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Sample records for ring-shaped protein explains

  1. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on...

  2. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions...

  3. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho...

  4. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric...

  5. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with...

  6. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Monday, 28 November 2011 14:52 Movement is fundamental to life. It...

  7. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported...

  8. Ring-shaped polariton lasing in pillar microcavities

    SciTech Connect (OSTI)

    Kalevich, V. K. Afanasiev, M. M.; Lukoshkin, V. A.; Kavokin, K. V.; Tsintzos, S. I.; Savvidis, P. G.; Kavokin, A. V.

    2014-03-07

    Optically generated exciton-polaritons in cylindric semiconductor pillar microcavity with embedded GaAs/AlGaAs quantum wells demonstrate a clear polariton lasing regime. When exciting in the center of the pillar, we detect a ring-shaped emission, where the peak of intensity can be separated from the excitation spot by more than 10 μm. The spatial coherence of the ring emission is verified by interferometry measurements. These observations are interpreted by drift of the exciton polariton condensate away from the excitation spot due to its repulsion from the exciton reservoir and by its spatial confinement by the pillar boundary.

  9. Peculiarity of convergence of shock wave generated by underwater electrical explosion of ring-shaped wire

    SciTech Connect (OSTI)

    Shafer, D.; Toker, G. R.; Gurovich, V. Tz.; Gleizer, S.; Krasik, Ya. E.

    2013-05-15

    Nanosecond timescale underwater electrical wire explosions of ring-shaped Cu wires were investigated using a pulsed generator with a current amplitude up to 50 kA. It was shown that this type of wire explosion results in the generation of a toroidal shock wave (SW). Time- and space-resolved optical diagnostics were used to determine azimuthal uniformity of the shock wave front and its velocity. It was found that the shock wave preserves its circular front shape in the range of radii 50?mexplaining the constant velocity of the shock wave.

  10. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    feature called the buttress that may play an important role in dynein's mechanical cycle. Yeast Yields Enable Protein Study The transportation of materials around a cell is...

  11. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    But the yield of protein from yeast was low, prompting researchers to try fed-batch fermentation, an approach used to make commercial yeast. In this method, a sugar solution is fed...

  12. Electromagnetic wave attenuation measurements in a ring-shaped inductively coupled air plasma

    SciTech Connect (OSTI)

    Xiaolong, Wei; Haojun, Xu; Min, Lin; Chen, Su; Jianhai, Li

    2015-05-28

    An aerocraft with the surface, inlet and radome covered large-area inductive coupled plasma (ICP) can attenuate its radar echo effectively. The shape, thickness, and electron density (N{sub e}) distribution of ICP are critical to electromagnetic wave attenuation. In the paper, an air all-quartz ICP generator in size of 20 × 20 × 7 cm{sup 3} without magnetic confinement is designed. The discharge results show that the ICP is amorphous in E-mode and ring-shaped in H-mode. The structure of ICP stratifies into core region and edge halo in H-mode, and its width and thickness changes from power and pressure. Such phenomena are explained by the distribution of RF magnetic field, the diffusion of negative ions plasma and the variation of skin depth. In addition, the theoretical analysis shows that the N{sub e} achieves nearly uniform within the electronegative core and sharply steepens in the edge. The N{sub e} of core region is diagnosed by microwave interferometer under varied conditions (pressure in range of 10–50 Pa, power in 300–700 W). Furthermore, the electromagnetic wave attenuation measurements were carried out with the air ICP in the frequencies of 4–5 GHz. The results show that the interspaced ICP is still effective to wave attenuation, and the wave attenuation increases with the power and pressure. The measured attenuation is approximately in accordance with the calculation data of finite-different time-domain simulations.

  13. Electrodynamics of a ring-shaped spiral resonator

    SciTech Connect (OSTI)

    Maleeva, N.; Karpov, A.; Averkin, A.; Fistul, M. V.; Zhuravel, A. P.; Jung, P.; Ustinov, A. V.

    2014-02-14

    We present analytical, numerical, and experimental investigations of electromagnetic resonant modes of a compact monofilar Archimedean spiral resonator shaped in a ring, with no central part. Planar spiral resonators are interesting as components of metamaterials for their compact deep-subwavelength size. Such resonators couple primarily to the magnetic field component of the incident electromagnetic wave, offering properties suitable for magnetic meta-atoms. Surprisingly, the relative frequencies of the resonant modes follow the sequence of the odd numbers as f{sub 1}:f{sub 2}:f{sub 3}:f{sub 4}… = 1:3:5:7…, despite the nearly identical boundary conditions for electromagnetic fields at the extremities of the resonator. In order to explain the observed spectrum of resonant modes, we show that the current distribution inside the spiral satisfies a particular Carleman type singular integral equation. By solving this equation, we obtain a set of resonant frequencies. The analytically calculated resonance frequencies and the current distributions are in good agreement with experimental data and the results of numerical simulations. By using low-temperature laser scanning microscopy of a superconducting spiral resonator, we compare the experimentally visualized ac current distributions over the spiral with the calculated ones. Theory and experiment agree well with each other. Our analytical model allows for calculation of a detailed three-dimensional magnetic field structure of the resonators.

  14. Cell culture arrays using micron-sized ferromagnetic ring-shaped thin films

    SciTech Connect (OSTI)

    Huang, Chen-Yu; Wei, Zung-Hang; Lai, Mei-Feng; Ger, Tzong-Rong

    2015-05-07

    Cell patterning has become an important technology for tissue engineering. In this research, domain walls are formed at the two ends of a ferromagnetic ring thin film after applying a strong external magnetic field, which can effectively attract magnetically labeled cells and control the position for biological cell. Magnetophoresis experiment was conducted to quantify the magnetic nanoparticle inside the cells. A ring-shaped magnetic thin films array was fabricated through photolithography. It is observed that magnetically labeled cells can be successfully attracted to the two ends of the ring-shaped magnetic thin film structure and more cells were attracted and further attached to the structures. The cells are co-cultured with the structure and kept proliferating; therefore, such ring thin film can be an important candidate for in-vitro biomedical chips or tissue engineering.

  15. Trapping two types of particles using a double-ring-shaped radially polarized beam

    SciTech Connect (OSTI)

    Zhang Yaoju; Ding Biaofeng; Suyama, Taikei

    2010-02-15

    An optical-trap method based on the illumination of a double-ring-shaped radially polarized beam (R-TEM{sub 11}*) is proposed. The numerical results based on the vector diffraction theory show that a highly focused R-TEM{sub 11}* beam not only can produce a bright spot but also can form an optical cage in the focal region by changing the truncation parameter {beta}, defined as the ratio of the radius of the aperture to the waist of the beam. The radiation forces acting on Rayleigh particles are calculated by using the Rayleigh scattering theory. The bright spot generated by the R-TEM{sub 11}* beam with a {beta} value close to 2 can three-dimensionally trap a particle with a refractive index larger than that of the ambient. An optical cage or three-dimensional dark spot generated by the R-TEM{sub 11}* beam with a {beta} value close to 1.3 can three-dimensionally trap a particle with refractive index smaller than that of the ambient. Because the adjustment of the truncation parameter can be actualized by simply changing the radius of a circular aperture inserted in the front of the lens, only one optical-trap system in the present method can be used to three-dimensionally trap two types of particles with different refractive indices.

  16. Criteria of radio-frequency ring-shaped hollow cathode discharge using H{sub 2} and Ar gases for plasma processing

    SciTech Connect (OSTI)

    Ohtsu, Yasunori; Kawasaki, Yujiro

    2013-01-21

    In order to achieve high-density capacitively coupled plasma, a radio-frequency (RF) ring-shaped hollow cathode discharge has been developed as a candidate for processing plasma sources. The plasma density in the hollow cathode discharge reaches a high magnitude of 10{sup 10}-10{sup 11} cm{sup -3}. The RF ring-shaped hollow cathode discharge depends on the pressure and mass of the working gas. Criteria required for producing a RF ring-shaped hollow cathode discharge have been investigated for various gas pressures using H{sub 2} and Ar gases for high-density plasma production. The results reveal that the criteria for the occurrence of the hollow cathode effect are that the trench width should be approximately equal to the sum of the electron-neutral mean free paths and twice the sheath thickness of the RF powered electrode.

  17. Transcriptional bursting explains the noise–versus–mean relationship in mRNA and protein levels

    DOE PAGES-Beta [OSTI]

    Dar, Roy; Shaffer, Sydney M.; Singh, Abhyudai; Razooky, Brandon S.; Simpson, Michael L.; Raj, Arjun; Weinberger, Leor S.

    2016-07-28

    Recent analysis demonstrates that the HIV-1 Long Terminal Repeat (HIV LTR) promoter exhibits a range of possible transcriptional burst sizes and frequencies for any mean-expression level. However, these results have also been interpreted as demonstrating that cell-tocell expression variability (noise) and mean are uncorrelated, a significant deviation from previous results. Here, we re-examine the available mRNA and protein abundance data for the HIV LTR and find that noise in mRNA and protein expression scales inversely with the mean along analytically predicted transcriptional burst-size manifolds. We then experimentally perturb transcriptional activity to test a prediction of the multiple burst-size model: thatmore » increasing burst frequency will cause mRNA noise to decrease along given burst-size lines as mRNA levels increase. In conclusion, the data show that mRNA and protein noise decrease as mean expression increases, supporting the canonical inverse correlation between noise and mean.« less

  18. Wedding ring shaped excitation coil

    DOE Patents [OSTI]

    MacLennan, Donald A.; Tsai, Peter

    2001-01-01

    A high frequency inductively coupled electrodeless lamp includes an excitation coil with an effective electrical length which is less than one half wavelength of a driving frequency applied thereto, preferably much less. The driving frequency may be greater than 100 MHz and is preferably as high as 915 MHz. Preferably, the excitation coil is configured as a non-helical, semi-cylindrical conductive surface having less than one turn, in the general shape of a wedding ring. At high frequencies, the current in the coil forms two loops which are spaced apart and parallel to each other. Configured appropriately, the coil approximates a Helmholtz configuration. The lamp preferably utilizes an bulb encased in a reflective ceramic cup with a pre-formed aperture defined therethrough. The ceramic cup may include structural features to aid in alignment and/or a flanged face to aid in thermal management. The lamp head is preferably an integrated lamp head comprising a metal matrix composite surrounding an insulating ceramic with the excitation integrally formed on the ceramic. A novel solid-state oscillator preferably provides RF power to the lamp. The oscillator is a single active element device capable of providing over 70 watts of power at over 70% efficiency.

  19. Proteins

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Proteins Scientists manipulate and mimic proteins for use in creating solutions for medicine, sustainable energy, and more Read caption + Los Alamos National Laboratory graduate student, Patricia Langan, changes the properties of a green fluorescent protein in order to create new fluorescent protein variants. Overview of Research and Highlights Scientists at Los Alamos apply a unique collection of tools and expertise to gain a comprehensive understanding of the structure and function of proteins

  20. Proteins

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Proteins Protein Engineering, Structure, and Function Los Alamos scientists seek a comprehensive understanding of the structure and function of proteins which can lead to a multitude of possibilities, such as enhancing cellulose degradation for biofuels or creating new therapeutics. Contact Us Tom Terwilliger Laboratory Fellow Email Andrew Bradbury Bioscience Group Leader Email Rebecca McDonald Bioscience Communications Email Los Alamos scientists are developing mosaic proteins that may one day

  1. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    normal density. A 75-liter fed-batch growth produced 14 kg of yeast and required a new freezer be purchased to store it all. With this massive increase in starting material, enough...

  2. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    normal density. A 75-liter fed-batch growth produced 14 kg of yeast and required a new freezer be purchased to store it all. With this massive increase in starting material,...

  3. Dark antiatoms can explain DAMA

    SciTech Connect (OSTI)

    Wallemacq, Quentin; Cudell, Jean-René E-mail: jr.cudell@ulg.ac.be

    2015-02-01

    We show that the existence of a sub-dominant form of dark matter, made of dark ''antiatoms'' of mass m∼ 1 TeV and size a-dot {sub 0}∼ 3 fm, can explain the results of direct detection experiments, with a positive signal in DAMA/NaI and DAMA/LIBRA and no signal in other experiments. The signal comes from the binding of the dark antiatoms to thallium, a dopant in DAMA, and is not present for the constituent atoms of other experiments. The dark antiatoms are made of two particles oppositely charged under a dark U(1) symmetry and can bind to terrestrial atoms because of a kinetic mixing between the photon and the massless dark photon, such that the dark particles acquire an electric millicharge ∼ ± 5.10{sup −4}e. This millicharge enables them to bind to high-Z atoms via radiative capture, after they thermalize in terrestrial matter through elastic collisions.

  4. Natural Aerosols Explain Seasonal and Spatial Patterns of Southern...

    Office of Scientific and Technical Information (OSTI)

    Natural Aerosols Explain Seasonal and Spatial Patterns of Southern Ocean Cloud Albedo Citation Details In-Document Search Title: Natural Aerosols Explain Seasonal and Spatial ...

  5. Assembling a ring-shaped crystal in a microfabricated surface ion trap

    DOE PAGES-Beta [OSTI]

    Stick, Daniel Lynn; Univ. of New Mexico, Albuquerque, NM; Tabakov, Boyan; Univ. of New Mexico, Albuquerque, NM; Benito, Francisco; Blain, Matthew; Clark, Craig R.; Clark, Susan; Haltli, Raymond A.; Maunz, Peter; et al

    2015-09-01

    We report on experiments with a microfabricated surface trap designed for confining a chain of ions in a ring. Uniform ion separation over most of the ring is achieved with a rotationally symmetric design and by measuring and suppressing undesired electric fields. After reducing stray fields, the ions are confined primarily by a radio-frequency pseudopotential and their mutual Coulomb repulsion. As a result, approximately 400 40Ca+ ions with an average separation of 9 μm comprise the ion crystal.

  6. Electronic and thermoelectric properties of van der Waals materials with ring-shaped valence bands

    SciTech Connect (OSTI)

    Wickramaratne, Darshana E-mail: rlake@ece.ucr.edu; Lake, Roger K. E-mail: rlake@ece.ucr.edu; Zahid, Ferdows

    2015-08-21

    The valence band of a variety of few-layer, two-dimensional materials consist of a ring of states in the Brillouin zone. The energy-momentum relation has the form of a “Mexican hat” or a Rashba dispersion. The two-dimensional density of states is singular at or near the band edge, and the band-edge density of modes turns on nearly abruptly as a step function. The large band-edge density of modes enhances the Seebeck coefficient, the power factor, and the thermoelectric figure of merit ZT. Electronic and thermoelectric properties are determined from ab initio calculations for few-layer III–VI materials GaS, GaSe, InS, InSe, for Bi{sub 2}Se{sub 3}, for monolayer Bi, and for bilayer graphene as a function of vertical field. The effect of interlayer coupling on these properties in few-layer III–VI materials and Bi{sub 2}Se{sub 3} is described. Analytical models provide insight into the layer dependent trends that are relatively consistent for all of these few-layer materials. Vertically biased bilayer graphene could serve as an experimental test-bed for measuring these effects.

  7. Assembling a ring-shaped crystal in a microfabricated surface ion trap

    SciTech Connect (OSTI)

    Stick, Daniel Lynn; Tabakov, Boyan; Benito, Francisco; Blain, Matthew; Clark, Craig R.; Clark, Susan; Haltli, Raymond A.; Maunz, Peter; Sterk, Jonathan D.; Tigges, Chris

    2015-09-01

    We report on experiments with a microfabricated surface trap designed for confining a chain of ions in a ring. Uniform ion separation over most of the ring is achieved with a rotationally symmetric design and by measuring and suppressing undesired electric fields. After reducing stray fields, the ions are confined primarily by a radio-frequency pseudopotential and their mutual Coulomb repulsion. As a result, approximately 400 40Ca+ ions with an average separation of 9 μm comprise the ion crystal.

  8. Good Fences Make Good Financing: Project Finance Explained | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Energy Good Fences Make Good Financing: Project Finance Explained Good Fences Make Good Financing: Project Finance Explained April 7, 2016 - 9:12am Addthis Good Fences Make Good Financing: Project Finance Explained David Feldman David Feldman Energy Analyst, Department of Energy's National Renewable Energy Laboratory At the U.S. Department of Energy, one of our key missions is supporting research, development and deployment of new technologies. How do we do this? We fund projects of all

  9. Biofuels: Ethanol and Biodiesel - Energy Explained, Your Guide...

    U.S. Energy Information Administration (EIA) (indexed site)

    Biodiesel Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws ... Biofuels: Ethanol & Biodiesel Ethanol Use of Ethanol Ethanol & the Environment Biodiesel ...

  10. Biodiesel and the Environment - Energy Explained, Your Guide...

    U.S. Energy Information Administration (EIA) (indexed site)

    Biodiesel & the Environment Energy Explained - Home What Is Energy? Forms of Energy ... Biofuels: Ethanol & Biodiesel Ethanol Use of Ethanol Ethanol & the Environment Biodiesel ...

  11. Energy Units - Energy Explained, Your Guide To Understanding...

    U.S. Energy Information Administration (EIA) (indexed site)

    Calculators Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  12. Hydrogen - Energy Explained, Your Guide To Understanding Energy...

    U.S. Energy Information Administration (EIA) (indexed site)

    Hydrogen Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  13. Solar - Energy Explained, Your Guide To Understanding Energy...

    U.S. Energy Information Administration (EIA) (indexed site)

    Solar Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  14. Ethanol - Energy Explained, Your Guide To Understanding Energy...

    U.S. Energy Information Administration (EIA) (indexed site)

    Ethanol Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  15. Geothermal Energy and the Environment - Energy Explained, Your...

    U.S. Energy Information Administration (EIA) (indexed site)

    Geothermal > Geothermal Energy & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion ...

  16. Energy Use in Homes - Energy Explained, Your Guide To Understanding...

    U.S. Energy Information Administration (EIA) (indexed site)

    Homes Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  17. Solar Energy and the Environment - Energy Explained, Your Guide...

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy and the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British ...

  18. Energy Use in Commercial Buildings - Energy Explained, Your Guide...

    U.S. Energy Information Administration (EIA) (indexed site)

    Commercial Buildings Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal ...

  19. Geothermal - Energy Explained, Your Guide To Understanding Energy...

    U.S. Energy Information Administration (EIA) (indexed site)

    Geothermal Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  20. Hydropower - Energy Explained, Your Guide To Understanding Energy...

    U.S. Energy Information Administration (EIA) (indexed site)

    Hydropower Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  1. Energy Use in Industry - Energy Explained, Your Guide To Understanding...

    U.S. Energy Information Administration (EIA) (indexed site)

    Industry Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  2. Energy Use for Transportation - Energy Explained, Your Guide...

    U.S. Energy Information Administration (EIA) (indexed site)

    For Transportation Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal ...

  3. Coal - Energy Explained, Your Guide To Understanding Energy ...

    U.S. Energy Information Administration (EIA) (indexed site)

    Coal Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  4. Biomass - Energy Explained, Your Guide To Understanding Energy...

    U.S. Energy Information Administration (EIA) (indexed site)

    Biomass Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  5. Nuclear - Energy Explained, Your Guide To Understanding Energy...

    U.S. Energy Information Administration (EIA) (indexed site)

    Nuclear Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  6. Electricity - Energy Explained, Your Guide To Understanding Energy...

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    Electricity Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) ...

  7. Crystal structure of a ;#8203;BRAF kinase domain monomer explains...

    Office of Scientific and Technical Information (OSTI)

    Crystal structure of a ;8203;BRAF kinase domain monomer explains basis for allosteric regulation Citation Details In-Document Search Title: Crystal structure of a ;8203;BRAF ...

  8. NREL Explains the Higher Cellulolytic Activity of a Vital Microorganis...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Explains the Higher Cellulolytic Activity of a Vital Microorganism Wide range of cellulase ... The scientists found the microorganism utilizes the common cellulase degradation ...

  9. Home - Energy Explained, Your Guide To Understanding Energy ...

    Gasoline and Diesel Fuel Update

    Use of Electricity Prices and Factors Affecting Prices Electricity & the Environment Hydrogen Production of Hydrogen Use of Hydrogen Help promote Energy Explained with the...

  10. Adsorption of Organic Molecules May Explain Growth of Newly Nucleated...

    Office of Scientific and Technical Information (OSTI)

    Adsorption of Organic Molecules May Explain Growth of Newly Nucleated Clusters and New Particle Formation Citation Details In-Document Search Title: Adsorption of Organic Molecules ...

  11. Physics of Intrinsic Plasma Rotation Explained for First Time

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Physics of Intrinsic Plasma Rotation Explained for First Time Physics of Intrinsic Plasma Rotation Explained for First Time Key understanding for modeling future fusion reactors such as ITER July 23, 2013 CHANG.JPG Flamelets or hot spots along the plasma edge (a) drive turbulence intensity (b), temperature intensity (c), and intrinsic torque (d) inward, converting heat into toroidal rotation. (S. Ku et al.) If humans could harness nuclear fusion, the process that powers stars like our sun, the

  12. Home - Energy Explained, Your Guide To Understanding Energy - Energy

    U.S. Energy Information Administration (EIA) (indexed site)

    Information Administration Explained Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook for Future

  13. How Energy Works: Explaining Game-Changing Energy Technologies | Department

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    of Energy Works: Explaining Game-Changing Energy Technologies How Energy Works: Explaining Game-Changing Energy Technologies June 16, 2014 - 10:50am Q&A What How Energy Works topic should we cover next? Vote Now! Addthis What How Energy Works topic should we cover next? <a href="/node/919166">Vote now</a> using our interactive voting tool. | Graphic by Sarah Gerrity, Energy Department. What How Energy Works topic should we cover next? Vote now using our interactive

  14. Measuring and Explaining Electricity Price Changes in Restructured States

    SciTech Connect (OSTI)

    Fagan, Mark L.

    2006-06-15

    An effort to determine the effect of restructuring on prices finds that, on average, prices for industrial customers in restructured states were lower, relative to predicted prices, than prices for industrial customers in non-restructured states. This preliminary analysis also finds that these price changes are explained primarily by high pre-restructuring prices, not whether or not a state restructured. (author)

  15. NREL Explains the Higher Cellulolytic Activity of a Vital Microorganism |

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Bioenergy | NREL NREL Explains the Higher Cellulolytic Activity of a Vital Microorganism Wide range of cellulase modalities in C. thermocellum makes it one of the most efficient biomass degraders February 5, 2016 Researchers at the Energy Department's National Renewable Energy Laboratory (NREL) and the BioEnergy Science Center (BESC) say better understanding of a bacterium could lead to cheaper production of cellulosic ethanol and other advanced biofuels. Their discovery was made during an

  16. Energy and the Environment - Energy Explained, Your Guide To Understanding

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy - Energy Information Administration Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook

  17. Nonrenewable Energy Sources - Energy Explained, Your Guide To Understanding

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy - Energy Information Administration Sources Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook for

  18. Renewable Energy Sources - Energy Explained, Your Guide To Understanding

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy - Energy Information Administration Sources Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook for

  19. Secondary Energy Sources - Energy Explained, Your Guide To Understanding

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    Energy - Energy Information Administration Sources Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook for

  20. Biodiesel - Energy Explained, Your Guide To Understanding Energy - Energy

    U.S. Energy Information Administration (EIA) (indexed site)

    Information Administration Biodiesel Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook for Future

  1. Biomass and the Environment - Energy Explained, Your Guide To Understanding

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy - Energy Information Administration Biomass & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases

  2. Ethanol and the Environment - Energy Explained, Your Guide To Understanding

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy - Energy Information Administration Ethanol & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases

  3. Gasoline and the Environment - Energy Explained, Your Guide To

    U.S. Energy Information Administration (EIA) (indexed site)

    Understanding Energy - Energy Information Administration Gasoline > Gasoline & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the

  4. Landfill Gas and Biogas - Energy Explained, Your Guide To Understanding

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy - Energy Information Administration Landfill Gas and Biogas Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come

  5. Natural Gas and the Environment - Energy Explained, Your Guide To

    U.S. Energy Information Administration (EIA) (indexed site)

    Understanding Energy - Energy Information Administration Gas > Natural Gas & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the

  6. Nuclear Power and the Environment - Energy Explained, Your Guide To

    U.S. Energy Information Administration (EIA) (indexed site)

    Understanding Energy - Energy Information Administration Nuclear > Nuclear Power & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on

  7. Nuclear forensics, explained: NNSA analytic chemists help keep the world

    National Nuclear Security Administration (NNSA)

    safe | National Nuclear Security Administration | (NNSA) forensics, explained: NNSA analytic chemists help keep the world safe Thursday, February 25, 2016 - 2:46pm One of the gravest threats the world faces is the possibility that terrorists will acquire nuclear weapons or the necessary materials to construct a weapon. Part of the work of NNSA's Office of Defense Nuclear Nonproliferation and the national laboratories is to support investigations into the diversion, trafficking, or illicit

  8. Wind - Energy Explained, Your Guide To Understanding Energy - Energy

    U.S. Energy Information Administration (EIA) (indexed site)

    Information Administration Wind Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook for Future Emissions

  9. Wind Energy and the Environment - Energy Explained, Your Guide To

    U.S. Energy Information Administration (EIA) (indexed site)

    Understanding Energy - Energy Information Administration Wind > Wind Energy & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the

  10. Vocational Rehabilitation -Value Added: Explaining What We Do,

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Vocational Rehabilitation -Value Added: Explaining What We Do, Craig Bock, MA, CRC Washington State IARP Quarterly Newsletter - June 2009 If you have an injury at work, do you know what happens next or how you would navigate the Workers' Compensation system should you need to? What does RCW 51.32.095 (state law) and WAC 296-19A-070 (administrative rules) mean to you? If you could not return to your job and had permanent physical or cognitive restrictions who would help you explore your return to

  11. Explaining the Cosmic-Ray E+/(E- + E+) and Anti-P/P Ratios Using...

    Office of Scientific and Technical Information (OSTI)

    Explaining the Cosmic-Ray E+(E- + E+) and Anti-PP Ratios Using a Steady-State Injection Model Citation Details In-Document Search Title: Explaining the Cosmic-Ray E+(E- + E+) ...

  12. High Poisson;s ratio of Earth;s inner core explained by carbon...

    Office of Scientific and Technical Information (OSTI)

    High Poisson;s ratio of Earth;s inner core explained by carbon alloying Citation Details In-Document Search Title: High Poisson;s ratio of Earth;s inner core explained by carbon ...

  13. ATLAS/BNL Physicist Marc-Andre Pleier Explains the Higgs Mechanism

    ScienceCinema (OSTI)

    Pleier,Marc-Andre

    2016-07-12

    ATLAS/BNL Physicist Marc-Andre Pleier explains his role in analyzing data from the Large Hadron Collider and the search for the Higgs boson

  14. ATLAS/BNL Physicist Marc-Andre Pleier Explains the Higgs Mechanism

    SciTech Connect (OSTI)

    Pleier,Marc-Andre

    2013-10-07

    ATLAS/BNL Physicist Marc-Andre Pleier explains his role in analyzing data from the Large Hadron Collider and the search for the Higgs boson

  15. Getting Ready for LEDs: LED Lighting Video Series Explains the Basics |

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Department of Energy Getting Ready for LEDs: LED Lighting Video Series Explains the Basics Getting Ready for LEDs: LED Lighting Video Series Explains the Basics November 26, 2012 - 3:09pm Addthis Part 1 of the ElectricTV.net video series. Part 2 of the ElectricTV.net video series. Roland Risser Roland Risser Deputy Assistant Secretary for Renewable Power How can I participate? Learn more about the advantages and accessiblity of LED lighting from this series of videos. If you haven't been

  16. Assessing Energetic Contributions to Binding from a Disordered Region in a Protein-Protein Interaction

    SciTech Connect (OSTI)

    S Cho; C Swaminathan; D Bonsor; M Kerzic; R Guan; J Yang; C Kieke; P Anderson; D Kranz; et al.

    2011-12-31

    Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.

  17. NREL Scientists Use In-Situ Characterization to Explain Perovskite Solar

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Cell Growth and Processing | PV | NREL Scientists Use In-Situ Characterization to Explain Perovskite Solar Cell Growth and Processing June 6, 2016 NREL scientists have helped to establish research capabilities to address several important scientific and practical questions concerning perovskite solar cells. Perovskites are an important class of next-generation photovoltaic materials exhibiting impressive light absorption, high device efficiencies, and low-cost, industry-scalable processing.

  18. U.S. Energy Facts - Energy Explained, Your Guide To Understanding Energy -

    U.S. Energy Information Administration (EIA) (indexed site)

    Energy Information Administration U.S. Energy Facts Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From Outlook

  19. Use of Energy in the United States - Energy Explained, Your Guide To

    U.S. Energy Information Administration (EIA) (indexed site)

    Understanding Energy - Energy Information Administration Energy Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come

  20. Magnetic Amplification in Cosmic Field Explained | U.S. DOE Office of

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Science (SC) Magnetic Amplification in Cosmic Field Explained Fusion Energy Sciences (FES) FES Home About Research Facilities Science Highlights Benefits of FES Funding Opportunities Fusion Energy Sciences Advisory Committee (FESAC) Community Resources Contact Information Fusion Energy Sciences U.S. Department of Energy SC-24/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-4941 F: (301) 903-8584 E: Email Us More Information » 08.01.15 Magnetic Amplification

  1. Magnetic Amplification in Cosmic Field Explained | U.S. DOE Office of

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Science (SC) Magnetic Amplification in Cosmic Field Explained Advanced Scientific Computing Research (ASCR) ASCR Home About Research Facilities Science Highlights Benefits of ASCR Funding Opportunities Advanced Scientific Computing Advisory Committee (ASCAC) Community Resources Contact Information Advanced Scientific Computing Research U.S. Department of Energy SC-21/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-7486 F: (301) 903-4846 E: Email Us More

  2. INL Director Explains How the National Labs Are Assisting With Japan's Nuclear Crisis

    SciTech Connect (OSTI)

    Grossenbacher, John

    2011-01-01

    Idaho National Laboratory's Director John Grossenbacher discusses the types of nuclear expertise and capabilities that exist within the U.S. Department of Energy's national labs to assist with the Japan nuclear crisis. He also explains how the labs will provide long-term research that will uncover lessons learned from the Fukushima nuclear plants. For more information about INL's nuclear energy research, visit http://www.facebook.com/idahonationallaboratory.

  3. INL Director Explains How the National Labs Are Assisting With Japan's Nuclear Crisis

    ScienceCinema (OSTI)

    Grossenbacher, John

    2013-05-28

    Idaho National Laboratory's Director John Grossenbacher discusses the types of nuclear expertise and capabilities that exist within the U.S. Department of Energy's national labs to assist with the Japan nuclear crisis. He also explains how the labs will provide long-term research that will uncover lessons learned from the Fukushima nuclear plants. For more information about INL's nuclear energy research, visit http://www.facebook.com/idahonationallaboratory.

  4. Waste-to-Energy (Municipal Solid Waste) - Energy Explained, Your Guide To

    U.S. Energy Information Administration (EIA) (indexed site)

    Understanding Energy - Energy Information Administration Waste-to-Energy (MSW) Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse

  5. Wood and Wood Waste - Energy Explained, Your Guide To Understanding Energy

    U.S. Energy Information Administration (EIA) (indexed site)

    - Energy Information Administration Wood and Wood Waste Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Greenhouse Gases Come From

  6. Can Magnetism Explain High Temperature Superconductivity? | U.S. DOE Office

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    of Science (SC) Can Magnetism Explain High Temperature Superconductivity? Basic Energy Sciences (BES) BES Home About Research Facilities Science Highlights Benefits of BES Funding Opportunities Basic Energy Sciences Advisory Committee (BESAC) Community Resources Contact Information Basic Energy Sciences U.S. Department of Energy SC-22/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-3081 F: (301) 903-6594 E: Email Us More Information » 05.01.12 Can Magnetism

  7. Shotgun protein sequencing.

    SciTech Connect (OSTI)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  8. Explaining the t - t¯ asymmetry with a light axigluon

    DOE PAGES-Beta [OSTI]

    Marques Tavares, Gustavo; Schmaltz, Martin

    2011-09-12

    We propose an axigluon with mass between 400 and 450 GeV and flavor-universal couplings to quarks to explain the Tevatron t -t¯ forward-backward asymmetry. The model predicts a small negative asymmetry for t - t¯ pairs with invariant mass below 450 GeV and a large positive asymmetry above 450 GeV. The asymmetry arises from interference between s-channel gluon and axigluon diagrams and requires a relatively weakly coupled axigluon (ga=gqcd/3). Axigluon-gluon interference does not contribute to the t - t¯ cross section. New contributions to the cross section arise only at fourth order in the axigluon coupling and are very smallmore » for a sufficiently broad axigluon. Dijet measurements do not significantly constrain the axigluon couplings. We propose several possible UV completions of the phenomenological axigluon which explain the required small couplings and large width. Such UV completions necessarily contain new colored fermions or scalars below the axigluon mass and predict multijet events with large cross sections at the Tevatron and LHC.« less

  9. Can surface cracks and unipolar arcs explain breakdown and gradient limits?

    SciTech Connect (OSTI)

    Insepov, Zeke; Norem, Jim

    2013-01-15

    The authors argue that the physics of unipolar arcs and surface cracks can help understand rf breakdown and vacuum arc data. They outline a model of the basic mechanisms involved in breakdown and explore how the physics of unipolar arcs and cracks can simplify the picture of breakdown and gradient limits in accelerators, tokamaks as well as laser ablation, micrometeorites, and other applications. Cracks are commonly seen in SEM images of arc damage and they are produced as the liquid metal cools. They can produce the required field enhancements to explain field emission data and can produce mechanical failure of the surface that would trigger breakdown events. Unipolar arcs can produce currents sufficient to short out rf structures, and can cause the sort of damage seen in SEM images. They should be unstable, and possibly self-quenching, as seen in optical fluctuations and surface damage. The authors describe some details and consider the predictions of this simple model.

  10. Engineering and Characterization of a Superfolder Green Fluorescent Protein

    SciTech Connect (OSTI)

    Pedelacq,J.; Cabantous, S.; Tran, T.; Terwilliger, T.; Waldo, G.

    2006-01-01

    Existing variants of green fluorescent protein (GFP) often misfold when expressed as fusions with other proteins. We have generated a robustly folded version of GFP, called 'superfolder' GFP, that folds well even when fused to poorly folded polypeptides. Compared to 'folding reporter' GFP, a folding-enhanced GFP containing the 'cycle-3' mutations and the 'enhanced GFP' mutations F64L and S65T, superfolder GFP shows improved tolerance of circular permutation, greater resistance to chemical denaturants and improved folding kinetics. The fluorescence of Escherichia coli cells expressing each of eighteen proteins from Pyrobaculum aerophilum as fusions with superfolder GFP was proportional to total protein expression. In contrast, fluorescence of folding reporter GFP fusion proteins was strongly correlated with the productive folding yield of the passenger protein. X-ray crystallographic structural analyses helped explain the enhanced folding of superfolder GFP relative to folding reporter GFP.

  11. Protein- protein interaction detection system using fluorescent protein microdomains

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

    The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

  12. New positron spectral features from supersymmetric dark matter: A way to explain the PAMELA data?

    SciTech Connect (OSTI)

    Bergstroem, Lars; Bringmann, Torsten; Edsjoe, Joakim

    2008-11-15

    The space-borne antimatter experiment PAMELA has recently reported a surprising rise in the positron to electron ratio at high energies. It has also recently been found that electromagnetic radiative corrections in some cases may boost the gamma-ray yield from supersymmetric dark-matter annihilations in the galactic halo by up to 3 or 4 orders of magnitude, providing distinct spectral signatures for indirect dark matter searches to look for. Here, we investigate whether the same type of corrections can also lead to sizeable enhancements in the positron yield. We find that this is indeed the case, albeit for a smaller region of parameter space than for gamma rays; selecting models with a small mass difference between the neutralino and sleptons, like in the stau-coannihilation region in mSUGRA, the effect becomes more pronounced. The resulting, rather hard positron spectrum with a relatively sharp cutoff may potentially fit the rising positron ratio measured by the PAMELA satellite. To do so, however, very large 'boost factors' have to be invoked that are not expected in current models of halo structure. If the predicted cutoff would also be confirmed by later PAMELA data or upcoming experiments, one could either assume nonthermal production in the early universe or nonstandard halo formation to explain such a spectral feature as an effect of dark-matter annihilation. At the end of the paper, we briefly comment on the impact of radiative corrections on other annihilation channels, in particular, antiprotons and neutrinos.

  13. Communication: Cosolvency and cononsolvency explained in terms of a Flory-Huggins type theory

    SciTech Connect (OSTI)

    Dudowicz, Jacek Freed, Karl F.; Douglas, Jack F.

    2015-10-07

    Standard Flory-Huggins (FH) theory is utilized to describe the enigmatic cosolvency and cononsolvency phenomena for systems of polymers dissolved in mixed solvents. In particular, phase boundaries (specifically upper critical solution temperature spinodals) are calculated for solutions of homopolymers B in pure solvents and in binary mixtures of small molecule liquids A and C. The miscibility (or immiscibility) patterns for the ternary systems are classified in terms of the FH binary interaction parameters (χ{sub αβ}) and the ratio r = ϕ{sub A}/ϕ{sub C} of the concentrations ϕ{sub A} and ϕ{sub C} of the two solvents. The trends in miscibility are compared to those observed for blends of random copolymers (A{sub x}C{sub 1−x}) with homopolymers (B) and to those deduced for A/B/C solutions of polymers B in liquid mixtures of small molecules A and C that associate into polymeric clusters (A{sub p}C{sub q}){sub i}, (i = 1, 2, …, ∞). Although the classic FH theory is able to explain cosolvency and cononsolvency phenomena, the theory does not include a consideration of the mutual association of the solvent molecules and the competitive association between the solvent molecules and the polymer. These interactions can be incorporated in refinements of the FH theory, and the present paper provides a foundation for such extensions for modeling the rich thermodynamics of polymers in mixed solvents.

  14. Allostery through protein-induced DNA bubbles

    DOE PAGES-Beta [OSTI]

    Traverso, Joseph J.; Manoranjan, Valipuram S.; Bishop, A. R.; Rasmussen, Kim Ø.; Voulgarakis, Nikolaos K.

    2015-03-12

    Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resultingmore » melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.« less

  15. IS COMPTON COOLING SUFFICIENT TO EXPLAIN EVOLUTION OF OBSERVED QUASI-PERIODIC OSCILLATIONS IN OUTBURST SOURCES?

    SciTech Connect (OSTI)

    Mondal, Santanu; Chakrabarti, Sandip K.; Debnath, Dipak E-mail: chakraba@bose.res.in

    2015-01-01

    In outburst sources, quasi-periodic oscillation (QPO) frequency is known to evolve in a certain way: in the rising phase, it monotonically goes up until a soft intermediate state is achieved. In the propagating oscillatory shock model, oscillation of the Compton cloud is thought to cause QPOs. Thus, in order to increase QPO frequency, the Compton cloud must collapse steadily in the rising phase. In decline phases, the exact opposite should be true. We investigate cause of this evolution of the Compton cloud. The same viscosity parameter that increases the Keplerian disk rate also moves the inner edge of the Keplerian component, thereby reducing the size of the Compton cloud and reducing the cooling timescale. We show that cooling of the Compton cloud by inverse Comptonization is enough for it to collapse sufficiently so as to explain the QPO evolution. In the two-component advective flow configuration of Chakrabarti-Titarchuk, centrifugal force-induced shock represents the boundary of the Compton cloud. We take the rising phase of 2010 outburst of Galactic black hole candidate H 1743-322 and find an estimation of variation of the α parameter of the sub-Keplerian flow to be monotonically rising from 0.0001 to 0.02, well within the range suggested by magnetorotational instability. We also estimate the inward velocity of the Compton cloud to be a few meters per second, which is comparable to what is found in several earlier studies of our group by empirically fitting the shock locations with the time of observations.

  16. Destabilized bioluminescent proteins

    DOE Patents [OSTI]

    Allen, Michael S.; Rakesh, Gupta; Gary, Sayler S.

    2007-07-31

    Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.

  17. The HPr Proteins from the Thermophile Bacillus stearothermophilus Can Form Domain-swapped Dimers

    SciTech Connect (OSTI)

    Sridharan, Sudharsan; Razvi, Abbas; Scholtz, J. Martin; Sacchettini, James C. (TAM)

    2010-07-20

    The study of proteins from extremophilic organisms continues to generate interest in the field of protein folding because paradigms explaining the enhanced stability of these proteins still elude us and such studies have the potential to further our knowledge of the forces stabilizing proteins. We have undertaken such a study with our model protein HPr from a mesophile, Bacillus subtilis, and a thermophile, Bacillus stearothermophilus. We report here the high-resolution structures of the wild-type HPr protein from the thermophile and a variant, F29W. The variant proved to crystallize in two forms: a monomeric form with a structure very similar to the wild-type protein as well as a domain-swapped dimer. Interestingly, the structure of the domain-swapped dimer for HPr is very different from that observed for a homologous protein, Crh, from B. subtilis. The existence of a domain-swapped dimer has implications for amyloid formation and is consistent with recent results showing that the HPr proteins can form amyloid fibrils. We also characterized the conformational stability of the thermophilic HPr proteins using thermal and solvent denaturation methods and have used the high-resolution structures in an attempt to explain the differences in stability between the different HPr proteins. Finally, we present a detailed analysis of the solution properties of the HPr proteins using a variety of biochemical and biophysical methods.

  18. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  19. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-11-29

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  20. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2012-05-01

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  1. Protein kinesis: The dynamics of protein trafficking and stability

    SciTech Connect (OSTI)

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  2. Pressure cryocooling protein crystals

    DOE Patents [OSTI]

    Kim, Chae Un; Gruner, Sol M.

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  3. Self assembling proteins

    DOE Patents [OSTI]

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  4. Algae Protein Fermentation

    Energy.gov (indexed) [DOE]

    Protein Fermentation March 24, 2015 Ryan W Davis, PhD Sandia National Laboratory This presentation does not contain any proprietary, confidential, or otherwise restricted ...

  5. LucY: A versatile new fluorescent reporter protein

    DOE PAGES-Beta [OSTI]

    Auldridge, Michele E.; Cao, Hongnan; Sen, Saurabh; Franz, Laura P.; Bingman, Craig A.; Yennamalli, Ragothaman M.; Phillips, Jr., George N.; Mead, David; Steinmetz, Eric J.; Michnick, Stephen W.

    2015-04-23

    We report on the discovery, isolation, and use of a novel yellow fluorescent protein. Lucigen Yellow (LucY) binds one FAD molecule within its core, thus shielding it from water and maintaining its structure so that fluorescence is 10-fold higher than freely soluble FAD. LucY displays excitation and emission spectra characteristic of FAD, with 3 excitation peaks at 276nm, 377nm, and 460nm and a single emission peak at 530nm. These excitation and emission maxima provide the large Stokes shift beneficial to fluorescence experimentation. LucY belongs to the MurB family of UDP-N-acetylenolpyruvylglucosamine reductases. The high resolution crystal structure shows that in contrastmore » to other structurally resolved MurB enzymes, LucY does not contain a potentially quenching aromatic residue near the FAD isoalloxazine ring, which may explain its increased fluorescence over related proteins. Using E. coli as a system in which to develop LucY as a reporter, we show that it is amenable to circular permutation and use as a reporter of protein-protein interaction. Fragmentation between its distinct domains renders LucY non-fluorescent, but fluorescence can be partially restored by fusion of the fragments to interacting protein domains. Thus, LucY may find application in Protein-fragment Complementation Assays for evaluating protein-protein interactions.« less

  6. CHANGES OF THE SOLAR MERIDIONAL VELOCITY PROFILE DURING CYCLE 23 EXPLAINED BY FLOWS TOWARD THE ACTIVITY BELTS

    SciTech Connect (OSTI)

    Cameron, R. H.; Schuessler, M.

    2010-09-10

    The solar meridional flow is an important ingredient in Babcock-Leighton type models of the solar dynamo. Global variations of this flow have been suggested to explain the variations in the amplitudes and lengths of the activity cycles. Recently, cycle-related variations in the amplitude of the P{sup 1}{sub 2} term in the Legendre decomposition of the observed meridional flow have been reported. The result is often interpreted in terms of an overall variation in the flow amplitude during the activity cycle. Using a semi-empirical model based upon the observed distribution of magnetic flux on the solar surface, we show that the reported variations of the P{sup 1}{sub 2} term can be explained by the observed localized inflows into the active region belts. No variation of the overall meridional flow amplitude is required.

  7. Protein crystallography prescreen kit

    DOE Patents [OSTI]

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2007-10-02

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  8. Protein crystallography prescreen kit

    DOE Patents [OSTI]

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2005-07-12

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  9. ProteinShop: A tool for interactive protein manipulation and...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: ProteinShop: A tool for interactive protein manipulation and steering ... DOE Contract Number: AC03-76SF00098 Resource Type: Journal Article Resource Relation: ...

  10. Protein Dynamics and Biocatalysis

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Protein Dynamics and Biocatalysis Protein Dynamics and Biocatalysis 1998 Annual Report Grand Challenge Projects biocatalysis.gif A model of the Michaelis complex for the TEM-1/penicillin system from molecular dynamics simulations. Investigators: P. A. Bash, Northwestern University Medical School and M. Karplus, Harvard University Research Objectives A guiding principle of molecular biology is that the structure of a biomolecule defines its function. This principle is especially true in the case

  11. Environmental Impact Statement Explained

    Energy.gov [DOE]

    The National Environmental Policy Act (NEPA) requires Federal agencies to prepare an Environmental Impact Statement (EIS) for all major Federal actions that may significantly affect the quality of...

  12. Comment Period Closed Explained

    Energy.gov [DOE]

    The public comment period on the Draft Environmental Impact Statement (EIS) has ended, and DOE is preparing a Final EIS. The Final EIS will consider and respond to all timely public comments on the...

  13. Solitons and protein folding: An In Silico experiment

    SciTech Connect (OSTI)

    Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  14. Amphiphiles for protein solubilization and stabilization (Patent...

    Office of Scientific and Technical Information (OSTI)

    The invention provides amphiphiles for manipulating membrane proteins. The amphiphiles can ... and stabilization of membrane proteins, including photosynthetic protein ...

  15. Purine inhibitors of protein kinases, G proteins and polymerases

    DOE Patents [OSTI]

    Gray, Nathanael S. (Berkeley, CA); Schultz, Peter (Oakland, CA); Kim, Sung-Hou (Moraga, CA); Meijer, Laurent (Roscoff, FR)

    2001-07-03

    The present invention relates to purine analogs that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such purine analogs to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  16. Purine inhibitors of protein kinases, G proteins and polymerases

    DOE Patents [OSTI]

    Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

    2001-07-03

    The present invention relates to purine analogs that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such purine analogs to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  17. Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    SciTech Connect (OSTI)

    Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.

    2015-08-01

    We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.

  18. Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    DOE PAGES-Beta [OSTI]

    Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.

    2015-08-01

    We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage.more » Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.« less

  19. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  20. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  1. Coadsorbed species explain the mechanism of methanol temperature-desorption on CeO2(111)

    DOE PAGES-Beta [OSTI]

    Sutton, Jonathan E.; Steven H. Overbury; Beste, Ariana

    2016-03-24

    Here, we have used density functional theory calculations to investigate the temperature-programmed desorption (TPD) of methanol from CeO2(111). For the first time, low-temperature water formation and high-temperature methanol desorption are explained by our calculations. High coverages of methanol, which correspond to experimental conditions, are required to properly describe these features of the TPD spectrum. We identify a mechanism for the low-temperature formation of water involving the dissociation of two methanol molecules on the same surface O atom and filling of the resulting surface vacancy with one of the methoxy products. After water desorption, methoxy groups are stabilized on the surfacemore » and react at higher temperatures to form methanol and formaldehyde by a disproportionation mechanism. Alternatively, the stabilized methoxy groups undergo sequential C–H scission reactions to produce formaldehyde. Calculated energy requirements and methanol/formaldehyde selectivity agree with the experimental data.« less

  2. Bayesian Estimator of Protein-Protein Association Probabilities

    Energy Science and Technology Software Center (OSTI)

    2008-05-28

    The Bayesian Estimator of Protein-Protein Association Probabilities (BEPro3) is a software tool for estimating probabilities of protein-protein association between bait and prey protein pairs using data from multiple-bait, multiple-replicate, protein LC-MS/MS affinity isolation experiments. BEPro3 is public domain software, has been tested on Windows XP and version 10.4 or newer of the Mac OS 10.4, and is freely available. A user guide, example dataset with analysis and additional documentation are included with the BEPro3 download.

  3. Purine inhibitors of protein kinases, G proteins and polymerases

    DOE Patents [OSTI]

    Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

    2004-10-12

    The present invention relates to 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  4. Bone morphogenetic protein

    SciTech Connect (OSTI)

    Xiao Yongtao; Xiang Lixin; Shao Jianzhong

    2007-10-26

    Bone morphogenetic proteins (BMPs) are multi-functional growth factors belonging to the transforming growth factor-beta superfamily. It has been demonstrated that BMPs had been involved in the regulation of cell proliferation, survival, differentiation and apoptosis. However, their hallmark ability is that play a pivotal role in inducing bone, cartilage, ligament, and tendon formation at both heterotopic and orthotopic sites. In this review, we mainly concentrate on BMP structure, function, molecular signaling and potential medical application.

  5. Stabilized polyacrylic saccharide protein conjugates

    DOE Patents [OSTI]

    Callstrom, Matthew R.; Bednarski, Mark D.; Gruber, Patrick R.

    1996-01-01

    This invention is directed to water soluble protein polymer conjugates which are stabile in hostile environments. The conjugate comprises a protein which is linked to an acrylic polymer at multiple points through saccharide linker groups.

  6. Stabilized polyacrylic saccharide protein conjugates

    DOE Patents [OSTI]

    Callstrom, M.R.; Bednarski, M.D.; Gruber, P.R.

    1996-02-20

    This invention is directed to water soluble protein polymer conjugates which are stable in hostile environments. The conjugate comprises a protein which is linked to an acrylic polymer at multiple points through saccharide linker groups. 16 figs.

  7. Validation of Shewanella oneidensis MR-1 Small Proteins by AMT Tag-based Proteome Analysis

    SciTech Connect (OSTI)

    Romine, Margaret F.; Elias, Dwayne A.; Monroe, Matthew E.; Auberry, Kenneth J.; Fang, Ruihua; Fredrickson, Jim K.; Anderson, Gordon A.; Smith, Richard D.; Lipton, Mary S.

    2004-09-01

    Using stringent criteria for protein identification by accurate mass and time (AMT) tag mass spectrometric methodology, we detected 36 proteins <101 amino acids in length, including 10 that were annotated as hypothetical proteins, in 172 global tryptic digests of Shewanella oneidensis MR-1 proteins analyzed. Peptides that map to the conserved, but functionally uncharacterized proteins SO4134 and SO2787, were the most frequently detected small proteins in these samples, while hypotheticals SO2669 and SO2063, conserved hypotheticals SO0335 and SO2176, and the SlyX protein (SO1063) were observed at frequencies similar to small expected abundant ribosomal proteins and translation initiation factor IF-1 and consequently, likely to encode important cellular functions. In addition, 30 proteins including three of the small proteins that map to genes predicted to encode frameshifts, point mutations, or recoding signals were detected. Of these 30 genes, peptides that map to positions beyond internal stop codons were detected in 13 genes (SO0101, SO0419, SO0590, SO0738, SO1113, SO1211, SO3079, SO3130, SO3240, SO4231, SO4328, SO4422, and SO4657). While expression of the full-length formate dehydrogenase encoded by SO0101 can be explained by incorporation of selenocysteine at the internal stop codon, the mechanism of translating downstream sequences in the remaining genes remains unknown.

  8. Protein subcellular localization assays using split fluorescent proteins

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2009-09-08

    The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

  9. First principles study of electronic structure for cubane-like and ring-shaped structures of M{sub 4}O{sub 4}, M{sub 4}S{sub 4} clusters (M = Mn, Fe, Co, Ni, Cu)

    SciTech Connect (OSTI)

    Datta, Soumendu; Rahaman, Badiur

    2015-11-15

    Spin-polarized DFT has been used to perform a comparative study of the geometric structures and electronic properties for isolated M{sub 4}X{sub 4} nano clusters between their two stable isomers - a planar rhombus-like 2D structure and a cubane-like 3D structure with M = Mn, Fe, Co, Ni, Cu ; X = O, S. These two structural patterns of the M{sub 4}X{sub 4} clusters are commonly found as building blocks in several poly-nuclear transition metal complexes in inorganic chemistry. The effects of the van der Waals corrections to the physical properties have been considered in the electronic structure calculations employing the empirical Grimme’s correction (DFT+D2). We report here an interesting trend in their relative structural stability - the isolated M{sub 4}O{sub 4} clusters prefer to stabilize more in the planar structure, while the cubane-like 3D structure is more favorable for most of the isolated M{sub 4}S{sub 4} clusters than their planar 2D counterparts. Our study reveals that this contrasting trend in the relative structural stability is expected to be driven by an interesting interplay between the s-d and p-d hybridization effects of the constituents’ valence electrons.

  10. Microsoft Word - Translocator_protein bh

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    November 2015 Translocator Protein Structure and Function Translocator protein (TSPO) is an ancient conserved protein whose functions in bacteria and higher eukaryotes are yet to...

  11. Mathematical methods for protein science

    SciTech Connect (OSTI)

    Hart, W.; Istrail, S.; Atkins, J.

    1997-12-31

    Understanding the structure and function of proteins is a fundamental endeavor in molecular biology. Currently, over 100,000 protein sequences have been determined by experimental methods. The three dimensional structure of the protein determines its function, but there are currently less than 4,000 structures known to atomic resolution. Accordingly, techniques to predict protein structure from sequence have an important role in aiding the understanding of the Genome and the effects of mutations in genetic disease. The authors describe current efforts at Sandia to better understand the structure of proteins through rigorous mathematical analyses of simple lattice models. The efforts have focused on two aspects of protein science: mathematical structure prediction, and inverse protein folding.

  12. Signature Product Code for Predicting Protein-Protein Interactions

    Energy Science and Technology Software Center (OSTI)

    2004-09-25

    The SigProdV1.0 software consists of four programs which together allow the prediction of protein-protein interactions using only amino acid sequences and experimental data. The software is based on the use of tensor products of amino acid trimers coupled with classifiers known as support vector machines. Essentially the program looks for amino acid trimer pairs which occur more frequently in protein pairs which are known to interact. These trimer pairs are then used to make predictionsmore » about unknown protein pairs. A detailed description of the method can be found in the paper: S. Martin, D. Roe, J.L. Faulon. "Predicting protein-protein interactions using signature products," Bioinformatics, available online from Advance Access, Aug. 19, 2004.« less

  13. Targeting diverse protein-protein interaction interfaces with...

    Office of Scientific and Technical Information (OSTI)

    targeting vascular endothelial growth factor (VEGF) can structurally and functionally ... -peptides that bind to two other protein partners, IgG and tumor necrosis factor-. ...

  14. Protein detection system

    DOE Patents [OSTI]

    Fruetel, Julie A.; Fiechtner, Gregory J.; Kliner, Dahv A. V.; McIlroy, Andrew

    2009-05-05

    The present embodiment describes a miniature, microfluidic, absorption-based sensor to detect proteins at sensitivities comparable to LIF but without the need for tagging. This instrument utilizes fiber-based evanescent-field cavity-ringdown spectroscopy, in combination with faceted prism microchannels. The combination of these techniques will increase the effective absorption path length by a factor of 10.sup.3 to 10.sup.4 (to .about.1-m), thereby providing unprecedented sensitivity using direct absorption. The coupling of high-sensitivity absorption with high-performance microfluidic separation will enable real-time sensing of biological agents in aqueous samples (including aerosol collector fluids) and will provide a general method with spectral fingerprint capability for detecting specific bio-agents.

  15. Developing algorithms for predicting protein-protein interactions of homology modeled proteins.

    SciTech Connect (OSTI)

    Martin, Shawn Bryan; Sale, Kenneth L.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2006-01-01

    The goal of this project was to examine the protein-protein docking problem, especially as it relates to homology-based structures, identify the key bottlenecks in current software tools, and evaluate and prototype new algorithms that may be developed to improve these bottlenecks. This report describes the current challenges in the protein-protein docking problem: correctly predicting the binding site for the protein-protein interaction and correctly placing the sidechains. Two different and complementary approaches are taken that can help with the protein-protein docking problem. The first approach is to predict interaction sites prior to docking, and uses bioinformatics studies of protein-protein interactions to predict theses interaction site. The second approach is to improve validation of predicted complexes after docking, and uses an improved scoring function for evaluating proposed docked poses, incorporating a solvation term. This scoring function demonstrates significant improvement over current state-of-the art functions. Initial studies on both these approaches are promising, and argue for full development of these algorithms.

  16. Molecular dynamics of membrane proteins.

    SciTech Connect (OSTI)

    Woolf, Thomas B.; Crozier, Paul Stewart; Stevens, Mark Jackson

    2004-10-01

    Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

  17. High throughput protein production screening

    DOE Patents [OSTI]

    Beernink, Peter T.; Coleman, Matthew A.; Segelke, Brent W.

    2009-09-08

    Methods, compositions, and kits for the cell-free production and analysis of proteins are provided. The invention allows for the production of proteins from prokaryotic sequences or eukaryotic sequences, including human cDNAs using PCR and IVT methods and detecting the proteins through fluorescence or immunoblot techniques. This invention can be used to identify optimized PCR and WT conditions, codon usages and mutations. The methods are readily automated and can be used for high throughput analysis of protein expression levels, interactions, and functional states.

  18. Johann Deisenhofer, Crystallography, and Proteins

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Johann Deisenhofer, Crystallography, and Proteins Resources with Additional Information Johann Deisenhofer Courtesy of UT Southwestern Medical Center "Johann Deisenhofer, Ph.D. is ...

  19. Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription

    SciTech Connect (OSTI)

    Vaidya, Anand T.; Chen, Chen-Hui; Dunlap, Jay C.; Loros, Jennifer J.; Crane, Brian R.

    2012-10-25

    Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.

  20. Structural Genomics of Protein Phosphatases

    SciTech Connect (OSTI)

    Almo,S.; Bonanno, J.; Sauder, J.; Emtage, S.; Dilorenzo, T.; Malashkevich, V.; Wasserman, S.; Swaminathan, S.; Eswaramoorthy, S.; et al

    2007-01-01

    The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.

  1. ProteinShop: A tool for interactive protein manipulation and steering

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect ProteinShop: A tool for interactive protein manipulation and steering Citation Details In-Document Search Title: ProteinShop: A tool for interactive protein manipulation and steering We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing

  2. Expression of multiple proteins in transgenic plants

    DOE Patents [OSTI]

    Vierstra, Richard D.; Walker, Joseph M.

    2002-01-01

    A method is disclosed for the production of multiple proteins in transgenic plants. A DNA construct for introduction into plants includes a provision to express a fusion protein of two proteins of interest joined by a linking domain including plant ubiquitin. When the fusion protein is produced in the cells of a transgenic plant transformed with the DNA construction, native enzymes present in plant cells cleave the fusion protein to release both proteins of interest into the cells of the transgenic plant. Since the proteins are produced from the same fusion protein, the initial quantities of the proteins in the cells of the plant are approximately equal.

  3. ProteinShop: A Tool for Interactive Protein

    Office of Scientific and Technical Information (OSTI)

    ... Also, it can be used to define the minimum and maximum per-atom energy values that will be mapped to ProteinShop's green-yellow-red color ramp, and to select any combination of ...

  4. Assigning protein functions by comparative genome analysis protein phylogenetic profiles

    DOE Patents [OSTI]

    Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

    2003-05-13

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  5. ProteinShop: A Tool for Interactive Protein

    Office of Scientific and Technical Information (OSTI)

    ... To guide the manipulation with an energy function, ProteinShop can be used with the AMBER ... of amino acids from the input file, and the atom positions from residue template files. ...

  6. Protein-Protein Binding Specificity | Argonne Leadership Computing Facility

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    This so-called computational microcalorimeter was employed to determine the standard binding constant of the proteins barstar and barnase Calorimetry has been part of the experimental chemist's toolbox for over two centuries. Using guided potential-of-mean-force calculations, the technique is now available to the computational chemist as well. This so-called computational microcalorimeter was employed to determine the standard binding constant of the proteins barstar and barnase. Chris Chipot,

  7. Adhesives from modified soy protein

    DOE Patents [OSTI]

    Sun, Susan; Wang, Donghai; Zhong, Zhikai; Yang, Guang

    2008-08-26

    The, present invention provides useful adhesive compositions having similar adhesive properties to conventional UF and PPF resins. The compositions generally include a protein portion and modifying ingredient portion selected from the group consisting of carboxyl-containing compounds, aldehyde-containing compounds, epoxy group-containing compounds, and mixtures thereof. The composition is preferably prepared at a pH level at or near the isoelectric point of the protein. In other preferred forms, the adhesive composition includes a protein portion and a carboxyl-containing group portion.

  8. Protein Flips Lipids Across Membranes

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Found ubiquitously in both bacteria and humans, membrane proteins of the adenosine ... head-over-tail from one side of the membrane to the other, on its way out of the cell. ...

  9. Small-Angle X-Ray Scattering From RNA, Proteins, And Protein...

    Office of Scientific and Technical Information (OSTI)

    Small-Angle X-Ray Scattering From RNA, Proteins, And Protein Complexes Citation Details In-Document Search Title: Small-Angle X-Ray Scattering From RNA, Proteins, And Protein ...

  10. Fast events in protein folding

    SciTech Connect (OSTI)

    Woodruff, W.; Callender, R.; Causgrove, T.; Dyer, R.; Williams, S.

    1996-04-01

    The primary objective of this work was to develop a molecular understanding of how proteins achieve their native three-dimensional (folded) structures. This requires the identification and characterization of intermediates in the protein folding process on all relevant timescales, from picoseconds to seconds. The short timescale events in protein folding have been entirely unknown. Prior to this work, state-of-the-art experimental approaches were limited to milliseconds or longer, when much of the folding process is already over. The gap between theory and experiment is enormous: current theoretical and computational methods cannot realistically model folding processes with lifetimes longer than one nanosecond. This unique approach to employ laser pump-probe techniques that combine novel methods of laser flash photolysis with time-resolved vibrational spectroscopic probes of protein transients. In this scheme, a short (picosecond to nanosecond) laser photolysis pulse was used to produce an instantaneous pH or temperature jump, thereby initiating a protein folding or unfolding reaction. Structure-specific, time-resolved vibrational probes were then used to identify and characterize protein folding intermediates.

  11. Microsecond Microfluidic Mixing for Investigation of Protein...

    Office of Scientific and Technical Information (OSTI)

    for Investigation of Protein Folding Kinetics Citation Details In-Document Search Title: Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics You ...

  12. SciTech Connect: "protein folding"

    Office of Scientific and Technical Information (OSTI)

    protein folding" Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: "protein folding" Semantic Semantic Term Title: Full Text: Bibliographic Data:...

  13. Elementary tetrahelical protein design for diverse oxidoreductase...

    Office of Scientific and Technical Information (OSTI)

    Elementary tetrahelical protein design for diverse oxidoreductase functions Citation Details In-Document Search Title: Elementary tetrahelical protein design for diverse...

  14. Amphiphiles for protein solubilization and stabilization (Patent...

    Office of Scientific and Technical Information (OSTI)

    Amphiphiles for protein solubilization and stabilization Citation Details In-Document Search Title: Amphiphiles for protein solubilization and stabilization The invention provides ...

  15. Protein Instability and Lou Gehrig's Disease

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins...

  16. Experimental Approach to Controllably Vary Protein Oxidation...

    Office of Scientific and Technical Information (OSTI)

    Vary Protein Oxidation While Minimizing Electrode Adsorption for Boron-Doped Diamond ... Vary Protein Oxidation While Minimizing Electrode Adsorption for Boron-Doped Diamond ...

  17. DOE Science Showcase - Understanding Protein Membranes | OSTI...

    Office of Scientific and Technical Information (OSTI)

    DOE Science Showcase - Understanding Protein Membranes Protein membrane simulation and ... Database DOE R&D Project Summaries DOE Data Explorer Visit the Science Showcase homepage.

  18. Oncoprotein protein kinase antibody kit (Patent) | DOEPatents

    Office of Scientific and Technical Information (OSTI)

    Oncoprotein protein kinase antibody kit Title: Oncoprotein protein kinase antibody kit An ... domain and polynucleotide sequences and method of detection of JNK are provided herein. ...

  19. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences

    DOE Patents [OSTI]

    Eisenberg, David; Marcotte, Edward M.; Pellegrini, Matteo; Thompson, Michael J.; Yeates, Todd O.

    2002-10-15

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  20. Manipulating and Visualizing Proteins Simon, Horst D. 59 BASIC...

    Office of Scientific and Technical Information (OSTI)

    ACIDS; CALIFORNIA; CHAINS; CHEMISTRY; DISEASES; FIBROSIS; FORECASTING; GENETICS; OPTIMIZATION; PROTEIN STRUCTURE; PROTEINS; QUEUES; SHAPE; SIMULATION PROTEIN STRUCTURE...

  1. Protein design for pathway engineering

    SciTech Connect (OSTI)

    Eriksen, DT; Lian, JZ; Zhao, HM

    2014-02-01

    Design and construction of biochemical pathways has increased the complexity of biosynthetically-produced compounds when compared to single enzyme biocatalysis. However, the coordination of multiple enzymes can introduce a complicated set of obstacles to overcome in order to achieve a high titer and yield of the desired compound. Metabolic engineering has made great strides in developing tools to optimize the flux through a target pathway, but the inherent characteristics of a particular enzyme within the pathway can still limit the productivity. Thus, judicious protein design is critical for metabolic and pathway engineering. This review will describe various strategies and examples of applying protein design to pathway engineering to optimize the flux through the pathway. The proteins can be engineered for altered substrate specificity/selectivity, increased catalytic activity, reduced mass transfer limitations through specific protein localization, and reduced substrate/product inhibition. Protein engineering can also be expanded to design biosensors to enable high through-put screening and to customize cell signaling networks. These strategies have successfully engineered pathways for significantly increased productivity of the desired product or in the production of novel compounds. (C) 2013 Elsevier Inc. All rights reserved.

  2. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01

    The three-dimensional structure of a protein is encoded in its linear sequence of amino acids. Studies of protein folding are aimed at understanding the nature of this code which translates one-dimensional information to three-dimensions. It is now well-established that protein folding intermediates exist and can be populated significantly under some conditions. A method to characterize kinetic folding intermediates is described. The method takes advantage of the decrease in exchange rates between amide protons (i.e., peptide backbone NH) and solvent water protons, when the amide proton is involved in structure. The feasibility of using amide proton exchange to pulse-label proteins during folding has been demonstrated using (/sup 3/H)-H/sub 2/O. The results with ribonuclease A (RNase A) support a framework model for folding, in which the secondary structure of a protein is formed before tertiary structure changes are complete. Extension of these studies using NMR should permit characterization of early secondary structure folding frameworks.

  3. Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures

    SciTech Connect (OSTI)

    Pyklinen, Anette; Boczkowska, Malgorzata; Zhao, Hongxia; Saarikangas, Juha; Rebowski, Grzegorz; Jansen, Maurice; Hakanen, Janne; Koskela, Essi V.; Pernen, Johan; Vihinen, Helena; Jokitalo, Eija; Salminen, Marjo; Ikonen, Elina; Dominguez, Roberto; Lappalainen, Pekka

    2013-05-29

    Bin/amphipysin/Rvs (BAR)-domain proteins sculpt cellular membranes and have key roles in processes such as endocytosis, cell motility and morphogenesis. BAR domains are divided into three subfamilies: BAR- and F-BAR-domain proteins generate positive membrane curvature and stabilize cellular invaginations, whereas I-BAR-domain proteins induce negative curvature and stabilize protrusions. We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane tubulation but promotes the formation of planar membrane sheets. Structural and mutagenesis analyses reveal that the BAR domain of Pinkbar has a relatively flat lipid-binding interface and that it assembles into sheet-like oligomers in crystals and in solution, which may explain its unique membrane-deforming activity.

  4. Protein folding in the ER.

    SciTech Connect (OSTI)

    Stevens, F. J.; Argon, Y.; Biosciences Division; Univ. of Chicago

    1999-10-01

    The endoplasmic reticulum (ER) is a major protein folding compartment for secreted, plasma membrane and organelle proteins. Each of these newly-synthesized polypeptides folds in a deterministic process, affected by the unique conditions that exist in the ER. An understanding of protein folding in the ER is a fundamental biomolecular challenge at two levels. The first level addresses how the amino acid sequence programs that polypeptide to efficiently arrive at a particular fold out of a multitude of alternatives, and how different sequences obtain similar folds. At the second level are the issues introduced by folding not in the cytosol, but in the ER, including the risk of aggregation in a molecularly crowded environment, accommodation of post-translational modifications and the compatibility with subsequent intracellular trafficking. This review discusses both the physicochemical and cell biological constraints of folding, which are the challenges that the ER molecular chaperones help overcome.

  5. Recombinant fluorescent protein microsphere calibration standard

    DOE Patents [OSTI]

    Nolan, John P.; Nolan, Rhiannon L.; Ruscetti, Teresa; Lehnert, Bruce E.

    2001-01-01

    A method for making recombinant fluorescent protein standard particles for calibration of fluorescence instruments.

  6. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    SciTech Connect (OSTI)

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  7. Using proteins as chainmail armor

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Using proteins as chainmail armor Click to share on Facebook (Opens in new window) Click to share on Twitter (Opens in new window) Click to share on Reddit (Opens in new window) Click to share on Pinterest (Opens in new window) Many bacteria and archaea encase themselves within a self-assembling protective shell of proteins, like chainmail armor. The process is a model for the self assembly of 2-D and 3-D organic and inorganic nanostructures, and could be used to make adhesive nanostructures

  8. Method for protein structure alignment

    DOE Patents [OSTI]

    Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

    2005-02-22

    This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

  9. Shining a spotlight on intact proteins

    SciTech Connect (OSTI)

    Pasa-Tolic, Ljiljana; Masselon, Christophe

    2014-05-01

    Cells react to cues from their environment using various mechanisms that include changes in metabolites, gene expression, protein binding partners, protein localization, and protein posttranslational modifications (PTMs), all of which contribute to altered cellular signatures that enable appropriate cellular responses. Given the seemingly infinite number of mechanisms available to affect protein function and modulate biological processes, the question arises as to how cells manage to interpret protein readouts to accomplish the appropriate cell-type specific response to a particular stimulus.

  10. Protein Dynamics Hit the Big Screen

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Protein Dynamics Hit the Big Screen Protein Dynamics Hit the Big Screen Now playing at a supercomputer near you: proteins in action June 29, 2005 Contact: Dan Krotz, dakrotz@lbl.gov 06tyrosinekinasechanging.jpg This simulation of a tyrosine kinase reveals how the protein changes shape. Scientists from Berkeley Lab and UC Berkeley are using one the world's most powerful computers to simulate how protein molecules move, rotate, and fold as they carry out life's most fundamental tasks.Although they

  11. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  12. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1998-02-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  13. Method for voltage-gated protein fractionation

    DOE Patents [OSTI]

    Hatch, Anson; Singh, Anup K.

    2012-04-24

    We report unique findings on the voltage dependence of protein exclusion from the pores of nanoporous polymer exclusion membranes. The pores are small enough that proteins are excluded from passage with low applied electric fields, but increasing the field enables proteins to pass through. The requisite field necessary for a change in exclusion is protein-specific with a correlation to protein size. The field-dependence of exclusion is important to consider for preconcentration applications. The ability to selectively gate proteins at exclusion membranes is also a promising means for manipulating and characterizing proteins. We show that field-gated exclusion can be used to selectively remove proteins from a mixture, or to selectively trap protein at one exclusion membrane in a series.

  14. Building Biochips: A Protein Production Pipeline

    SciTech Connect (OSTI)

    de Carvalho-Kavanagh, M; Albala, J S

    2004-02-09

    Protein arrays are emerging as a practical format in which to study proteins in high-throughput using many of the same techniques as that of the DNA microarray. The key advantage to array-based methods for protein study is the potential for parallel analysis of thousands of samples in an automated, high-throughput fashion. Building protein arrays capable of this analysis capacity requires a robust expression and purification system capable of generating hundreds to thousands of purified recombinant proteins. We have developed a method to utilize LLNL-I.M.A.G.E. cDNAs to generate recombinant protein libraries using a baculovirus-insect cell expression system. We have used this strategy to produce proteins for analysis of protein/DNA and protein/protein interactions using protein microarrays in order to understand the complex interactions of proteins involved in homologous recombination and DNA repair. Using protein array techniques, a novel interaction between the DNA repair protein, Rad51B, and histones has been identified.

  15. Proteins

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Such understanding could help scientists develop new antibiotics to battle "superbugs" such as MRSA (methicillin-resistant Staphylococcus aureus) infections, as well as engineered ...

  16. Proteins

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    ... Such understanding could help scientists develop new antibiotics to battle "superbugs" such as MRSA (methicillin-resistant Staphylococcus aureus) infections, as well as engineered ...

  17. Extracellular secretion of recombinant proteins

    DOE Patents [OSTI]

    Linger, Jeffrey G.; Darzins, Aldis

    2014-07-22

    Nucleic acids encoding secretion signals, expression vectors containing the nucleic acids, and host cells containing the expression vectors are disclosed. Also disclosed are polypeptides that contain the secretion signals and methods of producing polypeptides, including methods of directing the extracellular secretion of the polypeptides. Exemplary embodiments include cellulase proteins fused to secretion signals, methods to produce and isolate these polypeptides, and methods to degrade lignocellulosic biomass.

  18. A Designed Protein Maps Brain Activity

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    A Designed Protein Maps Brain Activity Print A team of scientists from the Howard Hughes ... a fluorescent protein (CaMPARI) that allows the permanent marking of active brain cells. ...

  19. A Designed Protein Maps Brain Activity

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    A Designed Protein Maps Brain Activity A Designed Protein Maps Brain Activity Print Wednesday, 28 October 2015 00:00 A team of scientists from the Howard Hughes Medical Institute's ...

  20. Microsecond Microfluidic Mixing for Investigation of Protein...

    Office of Scientific and Technical Information (OSTI)

    Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; COMPATIBILITY; DIFFUSION; FOCUSING; HYDRODYNAMICS; KINETICS; MIXERS; PROTEINS; REACTION KINETICS; ...

  1. Translocator Protein Structure and Function | Stanford Synchrotron

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Radiation Lightsource Translocator Protein Structure and Function Monday, November 30, 2015 Translocator protein (TSPO) is an ancient conserved protein whose functions in bacteria and higher eukaryotes are yet to be clearly defined in spite of more than 30 years of study. In mitochondria, it was first recognized as an outer membrane protein that binds benzodiazepine drugs, but distinct from the central nervous system site, the GABAA receptor(1). Originally called the peripheral

  2. Amphiphiles for protein solubilization and stabilization

    DOE Patents [OSTI]

    Gellman, Samuel Helmer; Chae, Pil Seok; Laible, Philip D.; Wander, Marc J.

    2012-09-11

    The invention provides amphiphiles for manipulating membrane proteins. The amphiphiles can feature carbohydrate-derived hydrophilic groups and branchpoints in the hydrophilic moiety and/or in a lipophilic moiety. Such amphiphiles are useful as detergents for solubilization and stabilization of membrane proteins, including photosynthetic protein superassemblies obtained from bacterial membranes.

  3. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Greg Hura

    2010-01-08

    The structure of a protein in days -- not months or years -- ushers in a new era in genomics research. Berkeley Lab scientists have developed a high-throughput protein pipeline that could expedite the development of biofuels and elucidate how proteins carry out lifes vital functions.

  4. Radioactive Lysine in Protein Metabolism Studies

    DOE R&D Accomplishments [OSTI]

    Miller, L. L.; Bale, W. F.; Yuile, C. L.; Masters, R. E.; Tishkoff, G. H.; Whipple,, G. H.

    1950-01-09

    Studies of incorporation of DL-lysine in various body proteins of the dog; the time course of labeled blood proteins; and apparent rate of disappearance of labeled plasma proteins for comparison of behavior of the plasma albumin and globulin fractions; shows more rapid turn over of globulin fraction.

  5. Protein Structures Revealed at Record Pace

    SciTech Connect (OSTI)

    Hura, Greg

    2009-01-01

    The structure of a protein in days -- not months or years -- ushers in a new era in genomics research. Berkeley Lab scientists have developed a high-throughput protein pipeline that could expedite the development of biofuels and elucidate how proteins carry out lifes vital functions.

  6. Amphiphiles for protein solubilization and stabilization

    SciTech Connect (OSTI)

    Gellman, Samuel Helmer; Chae, Pil Seok; Laible, Phillip D; Wander, Marc J

    2014-11-04

    The invention provides amphiphiles for manipulating membrane proteins. The amphiphiles can feature carbohydrate-derived hydrophilic groups and branchpoints in the hydrophilic moiety and/or in a lipophilic moiety. Such amphiphiles are useful as detergents for solubilization and stabilization of membrane proteins, including photosynthetic protein superassemblies obtained from bacterial membranes.

  7. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Hura, Greg

    2016-07-12

    The structure of a protein in days -- not months or years -- ushers in a new era in genomics research. Berkeley Lab scientists have developed a high-throughput protein pipeline that could expedite the development of biofuels and elucidate how proteins carry out lifes vital functions.

  8. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K.

    1997-01-01

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described.

  9. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, G.K.

    1997-04-29

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

  10. Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding

    SciTech Connect (OSTI)

    Huang, David M.; Chandler, David

    2000-04-01

    The Lum-Chandler-Weeks theory of hydrophobicity [J. Phys. Chem. 103, 4570 (1999)] is applied to treat the temperature dependence of hydrophobic solvation in water. The application illustrates how the temperature dependence for hydrophobic surfaces extending less than 1nm differs significantly from that for surfaces extending more than 1nm. The latter is the result of water depletion, a collective effect, that appears at length scales of 1nm and larger. Due to the contrasting behaviors at small and large length scales, hydrophobicity by itself can explain the variable behavior of protein folding.

  11. Method for voltage-gated protein fractionation (Patent) | DOEPatents

    Office of Scientific and Technical Information (OSTI)

    Method for voltage-gated protein fractionation Title: Method for voltage-gated protein fractionation We report unique findings on the voltage dependence of protein exclusion from ...

  12. Activity-Based Protein Profiling of Microbes

    SciTech Connect (OSTI)

    Sadler, Natalie C.; Wright, Aaron T.

    2015-02-01

    Activity-Based Protein Profiling (ABPP) in conjunction with multimodal characterization techniques has yielded impactful findings in microbiology, particularly in pathogen, bioenergy, drug discovery, and environmental research. Using small molecule chemical probes that react irreversibly with specific proteins or protein families in complex systems has provided insights in enzyme functions in central metabolic pathways, drug-protein interactions, and regulatory protein redox, for systems ranging from photoautotrophic cyanobacteria to mycobacteria, and combining live cell or cell extract ABPP with proteomics, molecular biology, modeling, and other techniques has greatly expanded our understanding of these systems. New opportunities for application of ABPP to microbial systems include: enhancing protein annotation, characterizing protein activities in myriad environments, and reveal signal transduction and regulatory mechanisms in microbial systems.

  13. Transient competitive complexation in biological kinetic isotope fractionation explains non-steady isotopic effects: Theory and application to denitrification in soils

    SciTech Connect (OSTI)

    Maggi, F.M.; Riley, W.J.

    2009-06-01

    The theoretical formulation of biological kinetic reactions in isotopic applications often assume first-order or Michaelis-Menten-Monod kinetics under the quasi-steady-state assumption to simplify the system kinetics. However, isotopic e ects have the same order of magnitude as the potential error introduced by these simpli cations. Both formulations lead to a constant fractionation factor which may yield incorrect estimations of the isotopic effect and a misleading interpretation of the isotopic signature of a reaction. We have analyzed the isotopic signature of denitri cation in biogeochemical soil systems by Menyailo and Hungate [2006], where high {sup 15}N{sub 2}O enrichment during N{sub 2}O production and inverse isotope fractionation during N{sub 2}O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with the quasi-steady-state Michaelis-Menten-Monod kinetics. When the quasi-steady-state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observations and aided in interpretation of experimental isotopic signatures. These results may imply a substantial revision in using the Rayleigh equation for interpretation of isotopic signatures and in modeling biological kinetic isotope fractionation with first-order kinetics or quasi-steady-state Michaelis-Menten-Monod kinetics.

  14. Coevolution of gene expression among interacting proteins

    SciTech Connect (OSTI)

    Fraser, Hunter B.; Hirsh, Aaron E.; Wall, Dennis P.; Eisen,Michael B.

    2004-03-01

    Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate previously uncharacterized coevolution of gene expression, adding a different dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein protein interactions.

  15. FUNCTIONAL INTERACTOMICS: DETERMINING THE ROLES PLAYED BY MEMBERS OF THE POPULAR BIOMASS PROTEIN-PROTEIN INTERACTOME

    SciTech Connect (OSTI)

    Beers, Eric; Brunner, Amy; Helm, Richard

    2015-07-31

    Proteins are molecular machines that are required for nearly all biological functions based on interactions with other molecules such as carbohydrates, lipids, other low molecular weight molecules, nucleic acids and other proteins. Here we map protein-protein interactions relevant to biomass production by focusing on proteins coexpressed in poplar xylem, the site of the majority of lignocellulose synthesis and hence biomass accumulation in poplar. Work proposed here will yield novel biological and bioinformatic resources that can benefit a variety of ongoing and future projects focusing on plant biomass/cell wall biology. The protein-protein interaction map that results from these studies will comprise an advanced view of protein-protein interactions in a model biomass tissue. Results will be made available to the biomass research community to serve as tools for developing new strategies for altering biomass quality and quantity.

  16. Cell-free system for synthesizing membrane proteins cell free method for synthesizing membrane proteins

    SciTech Connect (OSTI)

    Laible, Philip D; Hanson, Deborah K

    2013-06-04

    The invention provides an in vitro method for producing proteins, membrane proteins, membrane-associated proteins, and soluble proteins that interact with membrane-associated proteins for assembly into an oligomeric complex or that require association with a membrane for proper folding. The method comprises, supplying intracytoplasmic membranes from organisms; modifying protein composition of intracytoplasmic membranes from organism by modifying DNA to delete genes encoding functions of the organism not associated with the formation of the intracytoplasmic membranes; generating appropriate DNA or RNA templates that encode the target protein; and mixing the intracytoplasmic membranes with the template and a transcription/translation-competent cellular extract to cause simultaneous production of the membrane proteins and encapsulation of the membrane proteins within the intracytoplasmic membranes.

  17. Localization of peroxisomal matrix proteins by photobleaching

    SciTech Connect (OSTI)

    Buch, Charlotta; Hunt, Mary C.; Alexson, Stefan E.H.; Hallberg, Einar

    2009-10-16

    The distribution of some enzymes between peroxisomes and cytosol, or a dual localization in both these compartments, can be difficult to reconcile. We have used photobleaching in live cells expressing green fluorescent protein (GFP)-fusion proteins to show that imported bona fide peroxisomal matrix proteins are retained in the peroxisome. The high mobility of the GFP-fusion proteins in the cytosol and absence of peroxisomal escape makes it possible to eliminate the cytosolic fluorescence by photobleaching, to distinguish between exclusively cytosolic proteins and proteins that are also present at low levels in peroxisomes. Using this technique we found that GFP tagged bile acid-CoA:amino acid N-acyltransferase (BAAT) was exclusively localized in the cytosol in HeLa cells. We conclude that the cytosolic localization was due to its carboxyterminal non-consensus peroxisomal targeting signal (-SQL) since mutation of the -SQL to -SKL resulted in BAAT being efficiently imported into peroxisomes.

  18. Antimicrobial protein protects grapevines from pathogen

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Antimicrobial protein protects grapevines from pathogen Antimicrobial protein protects grapevines from pathogen Engineered grapevines produce a hybrid antimicrobial protein to block infection. February 21, 2012 Grapevines Goutam Gupta, from the Lab's Bioscience Division and the Center for Bio-security Science, along with researchers at the University of California at Davis (UCD), and the U.S. Department of Agriculture's Agricultural Research Service, have created specially engineered grapevines

  19. Hereditary thrombophilia: identification of nonsense and missense mutations in the protein C gene

    SciTech Connect (OSTI)

    Romeo, G.; Hassan, H.J.; Staempfli, S.; Roncuzzi, L.; Cianetti, L.; Leonardi, A.; Vicente, V.; Mannucci, P.M.; Bertina, R.; Peschile, C.; Cortese, R.

    1987-05-01

    The structure of the gene for protein C, an anticoagulant serine protease, was analyzed in 29 unrelated patients with hereditary thrombophilia and protein C deficiency. Gene deletion(s) or gross rearrangement(s) was not demonstrable by Southern blot hybridization to cDNA probes. However, two unrelated patients showed a variant restriction pattern after Pvu II or BamHi digestion, due to mutations in the last exon: analysis of their pedigrees, including three or seven heterozygotes, respectively, with approx.50% reduction of both enzymatic and antigen level, showed the abnormal restriction pattern in all heterozygous individuals, but not in normal relatives. Cloning of protein C gene and sequencing of the last exon allowed the authors to identify a nonsense and a missense mutation, respectively. In the first case, codon 306 (CGA, arginine) is mutated to an inframe stop codon, thus generating a new Pvu II recognition site. In the second case, a missense mutation in the BamHI palindrome (GGATCC ..-->.. GCATCC) leads to substitution of a key amino acid (a tryptophan to cysteine substitution at position 402), invariantly conserved in eukaryotic serine proteases. These point mutations may explain the protein C-deficiency phenotype of heterozygotes in the two pedigrees.

  20. An analysis framework for characterizing and explaining development of EIA legislation in developing countries-Illustrated for Georgia, Ghana and Yemen

    SciTech Connect (OSTI)

    Kolhoff, Arend J.; Driessen, Peter P.J.; Runhaar, Hens A.C.

    2013-01-15

    Actors in the field of international development co-operation supporting the development of EIA legislation in developing countries often do not achieve the results envisaged. The performance of EIA in these countries often remains weak. One reason, we assume, is that often those actors support the establishment of overly ambitious EIA legislation that cannot achieve its objectives in the light of constraining contexts. To provide more effective support we need to better understand the enabling and constraining contextual factors that influence the development of EIA legislation and to which support actors should align itself. In this article a new analysis framework for classifying, characterizing and explaining the development of EIA legislation is described, measured in terms of ambition levels. Ambitions are defined as intentions the EIA authorities aim to fulfill, expressed in formal EIA legislation. Three country cases, Yemen, Georgia and Ghana are used to illustrate the usefulness of our framework and as a first test to refine the framework. We have formulated the following five hypotheses that complement and refine our analysis framework. One, EIA legislation may develop multilinearly in terms of ambition levels. Two, ambitions in EIA legislation seem to be influenced to a great extent by the power and capacity of, on the one hand, the environmental authorities supporting EIA and, on the other hand, the sector authorities hindering the development of EIA. Three, the political system is the most important context factor influencing the rules of policy-making and the power of the different actors involved. Four, the importance of context factors on the development of ambitions is dependent on the phase of EIA system development. Five, some ambitions seem to be influenced by particular factors; for instance the ambitions for the object of study seem to be influenced by the level of environmental awareness of the sector ministries and parliament. The analysis

  1. Bayesian Proteoform Modeling Improves Protein Quantification...

    Office of Scientific and Technical Information (OSTI)

    Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Citation Details In-Document Search Title: Bayesian Proteoform Modeling Improves ...

  2. Orpinomyces xylanase proteins and coding sequences

    DOE Patents [OSTI]

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    1998-01-01

    Xylanases having high specific activities from Orpinomyces sp. strain PC-2 are provided as well as methods for their purification. DNA sequences encoding these proteins are also provided.

  3. Lipidic phase membrane protein serial femtosecond crystallography

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. ...

  4. Crystallization of Enantiomerically Pure Proteins from Quasi...

    Office of Scientific and Technical Information (OSTI)

    Crystallization of Enantiomerically Pure Proteins from Quasi-Racemic Mixtures: Structure Determination by X-Ray Diffraction of Isotope-Labeled Ester Insulin and Human Insulin ...

  5. Validating Computer-Designed Proteins for Vaccines

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Our immune systems, after all, are highly specialized and efficient producers of antibodies, those proteins that identify and kill the pathogens that are constantly attacking us ...

  6. DOE Science Showcase - Understanding Protein Membranes | OSTI...

    Office of Scientific and Technical Information (OSTI)

    Protein Research Documents from DOE Databases Information Bridge Energy Citations Database DOE R&D Accomplishments Database DOE R&D Project Summaries DOE Data Explorer Drug ...

  7. Protein Instability and Lou Gehrig's Disease

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    more prone to form clusters or aggregates, suggesting that strategies for stabilizing SOD proteins could be useful in treating or preventing SOD-linked ALS. The Other ALS...

  8. DIP: The Database of Interacting Proteins

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The DIP Database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. By interaction, the DIP Database creators mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organisation and complexity of the protein interaction network at the cellular level. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. It is a relational database that can be searched by protein, sequence, motif, article information, and pathBLAST. The website also serves as an access point to a number of projects related to DIP, such as LiveDIP, The Database of Ligand-Receptor Partners (DLRP) and JDIP. Users have free and open access to DIP after login. [Taken from the DIP Guide and the DIP website] (Specialized Interface) (Registration Required)

  9. Translocator Protein Structure and Function | Stanford Synchrotron...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    protein that binds benzodiazepine drugs, but distinct from the central nervous ... with anxiety-related diseases, making it a potential target for anxiolytic drugs. ...

  10. Year 2 Report: Protein Function Prediction Platform

    SciTech Connect (OSTI)

    Zhou, C E

    2012-04-27

    Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

  11. Protein Instability and Lou Gehrig's Disease

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    called superoxide dismutase (SOD). The study provides evidence that those proteins linked to more severe forms of the disease are less stable structurally and more prone to...

  12. A Designed Protein Maps Brain Activity

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    A Designed Protein Maps Brain Activity Print A team of scientists from the Howard Hughes Medical Institute's Janelia Research Campus designed and validated via x-ray...

  13. Protein Structure Suggests Role as Molecular Adapter

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Protein Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the...

  14. Energy barriers, cooperativity, and hidden intermediates in the folding of small proteins

    SciTech Connect (OSTI)

    Bai Yawen [Laboratory of Biochemistry, National Cancer Institute, NIH, Building 37, Room 6114E, Bethesda, MD 20892 (United States)]. E-mail: yawen@helix.nih.gov

    2006-02-17

    Current theoretical views of the folding process of small proteins (<{approx}100 amino acids) postulate that the landscape of potential mean force (PMF) for the formation of the native state has a funnel shape and that the free energy barrier to folding arises from the chain configurational entropy only. However, recent theoretical studies on the formation of hydrophobic clusters with explicit water suggest that a barrier should exist on the PMF of folding, consistent with the fact that protein folding generally involves a large positive activation enthalpy at room temperature. In addition, high-resolution structural studies of the hidden partially unfolded intermediates have revealed the existence of non-native interactions, suggesting that the correction of the non-native interactions during folding should also lead to barriers on PMF. To explore the effect of a PMF barrier on the folding behavior of proteins, we modified Zwanzig's model for protein folding with an uphill landscape of PMF for the formation of transition states. We found that the modified model for short peptide segments can satisfy the thermodynamic and kinetic criteria for an apparently two-state folding. Since the Levinthal paradox can be solved by a stepwise folding of short peptide segments, a landscape of PMF with a locally uphill search for the transition state and cooperative stabilization of folding intermediates/native state is able to explain the available experimental results for small proteins. We speculate that the existence of cooperative hidden folding intermediates in small proteins could be the consequence of the highly specific structures of the native state, which are selected by evolution to perform specific functions and fold in a biologically meaningful time scale.

  15. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

    Ben-Naim, A. (Hebrew Univ., Jerusalem (Israel))

    1990-08-23

    The solvent-induced forces between various groups on the protein are examined. It is found that the intramolecular hydrophilic forces are likely to be the strongest forces mediated through the solvent. It is argued that these are probably the most important solvent-induced driving forces in the process of protein folding.

  16. Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy - An Enhanced Method for Examining Protein Conformations and Protein Interactions

    SciTech Connect (OSTI)

    B Wallace; R Janes

    2011-12-31

    CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins, the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein-protein complex formation involving either induced-fit or rigid-body mechanisms, and protein-lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.

  17. Synthesizing Membrane Proteins Using In Vitro Methodology | Argonne

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    National Laboratory Membrane Proteins Using In Vitro Methodology Technology available for licensing: in vitro, cell-free expression system that caters to the production of protein types that are challenging to study: membrane proteins, membrane-associated proteins, and soluble proteins that require complex redox cofactors. A cell-free, in vitro protein synthesis method for targeting difficult-to-study proteins Quicker and easier than conventional methodologies, this system does not require

  18. Wide angle x-ray scattering of proteins : effect of beam exposure on protein integrity.

    SciTech Connect (OSTI)

    Fischetti, R. F.; Rodi, D. J.; Mirza, A.; Makowski, L.; Illinois Inst. of Tech.

    2003-01-01

    Wide-angle X-ray scattering patterns from proteins in solution contain information relevant to the determination of protein fold. At relevant scattering angles, however, these data are weak, and the degree to which they might be used to categorize the fold of a protein is unknown. Preliminary work has been performed at the BioCAT insertion-device beamline at the Advanced Photon Source which demonstrates that one can collect X-ray scattering data from proteins in solution to spacings of at least 2.2 {angstrom} (q = 2.8 {angstrom}-1). These data are sensitive to protein conformational states, and are in good agreement with the scattering predicted by the program CRYSOL using the known three-dimensional atomic coordinates of the protein. An important issue in the exploitation of this technique as a tool for structural genomics is the extent to which the high intensity of X-rays available at third-generation synchrotron sources chemically or structurally damage proteins. Various data-collection protocols have been investigated demonstrating conditions under which structural degradation of even sensitive proteins can be minimized, making this technique a viable tool for protein fold categorization, the study of protein folding, unfolding, protein-ligand interactions and domain movement.

  19. Structural effects of protein aging: Terminal marking by deamidation in human triosephosphate isomerase

    DOE PAGES-Beta [OSTI]

    Torres-Larios, Alfredo; Enríquez-Flores, Sergio; Méndez, Sara -Teresa; Castillo-Villanueva, Adriana; Gómez-Manzo, Saúl; Velázquez, Gabriel López-; Marcial-Quino, Jaime; Torres-Arroyo, Angélica; García-Torres, Itzhel; Reyes-Vivas, Horacio; et al

    2015-04-17

    Deamidation, the loss of the ammonium group of asparagine and glutamine to form aspartic and glutamic acid, is one of the most commonly occurring post-translational modifications in proteins. Since deamidation rates are encoded in the protein structure, it has been proposed that they can serve as molecular clocks for the timing of biological processes such as protein turnover, development and aging. Despite the importance of this process, there is a lack of detailed structural information explaining the effects of deamidation on the structure of proteins. Here, we studied the effects of deamidation on human triosephosphate isomerase (HsTIM), an enzyme formore » which deamidation of N15 and N71 has been long recognized as the signal for terminal marking of the protein. Deamidation was mimicked by site directed mutagenesis; thus, three mutants of HsTIM (N15D, N71D and N15D/N71D) were characterized. The results show that the N71D mutant resembles, structurally and functionally, the wild type enzyme. In contrast, the N15D mutant displays all the detrimental effects related to deamidation. The N15D/N71D mutant shows only minor additional effects when compared with the N15D mutation, supporting that deamidation of N71 induces negligible effects. The crystal structures show that, in contrast to the N71D mutant, where minimal alterations are observed, the N15D mutation forms new interactions that perturb the structure of loop 1 and loop 3, both critical components of the catalytic site and the interface of HsTIM. Based on a phylogenetic analysis of TIM sequences, we propose the conservation of this mechanism for mammalian TIMs.« less

  20. Orpinomyces xylanase proteins and coding sequences

    DOE Patents [OSTI]

    Li, X.L.; Ljungdahl, L.G.; Chen, H.

    1998-10-20

    Xylanases having high specific activities from Orpinomyces sp. strain PC-2 are provided as well as methods for their purification. DNA sequences encoding these proteins are also provided. 8 figs.

  1. Biomimetic materials for protein storage and transport

    DOE Patents [OSTI]

    Firestone, Millicent A.; Laible, Philip D.

    2012-05-01

    The invention provides a method for the insertion of protein in storage vehicles and the recovery of the proteins from the vehicles, the method comprising supplying isolated protein; mixing the isolated protein with a fluid so as to form a mixture, the fluid comprising saturated phospholipids, lipopolymers, and a surfactant; cycling the mixture between a first temperature and a second temperature; maintaining the mixture as a solid for an indefinite period of time; diluting the mixture in detergent buffer so as to disrupt the composition of the mixture, and diluting to disrupt the fluid in its low viscosity state for removal of the guest molecules by, for example, dialysis, filtering or chromatography dialyzing/filtering the emulsified solid.

  2. Protein Scaffolding for Small Molecule Catalysts

    SciTech Connect (OSTI)

    Baker, David

    2014-09-14

    We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to model novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine hydrogenase of DuBois et. al.We will enhance the hydrogenase activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematically modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.

  3. Mapping the Protein Universe | Argonne National Laboratory

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    of proteins do, and even less about how they do it. While the ability to scoop up microbes from the environment and sequence their DNA has been getting cheaper, we don't yet...

  4. Validating Computer-Designed Proteins for Vaccines

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Validating Computer-Designed Proteins for Vaccines Print In the struggle to keep up with microbes whose rapid mutations outpace our ability to produce vaccines, the human race has...

  5. Collaboration drives achievement in protein structure research

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Collaboration drives achievement in protein structure research Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit Collaboration drives achievement in protein structure research By tracking down how bacterial defense systems work, the scientists can potentially fight infectious diseases and genetic disorders November 1, 2014 Thomas Terwilliger Thomas Terwilliger Contact Linda Anderman Email When a recent print issue of

  6. Molecular Characterizations of Surface Proteins Hemagglutinin and

    Office of Scientific and Technical Information (OSTI)

    Neuraminidase from Recent H5Nx Avian Influenza Viruses (Journal Article) | SciTech Connect Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses Citation Details In-Document Search Title: Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses During 2014, a subclade 2.3.4.4 highly pathogenic avian influenza (HPAI) A(H5N8) virus caused poultry outbreaks around

  7. Exo-endo cellulase fusion protein

    DOE Patents [OSTI]

    Bower, Benjamin S.; Larenas, Edmund A.; Mitchinson, Colin

    2012-01-17

    The present invention relates to a heterologous exo-endo cellulase fusion construct, which encodes a fusion protein having cellulolytic activity comprising a catalytic domain derived from a fungal exo-cellobiohydrolase and a catalytic domain derived from an endoglucanase. The invention also relates to vectors and fungal host cells comprising the heterologous exo-endo cellulase fusion construct as well as methods for producing a cellulase fusion protein and enzymatic cellulase compositions.

  8. Positive modulator of bone morphogenic protein-2

    DOE Patents [OSTI]

    Zamora, Paul O.; Pena, Louis A.; Lin, Xinhua; Takahashi, Kazuyuki

    2009-01-27

    Compounds of the present invention of formula I and formula II are disclosed in the specification and wherein the compounds are modulators of Bone Morphogenic Protein activity. Compounds are synthetic peptides having a non-growth factor heparin binding region, a linker, and sequences that bind specifically to a receptor for Bone Morphogenic Protein. Uses of compounds of the present invention in the treatment of bone lesions, degenerative joint disease and to enhance bone formation are disclosed.

  9. Crystal Structure of a Protein Kinase A Complex

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Crystal Structure of a Protein Kinase A Complex Crystal Structure of a Protein Kinase A Complex Print Wednesday, 26 October 2005 00:00 Protein kinase A (PKA) is an enzyme that...

  10. A Tool for Interactive Protein Manipulation

    Energy Science and Technology Software Center (OSTI)

    2005-03-28

    ProteinShop is a graphical environment that facilitates a solution to the protein prediction problem through a combination of unique features and capabilities. These include: 1. Helping researchers automatically generate 3D protein structures from scratcW by using the sequence of amino acids and secondary structure specifications as input. 2. Enabling users to apply their accumulated biochemical knowledge and intuition during the interactive manipulation of structures. 3. FacIlitating interactive comparison and analysis of alternative structures through visualizationmore » of free energy computed during modeling. 4. Accelerating discovery of low-energy configurations by applying local optimizations plug-in to user-selected protein structures. ProteinShop v.2.0 includes the following new features: - Visualizes multiple-domain structures - Automatically creates a user-specified number of beta-sheet configurations - Provides the interface and the libraries for energy visualization and local minimization of protein structures - Reads standard POB files without previous editing« less

  11. Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

    SciTech Connect (OSTI)

    Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.; Machius, Mischa; Szyperski, Thomas; Kuhlman, Brian

    2015-10-15

    Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).

  12. Covalent agonists for studying G protein-coupled receptor activation...

    Office of Scientific and Technical Information (OSTI)

    Covalent agonists for studying G protein-coupled receptor activation Citation Details In-Document Search Title: Covalent agonists for studying G protein-coupled receptor activation ...

  13. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN ...

  14. On the predictability of the orientation of protein domains joined...

    Office of Scientific and Technical Information (OSTI)

    of protein domains joined by a spanning alpha-helical linker Citation Details In-Document Search Title: On the predictability of the orientation of protein domains ...

  15. Applications of molecular replacement to G protein-coupled receptors...

    Office of Scientific and Technical Information (OSTI)

    Applications of molecular replacement to G protein-coupled receptors Citation Details In-Document Search Title: Applications of molecular replacement to G protein-coupled receptors ...

  16. More grapes, less wrath: hybrid antimicrobial protein protects...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Hybrid antimicrobial protein protects grapevines from pathogen More grapes, less wrath: hybrid antimicrobial protein protects grapevines from pathogen Researchers has found a way...

  17. Robust, High-Throughput Analysis of Protein Structures

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Robust, High-Throughput Analysis of Protein Structures Print Scientists have developed a fast and efficient way to determine the structure of proteins, shortening a process that...

  18. From Protein Structure to Function: Ring Cycle for Dilating and...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore From Protein Structure to Function: Ring Cycle for Dilating and Constricting the...

  19. Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous...

    Office of Scientific and Technical Information (OSTI)

    Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic Citation Details In-Document Search Title: Renaturing Membrane Proteins in the Lipid Cubic ...

  20. Nantong BIOLUX Bioenergy Protein Feed Co Ltd | Open Energy Information

    Open Energy Information (Open El) [EERE & EIA]

    Nantong BIOLUX Bioenergy Protein Feed Co Ltd Jump to: navigation, search Name: Nantong BIOLUX Bioenergy Protein Feed Co Ltd Place: Nantong, Jiangsu Province, China Product: BIOLUX...

  1. Glucose-Neopentyl Glycol (GNG) amphiphiles for membrane protein...

    Office of Scientific and Technical Information (OSTI)

    Glucose-Neopentyl Glycol (GNG) amphiphiles for membrane protein study Citation Details In-Document Search Title: Glucose-Neopentyl Glycol (GNG) amphiphiles for membrane protein ...

  2. Structures for Three Membrane Transport Proteins Yield Functional...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Structures for Three Membrane Transport Proteins Yield Functional Insights Structures for Three Membrane Transport Proteins Yield Functional Insights Print Wednesday, 27 January ...

  3. Directed Spontaneous Assembly of Membrane Protein with Amphiphilic...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Directed Spontaneous Assembly of Membrane Protein with Amphiphilic Block Copolymers ... invention describes a method for using membrane proteins (MPs) in synthetic systems for ...

  4. Using Rhodobacter Bacteria to Express Membrane Proteins (ANL...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    to Express Membrane Proteins (ANL-IN-99-089) Argonne National Laboratory Contact ANL About This Technology

    A strategy to express heterologous membrane proteins by using ...

  5. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein...

  6. Compositions and methods for improved protein production (Patent...

    Office of Scientific and Technical Information (OSTI)

    Compositions and methods for improved protein production Title: Compositions and methods for improved protein production The present invention relates to the identification of ...

  7. Simplified Protein Models: Predicting Folding Pathways and Structure...

    Office of Scientific and Technical Information (OSTI)

    Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences Title: Simplified Protein Models: Predicting Folding Pathways and Structure Using ...

  8. Artificial oxygen transport protein (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Patent: Artificial oxygen transport protein Citation Details In-Document Search Title: Artificial oxygen transport protein This invention provides heme-containing peptides capable...

  9. New Crystal Structures Lift Fog around Protein Folding

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these...

  10. Robust, High-Throughput Analysis of Protein Structures

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    is sufficient to address key biological questions. For example, future synthetic biology efforts may involve taking a useful protein, or a network of proteins, from one...

  11. Towards a map of the Populus biomass protein-protein interaction network

    SciTech Connect (OSTI)

    Beers, Eric; Brunner, Amy; Helm, Richard; Dickerman, Allan

    2015-07-31

    Biofuels can be produced from a variety of plant feedstocks. The value of a particular feedstock for biofuels production depends in part on the degree of difficulty associated with the extraction of fermentable sugars from the plant biomass. The wood of trees is potentially a rich source fermentable sugars. However, the sugars in wood exist in a tightly cross-linked matrix of cellulose, hemicellulose, and lignin, making them largely recalcitrant to release and fermentation for biofuels production. Before breeders and genetic engineers can effectively develop plants with reduced recalcitrance to fermentation, it is necessary to gain a better understanding of the fundamental biology of the mechanisms responsible for wood formation. Regulatory, structural, and enzymatic proteins are required for the complicated process of wood formation. To function properly, proteins must interact with other proteins. Yet, very few of the protein-protein interactions necessary for wood formation are known. The main objectives of this project were to 1) identify new protein-protein interactions relevant to wood formation, and 2) perform in-depth characterizations of selected protein-protein interactions. To identify relevant protein-protein interactions, we cloned a set of approximately 400 genes that were highly expressed in the wood-forming tissue (known as secondary xylem) of poplar (Populus trichocarpa). We tested whether the proteins encoded by these biomass genes interacted with each other in a binary matrix design using the yeast two-hybrid (Y2H) method for protein-protein interaction discovery. We also tested a subset of the 400 biomass proteins for interactions with all proteins present in wood-forming tissue of poplar in a biomass library screen design using Y2H. Together, these two Y2H screens yielded over 270 interactions involving over 75 biomass proteins. For the second main objective we selected several interacting pairs or groups of interacting proteins for in

  12. Protein-Folding Landscapes in Multi-Chain Systems Cellmer, Troy...

    Office of Scientific and Technical Information (OSTI)

    37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; FREE ENERGY; MELTING; PROTEINS; THERMODYNAMICS; TOPOLOGY protein folding protein...

  13. Protein_folding.png | OSTI, US Dept of Energy Office of Scientific and

    Office of Scientific and Technical Information (OSTI)

    Technical Information Protein_folding

  14. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01

    Proteins, biological macromolecules composed of amino-acid building blocks, possess unique three dimensional shapes or conformations which are intimately related to their biological function. All of the information necessary to determine this conformation is stored in a protein`s amino acid sequence. The problem of understanding the process by which nature maps protein amino-acid sequences to three-dimensional conformations is known as the protein folding problem, and is one of the central unsolved problems in biophysics today. The possible applications of a solution are broad, ranging from the elucidation of thousands of protein structures to the rational modification and design of protein-based drugs. The scattering of X-rays by matter has long been useful as a tool for the characterization of physical properties of materials, including biological samples. The high photon flux available at synchrotron X-ray sources allows for the measurement of scattering cross-sections of dilute and/or disordered samples. Such measurements do not yield the detailed geometrical information available from crystalline samples, but do allow for lower resolution studies of dynamical processes not observable in the crystalline state. The main focus of the work described here has been the study of the protein folding process using time-resolved small-angle x-ray scattering measurements. The original intention was to observe the decrease in overall size which must accompany the folding of a protein from an extended conformation to its compact native state. Although this process proved too fast for the current time-resolution of the technique, upper bounds were set on the probable compaction times of several small proteins. In addition, an interesting and unexpected process was detected, in which the folding protein passes through an intermediate state which shows a tendency to associate. This state is proposed to be a kinetic molten globule folding intermediate.

  15. Amber Plug-In for Protein Shop

    Energy Science and Technology Software Center (OSTI)

    2004-05-10

    The Amber Plug-in for ProteinShop has two main components: an AmberEngine library to compute the protein energy models, and a module to solve the energy minimization problem using an optimization algorithm in the OPTI-+ library. Together, these components allow the visualization of the protein folding process in ProteinShop. AmberEngine is a object-oriented library to compute molecular energies based on the Amber model. The main class is called ProteinEnergy. Its main interface methods are (1) "init"more » to initialize internal variables needed to compute the energy. (2) "eval" to evaluate the total energy given a vector of coordinates. Additional methods allow the user to evaluate the individual components of the energy model (bond, angle, dihedral, non-bonded-1-4, and non-bonded energies) and to obtain the energy of each individual atom. The Amber Engine library source code includes examples and test routines that illustrate the use of the library in stand alone programs. The energy minimization module uses the AmberEngine library and the nonlinear optimization library OPT++. OPT++ is open source software available under the GNU Lesser General Public License. The minimization module currently makes use of the LBFGS optimization algorithm in OPT++ to perform the energy minimization. Future releases may give the user a choice of other algorithms available in OPT++.« less

  16. Protein expression, characterization and activity comparisons of wild type and mutant DUSP5 proteins

    DOE PAGES-Beta [OSTI]

    Nayak, Jaladhi; Gastonguay, Adam J.; Talipov, Marat R.; Vakeel, Padmanabhan; Span, Elise A.; Kalous, Kelsey S.; Kutty, Raman G.; Jensen, Davin R.; Pokkuluri, Phani Raj; Sem, Daniel S.; et al

    2014-12-18

    Background: The mitogen-activated protein kinases (MAPKs) pathway is critical for cellular signaling, and proteins such as phosphatases that regulate this pathway are important for normal tissue development. Based on our previous work on dual specificity phosphatase-5 (DUSP5), and its role in embryonic vascular development and disease, we hypothesized that mutations in DUSP5 will affect its function. Results: In this study, we tested this hypothesis by generating full-length glutathione-S-transferase-tagged DUSP5 and serine 147 proline mutant (S147P) proteins from bacteria. Light scattering analysis, circular dichroism, enzymatic assays and molecular modeling approaches have been performed to extensively characterize the protein form and function.more » We demonstrate that both proteins are active and, interestingly, the S147P protein is hypoactive as compared to the DUSP5 WT protein in two distinct biochemical substrate assays. Furthermore, due to the novel positioning of the S147P mutation, we utilize computational modeling to reconstruct full-length DUSP5 and S147P to predict a possible mechanism for the reduced activity of S147P. Conclusion: Taken together, this is the first evidence of the generation and characterization of an active, full-length, mutant DUSP5 protein which will facilitate future structure-function and drug development-based studies.« less

  17. The vaccinia virus E6 protein influences virion protein localization during virus assembly

    SciTech Connect (OSTI)

    Condit, Richard C. Moussatche, Nissin

    2015-08-15

    Vaccinia virus mutants in which expression of the virion core protein gene E6R is repressed are defective in virion morphogenesis. E6 deficient infections fail to properly package viroplasm into viral membranes, resulting in an accumulation of empty immature virions and large aggregates of viroplasm. We have used immunogold electron microscopy and immunofluorescence confocal microscopy to assess the intracellular localization of several virion structural proteins and enzymes during E6R mutant infections. We find that during E6R mutant infections virion membrane proteins and virion transcription enzymes maintain a normal localization within viral factories while several major core and lateral body proteins accumulate in aggregated virosomes. The results support a model in which vaccinia virions are assembled from at least three substructures, the membrane, the viroplasm and a “pre-nucleocapsid”, and that the E6 protein is essential for maintaining proper localization of the seven-protein complex and the viroplasm during assembly. - Highlights: • Mutation of E6 disrupts association of viral membranes with viral core proteins • Mutation of E6 does not perturb viral membrane biosynthesis • Mutation of E6 does not perturb localization of viral transcription enzymes • Mutation of E6 causes mis-localization and aggregation of viral core proteins • Vaccinia assembly uses three subassemblies: membranes, viroplasm, prenucleocapsid.

  18. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    SciTech Connect (OSTI)

    Fenglei Li

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  19. Functional Classification of Immune Regulatory Proteins

    SciTech Connect (OSTI)

    Rubinstein, Rotem; Ramagopal, Udupi A.; Nathenson, Stanley G.; Almo, Steven C.; Fiser, Andras

    2013-05-01

    Members of the immunoglobulin superfamily (IgSF) control innate and adaptive immunity and are prime targets for the treatment of autoimmune diseases, infectious diseases, and malignancies. We describe a computational method, termed the Brotherhood algorithm, which utilizes intermediate sequence information to classify proteins into functionally related families. This approach identifies functional relationships within the IgSF and predicts additional receptor-ligand interactions. As a specific example, we examine the nectin/nectin-like family of cell adhesion and signaling proteins and propose receptor-ligand interactions within this family. We were guided by the Brotherhood approach and present the high-resolution structural characterization of a homophilic interaction involving the class-I MHC-restricted T-cell-associated molecule, which we now classify as a nectin-like family member. The Brotherhood algorithm is likely to have a significant impact on structural immunology by identifying those proteins and complexes for which structural characterization will be particularly informative.

  20. Spectromicroscopy of self-assembled protein clusters

    SciTech Connect (OSTI)

    Schonschek, O.; Hormes, J.; Herzog, V.

    1997-04-01

    The aim of this project is to use synchrotron radiation as a tool to study biomedical questions concerned with the thyroid glands. The biological background is outlined in a recent paper. In short, Thyroglobulin (TG), the precursor protein of the hormone thyroxine, forms large (20 - 500 microns in diameter) clusters in the extracellular lumen of thyrocytes. The process of the cluster formation is still not well understood but is thought to be a main storage mechanism of TG and therefore thyroxine inside the thyroid glands. For human thyroids, the interconnections of the proteins inside the clusters are mainly disulfide bondings. Normally, sulfur bridges are catalyzed by an enzyme called Protein Disulfide Bridge Isomerase (PDI). While this enzyme is supposed to be not present in any extracellular space, the cluster formation of TG takes place in the lumen between the thyrocytes. A possible explanation is the autocatalysis of TG.

  1. Some thermodynamical aspects of protein hydration water

    SciTech Connect (OSTI)

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Stanley, H. Eugene; Chen, Sow-Hsin

    2015-06-07

    We study by means of nuclear magnetic resonance the self-diffusion of protein hydration water at different hydration levels across a large temperature range that includes the deeply supercooled regime. Starting with a single hydration shell (h = 0.3), we consider different hydrations up to h = 0.65. Our experimental evidence indicates that two phenomena play a significant role in the dynamics of protein hydration water: (i) the measured fragile-to-strong dynamic crossover temperature is unaffected by the hydration level and (ii) the first hydration shell remains liquid at all hydrations, even at the lowest temperature.

  2. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

    Campisi, Judith; Kim, Sahn-Ho

    2002-01-01

    The present invention provides a novel telomere associated protein (Trf1-interacting nuclear protein 2 "Tin2") that hinders the binding of Trf1 to its specific telomere repeat sequence and mediates the formation of a Tin2-Trf1-telomeric DNA complex that limits telomerase access to the telomere. Also included are the corresponding nucleic acids that encode the Tin2 of the present invention, as well as mutants of Tin2. Methods of making, purifying and using Tin2 of the present invention are described. In addition, drug screening assays to identify drugs that mimic and/or complement the effect of Tin2 are presented.

  3. Compositions and methods for improved protein production

    DOE Patents [OSTI]

    Bodie, Elizabeth A.; Kim, Steve Sungjin

    2014-06-03

    The present invention relates to the identification of novel nucleic acid sequences, designated herein as 7p, 8k, 7E, 9G, 8Q and 203, in a host cell which effect protein production. The present invention also provides host cells having a mutation or deletion of part or all of the gene encoding 7p, 8k, 7E, 9G, 8Q and 203, which are presented in FIG. 1, and are SEQ ID NOS.: 1-6, respectively. The present invention also provides host cells further comprising a nucleic acid encoding a desired heterologous protein such as an enzyme.

  4. Compositions and methods for improved protein production

    DOE Patents [OSTI]

    Bodie, Elizabeth A.; Kim, Steve

    2012-07-10

    The present invention relates to the identification of novel nucleic acid sequences, designated herein as 7p, 8k, 7E, 9G, 8Q and 203, in a host cell which effect protein production. The present invention also provides host cells having a mutation or deletion of part or all of the gene encoding 7p, 8k, 7E, 9G, 8Q and 203, which are presented in FIG. 1, and are SEQ ID NOS.: 1-6, respectively. The present invention also provides host cells further comprising a nucleic acid encoding a desired heterologous protein such as an enzyme.

  5. Robust expression of a bioactive mammalian protein in chlamydomonas chloroplast

    DOE Patents [OSTI]

    Mayfield, Stephen P.

    2010-03-16

    Methods and compositions are disclosed to engineer chloroplast comprising heterologous mammalian genes via a direct replacement of chloroplast Photosystem II (PSII) reaction center protein coding regions to achieve expression of recombinant protein above 5% of total protein. When algae is used, algal expressed protein is produced predominantly as a soluble protein where the functional activity of the peptide is intact. As the host algae is edible, production of biologics in this organism for oral delivery or proteins/peptides, especially gut active proteins, without purification is disclosed.

  6. Robust expression of a bioactive mammalian protein in Chlamydomonas chloroplast

    DOE Patents [OSTI]

    Mayfield, Stephen P

    2015-01-13

    Methods and compositions are disclosed to engineer chloroplast comprising heterologous mammalian genes via a direct replacement of chloroplast Photosystem II (PSII) reaction center protein coding regions to achieve expression of recombinant protein above 5% of total protein. When algae is used, algal expressed protein is produced predominantly as a soluble protein where the functional activity of the peptide is intact. As the host algae is edible, production of biologics in this organism for oral delivery of proteins/peptides, especially gut active proteins, without purification is disclosed.

  7. Structural determination of intact proteins using mass spectrometry

    DOE Patents [OSTI]

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  8. Fast computational methods for predicting protein structure from primary

    Office of Scientific and Technical Information (OSTI)

    amino acid sequence (Patent) | DOEPatents Fast computational methods for predicting protein structure from primary amino acid sequence Title: Fast computational methods for predicting protein structure from primary amino acid sequence The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible

  9. Tailoring a low-molecular weight protein tyrosine phosphatase into an efficient reporting protein

    SciTech Connect (OSTI)

    Liu, Xiao-Yan; Li, Lan-Fen [The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Science, Peking University, Beijing 100871 (China)] [The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Science, Peking University, Beijing 100871 (China); Su, Xiao-Dong, E-mail: xdsu@pku.edu.cn [The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Science, Peking University, Beijing 100871 (China) [The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Science, Peking University, Beijing 100871 (China); Shenzhen Graduate School of Peking University, Shenzhen 518055 (China)

    2009-05-15

    Fusion reporter methods are important tools for biology and biotechnology. An ideal reporter protein in a fusion system should have little effects on its fusion partner and provide an easy and accurate readout. Therefore, a small monomeric protein with high activity for detection assays often has advantages as a reporter protein. For this purpose, we have tailored the human B-form low-molecular-weight phosphotyrosyl phosphatase (HPTP-B) to increase its general applicability as a potent reporter protein. With the aim to eliminate interference from cysteine residues in the native HPTP-B, combined with a systematic survey of N- and C-terminal truncated variants, a series of cysteine to serine mutations were introduced, which allowed isolation of an engineered soluble protein with suitable biophysical properties. When we deleted both the first six residues and the last two residues, we still obtained a soluble mutant protein with correct folding and similar activity with wild-type protein. This mutant with two cysteine to serine mutations, HPTP-B{sup N{sub {Delta}}6-C{sub {Delta}}2-C90S-C109S}, has good potential as an optimal reporter.

  10. Transcriptional enhancer from milk protein genes

    DOE Patents [OSTI]

    Casperson, Gerald F.; Schmidhauser, Christian T.; Bissell, Mina J.

    1999-01-01

    The invention relates to novel enhancer nucleotide sequences which stimulate transcription of heterologous DNA in cells in culture. The enhancers are derived from major milk protein genes by the process of deletion mapping and functional analysis. The invention also relates to expression vectors containing the novel enhancers.

  11. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-07-11

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  12. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  13. Fusion proteins useful for producing pinene

    DOE Patents [OSTI]

    Peralta-Yahya, Pamela P.; Keasling, Jay D

    2016-06-28

    The present invention provides for a modified host cell comprising a heterologous pinene synthase (PS), or enzymatically active fragment or variant thereof, and optionally a geranyl pyrophosphate synthase (GPPS), or enzymatically active fragment or variant thereof, or a fusion protein comprising: (a) a PS and (b) a GPPS linked by a linker.

  14. The MORPHEUS II protein crystallization screen

    SciTech Connect (OSTI)

    Gorrec, Fabrice

    2015-06-27

    MORPHEUS II is a 96-condition initial crystallization screen formulated de novo. The screen incorporates reagents selected from the Protein Data Bank to yield crystals that are not observed in traditional conditions. In addition, the formulation facilitates the optimization and cryoprotection of crystals. High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.

  15. Corn Storage Protein - A Molecular Genetic Model

    SciTech Connect (OSTI)

    Messing, Joachim

    2013-05-31

    Corn is the highest yielding crop on earth and probably the most valuable agricultural product of the United States. Because it converts sun energy through photosynthesis into starch and proteins, we addressed energy savings by focusing on protein quality. People and animals require essential amino acids derived from the digestion of proteins. If proteins are relatively low in certain essential amino acids, the crop becomes nutritionally defective and has to be supplemented. Such deficiency affects meat and fish production and countries where corn is a staple. Because corn seed proteins have relatively low levels of lysine and methionine, a diet has to be supplemented with soybeans for the missing lysine and with chemically synthesized methionine. We therefore have studied genes expressed during maize seed development and their chromosomal organization. A critical technical requirement for the understanding of the molecular structure of genes and their positional information was DNA sequencing. Because of the length of sequences, DNA sequencing methods themselves were insufficient for this type of analysis. We therefore developed the so-called “DNA shotgun sequencing” strategy, where overlapping DNA fragments were sequenced in parallel and used to reconstruct large DNA molecules via overlaps. Our publications became the most frequently cited ones during the decade of 1981-1990 and former Associate Director of Science for the Office of Basic Energy Sciences Patricia M. Dehmer presented our work as one of the great successes of this program. A major component of the sequencing strategy was the development of bacterial strains and vectors, which were also used to develop the first biotechnology crops. These crops possessed new traits thanks to the expression of foreign genes in plants. To enable such expression, chimeric genes had to be constructed using our materials and methods by the industry. Because we made our materials and methods freely available to

  16. The interactions of peripheral membrane proteins with biological membranes

    DOE PAGES-Beta [OSTI]

    Johs, Alexander; Whited, A. M.

    2015-01-01

    The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approachesmore » continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.« less

  17. The interactions of peripheral membrane proteins with biological membranes

    SciTech Connect (OSTI)

    Johs, Alexander; Whited, A. M.

    2015-01-01

    The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approaches continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.

  18. Automated Analysis of Fluorescence Microscopy Images to Identify Protein-Protein Interactions

    DOE PAGES-Beta [OSTI]

    Venkatraman, S.; Doktycz, M. J.; Qi, H.; Morrell-Falvey, J. L.

    2006-01-01

    The identification of protein interactions is important for elucidating biological networks. One obstacle in comprehensive interaction studies is the analyses of large datasets, particularly those containing images. Development of an automated system to analyze an image-based protein interaction dataset is needed. Such an analysis system is described here, to automatically extract features from fluorescence microscopy images obtained from a bacterial protein interaction assay. These features are used to relay quantitative values that aid in the automated scoring of positive interactions. Experimental observations indicate that identifying at least 50% positive cells in an image is sufficient to detect a protein interaction.more » Based on this criterion, the automated system presents 100% accuracy in detecting positive interactions for a dataset of 16 images. Algorithms were implemented using MATLAB and the software developed is available on request from the authors.« less

  19. Deducing the Energetic Cost of Protein Folding in Zinc Finger Proteins Using Designed Metallopeptides

    SciTech Connect (OSTI)

    Reddi,A.; Guzman, T.; Breece, r.; Tierney, D.; Gibney, B.

    2007-01-01

    Zinc finger transcription factors represent the largest single class of metalloproteins in the human genome. Binding of Zn(II) to their canonical Cys4, Cys3His1, or Cys2His2 sites results in metal-induced protein folding events required to achieve their proper structure for biological activity. The thermodynamic contribution of Zn(II) in each of these coordination spheres toward protein folding is poorly understood because of the coupled nature of the metal-ligand and protein-protein interactions. Using an unstructured peptide scaffold, GGG, we have employed fluorimetry, potentiometry, and calorimetry to determine the thermodynamics of Zn(II) binding to the Cys4, Cys3His1, and Cys2His2 ligand sets with minimal interference from protein folding effects. The data show that Zn(II) complexation is entropy driven and modulated by proton release. The formation constants for Zn(II)-GGG with a Cys4, Cys3His1, or Cys2His2 site are 5.6 x 1016, 1.5 x 1015, or 2.5 x 1013 M-1, respectively. Thus, the Zn(II)-Cys4, Zn(II)-Cys3His1, and Zn(II)-Cys2His2 interactions can provide up to 22.8, 20.7, and 18.3 kcal/mol, respectively, in driving force for protein stabilization, folding, and/or assembly at pH values above the ligand pKa values. While the contributions from the three coordination motifs differ by 4.5 kcal/mol in Zn(II) affinity at pH 9.0, they are equivalent at physiological pH, ?G = -16.8 kcal/mol or a Ka = 2.0 x 1012 M-1. Calorimetric data show that this is due to proton-based enthalpy-entropy compensation between the favorable entropic term from proton release and the unfavorable enthalpic term due to thiol deprotonation. Since protein folding effects have been minimized in the GGG scaffold, these peptides possess nearly the tightest Zn(II) affinities possible for their coordination motifs. The Zn(II) affinities in each coordination motif are compared between the GGG scaffold and natural zinc finger proteins to determine the free energy required to fold the latter

  20. Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

    DOE PAGES-Beta [OSTI]

    Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; Otten, Renee; Higgins, Matthew K.; Schertler, Gebhard F. X.; Oprian, Daniel D.; Kern, Dorothee

    2015-12-24

    Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

  1. The coat protein complex II, COPII, protein Sec13 directly interacts with presenilin-1

    SciTech Connect (OSTI)

    Nielsen, Anders Lade

    2009-10-23

    Mutations in the human gene encoding presenilin-1, PS1, account for most cases of early-onset familial Alzheimer's disease. PS1 has nine transmembrane domains and a large loop orientated towards the cytoplasm. PS1 locates to cellular compartments as endoplasmic reticulum (ER), Golgi apparatus, vesicular structures, and plasma membrane, and is an integral member of {gamma}-secretase, a protein protease complex with specificity for intra-membranous cleavage of substrates such as {beta}-amyloid precursor protein. Here, an interaction between PS1 and the Sec13 protein is described. Sec13 takes part in coat protein complex II, COPII, vesicular trafficking, nuclear pore function, and ER directed protein sequestering and degradation control. The interaction maps to the N-terminal part of the large hydrophilic PS1 loop and the first of the six WD40-repeats present in Sec13. The identified Sec13 interaction to PS1 is a new candidate interaction for linking PS1 to secretory and protein degrading vesicular circuits.

  2. Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

    SciTech Connect (OSTI)

    Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; Otten, Renee; Higgins, Matthew K.; Schertler, Gebhard F. X.; Oprian, Daniel D.; Kern, Dorothee

    2015-12-24

    Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.

  3. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    SciTech Connect (OSTI)

    Xia, Kelin [Department of Mathematics, Michigan State University, Michigan 48824 (United States)] [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, Michigan 48824 (United States) [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States)

    2014-03-15

    This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction.

  4. Argonne explains nuclear recycling in 4 minutes

    SciTech Connect (OSTI)

    2012-01-01

    Currently, when using nuclear energy only about five percent of the uranium used in a fuel rod gets fissioned for energy; after that, the rods are taken out of the reactor and put into permanent storage. There is a way, however, to use almost all of the uranium in a fuel rod. Recycling used nuclear fuel could produce hundreds of years of energy from just the uranium we've already mined, all of it carbon-free. Problems with older technology put a halt to recycling used nuclear fuel in the United States, but new techniques developed by scientists at Argonne National Laboratory address many of those issues. For more information, visit http://www.anl.gov/energy/nuclear-energy.

  5. CARES Helps Explain Secondary Organic Aerosols

    SciTech Connect (OSTI)

    Zaveri, Rahul

    2014-03-28

    What happens when urban man-made pollution mixes with what we think of as pristine forest air? To know more about what this interaction means for the climate, the Carbonaceous Aerosol and Radiative Effects Study, or CARES, field campaign was designed in 2010. The sampling strategy during CARES was coordinated with CalNex 2010, another major field campaign that was planned in California in 2010 by the California Air Resources Board (CARB), the National Oceanic and Atmospheric Administration (NOAA), and the California Energy Commission (CEC). "We found two things. When urban pollution mixes with forest pollutions we get more secondary organic aerosols," said Rahul Zaveri, FCSD scientist and project lead on CARES. "SOAs are thought to be formed primarily from forest emissions but only when they interact with urban emissions. The data is saying that there will be climate cooling over the central California valley because of these interactions." Knowledge gained from detailed analyses of data gathered during the CARES campaign, together with laboratory experiments, is being used to improve existing climate models.

  6. Our Science Explained | The Ames Laboratory

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    The information is provided in a one-page, easy-to-read, "print-ready" pdf format. Lead-free Solder Magnetic Refrigeration Nanocatalysts Organic Light-emitting Devices (OLEDs) ...

  7. CARES Helps Explain Secondary Organic Aerosols

    ScienceCinema (OSTI)

    Zaveri, Rahul

    2014-06-02

    What happens when urban man-made pollution mixes with what we think of as pristine forest air? To know more about what this interaction means for the climate, the Carbonaceous Aerosol and Radiative Effects Study, or CARES, field campaign was designed in 2010. The sampling strategy during CARES was coordinated with CalNex 2010, another major field campaign that was planned in California in 2010 by the California Air Resources Board (CARB), the National Oceanic and Atmospheric Administration (NOAA), and the California Energy Commission (CEC). "We found two things. When urban pollution mixes with forest pollutions we get more secondary organic aerosols," said Rahul Zaveri, FCSD scientist and project lead on CARES. "SOAs are thought to be formed primarily from forest emissions but only when they interact with urban emissions. The data is saying that there will be climate cooling over the central California valley because of these interactions." Knowledge gained from detailed analyses of data gathered during the CARES campaign, together with laboratory experiments, is being used to improve existing climate models.

  8. Photovoltaics and Electricity - Energy Explained, Your Guide...

    U.S. Energy Information Administration (EIA) (indexed site)

    ... Photovoltaic cells convert sunlight into electricity A photovoltaic (PV) cell, commonly called a solar cell, is a nonmechanical device that converts sunlight directly into ...

  9. Report Explains How Bioenergy Supports Global Sustainability...

    Energy Savers

    ... and technologies to improve agricultural productivity and environmental health, and provides a vision for sustainably reducing poverty and reliance on dwindling fossil resources. ...

  10. Argonne explains nuclear recycling in 4 minutes

    ScienceCinema (OSTI)

    None

    2016-07-12

    Currently, when using nuclear energy only about five percent of the uranium used in a fuel rod gets fissioned for energy; after that, the rods are taken out of the reactor and put into permanent storage. There is a way, however, to use almost all of the uranium in a fuel rod. Recycling used nuclear fuel could produce hundreds of years of energy from just the uranium we've already mined, all of it carbon-free. Problems with older technology put a halt to recycling used nuclear fuel in the United States, but new techniques developed by scientists at Argonne National Laboratory address many of those issues. For more information, visit http://www.anl.gov/energy/nuclear-energy.

  11. The NIH rDNA Guidelines Explained

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    What Are the RAC and the OBA? The NIH OBA (Office of Biotechnology Activities) is an administrative arm responsible for carrying out the orders of the NIH Director with regard to ...

  12. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

    Zheng, Zhongzhou; Sosnick, Tobin R. (UC)

    2010-05-25

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu {yields} Glu{sup -}) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the {beta}5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  13. Protein detection system - Energy Innovation Portal

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    27,977 Site Map Printable Version Share this resource About Search Categories (15) Advanced Materials Biomass and Biofuels Building Energy Efficiency Electricity Transmission Energy Analysis Energy Storage Geothermal Hydrogen and Fuel Cell Hydropower, Wave and Tidal Industrial Technologies Solar Photovoltaic Solar Thermal Startup America Vehicles and Fuels Wind Energy Partners (27) Visual Patent Search Success Stories Find More Like This Return to Search Protein detection system United States

  14. Methods and devices for protein assays

    DOE Patents [OSTI]

    Chhabra, Swapnil; Cintron, Jose M.; Shediac, Renee

    2009-11-03

    Methods and devices for protein assays based on Edman degradation in microfluidic channels are disclosed herein. As disclosed, the cleaved amino acid residues may be immobilized in an array format and identified by detectable labels, such as antibodies, which specifically bind given amino acid residues. Alternatively, the antibodies are immobilized in an array format and the cleaved amino acids are labeled identified by being bound by the antibodies in the array.

  15. Nucleic acids encoding human trithorax protein

    DOE Patents [OSTI]

    Evans, Glen A.; Djabali, Malek; Selleri, Licia; Parry, Pauline

    2001-01-01

    In accordance with the present invention, there is provided an isolated peptide having the characteristics of human trithorax protein (as well as DNA encoding same, antisense DNA derived therefrom and antagonists therefor). The invention peptide is characterized by having a DNA binding domain comprising multiple zinc fingers and at least 40% amino acid identity with respect to the DNA binding domain of Drosophila trithorax protein and at least 70% conserved sequence with respect to the DNA binding domain of Drosophila trithorax protein, and wherein said peptide is encoded by a gene located at chromosome 11 of the human genome at q23. Also provided are methods for the treatment of subject(s) suffering from immunodeficiency, developmental abnormality, inherited disease, or cancer by administering to said subject a therapeutically effective amount of one of the above-described agents (i.e., peptide, antagonist therefor, DNA encoding said peptide or antisense DNA derived therefrom). Also provided is a method for the diagnosis, in a subject, of immunodeficiency, developmental abnormality, inherited disease, or cancer associated with disruption of chromosome 11 at q23.

  16. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions

    DOE PAGES-Beta [OSTI]

    Shatsky, Maxim; Dong, Ming; Liu, Haichuan; Yang, Lee Lisheng; Choi, Megan; Singer, Mary; Geller, Jil; Fisher, Susan; Hall, Steven; Hazen, Terry C.; et al

    2016-04-20

    Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification ofmore » endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.« less

  17. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    analysis. A small number of the top proteins were expressed and purified from E. coli, and further binding tests selected two proteins that bound to BHRF1 with acceptable...

  18. Crystal Structure of a Protein Kinase A Complex

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Crystal Structure of a Protein Kinase A Complex Print Protein kinase A (PKA) is an enzyme that regulates processes as diverse as growth, memory, and metabolism. In its unactivated...

  19. How the Membrane Protein AmtB Transports Ammonia

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    How the Membrane Protein AmtB Transports Ammonia Print Membrane proteins provide molecular-sized entry and exit portals for the various substances that pass into and out of cells. ...

  20. Folding and association of a homotetrameric protein complex in...

    Office of Scientific and Technical Information (OSTI)

    Folding and association of a homotetrameric protein complex in an all-atom Go model Title: Folding and association of a homotetrameric protein complex in an all-atom Go model ...

  1. Manipulating and Visualizing Proteins (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Manipulating and Visualizing Proteins Citation Details In-Document Search Title: Manipulating and Visualizing Proteins ProteinShop Gives Researchers a Hands-On Tool for Manipulating, Visualizing Protein Structures. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeup and genetic codes of living organisms. But in order to make sense of this raw data, researchers need software tools which let them explore

  2. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

    Threading Method (Thesis/Dissertation) | SciTech Connect Thesis/Dissertation: Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method Citation Details In-Document Search Title: Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation

  3. Brian K. Kobilka and G-protein-coupled Receptors (GPCR)

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Brian K. Kobilka and G-protein-coupled Receptors (GPCR) Resources with Additional Information Brian K. Kobilka Credit: Linda A. Cicero Stanford News Service 'Thanks in part to research performed at the U.S. Department of Energy's (DOE) Argonne National Laboratory, the 2012 Nobel Prize in Chemistry was awarded today to Americans Brian Kobilka and Robert Lefkowitz for their work on G-protein-coupled receptors. G-protein-coupled receptors, or GPCRs, are a large family of proteins embedded in a

  4. Translation-Coupling Cassette for Quickly and Reliably Monitoring Protein

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Translation in Host Cells - Energy Innovation Portal Translation-Coupling Cassette for Quickly and Reliably Monitoring Protein Translation in Host Cells Inventors: Brian Pfleger, Daniel Mendez Perez Great Lakes Bioenergy Research Center Contact GLBRC About This Technology Technology Marketing Summary Bacterial production of recombinant proteins is used commonly by researchers and commercial entities to manufacture a large variety of proteins. However, many proteins are not produced

  5. Interactive protein manipulation (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Interactive protein manipulation Citation Details In-Document Search Title: Interactive protein manipulation We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure

  6. De novo design of functional proteins: Toward artificial hydrogenases

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    De novo design of functional proteins: Toward artificial hydrogenases Authors: Faiella, M., Roy, A., Sommer, D., Ghirlanda, G. Title: De novo design of functional proteins: Toward artificial hydrogenases Source: Biopolymers Year: 2013 Volume: 100 Pages: 558 - 571 ABSTRACT: Over the last 25 years, de novo design has proven to be a valid approach to generate novel, well-folded proteins, and most recently, functional proteins. In response to societal needs, this approach is been used increasingly

  7. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

    Schultz, Peter G.; Wang, Lei

    2009-04-28

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  8. Photoswitchable method for the ordered attachment of proteins to surfaces

    DOE Patents [OSTI]

    Camarero, Julio A.; De Yoreo, James J.; Kwon, Youngeun

    2010-04-20

    Described herein is a method for the attachment of proteins to any solid support with control over the orientation of the attachment. The method is extremely efficient, not requiring the previous purification of the protein to be attached, and can be activated by UV-light. Spatially addressable arrays of multiple protein components can be generated by using standard photolithographic techniques.

  9. Photoswitchable method for the ordered attachment of proteins to surfaces

    DOE Patents [OSTI]

    Camarero, Julio A.; DeYoreo, James J.; Kwon, Youngeun

    2011-07-05

    Described herein is a method for the attachment of proteins to any solid support with control over the orientation of the attachment. The method is extremely efficient, not requiring the previous purification of the protein to be attached, and can be activated by UV-light. Spatially addressable arrays of multiple protein components can be generated by using standard photolithographic techniques.

  10. Recombinant HT.sub.m4 gene, protein and assays

    DOE Patents [OSTI]

    Lim, Bing; Adra, Chaker N.; Lelias, Jean-Michel

    1996-01-01

    The invention relates to a recombinant DNA molecule which encodes a HT.sub.m4 protein, a transformed host cell which has been stably transfected with a DNA molecule which encodes a HT.sub.m4 protein and a recombinant HT.sub.m4 protein. The invention also relates to a method for detecting the presence of a hereditary atopy.

  11. Methods for production of proteins in host cells

    DOE Patents [OSTI]

    Donnelly, Mark; Joachimiak, Andrzej

    2004-01-13

    The present invention provides methods for the production of proteins, particularly toxic proteins, in host cells. The invention provides methods which use a fusion protein comprising a chaperonin binding domain in host cells induced or regulated to have increased levels of chaperonin which binds the chaperonin binding domain.

  12. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

    Schultz, Peter G.; Wang, Lei

    2008-10-07

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  13. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

    Schultz, Peter G.; Wang, Lei

    2012-02-14

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  14. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

    Schultz, Peter G.; Wang, Lei

    2011-03-22

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  15. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

    Schultz, Peter G.; Wang, Lei

    2011-12-06

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  16. Protein-protein interactions in the cyanobacterial KaiABC circadian clock

    SciTech Connect (OSTI)

    Egli, M.; Pattanayek, R.; Pattanayek, S.

    2008-01-10

    The discovery that the central oscillator of the cyanobacterial KaiABC circadian clock can be reconstituted in vitro by the protein components KaiA, KaiB and KaiC renders this biological timer a unique target for biochemical and structural studies. The oscillator can be monitored through changes in the KaiC phosphorylation status that is modulated by KaiA and KaiB. As the 24-h period of the recombinant clock remains unaltered as a result of modest variation of temperature, interactions between the three Kai proteins not only form the basis for rhythmic control of levels of KaiC phosphorylation but also provide temperature compensation. A profound understanding of how this biological timer works requires a dissection of the functions of, and interactions between, the three proteins. Three-dimensional structures of the individual Kai proteins have been determined, and the KaiA-KaiC complex has been studied using hybrid structural methods. This chapter provides an overview of progress in the characterization of the cyanobacterial circadian clock with an emphasis on structural aspects of individual Kai proteins and the binary KaiA-KaiC complex.

  17. Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering

    SciTech Connect (OSTI)

    Close, Devin W.; Paul, Craig Don; Langan, Patricia S.; Wilce, Matthew C. J.; Traore, Daouda A. K.; Halfmann, Randal; Rocha, Reginaldo C.; Waldo, Geoffery S.; Payne, Riley J.; Rucker, Joseph B.; Prescott, Mark; Bradbury, Andrew R. M.

    2015-05-08

    In this paper, we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction of high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization.

  18. Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering

    DOE PAGES-Beta [OSTI]

    Close, Devin W.; Paul, Craig Don; Langan, Patricia S.; Wilce, Matthew C. J.; Traore, Daouda A. K.; Halfmann, Randal; Rocha, Reginaldo C.; Waldo, Geoffery S.; Payne, Riley J.; Rucker, Joseph B.; et al

    2015-05-08

    In this paper, we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction ofmore » high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization.« less

  19. Fast kinase domain-containing protein 3 is a mitochondrial protein essential for cellular respiration

    SciTech Connect (OSTI)

    Simarro, Maria; Gimenez-Cassina, Alfredo; Kedersha, Nancy; Lazaro, Jean-Bernard; Adelmant, Guillaume O.; Marto, Jarrod A.; Rhee, Kirsten; Tisdale, Sarah; Danial, Nika; Benarafa, Charaf; Orduna, Anonio; Anderson, Paul

    2010-10-22

    Research highlights: {yields} Five members of the FAST kinase domain-containing proteins are localized to mitochondria in mammalian cells. {yields} The FASTKD3 interactome includes proteins involved in various aspects of mitochondrial metabolism. {yields} Targeted knockdown of FASTKD3 significantly reduces basal and maximal mitochondrial oxygen consumption. -- Abstract: Fas-activated serine/threonine phosphoprotein (FAST) is the founding member of the FAST kinase domain-containing protein (FASTKD) family that includes FASTKD1-5. FAST is a sensor of mitochondrial stress that modulates protein translation to promote the survival of cells exposed to adverse conditions. Mutations in FASTKD2 have been linked to a mitochondrial encephalomyopathy that is associated with reduced cytochrome c oxidase activity, an essential component of the mitochondrial electron transport chain. We have confirmed the mitochondrial localization of FASTKD2 and shown that all FASTKD family members are found in mitochondria. Although human and mouse FASTKD1-5 genes are expressed ubiquitously, some of them are most abundantly expressed in mitochondria-enriched tissues. We have found that RNA interference-mediated knockdown of FASTKD3 severely blunts basal and stress-induced mitochondrial oxygen consumption without disrupting the assembly of respiratory chain complexes. Tandem affinity purification reveals that FASTKD3 interacts with components of mitochondrial respiratory and translation machineries. Our results introduce FASTKD3 as an essential component of mitochondrial respiration that may modulate energy balance in cells exposed to adverse conditions by functionally coupling mitochondrial protein synthesis to respiration.

  20. Protein-Based Nanomedicine Platforms for Drug Delivery

    SciTech Connect (OSTI)

    Ma Ham, Aihui; Tang, Zhiwen; Wu, Hong; Wang, Jun; Lin, Yuehe

    2009-08-03

    Drug delivery systems have been developed for many years, however some limitations still hurdle the pace of going to clinical phase, for example, poor biodistribution, drug molecule cytotoxicity, tissue damage, quick clearance from the circulation system, solubility and stability of drug molecules. To overcome the limitations of drug delivery, biomaterials have to be developed and applied to drug delivery to protect the drug molecules and to enhance the drugs efficacy. Protein-based nanomedicine platforms for drug delivery are platforms comprised of naturally self-assembled protein subunits of the same protein or a combination of proteins making up a complete system. They are ideal for drug delivery platforms due to their biocompatibility and biodegradability coupled with low toxicity. A variety of proteins have been used and characterized for drug delivery systems including the ferritin/apoferritin protein cage, plant derived viral capsids, the small Heat shock protein (sHsp) cage, albumin, soy and whey protein, collagen, and gelatin. There are many different types and shapes that have been prepared to deliver drug molecules using protein-based platforms including the various protein cages, microspheres, nanoparticles, hydrogels, films, minirods and minipellets. There are over 30 therapeutic compounds that have been investigated with protein-based drug delivery platforms for the potential treatment of various cancers, infectious diseases, chronic diseases, autoimmune diseases. In protein-based drug delivery platforms, protein cage is the most newly developed biomaterials for drug delivery and therapeutic applications. Their uniform sizes, multifunctions, and biodegradability push them to the frontier for drug delivery. In this review, the recent strategic development of drug delivery has been discussed with a special emphasis upon the polymer based, especially protein-based nanomedicine platforms for drug delivery. The advantages and disadvantages are also

  1. Multicomponent Protein Cage Architectures for Photocatalysis

    SciTech Connect (OSTI)

    Douglas, Trevor

    2014-11-21

    The central focus of the work performed under this award has been to develop the bacteriophage P22 viral capsid as a vehicle for the encapsulation of catalyticaly active cargo materials and study their utility towards economic energy harvesting systems. We have demonstrated that the capsid of the bacteriophage P22 can be used to genetically program the assembly and encapsulation of a range of inorganic nanoparticles and protein cargoes. The P22 capsid uses a scaffold protein (SP) to direct the assembly of its coat protein (CP) into icosahedral capsids. By creating a genetic fusion of a desired cargo enzyme or a small peptide that can act as a nucleation site for subsequent NP growth, we have demonstrated the co-assembly of these SP-fusions and CP into stable “nano-reactors”. The cargo is sequestered inside the engineered capsid and can either be used directly as a nanocatalyst or for the nucleation and growth of inorganic or organic nanoparticles or polymers. The synthetic cargos (NP or polymers) were shown to have photocatalytic activity. The time dependent photophysics of a select few of these systems were studied to determine the underlying mechanisms and efficiency of light harversting. Enzyme cargos encapsulated within the P22 were thermally activated catalysts and their kinetic behavior was characterized. During the course of this work we have demonstrated that the method is a robust means to harness biology for materials applications and have initiated work into assembling the P22 nanoreactors into hierarchically ordered materials. The successful implementation of the work performed under this DOE grant provides us with a great deal of knowledge and a library of components to go forward towards the development of bioinspired catalytic materials for energy harvesting.

  2. New insights into potential functions for the protein 4.1superfamily of proteins in kidney epithelium

    SciTech Connect (OSTI)

    Calinisan, Venice; Gravem, Dana; Chen, Ray Ping-Hsu; Brittin,Sachi; Mohandas, Narla; Lecomte, Marie-Christine; Gascard, Philippe

    2005-06-17

    Members of the protein 4.1 family of adapter proteins are expressed in a broad panel of tissues including various epithelia where they likely play an important role in maintenance of cell architecture and polarity and in control of cell proliferation. We have recently characterized the structure and distribution of three members of the protein 4.1 family, 4.1B, 4.1R and 4.1N, in mouse kidney. We describe here binding partners for renal 4.1 proteins, identified through the screening of a rat kidney yeast two-hybrid system cDNA library. The identification of putative protein 4.1-based complexes enables us to envision potential functions for 4.1 proteins in kidney: organization of signaling complexes, response to osmotic stress, protein trafficking, and control of cell proliferation. We discuss the relevance of these protein 4.1-based interactions in kidney physio-pathology in the context of their previously identified functions in other cells and tissues. Specifically, we will focus on renal 4.1 protein interactions with beta amyloid precursor protein (beta-APP), 14-3-3 proteins, and the cell swelling-activated chloride channel pICln. We also discuss the functional relevance of another member of the protein 4.1 superfamily, ezrin, in kidney physiopathology.

  3. Conservation of Oxidative Protein Stabilization in an Insect Homologue of Parkinsonism-Associated Protein DJ-1

    SciTech Connect (OSTI)

    Lin, Jiusheng; Prahlad, Janani; Wilson, Mark A.

    2012-08-21

    DJ-1 is a conserved, disease-associated protein that protects against oxidative stress and mitochondrial damage in multiple organisms. Human DJ-1 contains a functionally essential cysteine residue (Cys106) whose oxidation is important for regulating protein function by an unknown mechanism. This residue is well-conserved in other DJ-1 homologues, including two (DJ-1{alpha} and DJ-1{beta}) in Drosophila melanogaster. Because D. melanogaster is a powerful model system for studying DJ-1 function, we have determined the crystal structure and impact of cysteine oxidation on Drosophila DJ-1{beta}. The structure of D. melanogaster DJ-1{beta} is similar to that of human DJ-1, although two important residues in the human protein, Met26 and His126, are not conserved in DJ-1{beta}. His126 in human DJ-1 is substituted with a tyrosine in DJ-1{beta}, and this residue is not able to compose a putative catalytic dyad with Cys106 that was proposed to be important in the human protein. The reactive cysteine in DJ-1 is oxidized readily to the cysteine-sulfinic acid in both flies and humans, and this may regulate the cytoprotective function of the protein. We show that the oxidation of this conserved cysteine residue to its sulfinate form (Cys-SO{sub 2{sup -}}) results in considerable thermal stabilization of both Drosophila DJ-1{beta} and human DJ-1. Therefore, protein stabilization is one potential mechanism by which cysteine oxidation may regulate DJ-1 function in vivo. More generally, most close DJ-1 homologues are likely stabilized by cysteine-sulfinic acid formation but destabilized by further oxidation, suggesting that they are biphasically regulated by oxidative modification.

  4. TIGRFAMS: The TIGRFAMs database of protein families

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    TIGRFAMs are protein families based on Hidden Markov Models or HMMs. Use this page to see the curated seed alignmet for each TIGRFam, the full alignment of all family members and the cutoff scores for inclusion in each of the TIGRFAMs. Also use this page to search through the TIGRFAMs and HMMs for text in the TIGRFAMs Text Search or search for specific sequences in the TIGRFAMs Sequence Search.[Copied from the Overview at http://www.jcvi.org/cms/research/projects/tigrfams/overview/] See also TIGRFAMs ordered by the roles they play at http://cmr.jcvi.org/tigr-scripts/CMR/shared/EvidenceList.cgi?ev_type=TIGRFAM&order_type=role.

  5. Solving coiled-coil protein structures

    DOE PAGES-Beta [OSTI]

    Dauter, Zbigniew

    2015-02-26

    With the availability of more than 100,000 entries stored in the Protein Data Bank (PDB) that can be used as search models, molecular replacement (MR) is currently the most popular method of solving crystal structures of macromolecules. Significant methodological efforts have been directed in recent years towards making this approach more powerful and practical. This resulted in the creation of several computer programs, highly automated and user friendly, that are able to successfully solve many structures even by researchers who, although interested in structures of biomolecules, are not very experienced in crystallography.

  6. Gene encoding herbicide safener binding protein

    DOE Patents [OSTI]

    Walton, Jonathan D.; Scott-Craig, John S.

    1999-01-01

    The cDNA encoding safener binding protein (SafBP), also referred to as SBP1, is set forth in FIG. 5 and SEQ ID No. 1. The deduced amino acid sequence is provided in FIG. 5 and SEQ ID No. 2. Methods of making and using SBP1 and SafBP to alter a plant's sensitivity to certain herbicides or a plant's responsiveness to certain safeners are also provided, as well as expression vectors, transgenic plants or other organisms transfected with said vectors and seeds from said plants.

  7. Effective protein-protein interaction from structure factor data of a lysozyme solution

    SciTech Connect (OSTI)

    Abramo, M. C.; Caccamo, C.; Costa, D.; Ruberto, R.; Wanderlingh, U.; Cavero, M.; Pellicane, G.

    2013-08-07

    We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated.

  8. Protein-Folding Landscapes in Multi-Chain Systems (Journal Article...

    Office of Scientific and Technical Information (OSTI)

    contacts, suggesting that native topology plays a role in early stages of aggregation. ... MELTING; PROTEINS; THERMODYNAMICS; TOPOLOGY protein folding protein aggregation ...

  9. Analysis of crystallization data in the Protein Data Bank

    SciTech Connect (OSTI)

    Kirkwood, Jobie; Hargreaves, David; O’Keefe, Simon; Wilson, Julie

    2015-09-23

    In a large-scale study using data from the Protein Data Bank, some of the many reported findings regarding the crystallization of proteins were investigated. The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallization reagents were identified, the link between solution pH and the isoelectric point of the protein was investigated and the possibility of predicting whether a protein will crystallize was explored.

  10. Structure based alignment and clustering of proteins (STRALCP)

    DOE Patents [OSTI]

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  11. Graph representation of protein free energy landscape

    SciTech Connect (OSTI)

    Li, Minghai; Duan, Mojie; Fan, Jue; Huo, Shuanghong; Han, Li

    2013-11-14

    The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation of free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.

  12. Femtosecond X-ray protein nanocrystallography

    SciTech Connect (OSTI)

    Chapman, Henry N.; Barty, Anton; White, Thomas A.; Aquila, Andrew; Schulz, Joachim; DePonte, Daniel P.; Martin, Andrew V.; Coppola, Nicola; Liang, Mengning; Caleman, Carl; Gumprecht, Lars; Stern, Stephan; Nass, Karol; Fromme, Petra; Hunter, Mark S.; Grotjohann, Ingo; Fromme, Raimund; Kirian, Richard A.; Weierstall, Uwe; Doak, R. Bruce; Schmidt, Kevin E.; Wang, Xiaoyu; Spence, John C. H.; Schlichting, Ilme; Epp, Sascha W.; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Strüder, Lothar; Ullrich, Joachim; Krasniqi, Faton; Lomb, Lukas; Shoeman, Robert L.; Bott, Mario; Barends, Thomas R. M.; Kuhnel, Kai-Uwe; Schroter, Claus-Dieter; Hartmann, Robert; Holl, Peter; Reich, Christian; Soltau, Heike; Kimmel, Nils; Weidenspointner, Georg; Pietschner, Daniel; Hauser, Günter; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Andritschke, Robert; Boutet, Sébastien; Krzywinski, Jacek; Bostedt, Christoph; Messerschmidt, Marc; Bozek, John D.; Williams, Garth J.; Bogan, Michael J.; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Gorke, Hubert; Hau-Riege, Stefan P.; Frank, Matthias; Maia, Filipe R. N. C.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Holton, James M.; Marchesini, Stefano; Neutze, Richard; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Barthelmess, Miriam; Bajt, Saša; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn

    2011-02-03

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  13. PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction

    DOE PAGES-Beta [OSTI]

    Yao, Jianzhuang; Guo, Hong; Yang, Xiaohan

    2015-01-01

    Determining protein-protein interaction (PPI) in biological systems is of considerable importance, and prediction of PPI has become a popular research area. Although different classifiers have been developed for PPI prediction, no single classifier seems to be able to predict PPI with high confidence. We postulated that by combining individual classifiers the accuracy of PPI prediction could be improved. We developed a method called protein-protein interaction prediction classifiers merger (PPCM), and this method combines output from two PPI prediction tools, GO2PPI and Phyloprof, using Random Forests algorithm. The performance of PPCM was tested by area under the curve (AUC) using anmore » assembled Gold Standard database that contains both positive and negative PPI pairs. Our AUC test showed that PPCM significantly improved the PPI prediction accuracy over the corresponding individual classifiers. We found that additional classifiers incorporated into PPCM could lead to further improvement in the PPI prediction accuracy. Furthermore, cross species PPCM could achieve competitive and even better prediction accuracy compared to the single species PPCM. This study established a robust pipeline for PPI prediction by integrating multiple classifiers using Random Forests algorithm. This pipeline will be useful for predicting PPI in nonmodel species.« less

  14. Fermilab | Science at Fermilab | Experiments & Projects | Energy...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    ... The strength of the magnetic field must be increased. Ring-shaped particle accelerators operate the most powerful magnets in the world. The power of a ring-shaped proton ...

  15. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Mallick, Parag; Rice, Danny; Eisenberg, David

    How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  16. Exploring the conformational energy landscape of proteins

    SciTech Connect (OSTI)

    Nienhaus, G.U. |; Mueller, J.D.; McMahon, B.H.

    1997-04-01

    Proteins possess a complex energy landscape with a large number of local minima called conformational substates that are arranged in a hierarchical fashion. Here we discuss experiments aimed at the elucidation of the energy landscape in carbonmonoxy myoglobin (MbCO). In the highest tier of the hierarchy, a few taxonomic substates exist. Because of their small number, these substates are accessible to detailed structural investigations. Spectroscopic experiments are discussed that elucidate the role of protonations of amino acid side chains in creating the substates. The lower tiers of the hierarchy contain a large number of statistical substates. Substate interconversions are observed in the entire temperature range from below 1 K up to the denaturation temperature, indicating a wide spectrum of energy barriers that separate the substates.

  17. Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

    SciTech Connect (OSTI)

    Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S.; Reveco, S.A.; Fok, V.; Johanson, A.R.; Batth, T.S.; Singer, M.; Chandonia, J.M.; Joyner, D.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Singh, A.K.; Keasling, J.D.

    2011-05-01

    Proteinprotein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 pulled-down proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

  18. Interaction between a plasma membrane-localized ankyrin-repeat protein ITN1 and a nuclear protein RTV1

    SciTech Connect (OSTI)

    Sakamoto, Hikaru; Sakata, Keiko; Kusumi, Kensuke; Kojima, Mikiko; Sakakibara, Hitoshi; Iba, Koh

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer ITN1, a plasma membrane ankyrin protein, interacts with a nuclear DNA-binding protein RTV1. Black-Right-Pointing-Pointer The nuclear transport of RTV1 is partially inhibited by interaction with ITN1. Black-Right-Pointing-Pointer RTV1 can promote the nuclear localization of ITN1. Black-Right-Pointing-Pointer Both overexpression of RTV1 and the lack of ITN1 increase salicylic acids sensitivity in plants. -- Abstract: The increased tolerance to NaCl 1 (ITN1) protein is a plasma membrane (PM)-localized protein involved in responses to NaCl stress in Arabidopsis. The predicted structure of ITN1 is composed of multiple transmembrane regions and an ankyrin-repeat domain that is known to mediate protein-protein interactions. To elucidate the molecular functions of ITN1, we searched for interacting partners using a yeast two-hybrid assay, and a nuclear-localized DNA-binding protein, RTV1, was identified as a candidate. Bimolecular fluorescence complementation analysis revealed that RTV1 interacted with ITN1 at the PM and nuclei in vivo. RTV1 tagged with red fluorescent protein localized to nuclei and ITN1 tagged with green fluorescent protein localized to PM; however, both proteins localized to both nuclei and the PM when co-expressed. These findings suggest that RTV1 and ITN1 regulate the subcellular localization of each other.

  19. Analysis of Protein-RNA and Protein-Peptide Interactions in Equine Infectious Anemia

    SciTech Connect (OSTI)

    Jae-Hyung Lee

    2007-12-01

    Macromolecular interactions are essential for virtually all cellular functions including signal transduction processes, metabolic processes, regulation of gene expression and immune responses. This dissertation focuses on the characterization of two important macromolecular interactions involved in the relationship between Equine Infectious Anemia Virus (EIAV) and its host cell in horse: (1) the interaction between the EIAV Rev protein and its binding site, the Rev-responsive element (RRE) and (2) interactions between equine MHC class I molecules and epitope peptides derived from EIAV proteins. EIAV, one of the most divergent members of the lentivirus family, has a single-stranded RNA genome and carries several regulatory and structural proteins within its viral particle. Rev is an essential EIAV regulatory encoded protein that interacts with the viral RRE, a specific binding site in the viral mRNA. Using a combination of experimental and computational methods, the interactions between EIAV Rev and RRE were characterized in detail. EIAV Rev was shown to have a bipartite RNA binding domain contain two arginine rich motifs (ARMs). The RRE secondary structure was determined and specific structural motifs that act as cis-regulatory elements for EIAV Rev-RRE interaction were identified. Interestingly, a structural motif located in the high affinity Rev binding site is well conserved in several diverse lentiviral genoes, including HIV-1. Macromolecular interactions involved in the immune response of the horse to EIAV infection were investigated by analyzing complexes between MHC class I proteins and epitope peptides derived from EIAV Rev, Env and Gag proteins. Computational modeling results provided a mechanistic explanation for the experimental finding that a single amino acid change in the peptide binding domain of the quine MHC class I molecule differentially affectes the recognitino of specific epitopes by EIAV-specific CTL. Together, the findings in this

  20. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING

    Office of Scientific and Technical Information (OSTI)

    SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY (Conference) | SciTech Connect MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY The purpose of this study is to design, fabricate and optimize microfluidic mixers to investigate the kinetics of protein

  1. Microsecond Microfluidic Mixing for Investigation of Protein Folding

    Office of Scientific and Technical Information (OSTI)

    Kinetics (Conference) | SciTech Connect Conference: Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics Citation Details In-Document Search Title: Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first

  2. Recombinant HT{sub m4} gene, protein and assays

    DOE Patents [OSTI]

    Lim, B.; Adra, C.N.; Lelias, J.M.

    1996-09-03

    The invention relates to a recombinant DNA molecule which encodes a HT{sub m4} protein, a transformed host cell which has been stably transfected with a DNA molecule which encodes a HT{sub m4} protein and a recombinant HT{sub m4} protein. The invention also relates to a method for detecting the presence of a hereditary atopy. 2 figs.

  3. Femtosecond nanocrystallography using X-ray lasers for membrane protein

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    structure determination Femtosecond nanocrystallography using X-ray lasers for membrane protein structure determination Authors: Fromme, P., and Spence, J. C. H. Title: Femtosecond nanocrystallography using X-ray lasers for membrane protein structure determination Source: Current Opinion in Structural Biology Year: 2011 Volume: 21 Pages: 509-516 ABSTRACT: The invention of free electron X-ray lasers has opened a new era for membrane protein structure determination with the recent first

  4. Towards Breakthroughs in Protein Structure Calculation and Design | Argonne

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Leadership Computing Facility A metal-binding protein designed by the Baker laboratory. A metal-binding protein designed by the Baker laboratory, which uses a noncanonical amino acid, bipyradynl alanine, to coordinate the bound metal. Bound metals often play essential catalytic roles at enzyme active sites. Advances made in the current INCITE application will improve the ability to design with non-natural building blocks, and to add enzymatic or other functions to designed proteins. Vikram

  5. Modeling Feat Sheds Light on Protein Channel's Function

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Modeling Feat Sheds Light on Protein Channel's Function Modeling Feat Sheds Light on Protein Channel's Function November 1, 2012 NERSC Contact: Linda Vu, lvu@lbl.gov, +1 510 495 2402 nerscweb.png The ribosome (red-blue) in complex with the translocon channel (green), which is embedded in the cell membrane (yellow, white). Proteins that are inserted via the ribosome into the channel can either be laterally integrated into the cell membrane or secreted across the cell membrane (inset). (Image

  6. Transparent Gold as a Platform for Adsorbed Protein

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Spectroelectrochemistry: Investigation of Cytochrome c and Azurin Transparent Gold as a Platform for Adsorbed Protein Spectroelectrochemistry: Investigation of Cytochrome c and Azurin Authors: Ashur, I., Schulz, O., McIntosh, C. L., Pinkas, I., Ros, R., and Jones, A. K. Title: Transparent Gold as a Platform for Adsorbed Protein Spectroelectrochemistry: Investigation of Cytochrome c and Azurin Source: Langmuir Year: 2012 Volume: 28 Pages: 5861-5871 ABSTRACT: The majority of protein

  7. Computational Biology: A Recipe for Ligand-Binding Proteins

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Computational Biology: A Recipe for Ligand-Binding Proteins Authors: Ghirlanda, G. Title: Computational Biology: A Recipe for Ligand-Binding Proteins Source: Nature Year: 2013 Volume: 501 Pages: 177-178 ABSTRACT: Cellular cross-talk, enzymatic catalysis and regulation of gene expression all depend on molecular recognition. A method that allows the design of proteins with desired recognition sites could thus be revolutionary Date of online publication: Thu, 2013-09-12 Link online:

  8. Structure and Function of Microbial Metal-Reduction Proteins (Other) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Other: Structure and Function of Microbial Metal-Reduction Proteins Citation Details In-Document Search Title: Structure and Function of Microbial Metal-Reduction Proteins In this project, we proposed (i) identification of metal-reduction genes, (ii) development of new threading techniques and (iii) fold recognition and structure prediction of metal-reduction proteins. However, due to the reduction of the budget, we revised our plan to focus on two specific aims of (i)

  9. Biomimetic Materials for Protein Storage and Transport | Argonne National

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Laboratory Biomimetic Materials for Protein Storage and Transport Technology available for licensing: Unique, first-of-its-kind method for storing proteins in their native state for assay, application and delivery to sites outside of initial extraction and storage facilities. Enables delivery to sites outside of initial extraction and storage facilities Allows isolation, maintenance, and indefinite storage of protein in its native state PDF icon biomimetic_materials

  10. Structure of the enzyme-acyl carrier protein (ACP) substrate...

    Office of Scientific and Technical Information (OSTI)

    complex required for biotin synthesis Citation Details In-Document Search Title: Structure of the enzyme-acyl carrier protein (ACP) substrate gatekeeper complex required ...

  11. Development of a Fast Microfluidic Mixer for Studies of Protein...

    Office of Scientific and Technical Information (OSTI)

    be compatible with most commonly used spectroscopic methods. ... The mixers are used to study kinetics of fast protein ... Country of Publication: United States Language: English ...

  12. Structure and Function of Microbial Metal-Reduction Proteins...

    Office of Scientific and Technical Information (OSTI)

    Function of Microbial Metal-Reduction Proteins Xu, Ying; Crawford, Oakly H.; Xu, Dong; Larimer, Frank W.; Uberbacher, Edward C.; Zhou, Jizhong 97 MATHEMATICS AND COMPUTING; 59...

  13. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTIO...

    Office of Scientific and Technical Information (OSTI)

    ... As a graduate student, she studied the interactions between proteins required for Herpes simplex virus DNA replication. Following graduation, Dr. Trego was a postdoctoral fellow in ...

  14. Protein Structure Recognition: From Eigenvector Analysis to Structural...

    Office of Scientific and Technical Information (OSTI)

    ThesisDissertation: Protein Structure Recognition: From Eigenvector Analysis to ... The sensitivity and specificity of this method is discussed, along with a case of blind ...

  15. Modification of Lignin by Protein Cross-linking to Facilitate...

    Office of Scientific and Technical Information (OSTI)

    Production of Biofuels From Poplar Citation Details In-Document Search Title: Modification of Lignin by Protein Cross-linking to Facilitate Production of Biofuels From Poplar The ...

  16. Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL...

    Office of Scientific and Technical Information (OSTI)

    tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors Citation Details In-Document Search Title: Targeting Mycobacterium tuberculosis ...

  17. Non-destructively shattered mesoporous silica for protein drug...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Non-destructively shattered mesoporous silica for protein drug delivery Citation Details In-Document Search Title: Non-destructively shattered mesoporous silica ...

  18. New Crystal Structures Lift Fog around Protein Folding

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    genetic code embodied by the nucleotide sequences in DNA and collected in the form of genes is well known. Biological macromolecules like proteins comprise strings of amino acids...

  19. Crystal Structure of a Protein Kinase A Complex

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Regulating the Regulator Turn up the magnification, and the beehive of activity within a biological cell matches that in any large metropolis. Specialized proteins called enzymes...

  20. Phenylpropanoid related regulatory protein-regulatory region associations

    DOE Patents [OSTI]

    Apuya, Nestor; Bobzin, Steven Craig; Park, Joon-Hyun; Doukhanina, Elena

    2012-01-03

    Materials and methods for identifying lignin regulatory region-regulatory protein associations are disclosed. Materials and methods for modulating lignin accumulation are also disclosed.

  1. Brian K. Kobilka and G-protein-coupled Receptors (GPCR)

    Office of Scientific and Technical Information (OSTI)

    ... Additional information about Brian Kobilka and G-protein-coupled receptors (GPCR) is via publications and on the Web. Publication Information: Ligand-specific Regulation of the ...

  2. Visualization of Force Fields in Protein Structure Prediction...

    Office of Scientific and Technical Information (OSTI)

    WM KeckFoundation Country of Publication: United States Language: English Subject: 99 GENERAL AND MISCELLANEOUS molecular energy visualization protein structure prediction

  3. Monitoring Long-Range Electron Transfer Pathways in Proteins...

    Office of Scientific and Technical Information (OSTI)

    Published Article: Monitoring Long-Range Electron Transfer Pathways in Proteins by Stimulated Attosecond Broadband X-ray Raman Spectroscopy Title: Monitoring Long-Range Electron ...

  4. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

    RESIDUES; SENSITIVITY; SPECIFICITY In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for...

  5. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Kane, A; Hertzog, D; Baumgartel, P; Lengefeld, J; Horsley,...

  6. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Immortality is not a ... it more rigid, essentially locking it in the correct geometry for target interactions. ...

  7. X-ray Diffraction from Membrane Protein Nanocrystals

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    X-ray Diffraction from Membrane Protein Nanocrystals Authors: Hunter, M.S., DePonte, D.P., Shapiro, D.A., Kirian, R.A., Wang, X., Starodub, D., Marchesini, S., Weierstall, U., Doak, R.B., Spence, J.C.H., and Fromme, P. Title: X-ray Diffraction from Membrane Protein Nanocrystals Source: Biophysical Journal Year: 2011 Volume: 100 Pages: 198-206 ABSTRACT: Membrane proteins constitute >30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane

  8. Short-Time Glassy Dynamics in Viscous Protein Solutions with...

    Office of Scientific and Technical Information (OSTI)

    Short-Time Glassy Dynamics in Viscous Protein Solutions with Competing Interactions This content will become publicly available on November 23, 2016 Prev Next Title: ...

  9. Mapping protein collapse with single molecule fluorescence and...

    Office of Scientific and Technical Information (OSTI)

    spectroscopy Citation Details In-Document Search Title: Mapping protein collapse with single molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy ...

  10. Phthalimide conjugation as a strategy for in vivo target protein...

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Search Results Journal Article: Phthalimide conjugation as a strategy for in vivo target protein degradation Citation Details In-Document Search Title: Phthalimide ...

  11. Computational Design of Self-Assembling Protein Nanomaterials...

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Search Results Journal Article: Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy Citation Details In-Document Search Title: ...

  12. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE...

  13. New Crystal Structures Lift Fog around Protein Folding

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    incorrect or "misfolding" of proteins has been linked to many diseases, including Alzheimer's, Parkinson's, and some forms of cancer. So far, however, a complete...

  14. Computational Method for Detecting and Enhancing Protein Dynamics...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Marketing SummaryORNL researchers have developed a method that uses simulation and experimental data to detect, analyze, and manipulate protein activity. This approach enables...

  15. MTBreg: The Database of Conditionally Regulated Proteins in Mycobacterium Tuberculosis

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kaufman, Markus; Pal, Debnath; Eisenberg, David

    Proteins up- and down- regulated in Mycobacterium tuberculosis grown under conditions mimicking infection are included in this database. It also includes information on proteins that are regulated by selected transcription factors or other regulatory proteins. The literature data provided here is complimentary to the databases provided by Michael Strong that include recent TB computational functional linkages and the Prolinks Database by Peter Bowers. The experimental condition, the experimental dataset and a literature reference will be displayed, including links to the computationally linked proteins in the Prolinks Database and the entry in the Mycobacterium tuberculosis Structural Genomics Database.[Copied from information at http://www.doe-mbi.ucla.edu/Services/MTBreg/

  16. Kinks, loops, and protein folding, with protein A as an example

    SciTech Connect (OSTI)

    Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden)] [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Liwo, Adam, E-mail: adam@chem.univ.gda.pl [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland)] [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland); Maisuradze, Gia G., E-mail: gm56@cornell.edu; Scheraga, Harold A., E-mail: has5@cornell.edu [Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301 (United States); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours, France and Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2014-01-14

    The dynamics and energetics of formation of loops in the 46-residue N-terminal fragment of the B-domain of staphylococcal protein A has been studied. Numerical simulations have been performed using coarse-grained molecular dynamics with the united-residue (UNRES) force field. The results have been analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrdinger (DNLS) equation. In the case of proteins, the DNLS equation arises from a C{sup ?}-trace-based energy function. Three individual kink profiles were identified in the experimental three-?-helix structure of protein A, in the range of the Glu16-Asn29, Leu20-Asn29, and Gln33-Asn44 residues, respectively; these correspond to two loops in the native structure. UNRES simulations were started from the full right-handed ?-helix to obtain a clear picture of kink formation, which would otherwise be blurred by helix formation. All three kinks emerged during coarse-grained simulations. It was found that the formation of each is accompanied by a local free energy increase; this is expressed as the change of UNRES energy which has the physical sense of the potential of mean force of a polypeptide chain. The increase is about 7 kcal/mol. This value can thus be considered as the free energy barrier to kink formation in full ?-helical segments of polypeptide chains. During the simulations, the kinks emerge, disappear, propagate, and annihilate each other many times. It was found that the formation of a kink is initiated by an abrupt change in the orientation of a pair of consecutive side chains in the loop region. This resembles the formation of a Bloch wall along a spin chain, where the C{sup ?} backbone corresponds to the chain, and the amino acid side chains are interpreted as the spin variables. This observation suggests that nearest-neighbor side chainside chain interactions are responsible for initiation of loop formation. It was also found that the individual kinks are

  17. Protein Characterisation by Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy

    SciTech Connect (OSTI)

    Wallace, B.

    2009-01-01

    Circular dichroism (CD) spectroscopy is a well-established technique for the study of proteins. Synchrotron radiation circular dichroism (SRCD) spectroscopy extends the utility of conventional CD spectroscopy (i.e. using laboratory-based instruments) because the high light flux from a synchrotron enables collection of data to lower wavelengths, detection of spectra with higher signal-to-noise levels and measurements in the presence of strongly absorbing non-chiral components such as salts, buffers, lipids and detergents. This review describes developments in instrumentation, methodologies and bioinformatics that have enabled new applications of the SRCD technique for the study of proteins. It includes examples of the use of SRCD spectroscopy for providing static and dynamic structural information on molecules, including determinations of secondary structures of intact proteins and domains, assessment of protein stability, detection of conformational changes associated with ligand and drug binding, monitoring of environmental effects, examination of the processes of protein folding and membrane insertion, comparisons of mutant and modified proteins, identification of intermolecular interactions and complex formation, determination of the dispositions of proteins in membranes, identification of natively disordered proteins and their binding partners and examination of the carbohydrate components of glycoproteins. It also discusses how SRCD can be used in conjunction with macromolecular crystallography and other biophysical techniques to provide a more complete picture of protein structures and functions, including how proteins interact with other macromolecules and ligands. This review also includes a discussion of potential new applications in structural and functional genomics using SRCD spectroscopy and future instrumentation and bioinformatics developments that will enable such studies. Finally, the appendix describes a number of computational

  18. Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (VSP1) of Borrelia Turicatae

    SciTech Connect (OSTI)

    Lawson,C.; Yung, B.; Barbour, A.; Zuckert, W.

    2006-01-01

    Vsp surface lipoproteins are serotype-defining antigens of relapsing fever spirochetes that undergo multiphasic antigenic variation to allow bacterial persistence in spite of an immune response. Two isogenic serotypes of Borrelia turicatae strain Oz1 differ in their Vsp sequences and in disease manifestations in infected mice: Vsp1 is associated with the selection of a neurological niche, while Vsp2 is associated with blood and skin infection. We report here crystal structures of the Vsp1 dimer at 2.7 and 2.2 Angstroms. The structures confirm that relapsing fever Vsp proteins share a common helical fold with OspCs of Lyme disease-causing Borrelia. The fold features an inner stem formed by highly conserved N and C termini and an outer 'dome' formed by the variable central residues. Both Vsp1 and OspC structures possess small water-filled cavities, or pockets, that are lined largely by variable residues and are thus highly variable in shape. These features appear to signify tolerance of the Vsp-OspC fold for imperfect packing of residues at its antigenic surface. Structural comparison of Vsp1 with a homology model for Vsp2 suggests that observed differences in disease manifestation may arise in part from distinct differences in electrostatic surface properties; additional predicted positively charged surface patches on Vsp2 compared to Vsp1 may be sufficient to explain the relative propensity of Vsp2 to bind to acidic glycosaminoglycans.

  19. Construction of artificial pigment-protein antennae

    SciTech Connect (OSTI)

    Sibbald, J.

    1997-01-10

    Photosynthesis is a complex process which results in the conversion of solar radiation into chemical energy. This chemical energy is then used as the free energy source for all living organisms. In its basic form, photosynthesis can be described as the light-activated synthesis of carbohydrates from the simple molecules of water and carbon dioxide: 6H{sub 2}O + 6 CO{sub 2} light C{sub 6}H{sub 12}O{sub 6} + 6 O{sub 2} This basic mechanism actually requires numerous reaction steps. The two primary steps being: the capture of light by pigment molecules in light-harvesting antenna complexes and the transfer of this captured energy to the so-called photochemical reaction center. While the preferred pathway for energy absorbed by the chromophores in the antenna complexes is transfer to the reaction center, energy can be lost to competing processes such as internal conversion or radiative decay. Therefore, the energy transfer must be rapid, typically on the order of picoseconds, to successfully compete. The focus of the present work is on the construction of light-harvesting antenna complexes incorporating modular pigment-proteins.

  20. Orpinomyces cellulase celf protein and coding sequences

    DOE Patents [OSTI]

    Li, Xin-Liang; Chen, Huizhong; Ljungdahl, Lars G.

    2000-09-05

    A cDNA (1,520 bp), designated celF, consisting of an open reading frame (ORF) encoding a polypeptide (CelF) of 432 amino acids was isolated from a cDNA library of the anaerobic rumen fungus Orpinomyces PC-2 constructed in Escherichia coli. Analysis of the deduced amino acid sequence showed that starting from the N-terminus, CelF consists of a signal peptide, a cellulose binding domain (CBD) followed by an extremely Asn-rich linker region which separate the CBD and the catalytic domains. The latter is located at the C-terminus. The catalytic domain of CelF is highly homologous to CelA and CelC of Orpinomyces PC-2, to CelA of Neocallimastix patriciarum and also to cellobiohydrolase IIs (CBHIIs) from aerobic fungi. However, Like CelA of Neocallimastix patriciarum, CelF does not have the noncatalytic repeated peptide domain (NCRPD) found in CelA and CelC from the same organism. The recombinant protein CelF hydrolyzes cellooligosaccharides in the pattern of CBHII, yielding only cellobiose as product with cellotetraose as the substrate. The genomic celF is interrupted by a 111 bp intron, located within the region coding for the CBD. The intron of the celF has features in common with genes from aerobic filamentous fungi.

  1. Electrorheological crystallization of proteins and other molecules

    DOE Patents [OSTI]

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  2. Electrorheological crystallization of proteins and other molecules

    DOE Patents [OSTI]

    Craig, George D.; Rupp, Bernhard

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  3. Facilitating protein solubility by use of peptide extensions

    DOE Patents [OSTI]

    Freimuth, Paul I; Zhang, Yian-Biao; Howitt, Jason

    2013-09-17

    Expression vectors for expression of a protein or polypeptide of interest as a fusion product composed of the protein or polypeptide of interest fused at one terminus to a solubility enhancing peptide extension are provided. Sequences encoding the peptide extensions are provided. The invention further comprises antibodies which bind specifically to one or more of the solubility enhancing peptide extensions.

  4. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

    SciTech Connect (OSTI)

    Langkilde, Annette; Kristensen, Søren M.; Lo Leggio, Leila; Mølgaard, Anne; Jensen, Jan H.; Houk, Andrew R.; Navarro Poulsen, Jens-Christian; Kauppinen, Sakari; Larsen, Sine

    2008-08-01

    The short hydrogen bonds in rhamnogalacturonan acetylesterase have been investigated by structure determination of an active-site mutant, {sup 1}H NMR spectra and computational methods. Comparisons are made to database statistics. A very short carboxylic acid carboxylate hydrogen bond, buried in the protein, could explain the low-field (18 p.p.m.) {sup 1}H NMR signal. An extremely low-field signal (at approximately 18 p.p.m.) in the {sup 1}H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental {sup 1}H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK{sub a} values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest

  5. Method For Determining And Modifying Protein/Peptide Solubilty

    DOE Patents [OSTI]

    Waldo, Geoffrey S.

    2005-03-15

    A solubility reporter for measuring a protein's solubility in vivo or in vitro is described. The reporter, which can be used in a single living cell, gives a specific signal suitable for determining whether the cell bears a soluble version of the protein of interest. A pool of random mutants of an arbitrary protein, generated using error-prone in vitro recombination, may also be screened for more soluble versions using the reporter, and these versions may be recombined to yield variants having further-enhanced solubility. The method of the present invention includes "irrational" (random mutagenesis) methods, which do not require a priori knowledge of the three-dimensional structure of the protein of interest. Multiple sequences of mutation/genetic recombination and selection for improved solubility are demonstrated to yield versions of the protein which display enhanced solubility.

  6. Promoters and proteins from Clostridium thermocellum and uses thereof

    DOE Patents [OSTI]

    Wu, J. H. David; Newcomb, Michael

    2012-11-13

    The present invention relates to an inducible and a high expression nucleic acid promoter isolated from Clostridium thermocellum. These promoters are useful for directing expression of a protein or polypeptide encoded by a nucleic acid molecule operably associated with the nucleic acid promoters. The present invention also relates to nucleic acid constructs including the C. thermocellum promoters, and expression vectors and hosts containing such nucleic acid constructs. The present invention also relates to protein isolated from Clostridium thermocellum, including a repressor protein. The present invention also provides methods of using the isolated promoters and proteins from Clostridium thermocellum, including methods for directing inducible in vitro and in vivo expression of a protein or polypeptide in a host, and methods of producing ethanol from a cellulosic biomass.

  7. Elastic properties of protein functionalized nanoporous polymer films

    SciTech Connect (OSTI)

    Charles T. Black; Wang, Haoyu; Akcora, Pinar

    2015-12-16

    Retaining the conformational structure and bioactivity of immobilized proteins is important for biosensor designs and drug delivery systems. Confined environments often lead to changes in conformation and functions of proteins. In this study, lysozyme is chemically tethered into nanopores of polystyrene thin films, and submicron pores in poly(methyl methacrylate) films are functionalized with streptavidin. Nanoindentation experiments show that stiffness of streptavidin increases with decreasing submicron pore sizes. Lysozymes in polystyrene nanopores are found to behave stiffer than the submicron pore sizes and still retain their specific bioactivity relative to the proteins on flat surfaces. Lastly, our results show that protein functionalized ordered nanoporous polystyrene/poly(methyl methacrylate) films present heterogeneous elasticity and can be used to study interactions between free proteins and designed surfaces.

  8. A novel family of small proteins that affect plant development

    SciTech Connect (OSTI)

    John Charles Walker

    2011-04-29

    The DVL genes represent a new group of plant proteins that influence plant growth and development. Overexpression of DVL1, and other members of the DVL family, causes striking phenotypic changes. The DVL proteins share sequence homology in their C-terminal half. Point mutations in the C-terminal domain show it is necessary and deletion studies demonstrate the C-terminal domain is sufficient to confer the overexpression phenotypes. The phenotypes observed, and the conservation of the protein sequence in the plant kingdom, does suggest the DVL proteins have a role in modulating plant growth and development. Our working hypothesis is the DVL proteins function as regulators of cellular signaling pathways that control growth and development.

  9. Determining the role of hydration forces in protein folding

    SciTech Connect (OSTI)

    Sorenson, J.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry] [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Hura, G. [Univ. of California, Berkeley, CA (United States)] [Univ. of California, Berkeley, CA (United States); [Lawrence Berkeley National Lab., CA (United States). Life Sciences Div.; Soper, A.K. [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility] [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility; Pertsemlidis, A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry] [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Head-Gordon, T. [Lawrence Berkeley National Lab., CA (United States)] [Lawrence Berkeley National Lab., CA (United States)

    1999-07-01

    One of the primary issues in protein folding is determining what forces drive folding and eventually stabilize the native state. A delicate balance exists between electrostatic forces such as hydrogen bonding and salt bridges, and the hydrophobic effect, which are present for both intramolecular protein interactions and intermolecular contributions with the surrounding aqueous environment. This article describes a combined experimental, theoretical, and computational effort to show how the complexity of aqueous hydration can influence the structure, folding and aggregation, and stability of model protein systems. The unification of the theoretical and experimental work is the development or discovery of effective amino acid interactions that implicitly include the effects of aqueous solvent. The authors show that consideration of the full range of complexity of aqueous hydration forces such as many-body effects, long-ranged character of aqueous solvation, and the assumptions made about the degree of protein hydrophobicity can directly impact the observed structure, folding, and stability of model protein systems.

  10. Automating the determination of 3D protein structure

    SciTech Connect (OSTI)

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  11. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

    DOE PAGES-Beta [OSTI]

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; Chowdhury, Shatabdi Roy; Basu, Shibom; Boutet, Sébastien; Fromme, Petra; White, Thomas A.; Barty, Anton; Spence, John C. H.; et al

    2015-08-04

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is shown enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals deliveredmore » by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.« less

  12. Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

    DOE PAGES-Beta [OSTI]

    Yu, Peiqiang

    2006-01-01

    Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in

  13. The structures of synaptic cell adhesion proteins neuroligin-1 in isolation

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    and in complex with neurexin-1b reveal specific protein-protein and protein-Ca2+ interactions. The structures of synaptic cell adhesion proteins neuroligin-1 in isolation and in complex with neurexin-1b reveal specific protein-protein and protein-Ca2+ interactions. Autism is a neurodevelopmental disorder that impairs social interactions, and causes communication deficits and repetitive behaviors. About 1 in every 150 children is affected by autism. Genetic screens revealed that mutations in

  14. Protein Co-Expression Network Analysis (ProCoNA)

    SciTech Connect (OSTI)

    Gibbs, David L.; Baratt, Arie; Baric, Ralph; Kawaoka, Yoshihiro; Smith, Richard D.; Orwoll, Eric S.; Katze, Michael G.; Mcweeney, Shannon K.

    2013-06-01

    Biological networks are important for elucidating disease etiology due to their ability to model complex high dimensional data and biological systems. Proteomics provides a critical data source for such models, but currently lacks robust de novo methods for network construction, which could bring important insights in systems biology. We have evaluated the construction of network models using methods derived from weighted gene co-expression network analysis (WGCNA). We show that approximately scale-free peptide networks, composed of statistically significant modules, are feasible and biologically meaningful using two mouse lung experiments and one human plasma experiment. Within each network, peptides derived from the same protein are shown to have a statistically higher topological overlap and concordance in abundance, which is potentially important for inferring protein abundance. The module representatives, called eigenpeptides, correlate significantly with biological phenotypes. Furthermore, within modules, we find significant enrichment for biological function and known interactions (gene ontology and protein-protein interactions). Biological networks are important tools in the analysis of complex systems. In this paper we evaluate the application of weighted co-expression network analysis to quantitative proteomics data. Protein co-expression networks allow novel approaches for biological interpretation, quality control, inference of protein abundance, a framework for potentially resolving degenerate peptide-protein mappings, and a biomarker signature discovery.

  15. Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

    SciTech Connect (OSTI)

    Mereghetti, Paolo; Gabdoulline, Razif; Wade, Rebecca C.

    2010-12-01

    The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments.

  16. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  17. Stable isotope, site-specific mass tagging for protein identification

    DOE Patents [OSTI]

    Chen, Xian

    2006-10-24

    Proteolytic peptide mass mapping as measured by mass spectrometry provides an important method for the identification of proteins, which are usually identified by matching the measured and calculated m/z values of the proteolytic peptides. A unique identification is, however, heavily dependent upon the mass accuracy and sequence coverage of the fragment ions generated by peptide ionization. The present invention describes a method for increasing the specificity, accuracy and efficiency of the assignments of particular proteolytic peptides and consequent protein identification, by the incorporation of selected amino acid residue(s) enriched with stable isotope(s) into the protein sequence without the need for ultrahigh instrumental accuracy. Selected amino acid(s) are labeled with .sup.13C/.sup.15N/.sup.2H and incorporated into proteins in a sequence-specific manner during cell culturing. Each of these labeled amino acids carries a defined mass change encoded in its monoisotopic distribution pattern. Through their characteristic patterns, the peptides with mass tag(s) can then be readily distinguished from other peptides in mass spectra. The present method of identifying unique proteins can also be extended to protein complexes and will significantly increase data search specificity, efficiency and accuracy for protein identifications.

  18. Protein receptor-independent plasma membrane remodeling by HAMLET: A tumoricidal protein-lipid complex

    SciTech Connect (OSTI)

    Nadeem, Aftab; Sanborn, Jeremy; Gettel, Douglas L.; James, Ho C. S.; Rydström, Anna; Ngassam, Viviane N.; Klausen, Thomas Kjaer; Pedersen, Stine Falsig; Lam, Matti; Parikh, Atul N.; Svanborg, Catharina

    2015-11-12

    A central tenet of signal transduction in eukaryotic cells is that extra-cellular ligands activate specific cell surface receptors, which orchestrate downstream responses. This ‘’protein-centric” view is increasingly challenged by evidence for the involvement of specialized membrane domains in signal transduction. Here, we propose that membrane perturbation may serve as an alternative mechanism to activate a conserved cell-death program in cancer cells. This view emerges from the extraordinary manner in which HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) kills a wide range of tumor cells in vitro and demonstrates therapeutic efficacy and selectivity in cancer models and clinical studies. We identify a ‘’receptor independent” transformation of vesicular motifs in model membranes, which is paralleled by gross remodeling of tumor cell membranes. Furthermore, we find that HAMLET accumulates within these de novo membrane conformations and define membrane blebs as cellular compartments for direct interactions of HAMLET with essential target proteins such as the Ras family of GTPases. In conclusion, we demonstrate lower sensitivity of healthy cell membranes to HAMLET challenge. These features suggest that HAMLET-induced curvature-dependent membrane conformations serve as surrogate receptors for initiating signal transduction cascades, ultimately leading to cell death.

  19. Protein receptor-independent plasma membrane remodeling by HAMLET: A tumoricidal protein-lipid complex

    DOE PAGES-Beta [OSTI]

    Nadeem, Aftab; Sanborn, Jeremy; Gettel, Douglas L.; James, Ho C. S.; Rydström, Anna; Ngassam, Viviane N.; Klausen, Thomas Kjaer; Pedersen, Stine Falsig; Lam, Matti; Parikh, Atul N.; et al

    2015-11-12

    A central tenet of signal transduction in eukaryotic cells is that extra-cellular ligands activate specific cell surface receptors, which orchestrate downstream responses. This ‘’protein-centric” view is increasingly challenged by evidence for the involvement of specialized membrane domains in signal transduction. Here, we propose that membrane perturbation may serve as an alternative mechanism to activate a conserved cell-death program in cancer cells. This view emerges from the extraordinary manner in which HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) kills a wide range of tumor cells in vitro and demonstrates therapeutic efficacy and selectivity in cancer models and clinical studies. Wemore » identify a ‘’receptor independent” transformation of vesicular motifs in model membranes, which is paralleled by gross remodeling of tumor cell membranes. Furthermore, we find that HAMLET accumulates within these de novo membrane conformations and define membrane blebs as cellular compartments for direct interactions of HAMLET with essential target proteins such as the Ras family of GTPases. In conclusion, we demonstrate lower sensitivity of healthy cell membranes to HAMLET challenge. These features suggest that HAMLET-induced curvature-dependent membrane conformations serve as surrogate receptors for initiating signal transduction cascades, ultimately leading to cell death.« less

  20. The role of hydrogen bonds in protein folding and protein association

    SciTech Connect (OSTI)

    Ben-Naim, A. (National Inst. of Health, Bethesda, MD (USA))

    1991-02-07

    The contribution of a pair of functional groups that can form either intermolecular or intramolecular hydrogen bonds to the total standard free energy of the process of protein folding or protein association is examined. It is found that this contribution can be quite large, either positive or negative, depending on the particular process and on the solvent density. This is in contrast to the common belief that the hydrogen-bond energies tend to be compensated in these processes. For the binding process, in which the two functional groups are completely removed from the aqueous environment, the contribution of such a pair of functional groups to {Delta}G can be as high as +6.4 kcal/mol. This is the main reason why hydrophobic rather than hydrophilic surfaces tend to attach to each other. In contrast, when the two functional groups are only partially removed from the aqueous environment, as in the case of the formation of {alpha}-helix, their contribution to {Delta}G can be negative and of the order of about 1 kcal/mol.

  1. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

    SciTech Connect (OSTI)

    Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Datta, Susmita; Payne, Samuel H.; Kang, Jiyun; Bramer, Lisa M.; Nicora, Carrie D.; Shukla, Anil K.; Metz, Thomas O.; Rodland, Karin D.; Smith, Richard D.; Tardiff, Mark F.; McDermott, Jason E.; Pounds, Joel G.; Waters, Katrina M.

    2014-12-01

    As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

  2. Structural studies of human glioma pathogenesis-related protein 1

    SciTech Connect (OSTI)

    Asojo, Oluwatoyin A.; Koski, Raymond A.; Bonafé, Nathalie

    2011-10-01

    Structural analysis of a truncated soluble domain of human glioma pathogenesis-related protein 1, a membrane protein implicated in the proliferation of aggressive brain cancer, is presented. Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replacement solution could only be obtained by removing all loops from the search model. The native structure was refined to 1.85 Å resolution and that of a Zn{sup 2+} complex was refined to 2.2 Å resolution. The latter structure revealed that the putative binding cavity coordinates Zn{sup 2+} similarly to snake-venom CRISPs, which are involved in Zn{sup 2+}-dependent mechanisms of inflammatory modulation. Both sGLIPR1 structures have extensive flexible loop/turn regions and unique charge distributions that were not observed in any of the previously reported CAP protein structures. A model is also proposed for the structure of full-length membrane-bound GLIPR1.

  3. Hydration water dynamics and instigation of protein structuralrelaxation

    SciTech Connect (OSTI)

    Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

    2003-09-01

    Until a critical hydration level is reached, proteins do not function. This critical level of hydration is analogous to a similar lack of protein function observed for temperatures below a dynamical temperature range of 180-220K that also is connected to the dynamics of protein surface water. Restoration of some enzymatic activity is observed in partially hydrated protein powders, sometimes corresponding to less than a single hydration layer on the protein surface, which indicates that the dynamical and structural properties of the surface water is intimately connected to protein stability and function. Many elegant studies using both experiment and simulation have contributed important information about protein hydration structure and timescales. The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use experimental quasi-elastic neutron scattering (QENS) and molecular dynamics simulation to investigate hydration water dynamics near a greatly simplified protein system. We consider the hydration water dynamics near the completely deuterated N-acetyl-leucine-methylamide (NALMA) solute, a hydrophobic amino acid side chain attached to a polar blocked polypeptide backbone, as a function of concentration between 0.5M-2.0M under ambient conditions. We note that roughly 50-60% of a folded protein's surface is equally distributed between hydrophobic and hydrophilic domains, domains whose lengths are on the order of a few water diameters, that justify our study of hydration dynamics of this simple model protein system. The QENS experiment was performed at the NIST Center for Neutron Research, using the disk chopper time of flight spectrometer (DCS). In order to separate the translational and rotational components in the spectra, two sets of experiments were carried out using different incident neutron wavelengths of 7

  4. Water dynamics clue to key residues in protein folding

    SciTech Connect (OSTI)

    Gao, Meng [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Zhu, Huaiqiu, E-mail: hqzhu@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Yao, Xin-Qiu [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China) [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Department of Biophysics, Kyoto University, Sakyo Kyoto 606-8502 (Japan); She, Zhen-Su, E-mail: she@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)

    2010-01-29

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  5. Fast computational methods for predicting protein structure from...

    Office of Scientific and Technical Information (OSTI)

    independent of size of the protein, overcoming a significant limitation in the prior art. ...796,418 Contract Number: AC05-00OR22725 Research Org: UT-Battelle, LLC (Oak Ridge, TN) ...

  6. Protein scaffolds for selective enrichment of metal ions

    DOE Patents [OSTI]

    He, Chuan; Zhou, Lu; Bosscher, Michael

    2016-02-09

    Polypeptides comprising high affinity for the uranyl ion are provided. Methods for binding uranyl using such proteins are likewise provided and can be used, for example, in methods for uranium purification or removal.

  7. Protein Puzzles and Scientific Solutions | Department of Energy

    Energy Savers

    ... and serious computing power, the LCLS can be used to pull detailed structural information from protein crystals scarcely the size of a speck of dust (a micron) and even smaller. ...

  8. Serial femtosecond crystallography of soluble proteins in lipidic...

    Office of Scientific and Technical Information (OSTI)

    of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP...

  9. Deprotonated imidodiphosphate in AMPPNP-containing protein structures

    SciTech Connect (OSTI)

    Dauter, Miroslawa; Dauter, Zbigniew

    2011-12-01

    In certain AMPPNP-containing protein structures, the nitrogen bridging the two terminal phosphate groups can be deprotonated. Many different proteins utilize the chemical energy provided by the cofactor adenosine triphosphate (ATP) for their proper function. A number of structures in the Protein Data Bank (PDB) contain adenosine 5′-(β,γ-imido)triphosphate (AMPPNP), a nonhydrolysable analog of ATP in which the bridging O atom between the two terminal phosphate groups is substituted by the imido function. Under mild conditions imides do not have acidic properties and thus the imide nitrogen should be protonated. However, an analysis of protein structures containing AMPPNP reveals that the imide group is deprotonated in certain complexes if the negative charges of the phosphate moieties in AMPPNP are in part neutralized by coordinating divalent metals or a guanidinium group of an arginine.

  10. A Designed Supramolecular Protein Assembly with in-Vivo Enzymatic...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    A Designed Supramolecular Protein Assembly with in-Vivo Enzymatic Activity Thursday, April 30, 2015 A major goal in molecular design and engineering is the creation of new enzymes ...

  11. Protein Immobilization in Metal-Organic Frameworks by Covalent...

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Protein Immobilization in Metal-Organic Frameworks by Covalent Binding Previous Next List Xuan Wang, Trevor A. Makal and Hong-Cai Zhou, Aust. J. Chem. 67, 1629-1631 (2014) DOI:...

  12. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    The crystal structure of Epstein-Barr Viral BHRF1 (black) bound to a designed protein ... The study shows not just how to help defeat EBV, but also opens up a whole new way to ...

  13. A Novel Method for Sampling Alpha-Helical Protein Backbones

    DOE R&D Accomplishments [OSTI]

    Fain, Boris; Levitt, Michael

    2001-01-01

    We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.

  14. Determining protein function and interaction from genome analysis

    DOE Patents [OSTI]

    Eisenberg, David; Marcotte, Edward M.; Thompson, Michael J.; Pellegrini, Matteo; Yeates, Todd O.

    2004-08-03

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  15. Optimization of Xenon Biosensors for Detection of ProteinInteractions

    SciTech Connect (OSTI)

    Lowery, Thomas J.; Garcia, Sandra; Chavez, Lana; Ruiz, E.Janette; Wu, Tom; Brotin, Thierry; Dutasta, Jean-Pierre; King, David S.; Schultz, Peter G.; Pines, Alex; Wemmer, David E..

    2005-08-03

    Hyperpolarized 129Xe NMR can detect the presence of specific low-concentration biomolecular analytes by means of the xenon biosensor, which consists of a water-soluble, targeted cryptophane-A cage that encapsulates xenon. In this work we use the prototypical biotinylated xenon biosensor to determine the relationship between the molecular composition of the xenon biosensor and the characteristics of protein-bound resonances. The effects of diastereomer overlap, dipole-dipole coupling, chemical shift anisotropy, xenon exchange, and biosensor conformational exchange on protein-bound biosensor signal were assessed. It was found that optimal protein-bound biosensor signal can be obtained by minimizing the number of biosensor diastereomers and using a flexible linker of appropriate length. Both the linewidth and sensitivity of chemical shift to protein binding of the xenon biosensor were found to be inversely proportional to linker length.

  16. Elastic properties of protein functionalized nanoporous polymer films

    DOE PAGES-Beta [OSTI]

    Charles T. Black; Wang, Haoyu; Akcora, Pinar

    2015-12-16

    Retaining the conformational structure and bioactivity of immobilized proteins is important for biosensor designs and drug delivery systems. Confined environments often lead to changes in conformation and functions of proteins. In this study, lysozyme is chemically tethered into nanopores of polystyrene thin films, and submicron pores in poly(methyl methacrylate) films are functionalized with streptavidin. Nanoindentation experiments show that stiffness of streptavidin increases with decreasing submicron pore sizes. Lysozymes in polystyrene nanopores are found to behave stiffer than the submicron pore sizes and still retain their specific bioactivity relative to the proteins on flat surfaces. Lastly, our results show that proteinmore » functionalized ordered nanoporous polystyrene/poly(methyl methacrylate) films present heterogeneous elasticity and can be used to study interactions between free proteins and designed surfaces.« less

  17. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Immortality is not a good thing for cells, and in fact, cells will destroy themselves in a process called...

  18. In the OSTI Collections: Determining How Proteins Fold | OSTI...

    Office of Scientific and Technical Information (OSTI)

    ... Some of the research into how proteins fold has been funded by the Department of Energy ... in terms of how the object's energy would change if a force acted to change the shape. ...

  19. Structure and Function of Microbial Metal-Reduction Proteins

    Office of Scientific and Technical Information (OSTI)

    "Structure and Function of Microbial Metal-Reduction Proteins" PI: Ying Xu Co-PI: Oakley H. Crawford Dong Xu Frank W Larimer Edward C. Uberbacher Jizhong Zhou Descriptionabstract: ...

  20. Scientists ratchet up understanding of cellular protein factory

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Understanding of cellular protein factory Scientists ratchet up understanding of cellular protein factory The research could aid in development of new antibiotics used to fight multidrug resistant superbugs such as MRSA found in many U.S. hospitals. December 2, 2010 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to

  1. Theoretical Study on Catalysis by Protein Enzymes and Ribozyme

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Theoretical Study on Catalysis by Protein Enzymes and Ribozyme Theoretical Study on Catalysis by Protein Enzymes and Ribozyme 2000 NERSC Annual Report 17shkarplus.jpg The energetics were determined for three mechanisms proposed for TIM catalyzed reactions. Results from reaction path calculations suggest that the two mechanisms that involve an enediol intermediate are likely to occur, while the direct intra-substrate proton transfer mechanism (in green) is energetically unfavorable due to the

  2. Simplified Protein Models: Predicting Folding Pathways and Structure Using

    Office of Scientific and Technical Information (OSTI)

    Amino Acid Sequences (Journal Article) | DOE PAGES Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences Title: Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences Authors: Adhikari, Aashish N. ; Freed, Karl F. ; Sosnick, Tobin R. Publication Date: 2013-07-11 OSTI Identifier: 1103786 Type: Publisher's Accepted Manuscript Journal Name: Physical Review Letters Additional Journal Information: Journal Volume:

  3. Cellulosic Fiber Composites Using Protein Hydrolysates and Methods of

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Making Same - Energy Innovation Portal Advanced Materials Advanced Materials Find More Like This Return to Search Cellulosic Fiber Composites Using Protein Hydrolysates and Methods of Making Same Battelle Memorial Institute Contact BMI About This Technology Technology Marketing SummaryThis technology relates to cellulosic fiber composites using protein hydrolysates. DescriptionCellulosic fiber composites currently use petroleum-derived binders such as isocyanates and phenol formaldehyde.

  4. Cellulosic Fiber Composites Using Protein Hydrolysates and Methods of

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Making Same - Energy Innovation Portal Cellulosic Fiber Composites Using Protein Hydrolysates and Methods of Making Same Battelle Memorial Institute Contact BMI About This Technology Technology Marketing Summary This technology relates to cellulosic fiber composites using protein hydrolysates. Cellulosic fiber composites currently use petroleum-derived binders such as isocyanates and phenol formaldehyde. This work fills a need for a new fiber-adhesive, resin binder system that reduces the

  5. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    SciTech Connect (OSTI)

    Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

    2015-03-03

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  6. Methods and constructs for expression of foreign proteins in photosynthetic organisms

    DOE Patents [OSTI]

    Laible, Philip D.; Hanson, Deborah K.

    2002-01-01

    A method for expressing and purifying foreign proteins in photosynthetic organisms comprising the simultaneous expression of both the heterologous protein and a means for compartmentalizing or sequestering of the protein.

  7. The earliest events in protein folding: Helix dynamics in proteins and model peptides

    SciTech Connect (OSTI)

    Dyer, R.B.; Williams, S.; Woodruff, W.H. [Los Alamos National Lab., NM (United States)] [and others

    1996-12-31

    The earliest events in protein folding are critically important in determining the folding pathway, but have proved difficult to study by conventional approaches. We have developed new rapid initiation methods and structure-specific probes to interrogate the earliest events of protein folding. Our focus is the pathways. Folding or unfolding reactions are initiated on a fast timescale (10 ns) using a laser induced temperature jump (15 C) and probed with time-resolved infrared spectroscopy. We obtained the kinetics of the helix-coil transition for a model 21-residue peptide. The observed rate constant k{sub obs} = k{sub f} + k{sub u} for reversible kinetics; from the observed rate (6 x 10{sup 6} s{sup -1}) and the equilibrium constant favoring folding of 7.5 at 27 C, we calculate a folding lifetime of 180 ns and an unfolding lifetime of 1.4 {mu}s. The {open_quotes}molten globule{close_quotes} form of apomyoglobin (horse, pH*3, 0.15M NaCl) shows similar kinetics for helix that is unconstrained by tertiary structure (helix with an unusually low Amide I frequency, near 1633 cm{sup -1}). In {open_quotes}native{close_quotes} apomyoglobin (horse, pH*5.3, 10 mM NaCl) two very different rates (45 ns and 70 {mu}s) are observed and we infer that a third occurs on a timescales inaccessible to our experiment (> 1 ms). We suggest that the slower processes are due to helix formation that is rate-limited by the formation of tertiary structure.

  8. Applications of the second virial coefficient: protein crystallization and solubility

    SciTech Connect (OSTI)

    Wilson, William W.; DeLucas, Lawrence J.

    2014-04-30

    This article highlights some of the ground-based studies emanating from NASAs Microgravity Protein Crystal Growth (PCG) program, and includes a more detailed discussion of the history and the progress made in one of the NASA-funded PCG investigations involving the use of measured second virial coefficients (B values) as a diagnostic indicator of solution conditions conducive to protein crystallization. This article begins by highlighting some of the ground-based studies emanating from NASAs Microgravity Protein Crystal Growth (PCG) program. This is followed by a more detailed discussion of the history of and the progress made in one of the NASA-funded PCG investigations involving the use of measured second virial coefficients (B values) as a diagnostic indicator of solution conditions conducive to protein crystallization. A second application of measured B values involves the determination of solution conditions that improve or maximize the solubility of aqueous and membrane proteins. These two important applications have led to several technological improvements that simplify the experimental expertise required, enable the measurement of membrane proteins and improve the diagnostic capability and measurement throughput.

  9. Quantification of protein interaction kinetics in a micro droplet

    SciTech Connect (OSTI)

    Yin, L. L.; Wang, S. P. E-mail: njtao@asu.edu; Shan, X. N.; Tao, N. J. E-mail: njtao@asu.edu; Zhang, S. T.

    2015-11-15

    Characterization of protein interactions is essential to the discovery of disease biomarkers, the development of diagnostic assays, and the screening for therapeutic drugs. Conventional flow-through kinetic measurements need relative large amount of sample that is not feasible for precious protein samples. We report a novel method to measure protein interaction kinetics in a single droplet with sub microliter or less volume. A droplet in a humidity-controlled environmental chamber is replacing the microfluidic channels as the reactor for the protein interaction. The binding process is monitored by a surface plasmon resonance imaging (SPRi) system. Association curves are obtained from the average SPR image intensity in the center area of the droplet. The washing step required by conventional flow-through SPR method is eliminated in the droplet method. The association and dissociation rate constants and binding affinity of an antigen-antibody interaction are obtained by global fitting of association curves at different concentrations. The result obtained by this method is accurate as validated by conventional flow-through SPR system. This droplet-based method not only allows kinetic studies for proteins with limited supply but also opens the door for high-throughput protein interaction study in a droplet-based microarray format that enables measurement of many to many interactions on a single chip.

  10. The nucleocapsid protein of measles virus blocks host interferon response

    SciTech Connect (OSTI)

    Takayama, Ikuyo; Sato, Hiroki; Watanabe, Akira; Omi-Furutani, Mio; Sugai, Akihiro; Kanki, Keita; Yoneda, Misako; Kai, Chieko

    2012-03-01

    Measles virus (MV) belongs to the genus Morbillivirus of the family Paramyxoviridae. A number of paramyxoviruses inhibit host interferon (IFN) signaling pathways in host immune systems by various mechanisms. Inhibition mechanisms have been described for many paramyxoviruses. Although there are inconsistencies among previous reports concerning MV, it appears that P/V/C proteins interfere with the pathways. In this study, we confirmed the effects of MV P gene products of a wild MV strain on IFN pathways and examined that of other viral proteins on it. Interestingly, we found that N protein acts as an IFN-{alpha}/{beta} and {gamma}-antagonist as strong as P gene products. We further investigated the mechanisms of MV-N inhibition, and revealed that MV-N blocks the nuclear import of activated STAT without preventing STAT and Jak activation or STAT degradation, and that the nuclear translocation of MV-N is important for the inhibition. The inhibitory effect of the N protein was observed as a common feature of other morbilliviruses. The results presented in this report suggest that N protein of MV as well as P/V/C proteins is involved in the inhibition of host IFN signaling pathways.

  11. Towards understanding of Nipah virus attachment protein assembly and the role of protein affinity and crowding for membrane curvature events.

    SciTech Connect (OSTI)

    Stachowiak, Jeanne C.; Hayden, Carl C.; Negrete, Oscar A.; Davis, Ryan Wesley; Sasaki, Darryl Yoshio

    2013-10-01

    Pathogenic viruses are a primary threat to our national security and to the health and economy of our world. Effective defense strategies to combat viral infection and spread require the development of understanding of the mechanisms that these pathogens use to invade the host cell. We present in this report results of our research into viral particle recognition and fusion to cell membranes and the role that protein affinity and confinement in lipid domains plays in membrane curvature in cellular fusion and fission events. Herein, we describe 1) the assembly of the G attachment protein of Nipah virus using point mutation studies to define its role in viral particle fusion to the cell membrane, 2) how lateral pressure of membrane bound proteins induce curvature in model membrane systems, and 3) the role of membrane curvature in the selective partitioning of molecular receptors and specific affinity of associated proteins.

  12. High-Order Membrane Complexes from Activated G-Protein Subunits

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    High-Order Membrane Complexes from Activated G-Protein Subunits Print Many physiological ... (GPCRs), proteins integral to the cell membrane, sense the signal and activate G ...

  13. Structural analysis of flexible proteins in solution by SmallAngle...

    Office of Scientific and Technical Information (OSTI)

    of mass, radius, conformations, assembly, and shape changes associated with protein folding and functions. SAXS can efficiently reveal the spatial organization of protein...

  14. Report on the research conducted under the funding of the Sloan foundation postdoctoral fellowship in Computational Molecular Biology [Systematic study of protein-protein complexes] Final report

    SciTech Connect (OSTI)

    Sheinerman, Felix

    2001-06-01

    A central question in molecular biology is what structural features are common at protein-protein interfaces and what energetic factors define the affinity and specificity of protein-protein association. Analysis of structural and mutational data on protein-protein interfaces revealed that protein-protein interfaces of different functional classes contain many more energetically important charged and polar residues than was previously thought. Since, in the context of protein folding studies, polar interactions are believed to destabilize the folded proteins, this observation raised the question as to the forces that determine the stability of protein complexes. To investigate this issue in detail, the authors developed a number of partitioning schemes that allowed them to investigate the role of selected residues, ion pairs, and networks of polar interactions in protein-protein association. The methods developed were applied to the analysis of four different protein-protein interfaces: the ribonuclease barnase and its inhibitor barstar, the human growth hormone and its receptor, subtype N9 influenze virus neuraminidase and NC41 antibody, and the Ras Binding Domain of kinase cRaf and a Ras homologue Rap1A. The calculations revealed a surprising variability in how polar interactions affect the stability of different complexes. The finding that positions of charged and polar residues on protein-protein interfaces are optimized with respect to electrostatic interactions suggests that this property can be employed for the discrimination between native conformations and trial complexes generated by a docking algorithm. Analysis indicated the presence of SH2 domains in Janus family of non-receptor protein tyrosine kinases.

  15. Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition

    SciTech Connect (OSTI)

    Wang, Jin; Lu, Qiang N.; Lu, H PETER.

    2006-07-01

    The study of associations between two biomolecules is the key to understand molecular recognition and function. Molecular function is often thought to be determined by the underlying structures. Here, combining single molecule study of protein binding with an energy landscape inspired microscopic model, we found strong evidences that bio-molecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse grained molecular dynamics performed on the residue level with the energy function biased towards the native binding structure (Go model). With our model, the underlying free energy landscape of the binding can be explored. Two distinct conformational states as free energy minimum, one with partially folding of CBD and significant binding of CBD to CDC42, and another with native folding of CBD and native binding of CBD to CDC42, are clearly seen. This shows the binding process proceeds with significant interface binding of CBD with CDC42 first without complete folding of CBD. Finally binding and folding are coupled with each other cooperatively to reach the native binding state. The single molecule experimental finding of the dynamic fluctuations between the loosely bound and closely bound conformational states can be identified with theoretically calculated free energy minimum and quantitatively explained in our model as a result of binding associated with large conformational changes. Theoretical predictions have identified certain key residues for binding which are consistent with mutational experiments. The combined study provides a test ground for fundamental mechanisms as well as insights into design and further explorations on biomolecular recognition with large conformational changes.

  16. Rab proteins: The key regulators of intracellular vesicle transport

    SciTech Connect (OSTI)

    Bhuin, Tanmay; Roy, Jagat Kumar

    2014-10-15

    Vesicular/membrane trafficking essentially regulates the compartmentalization and abundance of proteins within the cells and contributes in many signalling pathways. This membrane transport in eukaryotic cells is a complex process regulated by a large and diverse array of proteins. A large group of monomeric small GTPases; the Rabs are essential components of this membrane trafficking route. Most of the Rabs are ubiquitously expressed proteins and have been implicated in vesicle formation, vesicle motility/delivery along cytoskeleton elements and docking/fusion at target membranes through the recruitment of effectors. Functional impairments of Rabs affecting transport pathways manifest different diseases. Rab functions are accompanied by cyclical activation and inactivation of GTP-bound and GDP-bound forms between the cytosol and membranes which is regulated by upstream regulators. Rab proteins are characterized by their distinct sub-cellular localization and regulate a wide variety of endocytic, transcytic and exocytic transport pathways. Mutations of Rabs affect cell growth, motility and other biological processes. - Highlights: Rab proteins regulate different signalling pathways. Deregulation of Rabs is the fundamental causes of a variety of human diseases. This paper gives potential directions in developing therapeutic targets. This paper also gives ample directions for modulating pathways central to normal physiology. These are the huge challenges for drug discovery and delivery in near future.

  17. Hemin as a generic and potent protein misfolding inhibitor

    SciTech Connect (OSTI)

    Liu, Yanqin; Carver, John A.; Ho, Lam H.; Elias, Abigail K.; Musgrave, Ian F.; Pukala, Tara L.

    2014-11-14

    Highlights: • Hemin prevents Aβ42, α-synuclein and RCM-κ-casein forming amyloid fibrils. • Hemin inhibits the β-sheet structure formation of Aβ42. • Hemin reduces the cell toxicity caused by fibrillar Aβ42. • Hemin dissociates partially formed Aβ42 fibrils. • Hemin prevents amorphous aggregation by ADH, catalase and γs-crystallin. - Abstract: Protein misfolding causes serious biological malfunction, resulting in diseases including Alzheimer’s disease, Parkinson’s disease and cataract. Molecules which inhibit protein misfolding are a promising avenue to explore as therapeutics for the treatment of these diseases. In the present study, thioflavin T fluorescence and transmission electron microscopy experiments demonstrated that hemin prevents amyloid fibril formation of kappa-casein, amyloid beta peptide and α-synuclein by blocking β-sheet structure assembly which is essential in fibril aggregation. Further, inhibition of fibril formation by hemin significantly reduces the cytotoxicity caused by fibrillar amyloid beta peptide in vitro. Interestingly, hemin degrades partially formed amyloid fibrils and prevents further aggregation to mature fibrils. Light scattering assay results revealed that hemin also prevents protein amorphous aggregation of alcohol dehydrogenase, catalase and γs-crystallin. In summary, hemin is a potent agent which generically stabilises proteins against aggregation, and has potential as a key molecule for the development of therapeutics for protein misfolding diseases.

  18. Multidimensional profiling of cell surface proteins and nuclear markers

    SciTech Connect (OSTI)

    Han, Ju; Chang, Hang; Andarawewa, Kumari; Yaswen, Paul; Helen Barcellos-Hoff, Mary; Parvin, Bahram

    2009-01-30

    Cell membrane proteins play an important role in tissue architecture and cell-cell communication. We hypothesize that segmentation and multidimensional characterization of the distribution of cell membrane proteins, on a cell-by-cell basis, enable improved classification of treatment groups and identify important characteristics that can otherwise be hidden. We have developed a series of computational steps to (i) delineate cell membrane protein signals and associate them with a specific nucleus; (ii) compute a coupled representation of the multiplexed DNA content with membrane proteins; (iii) rank computed features associated with such a multidimensional representation; (iv) visualize selected features for comparative evaluation through heatmaps; and (v) discriminate between treatment groups in an optimal fashion. The novelty of our method is in the segmentation of the membrane signal and the multidimensional representation of phenotypic signature on a cell-by-cell basis. To test the utility of this method, the proposed computational steps were applied to images of cells that have been irradiated with different radiation qualities in the presence and absence of other small molecules. These samples are labeled for their DNA content and E-cadherin membrane proteins. We demonstrate that multidimensional representations of cell-by-cell phenotypes improve predictive and visualization capabilities among different treatment groups, and identify hidden variables.

  19. TOWARDS A PROBABILISTIC RECOGNITION CODE FOR PROTEIN-DNA INTERACTIONS

    SciTech Connect (OSTI)

    P. BENOS; ET AL

    2000-09-01

    We are investigating the rules that govern protein-DNA interactions, using a statistical mechanics based formalism that is related to the Boltzmann Machine of the neural net literature. Our approach is data-driven, in which probabilistic algorithms are used to model protein-DNA interactions, given SELEX and phage data as input. Under the ''one-to-one'' model for interactions (i.e. one amino acid contacts one base), we can successfully identify the wild-type binding sites of EGR and MIG protein families. The predictions using our method are the same or better than that of methods existing in the literature, however our methodology offers the potential to capitalize in quantitative detail on more data as it becomes available.

  20. Heterologous protein production using the twin arginine translocation pathway

    DOE Patents [OSTI]

    Pohlschroder, Mechtild; Kissinger, Jessica C; Rose, R. Wesley; Brueser, Thomas; Dilks, Kieran

    2008-11-04

    Provided are means for evaluating and identifying putative substrates of the twin arginine translocation (Tat) secretory pathway in Streptomyces and other bacterial species. Also provided, therefore, are simple ways to express, secrete and purify correctly folded heterologous proteins on a large scale using host microorganisms, such as, Streptomyces and the Tat pathway therein. Many of the thus-produced proteins are of significant therapeutic value in the pharmaceutical and biochemical industries, particularly when they can be secreted from the host in fully-folded active form. Accordingly, there are further provided the heterologous proteins produced by the Tat secretion pathway using the foregoing methods, and the computer algorithm used to identify the Tat signal sequence and putative substrates.

  1. Shock wave induced damage of a protein by void collapse

    DOE PAGES-Beta [OSTI]

    Lau, Edmond Y.; Berkowitz, Max L.; Schwegler, Eric R.

    2016-01-05

    In this study, we report on a series of molecular dynamics simulations that were used to examine the effects of shockwaves on a membrane bound ion channel. A planar shockwave was found to compress the ion channel upon impact but the protein geometry resembles the initial structure as soon as the solvent density begins to dissipate. When a void was placed in close proximity to the membrane, the shockwave proved to be much more destructive to the protein due to formation of a nanojet that results from the asymmetric collapse of the void. The nanojet was able to cause significantmore » structural changes to the protein even at low particle velocities that are not able to directly cause poration of the membrane.« less

  2. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist invariants across lattices related to fundamental properties of the protein folding process. This paper considers whether performance-guaranteed approximability is such an invariant for HP lattice models. The authors define a master approximation algorithm that has provable performance guarantees provided that a specific sublattice exists within a given lattice. They describe a broad class of crystal lattices that are approximable, which further suggests that approximability is a general property of HP lattice models.

  3. Protein structure and hydration probed by SANS and osmotic stress

    SciTech Connect (OSTI)

    Rau, Dr. Donald [National Institutes of Health

    2008-01-01

    Interactions governing protein folding, stability, recognition, and activity are mediated by hydration. Here, we use small-angle neutron scattering coupled with osmotic stress to investigate the hydration of two proteins, lysozyme and guanylate kinase (GK), in the presence of solutes. By taking advantage of the neutron contrast variation that occurs upon addition of these solutes, the number of protein-associated (solute-excluded) water molecules can be estimated from changes in both the zero-angle scattering intensity and the radius of gyration. Poly(ethylene glycol) exclusion varies with molecular weight. This sensitivity can be exploited to probe structural features such as the large internal GK cavity. For GK, small-angle neutron scattering is complemented by isothermal titration calorimetry with osmoticstress to also measure hydration changes accompanying ligand binding. These results provide a framework for studying other biomolecular systems and assemblies using neutron scattering together with osmotic stress.

  4. Zero-length Cross-linking in Solid State as an Approach for Analysis of Protein -Protein Interactions

    SciTech Connect (OSTI)

    Elshafey, Ahmed; Tolic, Nikola; Young, Malin M.; Sale, Kenneth L.; Smith, Richard D.; Kery, Vladimir

    2006-03-01

    Analyzing the architecture of protein complexes is a difficult task. Chemical cross-linking is often used in combination with mass spectrometric analysis to elucidate the interaction interfaces between proteins. We have developed a new approach for the analysis of interacting interfaces in protein complexes based on cross-linking in the solid state. Protein complexes are freeze-dried under vacuum and cross-links are introduced in the solid phase by dehydrating the protein in a non-water solvent, thus, creating peptide bonds between amino and carboxyl groups of the interacting peptides. Cross-linked proteins are digested into peptides with trypsin in both H216O and H218O and then readily distinguished in mass spectra by characteristic 8 atomic mass unit (amu) shifts reflecting incorporation of two 18O atoms into each C-terminus of proteolytic peptides. Computer analysis of mass spectrometry (MS) and MS/MS data is used to identify the cross-linked peptides.We demonstrated our method by cross-linking homooligomeric protein complexes alone or in a mixture of many other proteins. Cross-linking in the solid state was shown to be specific and reproducible. Glutathione-S-transferase (GST) from Schistosoma japonicum was studied in more detail. Twenty-seven unique intra-molecular and two inter-molecular cross-linked peptides were identified using tryptic mapping followed by LTQ-MS analysis. Identified cross-links were predominantly of amide origin, but six esters and thioesters were also found. Identified cross-linked peptides were validated by computational (visualization of cross-links in the three-dimensional [3D] structure of GST) and experimental (MS/MS) analyses. Most of the identified cross-links matched interacting peptides in the native 3D structure of GST indicating that the structure of GST and its oligomeric complex remained primarily intact after freeze drying. The pattern of oligomeric GST obtained in solid state was the same as that obtained in solution by Ru

  5. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S.

    1995-12-11

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist ``invariants`` across lattices that define fundamental properties of protein folding process; an invariant defines a property that transcends particular lattice formulations. This paper identifies two classes of invariants, defined in terms of sublattices that are related to the design of algorithms for the structure prediction problem. The first class of invariants is, used to define a master approximation algorithm for which provable performance guarantees exist. This algorithm can be applied to generalizations of the hydrophobic-hydrophilic model that have lattices other than the cubic lattice, including most of the crystal lattices commonly used in protein folding lattice models. The second class of invariants applies to a related lattice model. Using these invariants, we show that for this model the structure prediction problem is intractable across a variety of three-dimensional lattices. It`` turns out that these two classes of invariants are respectively sublattices of the two- and three-dimensional square lattice. As the square lattices are the standard lattices used in empirical protein folding` studies, our results provide a rigorous confirmation of the ability of these lattices to provide insight into biological phenomenon. Our results are the first in the literature that identify algorithmic paradigms for the protein structure prediction problem which transcend particular lattice formulations.

  6. Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8

    SciTech Connect (OSTI)

    Wang, Chengliang; Zhang, Qiongdi; Hang, Tianrong; Tao, Yue; Ma, Xukai; Wu, Minhao; Zhang, Xuan Zang, Jianye

    2015-08-28

    The structure of the complex of NO66 and Rpl8 was solved in the native state and NO66 recognizes the consensus motif NHXH . Tetramerization is required for efficient substrate binding and catalysis by NO66. The JmjC domain-containing proteins belong to a large family of oxygenases possessing distinct substrate specificities which are involved in the regulation of different biological processes, such as gene transcription, RNA processing and translation. Nucleolar protein 66 (NO66) is a JmjC domain-containing protein which has been reported to be a histone demethylase and a ribosome protein 8 (Rpl8) hydroxylase. The present biochemical study confirmed the hydroxylase activity of NO66 and showed that oligomerization is required for NO66 to efficiently catalyze the hydroxylation of Rpl8. The structures of NO66{sup 176–C} complexed with Rpl8{sup 204–224} in a tetrameric form and of the mutant protein M2 in a dimeric form were solved. Based on the results of structural and biochemical analyses, the consensus sequence motif NHXH recognized by NO66 was confirmed. Several potential substrates of NO66 were found by a BLAST search according to the consensus sequence motif. When binding to substrate, the relative positions of each subunit in the NO66 tetramer shift. Oligomerization may facilitate the motion of each subunit in the NO66 tetramer and affect the catalytic activity.

  7. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2015-07-14

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  8. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2014-04-01

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  9. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2011-06-07

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  10. Methods and compositions for protein detection using nanoparticle-fluorescent polymer complexes

    DOE Patents [OSTI]

    Rotello, Vincent; Bunz, Uwe; You, Chang-Cheng; Miranda, Oscar; Kim, Ik-Bum

    2011-09-20

    Compositions, methods and related apparatus, as can be used for selective protein detection and identification.

  11. Divinyl ether synthase gene and protein, and uses thereof

    SciTech Connect (OSTI)

    Howe, Gregg A.; Itoh, Aya

    2011-09-13

    The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.

  12. Divinyl ether synthase gene, and protein and uses thereof

    DOE Patents [OSTI]

    Howe, Gregg A.; Itoh, Aya

    2006-12-26

    The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.

  13. Photoconversion of organic materials into single-cell protein

    DOE Patents [OSTI]

    Weaver, Paul F.

    2001-01-01

    A process is described for converting organic materials (such as biomass wastes) into sterile, high-grade bacterial protein suitable for use an animal feed or human food supplements. In a preferred embodiment the process involves thermally gasifying the organic material into primarily carbon monoxide, hydrogen and nitrogen products, followed by photosynthetic bacterial assimilation of the gases into cell material, which can be as high as 65% protein. The process is ideally suited for waste recycling and for food production under zero-gravity or extra-terrestrial conditions.

  14. Laser-induced breakdown spectroscopy of alcohols and protein solutions

    SciTech Connect (OSTI)

    Melikechi, N.; Ding, H.; Marcano, O. A.; Rock, S.

    2008-04-15

    We report on the use of laser-induced breakdown spectroscopy for the study of organic samples that exhibit similar elemental composition. We evaluate the method for its potential application for the measurement of small spectroscopic differences between samples such as alcohols and water solution of proteins. We measure differences in the relative amplitudes of the oxygen peaks for alcohols and find that these correlate with the relative amount of oxygen atoms within the molecule. We also show that the spectra of proteins reveal differences that can be used for their detection and identification.

  15. Use of Galerina marginata genes and proteins for peptide production

    DOE Patents [OSTI]

    Hallen-Adams, Heather E.; Scott-Craig, John S.; Walton, Jonathan D.; Luo, Hong

    2016-03-01

    The present invention relates to compositions and methods comprising genes and peptides associated with cyclic peptides and cyclic peptide production in mushrooms. In particular, the present invention relates to using genes and proteins from Galerina species encoding peptides specifically relating to amatoxins in addition to proteins involved with processing cyclic peptide toxins. In a preferred embodiment, the present invention also relates to methods for making small peptides and small cyclic peptides including peptides similar to amanitin. Further, the present inventions relate to providing kits for making small peptides.

  16. Fast computational methods for predicting protein structure from primary amino acid sequence

    DOE Patents [OSTI]

    Agarwal, Pratul Kumar

    2011-07-19

    The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

  17. Uniform {sup 15}N- and {sup 15}N/{sup 13}C-labeling of proteins in mammalian cells and solution structure of the amino terminal fragment of u-PA

    SciTech Connect (OSTI)

    Hansen, A.P.; Petros, A.M.; Meadows, R.P.; Mazar, A.P.; Nettesheim, D.G.; Pederson, T.M.; Fesik, S.W.

    1994-12-01

    Urokinase-type plasminogen activator (u-PA) is a 54-kDa glycoprotein that catalyzes the conversion of plasminogen to plasmin, a broad-specificity protease responsible for the degradation of fibrin clots and extracellular matrix components. The u-PA protein consists of three individual modules: a growth factor domain (GFD), a kringle, and a serine protease domain. The amino terminal fragment (ATF) includes the GFD-responsible for u-PA binding to its receptor-and the kringle domains. This protein was expressed and uniformly {sup 15}N-and {sup 15}N/{sup 13}C-labeled in mammalian cells by methods that will be described. In addition, we present the three-dimensional structure of ATF that was derived from 1299 NOE-derived distance restraints along with the {phi} angle and hydrogen bonding restraints. Although the individual domains in the structures were highly converged, the two domains are structurally independent. The overall structures of the individual domains are very similar to the structures of homologous proteins. However, important structural differences between the growth factor domain of u-PA and other homologous proteins were observed in the region that has been implicated in binding the urokinase receptor. These results may explain, in part, why other growth factors show no appreciable affinity for the urokinase receptor.

  18. Crystal structure of the β2 adrenergic receptor-Gs protein complex

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    (Journal Article) | SciTech Connect Crystal structure of the β2 adrenergic receptor-Gs protein complex Citation Details In-Document Search Title: Crystal structure of the β2 adrenergic receptor-Gs protein complex G protein-coupled receptors (GPCRs) are responsible for the majority of cellular responses to hormones and neurotransmitters as well as the senses of sight, olfaction and taste. The paradigm of GPCR signalling is the activation of a heterotrimeric GTP binding protein (G protein)

  19. Protein-Folding Landscapes in Multi-Chain Systems (Journal Article) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Protein-Folding Landscapes in Multi-Chain Systems Citation Details In-Document Search Title: Protein-Folding Landscapes in Multi-Chain Systems Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the

  20. Methods to alter levels of a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-10-17

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  1. Methods of use of cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1997-09-23

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  2. Methods of use of cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1997-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  3. Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

    SciTech Connect (OSTI)

    Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei; Forouhar, Farhad; Mesyanzhinov, Vadim V.; Tong, Liang; Rossmann, Michael G.

    2012-02-21

    Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.

  4. Heavy metal ions are potent inhibitors of protein folding

    SciTech Connect (OSTI)

    Sharma, Sandeep K. [Biochemisches Institut, Universitaet Zuerich, CH-8057 Zuerich (Switzerland); Departement de Biologie Moleculaire Vegetale, Universite de Lausanne, CH-1015 Lausanne (Switzerland); Goloubinoff, Pierre [Departement de Biologie Moleculaire Vegetale, Universite de Lausanne, CH-1015 Lausanne (Switzerland); Christen, Philipp [Biochemisches Institut, Universitaet Zuerich, CH-8057 Zuerich (Switzerland)], E-mail: christen@bioc.uzh.ch

    2008-07-25

    Environmental and occupational exposure to heavy metals such as cadmium, mercury and lead results in severe health hazards including prenatal and developmental defects. The deleterious effects of heavy metal ions have hitherto been attributed to their interactions with specific, particularly susceptible native proteins. Here, we report an as yet undescribed mode of heavy metal toxicity. Cd{sup 2+}, Hg{sup 2+} and Pb{sup 2+} proved to inhibit very efficiently the spontaneous refolding of chemically denatured proteins by forming high-affinity multidentate complexes with thiol and other functional groups (IC{sub 50} in the nanomolar range). With similar efficacy, the heavy metal ions inhibited the chaperone-assisted refolding of chemically denatured and heat-denatured proteins. Thus, the toxic effects of heavy metal ions may result as well from their interaction with the more readily accessible functional groups of proteins in nascent and other non-native form. The toxic scope of heavy metals seems to be substantially larger than assumed so far.

  5. Protein structure prediction enhanced with evolutionary diversity : SPEED.

    SciTech Connect (OSTI)

    DeBartolo, J.; Hocky, G.; Wilde, M.; Xu, J.; Freed, K. F.; Sosnick, T. R.; Univ. of Chicago; Toyota Technological Inst. at Chicago

    2010-03-01

    For naturally occurring proteins, similar sequence implies similar structure. Consequently, multiple sequence alignments (MSAs) often are used in template-based modeling of protein structure and have been incorporated into fragment-based assembly methods. Our previous homology-free structure prediction study introduced an algorithm that mimics the folding pathway by coupling the formation of secondary and tertiary structure. Moves in the Monte Carlo procedure involve only a change in a single pair of {phi},{psi} backbone dihedral angles that are obtained from a Protein Data Bank-based distribution appropriate for each amino acid, conditional on the type and conformation of the flanking residues. We improve this method by using MSAs to enrich the sampling distribution, but in a manner that does not require structural knowledge of any protein sequence (i.e., not homologous fragment insertion). In combination with other tools, including clustering and refinement, the accuracies of the predicted secondary and tertiary structures are substantially improved and a global and position-resolved measure of confidence is introduced for the accuracy of the predictions. Performance of the method in the Critical Assessment of Structure Prediction (CASP8) is discussed.

  6. Effect of cosolvent on protein stability: A theoretical investigation

    SciTech Connect (OSTI)

    Chalikian, Tigran V.

    2014-12-14

    We developed a statistical thermodynamic algorithm for analyzing solvent-induced folding/unfolding transitions of proteins. The energetics of protein transitions is governed by the interplay between the cavity formation contribution and the term reflecting direct solute-cosolvent interactions. The latter is viewed as an exchange reaction in which the binding of a cosolvent to a solute is accompanied by release of waters of hydration to the bulk. Our model clearly differentiates between the stoichiometric and non-stoichiometric interactions of solvent or co-solvent molecules with a solute. We analyzed the urea- and glycine betaine (GB)-induced conformational transitions of model proteins of varying size which are geometrically approximated by a sphere in their native state and a spherocylinder in their unfolded state. The free energy of cavity formation and its changes accompanying protein transitions were computed based on the concepts of scaled particle theory. The free energy of direct solute-cosolvent interactions were analyzed using empirical parameters previously determined for urea and GB interactions with low molecular weight model compounds. Our computations correctly capture the mode of action of urea and GB and yield realistic numbers for (??G/?a{sub 3}){sub T,P} which are related to the m-values of protein denaturation. Urea is characterized by negative values of (??G/?a{sub 3}){sub T,P} within the entire range of urea concentrations analyzed. At concentrations below ?1 M, GB exhibits positive values of (??G/?a{sub 3}){sub T,P} which turn positive at higher GB concentrations. The balance between the thermodynamic contributions of cavity formation and direct solute-cosolvent interactions that, ultimately, defines the mode of cosolvent action is extremely subtle. A 20% increase or decrease in the equilibrium constant for solute-cosolvent binding may change the sign of (??G/?a{sub 3}){sub T,P} thereby altering the mode of cosolvent action (stabilizing

  7. System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors

    DOE Patents [OSTI]

    Trabanino, Rene J; Vaidehi, Nagarajan; Hall, Spencer E; Goddard, William A; Floriano, Wely

    2013-02-05

    The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.

  8. Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein

    SciTech Connect (OSTI)

    Shaikh, Afshan; Shaikh, Afshan S.; Tang, Yinjie; Mukhopadhyay, Aindrila; Keasling, Jay D.

    2008-06-27

    {sup 13}C-based metabolic flux analysis provides valuable information about bacterial physiology. Though many biological processes rely on the synergistic functions of microbial communities, study of individual organisms in a mixed culture using existing flux analysis methods is difficult. Isotopomer-based flux analysis typically relies on hydrolyzed amino acids from a homogeneous biomass. Thus metabolic flux analysis of a given organism in a mixed culture requires its separation from the mixed culture. Swift and efficient cell separation is difficult and a major hurdle for isotopomer-based flux analysis of mixed cultures. Here we demonstrate the use of a single highly-expressed protein to analyze the isotopomer distribution of amino acids from one organism. Using the model organism E. coli expressing a plasmid-borne, his-tagged Green Fluorescent Protein (GFP), we show that induction of GFP does not affect E. coli growth kinetics or the isotopomer distribution in nine key metabolites. Further, the isotopomer labeling patterns of amino acids derived from purified GFP and total cell protein are indistinguishable, indicating that amino acids from a purified protein can be used to infer metabolic fluxes of targeted organisms in a mixed culture. This study provides the foundation to extend isotopomer-based flux analysis to study metabolism of individual strains in microbial communities.

  9. Development of a Chemoenzymatic-like and Photoswitchable Method for the High-Throughput creation of Protein Microarrays. Application to the Analysis of the Protein/Protein Interactions Involved in the YOP Virulon from Yersinia pestis.

    SciTech Connect (OSTI)

    Camarero, J A

    2006-12-07

    Protein arrays are ideal tools for the rapid analysis of whole proteomes as well as for the development of reliable and cheap biosensors. The objective of this proposal is to develop a new ligand assisted ligation method based in the naturally occurring protein trans-splicing process. This method has been used for the generation of spatially addressable arrays of multiple protein components by standard micro-lithographic techniques. Key to our approach is the use of the protein trans-splicing process. This naturally occurring process allows the development of a truly generic and highly efficient method for the covalent attachment of proteins through its C-terminus to any solid support. This technology has been used for the creation of protein chips containing several virulence factors from the human pathogen Y. pestis.

  10. High-throughput method for optimum solubility screening for homogeneity and crystallization of proteins

    SciTech Connect (OSTI)

    Kim, Sung-Hou; Kim, Rosalind; Jancarik, Jamila

    2012-01-31

    An optimum solubility screen in which a panel of buffers and many additives are provided in order to obtain the most homogeneous and monodisperse protein condition for protein crystallization. The present methods are useful for proteins that aggregate and cannot be concentrated prior to setting up crystallization screens. A high-throughput method using the hanging-drop method and vapor diffusion equilibrium and a panel of twenty-four buffers is further provided. Using the present methods, 14 poorly behaving proteins have been screened, resulting in 11 of the proteins having highly improved dynamic light scattering results allowing concentration of the proteins, and 9 were crystallized.

  11. Similar Energetic Contributions of Packing in the Core of Membrane and Water-Soluble Proteins

    SciTech Connect (OSTI)

    Joh, Nathan H.; Oberai, Amit; Yang, Duan; Whitelegge, Julian P.; Bowie, James U.; (UCLA)

    2009-09-15

    A major driving force for water-soluble protein folding is the hydrophobic effect, but membrane proteins cannot make use of this stabilizing contribution in the apolar core of the bilayer. It has been proposed that membrane proteins compensate by packing more efficiently. We therefore investigated packing contributions experimentally by observing the energetic and structural consequences of cavity creating mutations in the core of a membrane protein. We observed little difference in the packing energetics of water and membrane soluble proteins. Our results imply that other mechanisms are employed to stabilize the structure of membrane proteins.

  12. Large-volume protein crystal growth for neutron macromolecular crystallography

    SciTech Connect (OSTI)

    Ng, Joseph D.; Baird, James K.; Coates, Leighton; Garcia-Ruiz, Juan M.; Hodge, Teresa A.; Huang, Sijay

    2015-03-30

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  13. Rotational order–disorder structure of fluorescent protein FP480

    SciTech Connect (OSTI)

    Pletnev, Sergei; Morozova, Kateryna S.; Verkhusha, Vladislav V.; Dauter, Zbigniew

    2009-09-01

    An analysis of the rotational order–disorder structure of fluorescent protein FP480 is presented. In the last decade, advances in instrumentation and software development have made crystallography a powerful tool in structural biology. Using this method, structural information can now be acquired from pathological crystals that would have been abandoned in earlier times. In this paper, the order–disorder (OD) structure of fluorescent protein FP480 is discussed. The structure is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, namely rotated 90° with respect to each other around the crystal c axis, with tetramer axes coincident with crystallographic twofold axes. The random distribution of alternatively oriented tetramers in the crystal creates a rotational OD structure with statistically averaged I422 symmetry, although the presence of very weak and diffuse additional reflections suggests that the randomness is only approximate.

  14. Kinetic evidence for protein clustering at a surface

    SciTech Connect (OSTI)

    Ramsden, J.J. ); Bachmanova, G.I.; Archakov, A.I. )

    1994-12-01

    The molecules designated 1A2 and 2B4 belong to the cytochrome P450 protein superfamily. They can interact specifically with lipid bilayers via the penetration of part of their amino acid chains into the bilayer. The kinetics of their irreversible adsorption from solution to phospholipid bilayers, accurately measured in the low to intermediate coverage range using an integrated optics reflectance technique, differ significantly: at intermediate bulk solution concentrations, 2B4 shows typical random sequential adsorption (RSA) kinetics, whereas 1A2 shows Langmuir kinetics. At higher bulk concentration the behavior of 1[ital A]2 switches to RSA kinetics, and at very low concentrations 2[ital B]4 switches to Langmuir kinetics. The Langmuir kinetics provides strong evidence for clustering of the molecules at the bilayer surface, and the observed concentration dependence of the kinetics is consistent with the clusters arising through lateral diffusion of the proteins on the surface.

  15. Recombinant human bone morphogenetic protein induces bone formation

    SciTech Connect (OSTI)

    Wang, E.A.; Rosen, V.; D'Alessandro, J.S.; Bauduy, M.; Cordes, P.; Harada, T.; Israel, D.I.; Hewick, R.M.; Kerns, K.M.; LaPan, P.; Luxenberg, D.P.; McQuaid, D.; Moutsatsos, I.K.; Nove, J.; Wozney, J.M. )

    1990-03-01

    The authors have purified and characterized active recombinant human bone morphogenetic protein (BMP) 2A. Implantation of the recombinant protein in rats showed that a single BMP can induce bone formation in vivo. A dose-response and time-course study using the rat ectopic bone formation assay revealed that implantation of 0.5-115 {mu}g of partially purified recombinant human BMP-2A resulted in cartilage by day 7 and bone formation by day 14. The time at which bone formation occurred was dependent on the amount of BMP-2A implanted; at high doses bone formation could be observed at 5 days. The cartilage- and bone-inductive activity of the recombinant BMP-2A is histologically indistinguishable from that of bone extracts. Thus, recombinant BMP-2A has therapeutic potential to promote de novo bone formation in humans.

  16. Large-volume protein crystal growth for neutron macromolecular crystallography

    DOE PAGES-Beta [OSTI]

    Ng, Joseph D.; Baird, James K.; Coates, Leighton; Garcia-Ruiz, Juan M.; Hodge, Teresa A.; Huang, Sijay

    2015-03-30

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for themore » growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.« less

  17. Metal binding proteins, recombinant host cells and methods

    DOE Patents [OSTI]

    Summers, Anne O.; Caguiat, Jonathan J.

    2004-06-15

    The present disclosure provides artificial heavy metal binding proteins termed chelons by the inventors. These chelons bind cadmium and/or mercuric ions with relatively high affinity. Also disclosed are coding sequences, recombinant DNA molecules and recombinant host cells comprising those recombinant DNA molecules for expression of the chelon proteins. In the recombinant host cells or transgenic plants, the chelons can be used to bind heavy metals taken up from contaminated soil, groundwater or irrigation water and to concentrate and sequester those ions. Recombinant enteric bacteria can be used within the gastrointestinal tracts of animals or humans exposed to toxic metal ions such as mercury and/or cadmium, where the chelon recombinantly expressed in chosen in accordance with the ion to be rededicated. Alternatively, the chelons can be immobilized to solid supports to bind and concentrate heavy metals from a contaminated aqueous medium including biological fluids.

  18. Palmitoylation of POTE family proteins for plasma membrane targeting

    SciTech Connect (OSTI)

    Das, Sudipto; Ise, Tomoko; Nagata, Satoshi; Maeda, Hiroshi; Bera, Tapan K.; Pastan, Ira

    2007-11-23

    The POTE gene family is composed of 13 paralogs and likely evolved by duplications and remodeling of the human genome. One common property of POTE proteins is their localization on the inner aspect of the plasma membrane. To determine the structural elements required for membrane localization, we expressed mutants of different POTEs in 293T cells as EGFP fusion proteins. We also tested their palmitoylation by a biotin-switch assay. Our data indicate that the membrane localizations of different POTEs are mediated by similar 3-4 short cysteine rich repeats (CRRs) near the amino-terminuses and that palmitoylation on paired cysteine residues in each CRR motif is responsible for the localization. Multiple palmitoylation in the small CRRs can result in the strong association of whole POTEs with plasma membrane.

  19. Collective aspects of protein folding illustrated by a toy model

    SciTech Connect (OSTI)

    Stillinger, F.H. [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States)] [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States); Head-Gordon, T. [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)] [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)

    1995-09-01

    A simple toy model for polypeptides serves as a testbed to illuminate some nonlocal, or collective, aspects of protein folding phenomena. The model is two dimensional and has only two amino acids, but involves a continuous range of backbone bend angles. Global potential energy minima and their folding structures have been determined for leading members of two special and contrasting polypeptide sequences, center doped and Fibonacci, named descriptively for their primary structures. The results display the presence of spontaneous symmetry breaking, elastic strain, and substantial conformational variation for specific embedded amino acid strings. We conclude that collective variables generated by the primary amino acid structure may be required for fully effective protein folding predictors, including those based on neural networks.

  20. Heteropolymer freezing and design: Towards physical models of protein folding

    SciTech Connect (OSTI)

    Pande, Vijay S. [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States)] [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States); Grosberg, Alexander Yu. [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States)] [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Tanaka, Toyoichi [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2000-01-01

    Protein folding has become one of the most actively studied problems in modern molecular biophysics. Approaches to the problem combine ideas from the physics of disordered systems, polymer physics, and molecular biology. Much can be learned from the statistical properties of model heteropolymers, the chain molecules having different monomers in irregular sequences. Even in highly evolved proteins, there is a strong random element in the sequences, which gives rise to a statistical ensemble of sequences for a given folded shape. Simple analytic models give rise to phase transitions between random, glassy, and folded states, depending on the temperature T and the design temperature T{sup des} of the ensemble of sequences. Besides considering the analytic results obtainable in a random-energy model and in the Flory mean-field model of polymers, the article reports on confirming numerical simulations. (c) 2000 The American Physical Society.

  1. Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding

    SciTech Connect (OSTI)

    Garde, S.; Hummer, G.; Garcia, A.E.; Paulaitis, M.E.; Pratt, L.R. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); [Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716 (United States); [Department of Chemical Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    1996-12-01

    An information theory model of hydrophobic effects is used to construct a molecular explanation why hydrophobic solvation entropies of protein unfolding measured by high sensitivity calorimetry converge to zero at a common convergence temperature. The entropy convergence follows directly from the weak temperature dependence of occupancy fluctuations {l_angle}{delta}{ital n}{sup 2}{r_angle} for molecular-scale volumes in water. The macroscopic expression of the contrasting entropic behavior of water relative to common organic solvents is the {ital relative} temperature insensitivity of the water isothermal compressibility compared to hydrocarbon liquids. The information theory model used provides a quantitative description of small molecule hydration and, in addition, predicts that the value of the entropy at convergence is slightly {ital negative}. Interpretations of entropic contributions to protein folding should account for this result. {copyright} {ital 1996 The American Physical Society.}

  2. Structural Rearrangement in Ebola Virus Protein VP40 Creates Multiple

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    Functions | Stanford Synchrotron Radiation Lightsource Structural Rearrangement in Ebola Virus Protein VP40 Creates Multiple Functions Monday, March 31, 2014 Figure 1. Three structures of VP40. Top, a butterfly-shaped dimer structure critical for membrane trafficking. Middle, a rearranged hexameric structure essential for building and releasing nascent virions. Bottom, an RNA-binding octameric ring that controls transcription in infected cells. As x-ray crystallographers, we often assume

  3. Protein tyrosine adduct in humans self-poisoned by chlorpyrifos

    SciTech Connect (OSTI)

    Li, Bin; Eyer, Peter; Eddleston, Michael; Jiang, Wei; Schopfer, Lawrence M.; Lockridge, Oksana

    2013-06-15

    Studies of human cases of self-inflicted poisoning suggest that chlorpyrifos oxon reacts not only with acetylcholinesterase and butyrylcholinesterase but also with other blood proteins. A favored candidate is albumin because in vitro and animal studies have identified tyrosine 411 of albumin as a site covalently modified by organophosphorus poisons. Our goal was to test this proposal in humans by determining whether plasma from humans poisoned by chlorpyrifos has adducts on tyrosine. Plasma samples from 5 self-poisoned humans were drawn at various time intervals after ingestion of chlorpyrifos for a total of 34 samples. All 34 samples were analyzed for plasma levels of chlorpyrifos and chlorpyrifos oxon (CPO) as a function of time post-ingestion. Eleven samples were analyzed for the presence of diethoxyphosphorylated tyrosine by mass spectrometry. Six samples yielded diethoxyphosphorylated tyrosine in pronase digests. Blood collected as late as 5 days after chlorpyrifos ingestion was positive for CPO-tyrosine, consistent with the 20-day half-life of albumin. High plasma CPO levels did not predict detectable levels of CPO-tyrosine. CPO-tyrosine was identified in pralidoxime treated patients as well as in patients not treated with pralidoxime, indicating that pralidoxime does not reverse CPO binding to tyrosine in humans. Plasma butyrylcholinesterase was a more sensitive biomarker of exposure than adducts on tyrosine. In conclusion, chlorpyrifos oxon makes a stable covalent adduct on the tyrosine residue of blood proteins in humans who ingested chlorpyrifos. - Highlights: • Chlorpyrifos-poisoned patients have adducts on protein tyrosine. • Diethoxyphosphate-tyrosine does not lose an alkyl group. • Proteins in addition to AChE and BChE are modified by organophosphates.

  4. Two protein studies discover molecular secrets to recycling carbon and

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    healing cells | Argonne National Laboratory You may also like Cancer's big data problem October 19, 2016 Two protein studies discover molecular secrets to recycling carbon and healing cells September 9, 2016 Two Argonne-led projects among $39.8 million in first-round Exascale Computing Project awards September 7, 2016 X-rays reveal the photonic crystals in butterfly wings that create color June 10, 2016 New Microbiome Center to combine UChicago, Marine Biological Laboratory and Argonne

  5. The utility of protein and mRNA correlation

    SciTech Connect (OSTI)

    Payne, Samuel H.

    2015-01-01

    Transcriptomic, proteomic and metabolomic measurements are revolutionizing the way we model and predict cellular behavior, and multi-omic comparisons are being published with increased regularity. Some have expected a trivial and predictable correlation between mRNA and protein; however the manifest complexity of biological regulation suggests a more nuanced relationship. Indeed, observing this lack of strict correlation provides clues for new research topics, and has the potential for transformative biological insight.

  6. Combined approach to the inverse protein folding problem. Final report

    SciTech Connect (OSTI)

    Ruben A. Abagyan

    2000-06-01

    The main scientific contribution of the project ''Combined approach to the inverse protein folding problem'' submitted in 1996 and funded by the Department of Energy in 1997 is the formulation and development of the idea of the multilink recognition method for identification of functional and structural homologues of newly discovered genes. This idea became very popular after they first announced it and used it in prediction of the threading targets for the CASP2 competition (Critical Assessment of Structure Prediction).

  7. Architectures of Whole-module and Bimodular Proteins from

    U.S. Department of Energy (DOE) all webpages (Extended Search)

    6-Deoxyerythronolide B Synthase | Stanford Synchrotron Radiation Lightsource Architectures of Whole-module and Bimodular Proteins from 6-Deoxyerythronolide B Synthase Thursday, July 31, 2014 Secondary metabolites produced by microorganisms have a market value of over $30 billion annually, and nearly half of these compounds are naturally produced by bacteria in the phylum Actinobacteria1. Phylum is a taxonomic rank in biology. It is below kingdom (e.g. Animal, Plant, Fungi etc.) and above

  8. Analysis of differential protein expression in normal and neoplastic human breast epithelial cell lines

    SciTech Connect (OSTI)

    Williams, K.; Chubb, C.; Huberman, E.; Giometti, C.S.

    1997-07-01

    High resolution two dimensional get electrophoresis (2DE) and database analysis was used to establish protein expression patterns for cultured normal human mammary epithelial cells and thirteen breast cancer cell lines. The Human Breast Epithelial Cell database contains the 2DE protein patterns, including relative protein abundances, for each cell line, plus a composite pattern that contains all the common and specifically expressed proteins from all the cell lines. Significant differences in protein expression, both qualitative and quantitative, were observed not only between normal cells and tumor cells, but also among the tumor cell lines. Eight percent of the consistently detected proteins were found in significantly (P < 0.001) variable levels among the cell lines. Using a combination of immunostaining, comigration with purified protein, subcellular fractionation, and amino-terminal protein sequencing, we identified a subset of the differentially expressed proteins. These identified proteins include the cytoskeletal proteins actin, tubulin, vimentin, and cytokeratins. The cell lines can be classified into four distinct groups based on their intermediate filament protein profile. We also identified heat shock proteins; hsp27, hsp60, and hsp70 varied in abundance and in some cases in the relative phosphorylation levels among the cell lines. Finally, we identified IMP dehydrogenase in each of the cell lines, and found the levels of this enzyme in the tumor cell lines elevated 2- to 20-fold relative to the levels in normal cells.

  9. Interaction between human BAP31 and respiratory syncytial virus small hydrophobic (SH) protein

    SciTech Connect (OSTI)

    Li, Yan; Jain, Neeraj; Limpanawat, Suweeraya; To, Janet; Quistgaard, Esben M.; Nordlund, Par; Thanabalu, Thirumaran; Torres, Jaume

    2015-08-15

    The small hydrophobic (SH) protein is a short channel-forming polypeptide encoded by the human respiratory syncytial virus (hRSV). Deletion of SH protein leads to the viral attenuation in mice and primates, and delayed apoptosis in infected cells. We have used a membrane-based yeast two-hybrid system (MbY2H) and a library from human lung cDNA to detect proteins that bind SH protein. This led to the identification of a membrane protein, B-cell associated protein 31 (BAP31). Transfected SH protein co-localizes with transfected BAP31 in cells, and pulls down endogenous BAP31. Titration of purified C-terminal endodomain of BAP31 against isotopically labeled SH protein in detergent micelles suggests direct interaction between the two proteins. Given the key role of BAP31 in protein trafficking and its critical involvement in pro- and anti-apoptotic pathways, this novel interaction may constitute a potential drug target. - Highlights: • A yeast two-hybrid system (MbY2H) detected BAP31 as a binder of RSV SH protein. • Transfected SH and BAP31 co-localize in lung epithelial cells. • Endogenous BAP31 is pulled down by RSV SH protein. • BAP31 endodomain interacts with the N-terminal α-helix of SH protein in micelles. • This interaction is proposed to be a potential drug target.

  10. Protein interaction reporter agents and methods for using same

    DOE Patents [OSTI]

    Bruce, James E.; Tang, Xiaoting; Munske,Gerhard

    2009-04-28

    Particular aspects provide novel protein interaction reporter (PIR) compounds (e.g., formulas I and II), comprising at least two protein reactive moieties (e.g., N-hydroxysuccinamide), each linked to a reporter moiety (e.g., mass reporter) by a covalent labile bond that is differentially cleavable with respect to peptide bonds (e.g., by a method such as collisional activation in a mass spectrometer, activation by electron capture dissociation (ECD), photoactivation, etc.), wherein the reporter moiety is operatively releasable from the PIR agent upon cleavage of the labile bonds, the released reporter moiety having a characteristic identifying property or label (e.g., m/z value). Particular PIRs comprise a mass reporter moiety, and further comprise an affinity group, (e.g., biotin), linked to the PIR (e.g., to the mass reporter moiety) by a selectively cleavable bone (e.g. photo-labile bond)). Additional aspects provide methods for characterizing intermolecular or intramolecular protein interactions using one or more inventive PIR compounds.

  11. The development and application of engineered proteins for bioremediation

    SciTech Connect (OSTI)

    Trewhella, J.

    1995-09-26

    Clean up of the toxic legacy of the Cold War is projected to be the most expensive domestic project the nation has yet undertaken. Remediation of the Department of Energy and Department of Defense toxic waste sites alone are projected to cost {approximately}$1 trillion over a 20-30 year period. New, cost effective technologies are needed to attack this enormous problem. Los Alamos has put together a cross-divisional team of scientist to develop science based bioremediation technology to work toward this goal. In the team we have expertise in: (1) molecular, ecosystem and transport modeling; (2) genetic and protein engineering; (3) microbiology and microbial ecology; (4) structural biology; and (5) bioinorganic chemistry. This document summarizes talks at a workshop of different aspects of bioremediation technology including the following: Introducing novel function into a Heme enzyme: engineering by excavation; cytochrome P-450: ideal systems for bioremediation?; selection and development of bacterial strains for in situ remediation of cholorinated solvents; genetic analysis and preparation of toluene ortho-monooxygenase for field application in remediation of trichloroethylene; microbial ecology and diversity important to bioremediation; engineering haloalkane dehalogenase for bioremediation; enzymes for oxidative biodegradation; indigenous bacteria as hosts for engineered proteins; performance of indigenous bacterial, hosting engineered proteins in microbial communities.

  12. Microbial Protein-Protein Interactions (MiPPI) Data from the Genomics: GTL Center for Molecular and Cellular Systems (CMCS)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Genomic Science Center for Molecular and Cellular Systems (CMCS), established in 2002, seeks to identify and characterize the complete set of protein complexes within a cell to provide a mechanistic basis for the understanding of biochemical functions. The CMCS is anchored at ORNL and PNNL. CMCS initially focused on the identification and characterization of protein complexes in two microbial systems,Rhodopseudomonas palustris (R. palustris) and Shewanella oneidensis (S. oneidensis). These two organisms have also been the focus of major DOE Genomic Science/Microbial Cell Program (MCP) projects. To develop an approach for identifying the diverse types of complexes present in microbial organisms, CMCS incorporates a number of molecular biology, microbiology, analytical and computational tools in an integrated pipeline.

  13. Depletion of cellular poly (A) binding protein prevents protein synthesis and leads to apoptosis in HeLa cells

    SciTech Connect (OSTI)

    Thangima Zannat, Mst.; Bhattacharjee, Rumpa B.; Bag, Jnanankur

    2011-05-13

    Highlights: {yields} Depletion of cellular PABP level arrests mRNA translation in HeLa cells. {yields} PABP knock down leads to apoptotic cell death. {yields} PABP depletion does not affect transcription. {yields} PABP depletion does not lead to nuclear accumulation of mRNA. -- Abstract: The cytoplasmic poly (A) binding protein (PABP) is important in mRNA translation and stability. In yeast, depletion of PABP leads to translation arrest. Similarly, the PABP gene in Drosophila is important for proper development. It is however uncertain, whether mammalian PABP is essential for mRNA translation. Here we showed the effect of PABP depletion on mRNA metabolism in HeLa cells by using a small interfering RNA. Our results suggest that depletion of PABP prevents protein synthesis and consequently leads to cell death through apoptosis. Interestingly, no detectable effect of PABP depletion on transcription, transport and stability of mRNA was observed.

  14. Ran GTPase protein promotes human pancreatic cancer proliferation by deregulating the expression of Survivin and cell cycle proteins

    SciTech Connect (OSTI)

    Deng, Lin; Lu, Yuanyuan; Zhao, Xiaodi; Sun, Yi; Shi, Yongquan; Fan, Hongwei; Liu, Changhao; Zhou, Jinfeng; Nie, Yongzhan; Wu, Kaichun; Fan, Daiming; Guo, Xuegang

    2013-10-18

    Highlights: •Overexpression of Ran in pancreatic cancer was correlated with histological grade. •Downregulation of Ran could induce cell apoptosis and inhibit cell proliferation. •The effects were mediated by cell cycle proteins, Survivin and cleaved Caspase-3. -- Abstract: Ran, a member of the Ras GTPase family, has important roles in nucleocytoplasmic transport. Herein, we detected Ran expression in pancreatic cancer and explored its potential role on tumour progression. Overexpressed Ran in pancreatic cancer tissues was found highly correlated with the histological grade. Downregulation of Ran led to significant suppression of cell proliferation, cell cycle arrest at the G1/S phase and induction of apoptosis. In vivo studies also validated that result. Further studies revealed that those effects were at least partly mediated by the downregulation of Cyclin A, Cyclin D1, Cyclin E, CDK2, CDK4, phospho-Rb and Survivin proteins and up regulation of cleaved Caspase-3.

  15. Protein-Style Dynamical Transition in a non-Biological Polymer...

    Office of Scientific and Technical Information (OSTI)

    Protein-Style Dynamical Transition in a non-Biological Polymer and a non-Aqueous Solvent ... This content will become publicly available on January 1, 2017 Title: Protein-Style ...

  16. Discovering The Folding Rules That Proteins Obey FY08 LDRD Final...

    Office of Scientific and Technical Information (OSTI)

    Discovering The Folding Rules That Proteins Obey FY08 LDRD Final Report Citation Details In-Document Search Title: Discovering The Folding Rules That Proteins Obey FY08 LDRD Final ...

  17. Cross-linking proteins with bimetallic tetracarboxylate compounds of transition metals

    DOE Patents [OSTI]

    Kostic, Nenad M.; Chen, Jian

    1991-03-05

    Stable cross-linked complexes of transition-metal tetracarboxylates and proteins are formed. The preferred transition-metal is rhodium. The protein may be collagen or an enzyme such as a proteolytic enzyme.

  18. Femtosecond X-ray Diffraction From Two-Dimensional Protein Crystals...

    Office of Scientific and Technical Information (OSTI)

    Femtosecond X-ray Diffraction From Two-Dimensional Protein Crystals Citation Details In-Document Search Title: Femtosecond X-ray Diffraction From Two-Dimensional Protein Crystals...

  19. Methods for validating the presence of and characterizing proteins deposited onto an array

    DOE Patents [OSTI]

    Schabacker, Daniel S.

    2010-09-21

    A method of determining if proteins have been transferred from liquid-phase protein fractions to an array comprising staining the array with a total protein stain and imaging the array, optionally comparing the staining with a standard curve generated by staining known amounts of a known protein on the same or a similar array; a method of characterizing proteins transferred from liquid-phase protein fractions to an array including staining the array with a post-translational modification-specific (PTM-specific) stain and imaging the array and, optionally, after staining the array with a PTM-specific stain and imaging the array, washing the array, re-staining the array with a total protein stain, imaging the array, and comparing the imaging with the PTM-specific stain with the imaging with the total protein stain; stained arrays; and images of stained arrays.

  20. Structure of active [beta]-arrestin-1 bound to a G-protein-coupled...

    Office of Scientific and Technical Information (OSTI)

    bound to a G-protein-coupled receptor phosphopeptide Citation Details In-Document Search Title: Structure of active beta-arrestin-1 bound to a G-protein-coupled ...