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Sample records for ring-shaped protein explains

  1. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office 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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein Structures PrintRooftopRotary Firing in Ring-Shaped

  3. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein Structures PrintRooftop

  4. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein Structures PrintRooftop DiagnosticianRoomWPSSRotary

  5. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein Structures PrintRooftopRotary Firing in

  6. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein Structures PrintRooftopRotary Firing inRotary Firing

  7. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein Structures PrintRooftopRotary Firing inRotary

  8. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein Structures PrintRooftopRotary Firing inRotaryRotary

  9. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior....

  10. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) byMultidayAlumni > The Energy MaterialsRooftop Solar Challenge

  11. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) byMultidayAlumni > The Energy MaterialsRooftop Solar ChallengeRotary

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

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  13. 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 ?m. 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.

  14. 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.

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from...

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of...

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny...

  18. 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.

  19. The Quaternary Structure of Amalgam, a Drosophila Neuronal Adhesion Protein, Explains Its Dual Adhesion Properties

    E-Print Network [OSTI]

    Sussman, Joel L.

    The Quaternary Structure of Amalgam, a Drosophila Neuronal Adhesion Protein, Explains Its Dual Adhesion Properties Tzviya Zeev-Ben-Mordehai, Efstratios Mylonas,{ Aviv Paz, Yoav Peleg,§ Lilly Toker) is a secreted neuronal adhesion protein that contains three tandem immunoglobulin domains. It has both

  20. Energy spectra of Hartmann and ring-shaped oscillator potentials using the quantum Hamilton-Jacobi formalism

    E-Print Network [OSTI]

    Abdelhakim Gharbi; Ahmed Bouda

    2013-11-30

    In the present work, we apply the exact quantization condition, introduced within the framework of Padgett and Leacock's quantum Hamilton-Jacobi formalism, to angular and radial quantum action variables in the context of the Hartmann and the ring-shaped oscillator potentials which are separable and non central. The energy spectra of the two systems are exactly obtained.

  1. Wedding ring shaped excitation coil

    DOE Patents [OSTI]

    MacLennan, Donald A. (Gaithersburg, MD); Tsai, Peter (Olney, MD)

    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.

  2. Proteins

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  3. Proteins

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  4. Proteins

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the BigProteinProteins Scientists

  5. Proteins

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-Rich MatricesstudentsProjectsPropertymaterialsProteins Protein

  6. Dark antiatoms can explain DAMA

    E-Print Network [OSTI]

    Quentin Wallemacq; Jean-René Cudell

    2014-11-12

    We show that the existence of a sub-dominant form of dark matter, made of dark antiatoms of mass and size of the order of 1 TeV and 30 fm respectively, 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 of the order of 0.0005e. This millicharge enables them to bind to high-Z atoms via radiative capture, after they thermalize in terrestrial matter through elastic collisions.

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB PacketDieselAbsorption Techniques |Dr.Dr.Durathon(tm)Dynein Motor

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB PacketDieselAbsorption Techniques |Dr.Dr.Durathon(tm)Dynein

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor Domain Shows

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor Domain ShowsDynein

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor Domain

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor DomainDynein Motor

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor DomainDynein

  14. A Direct Manipulation Language for Explaining Algorithms

    E-Print Network [OSTI]

    Scott, Jeremy

    Instructors typically explain algorithms in computer science by tracing their behavior, often on blackboards, sometimes with algorithm visualizations. Using blackboards can be tedious because they do not facilitate ...

  15. NonEquilibrium Thermodynamics Explains Semiotic Shapes

    E-Print Network [OSTI]

    Kreinovich, Vladik

    Non­Equilibrium Thermodynamics Explains Semiotic Shapes: Applications to Astronomy and to Non­equilibrium thermodynamics, non­destructive testing, aerospace structures 1. SEMIOTIC SHAPES IN ASTRONOMY: FORMULATION by using the fundamental physical ideas of symmetry and non­equilibrium thermodynamics. 2. MAIN PHYSICAL

  16. Type-IV Pilus Deformation Can Explain Retraction Behavior

    E-Print Network [OSTI]

    Ranajay Ghosh; Aloke Kumar; Ashkan Vaziri

    2014-09-18

    Polymeric filament like type IV Pilus (TFP) can transfer forces in excess of 100pN during their retraction before stalling, powering surface translocation(twitching). Single TFP level experiments have shown remarkable nonlinearity in the retraction behavior influenced by the external load as well as levels of PilT molecular motor protein. This includes reversal of motion near stall forces when the concentration of the PilT protein is lowered significantly. In order to explain this behavior, we analyze the coupling of TFP elasticity and interfacial behavior with PilT kinetics. We model retraction as reaction controlled and elongation as transport controlled process. The reaction rates vary with TFP deformation which is modeled as a compound elastic body consisting of multiple helical strands under axial load. Elongation is controlled by monomer transport which suffer entrapment due to excess PilT in the cell periplasm. Our analysis shows excellent agreement with a host of experimental observations and we present a possible biophysical relevance of model parameters through a mechano-chemical stall force map

  17. Severe osmotic compression triggers a slowdown of intracellular signaling, which can be explained

    E-Print Network [OSTI]

    Hersen, Pascal - Laboratoire Matière et Systèmes Complexes, Université Paris 7

    Severe osmotic compression triggers a slowdown of intracellular signaling, which can be explained by severe osmotic stress, slows down the dynamics of several signaling cascades, including the stress-response pathways required for osmotic adaptation. We show that increasing osmotic compression decreases protein

  18. PeriodicitiesinSequenceResidueHydropathyandtheImplicationsonProteinFolds Nancy Zhang

    E-Print Network [OSTI]

    Brutlag, Doug

    1 PeriodicitiesinSequenceResidueHydropathyandtheImplicationsonProteinFolds Nancy Zhang March, 2000 algorithms is that there are hidden variables effecting the protein folding mechanism and explain why it is crucial to a protein's fold. In section III, I will explain how the Fourier transform

  19. Explaining the causes and consequences of internationally monitored elections

    E-Print Network [OSTI]

    Hyde, Susan Dayton

    2006-01-01

    2003. "Electoral Fraud: Causes, Types, and Consequences."Observing Norms: Explaining the Causes and Consequences ofW. 1998. "The International Causes of Democratization, 1974-

  20. EXPLAINING THE PRICE OF VOLUNTARY CARBON OFFSETS MARC N. CONTE

    E-Print Network [OSTI]

    Kotchen, Matthew J.

    EXPLAINING THE PRICE OF VOLUNTARY CARBON OFFSETS MARC N. CONTE Stanford University, Stanford, CA matthew.kotchen@yale.edu This paper identifies factors that explain the large variability in the price of voluntary carbon offsets. We estimate hedonic price functions using a variety of provider- and project

  1. Edinburgh Research Explorer Forecasting and explaining aggregate consumer credit

    E-Print Network [OSTI]

    Millar, Andrew J.

    one year. It is important for lenders to be able to explain and to predict aggregate consumer. A significant increase in delinquencies may cause lenders with low capital adequacy ratios to become insolvent

  2. Ring shaped 6.7 GHz methanol maser emission around a young high-mass star

    E-Print Network [OSTI]

    A. Bartkiewicz; M. Szymczak; H. J. van Langevelde

    2005-09-21

    We report on EVN imaging of the 6.7 GHz methanol maser emission from the candidate high-mass protostar G23.657-0.127. The masers originate in a nearly circular ring of 127 mas radius and 12 mas width. The ring structure points at a central exciting object which characteristics are typical for a young massive star; its bolometric luminosity is estimated to be methanol masers originate in a spherical bubble or in a rotating disc seen nearly face-on.

  3. Collagen Bundle Orientation Explains Aortic Valve Leaflet Coaptation

    E-Print Network [OSTI]

    Collagen Bundle Orientation Explains Aortic Valve Leaflet Coaptation Peter E. Hammer1 , Christina A. The aortic valve owes its strength and durability to a network of collagen fibers within the leaflets. However, the pattern of these fibers and their role in valve function is not well understood. We imaged

  4. Representation Sharpening Can Explain Perceptual Priming Samat Moldakarimov,

    E-Print Network [OSTI]

    Bazhenov, Maxim

    , we developed a rate-based network model of visual processing. In the model, decreased neural activity. The model explained a wide range of psychophysical and physiological data observed in priming experiments). Priming is an unconscious form of memory that has been observed in perceptual, semantic, and conceptual

  5. Variability in Color Discrimination Data Explained by a Generic

    E-Print Network [OSTI]

    Alleysson, David

    on adapting backgrounds, using matching lights that varied both in chromaticity and luminance. First, weVariability in Color Discrimination Data Explained by a Generic Model with Nonlinear and Adaptive: A generic model of color discrimination is pre- sented. It involves adaptive nonlinearities at photoreceptor

  6. Calorimetric glass transition explained by hierarchical dynamic facilitation

    E-Print Network [OSTI]

    Garrahan, Juan P.

    Calorimetric glass transition explained by hierarchical dynamic facilitation Aaron S. Keysa Contributed by David Chandler, February 11, 2013 (sent for review November 15, 2012) The glass transition different on cooling than on heating, and the response to melting a glass depends markedly on the cooling

  7. Explaining The Operation of A Home Care System

    E-Print Network [OSTI]

    Turner, Ken

    (e.g. for communication, speech input-output, or weather forecasts). A home care system is able are living normally at home. For example, non-intrusive sensing can confirm that the individual is sleepingExplaining The Operation of A Home Care System Kenneth J. Turner, Computing Science and Mathematics

  8. 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)

  9. A Pionic Hadron Explains the Muon Magnetic Moment Anomaly

    E-Print Network [OSTI]

    Rainer W. Schiel; John P. Ralston

    2007-10-01

    A significant discrepancy exists between experiment and calculations of the muon's magnetic moment. We find that standard formulas for the hadronic vacuum polarization term have overlooked pionic states known to exist. Coulomb binding alone guarantees $\\pi^+ \\pi^-$ states that quantum mechanically mix with the $\\rho$ meson. A simple 2-state mixing model explains the magnetic moment discrepancy for a mixing angle of order $\\alpha \\sim 10^{-2}$. The relevant physical state is predicted to give a tiny observable bump in the ratio R(s) of $e^+ e^-$ annihilation at a low energy not previously searched. The burden of proof is reversed for claims that conventional physics cannot explain the muon's anomalous moment.

  10. Cometary panspermia explains the red rain of Kerala

    E-Print Network [OSTI]

    Godfrey Louis; A. Santhosh Kumar

    2003-10-05

    Red coloured rain occurred in many places of Kerala in India during July to September 2001 due to the mixing of huge quantity of microscopic red cells in the rainwater. Considering its correlation with a meteor airbust event, this phenomenon raised an extraordinary question whether the cells are extraterrestrial. Here we show how the observed features of the red rain phenomenon can be explained by considering the fragmentation and atmospheric disintegration of a fragile cometary body that presumably contains a dense collection of red cells. Slow settling of cells in the stratosphere explains the continuation of the phenomenon for two months. The red cells under study appear to be the resting spores of an extremophilic microorganism. Possible presence of these cells in the interstellar clouds is speculated from its similarity in UV absorption with the 217.5 nm UV extinction feature of interstellar clouds.

  11. potentially explain the discrepancy observed. One obvious difference is the

    E-Print Network [OSTI]

    Millar, Andrew J.

    Biotechnological and Biological Science Research Council (B.B.S.R.C). References 1 Lawrence, M.J. (2000) Population Phytol. 151, 565­584 3 Stein, J.C. et al. (1991) Molecular cloning of a putative receptor protein interactions in Brassica self- incompatibility. Science 293, 1824­1826 9 Takayama S. et al. (2001) Direct

  12. A third alternative to explain recent observations: Future deceleration

    E-Print Network [OSTI]

    Subenoy Chakraborty; Supriya Pan; Subhajit Saha

    2014-10-30

    In the present work we discuss a third alternative to explain the latest observational data concerning the accelerating Universe and its different stages. The particle creation mechanism in the framework of non-equilibrium thermodynamics is considered as a basic cosmic mechanism acting on the flat FRW geometry. By assuming that the gravitationally induced particle production occurs under "adiabatic" conditions, the deceleration parameter is expressed in terms of the particle creation rate which is chosen as a truncated power series of the Hubble parameter. The model shows the evolution of the Universe starting from inflation to the present late time acceleration and it also predicts future decelerating stage.

  13. Property:If Yes, Please Explain | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QAsource History ViewMayo,AltFuelVehicle2 Jump to: navigation, search ThisHeadquartersState JumpPlease Explain Jump

  14. Property:EstimatedTimeExplained | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTION JEnvironmental Jump to: navigation, searchEnvironmentalMitigation JumpEstimatedTimeExplained Jump

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Marques Tavares, Gustavo; Schmaltz, Martin

    2011-09-01

    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

  16. Mesoscale symmetries explain dynamical equivalence of food webs

    E-Print Network [OSTI]

    Aufderheide, Helge; Gross, Thilo

    2012-01-01

    A present challenge in complex systems is to identify mesoscale structures that have distinct dynamical implications. In this paper we present a detailed investigation of a previously observed dynamical equivalence of certian ecological food webs. We show that this equivalence is rooted in mesoscale symmetries that exist in these webs. Certain eigenvectors of the Jacobian describing dynamical modes of the system, such as specific instabilities or responses to perturbations, localize on these symmetric motifs. On the one hand this means that by removing a symmetry from the network one obtains a system which has identical dynamics except for the removal of the localized mode. This explains the previously observed equivalence. On the other hand it means that we can identify dynamical modes that only depend on the symmetric motif. Symmetric structures thus provide an example for mesoscale network motifs having distinct and exact implications for the dynamics.

  17. Man made global warming explained - closing the blinds

    E-Print Network [OSTI]

    Sloan, T

    2010-01-01

    One of the big problems of the age concerns 'Global Warming', and whether it is 'man-made' or 'natural'. Most climatologists believe that it is very likely to be the former but some scientists (mostly non-climatologists) subscribe to the latter. Unsurprisingly, the population at large is often confused and and is not convinced either way. Here we try to explain the principles of man-made global warming in a simple way. Our purpose is to try to understand the story which the climatologists are telling us through their rather complicated general circulation models. Although the effects in detail are best left to the climatologists' models, we show that for the Globe as a whole the effects of man-made global warming can be demonstrated in a simple way. The simple model of only the direct heating from the absorption of infrared radiation, illustrates the main principles of the science involved. The predicted temperature increase due to the increase of greenhouse gases in the atmosphere over the last century descr...

  18. Failed supernovae explain the compact remnant mass function

    SciTech Connect (OSTI)

    Kochanek, C. S. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210, USAAND (United States); Center for Cosmology and AstroParticle Physics, The Ohio State University, 191 W. Woodruff Avenue, Columbus, OH 43210 (United States)

    2014-04-10

    One explanation for the absence of higher mass red supergiants (16.5 M {sub ?} ? M ? 25 M {sub ?}) as the progenitors of Type IIP supernovae (SNe) is that they die in failed SNe creating black holes. Simulations show that such failed SNe still eject their hydrogen envelopes in a weak transient, leaving a black hole with the mass of the star's helium core (5-8 M {sub ?}). Here we show that this naturally explains the typical masses of observed black holes and the gap between neutron star and black hole masses without any fine-tuning of stellar mass loss, binary mass transfer, or the SN mechanism, beyond having it fail in a mass range where many progenitor models have density structures that make the explosions more likely to fail. There is no difficulty including this ?20% population of failed SNe in any accounting of SN types over the progenitor mass function. And, other than patience, there is no observational barrier to either detecting these black hole formation events or limiting their rates to be well below this prediction.

  19. Jumping Neptune Can Explain the Kuiper Belt Kernel

    E-Print Network [OSTI]

    Nesvorny, David

    2015-01-01

    The Kuiper belt is a population of icy bodies beyond the orbit of Neptune. A particularly puzzling and up-to-now unexplained feature of the Kuiper belt is the so-called `kernel', a concentration of orbits with semimajor axes a~44 AU, eccentricities e~0.05, and inclinations ibelt kernel can be explained if Neptune's otherwise smooth migration was interrupted by a discontinuous change of Neptune's semimajor axis when Neptune reached ~28 AU. Before the discontinuity happened, planetesimals located at ~40 AU were swept into Neptune's 2:1 resonance, and were carried with the migrating resonance outwards. The 2:1 resonance was at ~44 AU when Neptune reached ~28 AU. If Neptune's semimajor axis changed by fraction of AU at this point, perhaps because Neptune was scattered off of another planet, the 2:1 population would have been released at ~44 AU, and would remain there to this day. We show that the orbital distribution of bodies produced in this model provides a good match to...

  20. Materiomics: biological protein materials, from nano to macro

    E-Print Network [OSTI]

    Cranford, Steven Wayne

    Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain ...

  1. Protein Assay Technical Handbook

    E-Print Network [OSTI]

    Lebendiker, Mario

    Protein Assay Technical Handbook #12;Table of Contents Total Protein Assays Quick Technical......................................................................6 Selection of a Protein Standard....................................................................7 Standards for Total Protein Assay

  2. Introduzione alle Proteine e al Protein Folding

    E-Print Network [OSTI]

    Giannozzi, Paolo

    Chapter 4 Introduzione alle Proteine e al Protein Folding 4.1 Proteine: propriet`a strutturali Le protein folding `e il cosiddetto modello HP, nel quale a ogni amino acido `e assegnata l'etichetta di

  3. Mick Jagger Explains High Crude Oil Prices How can Mick Jagger of The Rolling Stones help explain the current high crude oil

    E-Print Network [OSTI]

    Ahmad, Sajjad

    Mick Jagger Explains High Crude Oil Prices How can Mick Jagger of The Rolling Stones help explain the current high crude oil price? It does not relate to Mick' short stint at the London School of Economics for crude oil, that they attempted to control the price of crude on international markets. Their ability

  4. CAN STELLAR MIXING EXPLAIN THE LACK OF TYPE Ib SUPERNOVAE IN...

    Office of Scientific and Technical Information (OSTI)

    CAN STELLAR MIXING EXPLAIN THE LACK OF TYPE Ib SUPERNOVAE IN LONG-DURATION GAMMA-RAY BURSTS? Citation Details In-Document Search Title: CAN STELLAR MIXING EXPLAIN THE LACK OF TYPE...

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

    Broader source: Energy.gov [DOE]

    A new video series from ElectricTV.net explains the changes and opportunities offered by LED lighting.

  6. 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.

  7. Engineering novel fluorescent proteins

    E-Print Network [OSTI]

    Shaner, Nathan Christopher

    2006-01-01

    to Choosing Fluorescent Proteins. Nat. Methods. 2 (12): 905-Dynamics of Z-band based proteins in developing skeletaland yellow fluorescent proteins derived from Discosoma sp.

  8. Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks Gregg Lois,1,2

    E-Print Network [OSTI]

    O'Hern, Corey S.

    Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks Gregg a protein fold reliably to its native conforma- tion even though a large number of metastable states exist the funneled energy landscape may explain how some proteins fold reliably 7 , a different picture, i.e., rugged

  9. 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

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

    ScienceCinema (OSTI)

    Pleier,Marc-Andre

    2014-06-04

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

  11. Emergence Explained

    E-Print Network [OSTI]

    Russ Abbott

    2006-02-12

    Emergence (macro-level effects from micro-level causes) is at the heart of the conflict between reductionism and functionalism. How can there be autonomous higher level laws of nature (the functionalist claim) if everything can be reduced to the fundamental forces of physics (the reductionist position)? We cut through this debate by applying a computer science lens to the way we view nature. We conclude (a) that what functionalism calls the special sciences (sciences other than physics) do indeed study autonomous laws and furthermore that those laws pertain to real higher level entities but (b) that interactions among such higher-level entities is epiphenomenal in that they can always be reduced to primitive physical forces. In other words, epiphenomena, which we will identify with emergent phenomena, do real higher-level work. The proposed perspective provides a framework for understanding many thorny issues including the nature of entities, stigmergy, the evolution of complexity, phase transitions, supervenience, and downward entailment. We also discuss some practical considerations pertaining to systems of systems and the limitations of modeling.

  12. From%laggard%to%leader:%% Explaining%offshore%wind%developments%in%

    E-Print Network [OSTI]

    Sussex, University of

    From%laggard%to%leader:%% Explaining%offshore%wind%developments%in% the%UK% Florian!laggard!to!leader:!Explaining! offshore!wind!developments!in!the!UK! Florian Kern1* , Adrian Smith1 , Chris Shaw1 , Rob Raven2 and Bram for publication in Energy Policy, 19 Feb 2014 Abstract Offshore wind technology has recently undergone rapid

  13. Explaining ethnic conflict in the South Caucasus : Mountainous Karabagh, Abkhazia, and South Ossetia

    E-Print Network [OSTI]

    Welt, Cory

    2004-01-01

    (cont.) the USSR and finds that a focus on opportunity provides the best explanation for the presence or absence of mass mobilization. Finally, the dissertation argues that conventional state security concerns best explain ...

  14. i-Seek : an intelligent system for eliciting and explaining knowledge

    E-Print Network [OSTI]

    Kumar, Ashwani, S.M. Massachusetts Institute of Technology

    2005-01-01

    We propose i-Seek, an Intelligent System for Eliciting and Explaining Knowledge that leverages the OpenMind [1] Commonsense knowledge base in conjunction with domain- specific knowledge in Personal Finance, Technical Help, ...

  15. VARIATION IN ANATOMICAL AND MATERIAL PROPERTIES EXPLAINS DIFFERENCES IN HYDRODYNAMIC PERFORMANCES OF FOLIOSE RED

    E-Print Network [OSTI]

    Martone, Patrick T.

    VARIATION IN ANATOMICAL AND MATERIAL PROPERTIES EXPLAINS DIFFERENCES IN HYDRODYNAMIC PERFORMANCES that material properties of seaweed tissues may influence their fitness. Because hydrodynamic forces are likely difficult to disentangle the effects of materials properties on seaweed performance because size, shape

  16. MRF Technical Note # 49 Can desert dust explain the anomalous greenhouse

    E-Print Network [OSTI]

    Allan, Richard P.

    MRF Technical Note # 49 Can desert dust explain the anomalous greenhouse effect observed over greenhouse effect observed over the Sahara during July 2003 revealed by GERB/UM intercomparisons? Jim M

  17. Explaining low sulfur dioxide allowance prices : the effect of expectation errors and irreversibility

    E-Print Network [OSTI]

    Montero, Juan-Pablo

    1998-01-01

    The low price of allowances has been a frequently noted featured of the implementation of the sulfur dioxide emissions market of the U.S. Acid Rain Program. This paper presents theoretical and numerical analyses that explain ...

  18. Explaining households' economic hardship -an interplay of demography and housing system

    E-Print Network [OSTI]

    Birmingham, University of

    Explaining households' economic hardship - an interplay of demography and housing system Paper on research conducted in the EU 7th Framework Program DEMHOW Demographic Change and Housing Wealth (Grant. Demography and housing in the two-level model..............................................................6

  19. From hutong to hi-rise : explaining the transformation of Old Beijing, 1990-2002

    E-Print Network [OSTI]

    Goldman, Jasper, 1978-

    2003-01-01

    This thesis attempts to explain the redevelopment of Old Beijing during the period 1990-2002. During this time, at least one third of the Old City was transformed from an urban fabric consisting principally of courtyard ...

  20. Bankruptcy, guns or campaigns : explaining armed organizations' post-war trajectories

    E-Print Network [OSTI]

    Daly, Sarah Zukerman

    2011-01-01

    This project seeks to explain what happens to armed organizations after they sign peace accords. Why do they dissolve, return to war, or form non-violent socio-political entities (political parties or civic associations)? ...

  1. Why do they fight? Explaining participation in the War in Croatia

    E-Print Network [OSTI]

    Brown, Cody McClain

    2013-08-31

    This project explains voluntary participation in the War in Croatia, using a data set of daily interval event data and interviews with Croatian war veterans. It challenges the previous findings of macro level based research on conflict...

  2. Culex quinquefasciatus Storage Proteins

    E-Print Network [OSTI]

    2013-01-01

    and hemolymph proteins of Cx. quinquefasciatus . A and B:of typical storage proteins in Cx. quinquefasciatus.Fourth-instar Cx. quinquefasciatus larvae and early pupae

  3. Implied motion activation in cortical area MT can be explained by visual low-level features

    E-Print Network [OSTI]

    Oram, Mike

    ForReview Only Implied motion activation in cortical area MT can be explained by visual low Neuroscience #12;ForReview Only 1 Implied motion activation in cortical area MT can be explained by visual low, The Netherlands Page 1 of 51 Jounal of Cognitive Neuroscience 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

  4. 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.

  5. Protein Design Zhilei Chen

    E-Print Network [OSTI]

    Zhao, Huimin

    Protein Design Zhilei Chen Center for Biophysics and Computational Biology, University of Illinois of Illinois, Urbana, Illinois, U.S.A. INTRODUCTION Protein design refers to the ability to alter protein, and selectivity. To overcome this lim- itation, tailor-made biocatalysts must be developed by protein design

  6. Protein content of grains of different size fractions in malting barley

    E-Print Network [OSTI]

    Nacional de San Luis, Universidad

    of the variation observed in protein content was explained by the ratio of nitrogen availability to grain yield content is not due to the presence of a high proportion of thin grains, because thin grains do not always requirements, barley grain must have a specific protein level and high grain size (i.e. a high proportion

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

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)

    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.

  8. Variation in forest richness, density, and size is explained by environmental gradients from the plot to landscape scale

    E-Print Network [OSTI]

    Fricker, Geoffrey Andrew

    2015-01-01

    composed the largest proportion of variation in tree speciesto explain higher proportions of variation in tree species

  9. ACARYOCHLORIS EXPLAINING THE RIDDLE OF CHLOROPHYLL D IN RED ALGAE AND EXPANDING PAR FOR OXYGENIC PHOTOSYNTHESIS

    E-Print Network [OSTI]

    Oregon, University of

    ACARYOCHLORIS ­ EXPLAINING THE RIDDLE OF CHLOROPHYLL D IN RED ALGAE AND EXPANDING PAR FOR OXYGENIC strain is shown to live epi- phytically on the red alga Gelidium caulacantheum, which itself is harvested by the red alga. Availability of far red light, however, is relatively unaffected by DOM or red

  10. Unit 15: Risk Management To explain the concept of risk & to develop its role

    E-Print Network [OSTI]

    Finkelstein, Anthony

    1 Unit 15: Risk Management Objectives Ð To explain the concept of risk & to develop its role within the software development process Ð To introduce the use of risk management as a means of identifying ¥ Techniques & heuristics for the identification, analysis, treatment & monitoring of risk ¥ Risk management

  11. Better Technologies Key to Addressing Climate Change Energy Department official explains U.S. initiatives

    E-Print Network [OSTI]

    is a multilateral effort to develop the next generation of economical and safe nuclear reactors, and the ITERBetter Technologies Key to Addressing Climate Change Energy Department official explains U.S. initiatives 17 December 2004 More energy-efficient technologies will be key to reducing greenhouse gas

  12. Creating a Journal Article This cheatsheet will explain how to enter a Journal Article into IRMA.

    E-Print Network [OSTI]

    Creating a Journal Article This cheatsheet will explain how to enter a Journal Article into IRMA (MAIS ID (Staff, Student or MAIS other number)) and MAIS Password. Creating new journal article record) In the Publication Output field, click to choose Journal. Have a look at the table below to work out which

  13. Explaining Long-Run Changes in the Energy Intensity of the U.S. Economy

    E-Print Network [OSTI]

    Sue Wing, Ian.

    Recent events have revived interest in explaining the long-run changes in the energy intensity of the U.S. economy. We use a KLEM dataset for 35 industries over 39 years to decompose changes in the aggregate energy-GDP ...

  14. Favorable Climate Change Response Explains Non-Native Species' Success in Thoreau's Woods

    E-Print Network [OSTI]

    Davis, Charles

    Favorable Climate Change Response Explains Non-Native Species' Success in Thoreau's Woods Charles G Invasive species have tremendous detrimental ecological and economic impacts. Climate change may exacerbate species invasions across communities if non-native species are better able to respond to climate changes

  15. No available theories currently explain all adult-child cue weighting differences Catherine Mayo & Alice Turk

    E-Print Network [OSTI]

    Edinburgh, University of

    these hypotheses in two ways. First, we examined adults' and three- to seven-year-old chil- dren's weighting- text and the spectral distinctiveness of the transition. Sec- ond, we examined adults' and five-year-oldNo available theories currently explain all adult-child cue weighting differences Catherine Mayo

  16. Simple Quantum Model of Learning Explains the Yerkes-Dodson Law in Psychology

    E-Print Network [OSTI]

    E. D. Vol

    2012-02-09

    We propose the simple model of learning based on which we derive and explain the Yerkes-Dodson law - one of the oldest laws of experimental psychology. The approach uses some ideas of quantum theory of open systems (QTOS) and develops the method of statistical description of psychological systems that was proposed by author earlier.

  17. Introduction: Explaining the EU Political System The EU: a political system but not a state

    E-Print Network [OSTI]

    Franz, Sven Oliver

    but not a state How the EU political system works Actors, institutions and outcomes: the basics of modern1 Chapter 1 Introduction: Explaining the EU Political System The EU: a political system political science Theories of European integration and EU politics The allocation of policy competences

  18. A graphical technique for explaining the relationship between energy security and greenhouse gas emissions

    E-Print Network [OSTI]

    Hughes, Larry

    ERG/200806 A graphical technique for explaining the relationship between energy security and greenhouse gas emissions Larry Hughes and Nikita Sheth Energy Research Group Department of Electrical the relationship between energy security and greenhouse gas emissions Larry Hughes and Nikita Sheth Abstract

  19. Low light reflectance may explain the attraction of birds to defoliated trees

    E-Print Network [OSTI]

    Laaksonen, Toni

    Low light reflectance may explain the attraction of birds to defoliated trees Elina Ma¨ntyla¨, Tero autumnata) in nontest branches. Species, age, or sex of the experimental bird or lighting (ultraviolet [UV light than the herbivore trees, whereas no such difference was found in the shadier forest patch trees

  20. Modeling West Nile Virus One Host Infections Explaining Survival Curve Data

    E-Print Network [OSTI]

    Peterson, James K

    Modeling West Nile Virus One Host Infections Explaining Survival Curve Data James K. Peterson healthy cells also. The cells in G1 state are not upregulated as much and so virus hides in them and hence is decoyed into preferentially recognizing the upregulated cells while the virus actively propagates

  1. Modeling West Nile Virus One Host Infections Explaining Survival Curve Data

    E-Print Network [OSTI]

    Peterson, James K

    Modeling West Nile Virus One Host Infections Explaining Survival Curve Data James K. Peterson virus hides in them and hence is propagated upon rupture. Hence, this type of model is referred while the virus actively propagates in another small, but important, cell population. The development

  2. LETTER Colonisation and competition dynamics can explain incomplete sterilisation parasitism in antplant symbioses

    E-Print Network [OSTI]

    Palmer, Todd M.

    LETTER Colonisation and competition dynamics can explain incomplete sterilisation parasitism in ant-mail: ctarnita@princeton.edu Abstract Sterilisation of parasites prevents host reproduction, thereby diverting virulence, yet hosts are often incompletely sterilised. Whereas prior attempts to resolve this paradox have

  3. Mathematics Education in Iceland: Explaining the Non-homogeneity in a Homogenous System

    E-Print Network [OSTI]

    Bardsley, John

    Mathematics Education in Iceland: Explaining the Non-homogeneity in a Homogenous System Guðný Helga Gunnarsdóttir, Guðbjörg Pálsdóttir University of Iceland, School of Education & Bharath Sriraman The University of Montana Abstract: In this opening salvo to the Icelandic section, we synthesize some

  4. Journal of Mammalogy, 93(4):10991109, 2012 Keystone resource (Ficus) chemistry explains lick visitation by

    E-Print Network [OSTI]

    Harms, Kyle E.

    Journal of Mammalogy, 93(4):1099­1109, 2012 Keystone resource (Ficus) chemistry explains lick licks belong to the subfamily Stenodermatinae and are specialists on Ficus fruits--a keystone resource-borne resources available. Because sodium is an essential nutrient for vertebrates and Ficus is a keystone

  5. Structural parameters The analytical model proposed here can explain high fracture

    E-Print Network [OSTI]

    Barthelat, Francois

    Structural parameters · The analytical model proposed here can explain high fracture toughness, P.J., et al., Engineering Fracture Mechanics, 2007. 74: p. 19281941. 4. Ritchie, R.O., et al Tensile strength Fracture toughness Composite properties E max S )~( ~ aJ III. Fracture toughness

  6. 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.

  7. Allostery through protein-induced DNA bubbles

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  8. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17

    We have developed a simple, phenomenological, Monte-Carlo code that predicts the three-dimensional structure of globular proteins from the DNA sequences that define them. We have applied this code to two small proteins, the villin headpiece (1VII) and cole1 rop (1ROP). Our code folds both proteins to within 5 A rms of their native structures.

  9. Explaining the Power-law Distribution of Human Mobility Through Transportation Modality Decomposition

    E-Print Network [OSTI]

    Zhao, Kai; Hui, Pan; Rao, Weixiong; Tarkoma, Sasu

    2014-01-01

    Human mobility has been empirically observed to exhibit Levy flight characteristics and behaviour with power-law distributed jump size. The fundamental mechanisms behind this behaviour has not yet been fully explained. In this paper, we analyze urban human mobility and we propose to explain the Levy walk behaviour observed in human mobility patterns by decomposing them into different classes according to the different transportation modes, such as Walk/Run, Bicycle, Train/Subway or Car/Taxi/Bus. Our analysis is based on two real-life GPS datasets containing approximately 10 and 20 million GPS samples with transportation mode information. We show that human mobility can be modelled as a mixture of different transportation modes, and that these single movement patterns can be approximated by a lognormal distribution rather than a power-law distribution. Then, we demonstrate that the mixture of the decomposed lognormal flight distributions associated with each modality is a power-law distribution, providing an e...

  10. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

    Bradbury, Andrew M. (Santa Fe, NM); Waldo, Geoffrey S. (Santa Fe, NM); Kiss, Csaba (Los Alamos, NM)

    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.

  11. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

    Bradbury, Andrew M. (Santa Fe, NM); Waldo, Geoffrey S. (Santa Fe, NM); Kiss, Csaba (Los Alamos, NM)

    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.

  12. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

    Bradbury, Andrew M. (Santa Fe, NM); Waldo, Geoffrey S. (Santa Fe, NM); Kiss, Csaba (Los Alamos, NM)

    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.

  13. 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.

  14. 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.

  15. Does Weather Explain the Cost and Quality? An Analysis of UK Electricity Distribution Companies

    E-Print Network [OSTI]

    Yu, William; Jamasb, Tooraj; Pollitt, Michael G.

    O R K IN G P A P E R Abstract Does Weather Explain the Cost and Quality Performance? An Analysis of UK Electricity Distribution Companies EPRG Working Paper 0827 Cambridge Working Paper in Economics 0858 William Yu*, Tooraj Jamasb... are influenced by contextual factors. Among these, weather factors are frequently discussed as being important. We use Factor Analysis and two-stage Data Envelopment Analysis techniques to examine the effect of a set of important weather factors (gale, hail...

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

    SciTech Connect (OSTI)

    NONE

    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.

  17. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01

    Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to theoretical modeling and computer simulations. The present work introduces molecular nonlinear dynamics (MND), or molecular chaotic dynamics, as a theoretical framework for describing and analyzing protein folding. We unveil the existence of intrinsically low dimensional manifolds (ILDMs) in the chaotic dynamics of folded proteins. Additionally, we reveal that the transition from disordered to ordered conformations in protein folding increases the transverse stability of the ILDM. Stated differently, protein folding reduces the chaoticity of the nonlinear dynamical system, and a folded protein has the best ability to tame chaos. Additionally, we bring to light the connection between the ILDM stability and the thermodynamic stability, which enables us to quantify the disorderli...

  18. New reporters of protein trafficking and protein-protein interactions in live cells

    E-Print Network [OSTI]

    Fernández Suárez, Marta

    2008-01-01

    Here, we describe our attempts to harness the exquisite specificity of natural protein and RNA enzymes to develop improved methods to study protein localization and protein-protein interactions in live cells. We first ...

  19. LucY: A versatile new fluorescent reporter protein

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  20. 8. EXPLAIN HOW YOU BELIEVE YOU WERE DISCRIMINATED AGAINST (TREATED DIFFERENTLY FROM OTHER EMPLOYEES OR

    Broader source: Energy.gov (indexed) [DOE]

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of Natural GasAdjustmentsShirley Ann JacksonDepartment| Department ofApplianceU.S.Department of5th quarterly EXPLAIN HOW YOU

  1. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12

    We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random heteropolymeric description of these non random biomolecules. Various kinds of randomness are investigated, and the connection with disordered systems is discussed. We conclude by a brief study of the dynamics of proteins.

  2. Algae Protein Fermentation

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of microalgal proteins to mixed alcohol liquid fuels * Increase the yield of algae biofuel intermediates by integrated conversion of all of the major algal biochemical...

  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. Inferring the Rate-Length Law of Protein Folding

    E-Print Network [OSTI]

    Lane, Thomas J

    2013-01-01

    We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. We demonstrate that chain length is a dominant factor determining folding times, and that the unambiguous determination of the way chain length corre- lates with folding times could provide key mechanistic insight into the folding process. Four specific proposed laws (power law, exponential, and two stretched exponentials) are tested against one an- other, and it is found that the power law best explains the data. At the same time, the fit power law results in rates that are very fast, nearly unreasonably so in a biological context. We show that any of the proposed forms are viable, conclude that more data is necessary to unequivocally infer the rate-length law, and that such data could be obtained through a small number of protein folding experiments on large protein domains.

  5. Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments

    E-Print Network [OSTI]

    Haspel, Nurit

    Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments Nurit Haspel,1 folding model. The model postulates that protein folding is a hierarchical top-down pro- cess. The basic words: protein folding; building blocks; pro- tein structure prediction; hierarchical folding; protein

  6. Recombinant Protein Purification Handbook

    E-Print Network [OSTI]

    Lebendiker, Mario

    Recombinant Protein Purification Handbook Principles and Methods GE Healthcare #12;GST Gene Fusion System Handbook 18-1157-58 Hydrophobic Interaction and Reversed Phase Chromatography Principles-6429-60 Microcarrier Cell Culture Principles and Methods 18-1140-62 Challenging Protein Purification Handbook 28

  7. Low energy cosmic ray positron fraction explained by charge-sign dependent solar modulation

    E-Print Network [OSTI]

    Luca Maccione

    2013-01-24

    We compute cosmic ray (CR) nuclei, proton, antiproton, electron and positron spectra below 1 TeV at Earth by means of a detailed transport description in the galaxy and in the solar system. CR spectra below 10 GeV are strongly modified by charge-sign dependent propagation effects. These depend on the polarity of the solar magnetic field and therefore vary with the solar cycle. The puzzling discrepancy between the low-energy positron fraction measured by PAMELA and AMS-01 is then easily explained by their different data-taking epochs. We reproduce the observed spectra of CR light nuclei within the same galactic and solar-system propagation model.

  8. 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.

  9. Interfacial rheology of globular proteins

    E-Print Network [OSTI]

    Jaishankar, Aditya

    2011-01-01

    Protein-surfactant mixtures appear in many industrial and biological applications. Indeed, a fluid as vital as blood contains a mixture of serum albumin proteins with various other smaller surface-active components. Proteins ...

  10. Protein crystallography prescreen kit

    DOE Patents [OSTI]

    Segelke, Brent W. (San Ramon, CA); Krupka, Heike I. (Livermore, CA); Rupp, Bernhard (Livermore, CA)

    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.

  11. Protein Flips Lipids Across Membranes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Flips Lipids Across Membranes Print Found ubiquitously in both bacteria and humans, membrane proteins of the adenosine triphosphate (ATP)-binding cassette (ABC) transporter...

  12. Increasing Confidence of Protein-Protein Interactomes 1 Increasing Confidence of Protein-Protein Interactomes

    E-Print Network [OSTI]

    Wong, Limsoon

    associated with true-positive protein interactions--e.g., "new interaction gener- ality" (IG2) and "meso-scale comprises the "new interaction generality" (IG2) and "meso-scale motifs" (NeMoFinder) indices. This g

  13. Protein folding and cosmology

    E-Print Network [OSTI]

    P. F. Gonzalez-Diaz; C. L. Siguenza

    1997-06-04

    Protein denaturing induced by supercooling is interpreted as a process where some or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape becomes temperature-dependent and describes a phase transition. The idea that deformed vortices could be produced in the transition induced by temperature quenching, from native proteins to unfolded conformations is discussed in terms of the Zurek mechanism that implements the analogy between vortices, created in the laboratory at low energy, and the cosmic strings which are thought to have been left after symmetry breaking phase transitions in the early universe. An experiment is proposed to test the above idea which generalizes the cosmological analogy to also encompass biological systems and push a step ahead the view that protein folding is a biological equivalent of the big bang.

  14. MOLECULAR MODELING OF PROTEINS AND MATHEMATICAL PREDICTION OF PROTEIN STRUCTURE

    E-Print Network [OSTI]

    Neumaier, Arnold

    MOLECULAR MODELING OF PROTEINS AND MATHEMATICAL PREDICTION OF PROTEIN STRUCTURE ARNOLD NEUMAIER­called protein folding problem. The static aspect is concerned with how to predict the folded (native, tertiary) structure of a protein, given its sequence of amino acids. The dynamic aspect asks about the possible

  15. MOLECULAR MODELING OF PROTEINS AND MATHEMATICAL PREDICTION OF PROTEIN STRUCTURE

    E-Print Network [OSTI]

    Neumaier, Arnold

    MOLECULAR MODELING OF PROTEINS AND MATHEMATICAL PREDICTION OF PROTEIN STRUCTURE ARNOLD NEUMAIER-called protein folding problem. The static aspect is concerned with how to predict the folded (native, tertiary) structure of a protein, given its sequence of amino acids. The dynamic aspect asks about the possible

  16. Winter 2011 Evaluating Protein-Protein Docking Web Servers

    E-Print Network [OSTI]

    Nina Ly Winter 2011 Evaluating Protein-Protein Docking Web Servers Proteins are involved in many protein docking web servers: PIPER, GRAMM-X, 3D Garden, SmoothDock and PatchDock. I #12;will also perform structure. All of these web servers are freely available with no requirement to have an account

  17. 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.

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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. Clade Age and Diversification Rate Variation Explain Disparity in Species Richness among Water Scavenger Beetle (Hydrophilidae) Lineages

    E-Print Network [OSTI]

    Bloom, Devin D.; Fiká ?ek, Martin; Short, Andrew E. Z.

    2014-06-02

    Explaining the disparity of species richness across the tree of life is one of the great challenges in evolutionary biology. Some lineages are exceptionally species rich, while others are relatively species poor. One ...

  20. Explaining the pearl necklace of SNR 1987A by coherent optics

    E-Print Network [OSTI]

    Jacques Moret-Bailly

    2007-02-09

    A lot of beautiful observations of Supernova remnant 1987A give a precise idea of its structure and its evolution. The regular interpretations of the observations set that the large energy needed to explain the brightness of the pearl necklaces is provided by shock waves involving remnants of a first explosion and a wave produced by the observed explosion although the existence of this wave is discussed. We develop the alternative explanation of the necklaces by photoionization. Our main hypothesis is that the explosion of the blue supergiant progenitor produces two neutron stars and a central brilliant object, a linear system similar to those which were observed by Halton Arp. We suppose that these stars remains bright in extreme UV, to maintain the strong ionization of a bubble of hot hydrogen nearly transparent in far UV (defined as the range of Lyman frequencies of atomic hydrogen). Outside the bubbles, three shells containing atomic hydrogen generate resonant, superradiant scatterings at Lyman frequencies, in tangential competing modes. The superradiance cools the gas and absorbs strongly the radial far UV light, hiding the stars. The shells may be identified with the inner active shells found from light echoes.

  1. Can photo-ionization explain the decreasing fraction of X-ray obscured AGN with luminosity?

    E-Print Network [OSTI]

    A. Akylas; I. Georgantopoulos

    2008-01-30

    Chandra and XMM surveys show that the fraction of obscured AGN decreases rapidly with increasing luminosity. Although this is usually explained by assuming that the covering factor of the central engine is much smaller at luminous QSOs, the exact origin of this effect remains unknown. We perform toy simulations to test whether photo-ionisation of the obscuring screen in the presence of a strong radiation field can reproduce this effect. In particular, we create X-ray spectral simulations using a warm absorber model assuming a range of input column densities and ionization parameters. We fit instead the simulated spectra with a simple cold absorption power-law model that is the standard practice in X-ray surveys. We find that the fraction of absorbed AGN should fall with luminosity as $L^{-0.16\\pm0.03}$ in rough agreement with the observations. Furthermore, this apparent decrease in the obscuring material is consistent with the dependence of the FeK$\\alpha$ narrow-line equivalent width on luminosity, ie. the X-ray Baldwin effect.

  2. Horizon-Scale Lepton Acceleration in Jets: Explaining the Compact Radio Emission in M87

    E-Print Network [OSTI]

    Tchekhovskoy, Alexander

    2015-01-01

    It has now become clear that the radio jet in the giant elliptical galaxy M87 must turn on very close to the black hole. This implies the efficient acceleration of leptons within the jet at scales much smaller than feasible by the typical dissipative events usually invoked to explain jet synchrotron emission. Here we show that the stagnation surface, the separatrix between material that falls back into the black hole and material that is accelerated outward forming the jet, is a natural site of pair formation and particle acceleration. This occurs via an inverse-Compton pair catastrophe driven by unscreened electric fields within the charge-starved region about the stagnation surface and substantially amplified by a post-gap cascade. For typical estimates of the jet properties in M87, we find excellent quantitive agreement between the predicted relativistic lepton densities and those required by recent high-frequency radio observations of M87. This mechanism fails to adequately fill a putative jet from Sagitt...

  3. New Positron Spectral Features from Supersymmetric Dark Matter - a Way to Explain the PAMELA Data?

    E-Print Network [OSTI]

    Lars Bergstrom; Torsten Bringmann; Joakim Edsjo

    2008-11-13

    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 three or four 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 non-thermal production in the early universe or non-standard 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.

  4. 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.

  5. Computer Simulations of Protein Folding

    E-Print Network [OSTI]

    Sorin, Eric J.

    CHAPTER 8 Computer Simulations of Protein Folding VIJAY S. PANDE , ERIC J. SORIN , CHRISTOPHER D, CA 94305, USA 8.1 Introduction: Goals and Challenges of Simulating Protein Folding Computer as well as recent applications of this methodology. 8.1.1 Simulating Protein Folding Proteins play

  6. INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION

    E-Print Network [OSTI]

    Halligan, Daniel

    INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION AND TIE KNOTS Thomas M. A. Fink st. john Introduction 3 1.1 Inverse Protein Folding 3 1.2 Hierarchical Optimisation 5 1.3 Tie Knots 6 1.4 Schematic Organisation 6 1.5 Publications 9 2 Protein Folding, Inverse Protein Folding and Energy Landscapes 10 2

  7. Expression of Recombinant Proteins in Microalgae

    E-Print Network [OSTI]

    Mayfield, Stephen P.; Franklin, Scott E.

    2003-01-01

    Recombinant Proteins in Microalgae Publications Stephen P.Recombinant Proteins in Microalgae Final Narrative for Sea

  8. Tensile Forces and Shape Entropy Explain Observed Crista Structure in Mitochondria

    E-Print Network [OSTI]

    M. Ghochani; J. D. Nulton; P. Salamon; T. G. Frey; A. Rabinovitch; A. R. C. Baljon

    2010-04-03

    A model is presented from which the observed morphology of the inner mitochondrial membrane can be inferred as minimizing the system's free energy. Besides the usual energetic terms for bending, surface area, and pressure difference, our free energy includes terms for tension that we believe to be exerted by proteins and for an entropic contribution due to many dimensions worth of shapes available at a given energy. In order to test the model, we measured the structural features of mitochondria in HeLa cells and mouse embryonic fibroblasts using 3D electron tomography. Such tomograms reveal that the inner membrane self-assembles into a complex structure that contains both tubular and flat lamellar crista components. This structure, which contains one matrix compartment, is believed to be essential to the proper functioning of mitochondria as the powerhouse of the cell. We find that tensile forces of the order of 10 pN are required to stabilize a stress-induced coexistence of tubular and flat lamellar cristae phases. The model also predicts \\Deltap = -0.036 \\pm 0.004 atm and \\sigma=0.09 \\pm 0.04 pN/nm.

  9. Protein Dynamics and Biocatalysis

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen Protein Dynamics

  10. Report on Ngai et al.: Change of Caged Dynamics at Tg in hydrated proteins found after suppressing the methyl group rotation contribution"

    E-Print Network [OSTI]

    Doster, Wolfgang

    neutron scattering data of solvated proteins, the solvent is now restricted to hydration water: The authors belong to the elastic neutron scattering community, which intends to explain protein dynamics of dynamic information. The full dynamic information derivable from neutron scattering experiments

  11. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

    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 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.

  13. Protein knot server: detection of knots in protein structures

    E-Print Network [OSTI]

    Kolesov, Grigory

    KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding ...

  14. Identifying protein-protein interactions of a cell cycle regulator 

    E-Print Network [OSTI]

    Amos, Joseph Edward

    2013-02-22

    The role of anachronism (ana) protein in stem cell division of Drosophila melanogaster was examined. Synthesis of identifiable ana protein was necessary. The identifying method exploited was that of antibody tagging using ...

  15. Structure-based algorithms for protein-protein interaction prediction

    E-Print Network [OSTI]

    Hosur, Raghavendra

    2012-01-01

    Protein-protein interactions (PPIs) play a central role in all biological processes. Akin to the complete sequencing of genomes, complete descriptions of interactomes is a fundamental step towards a deeper understanding ...

  16. 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.

  17. An alternative scenario for the formation of specialized protein nano-domains (cluster phases) in biomembranes

    E-Print Network [OSTI]

    Nicolas Destainville

    2010-09-28

    We discuss a realistic scenario, accounting for the existence of sub-micrometric protein domains in cell membranes. At the biological level, such membrane domains have been shown to be specialized, in order to perform a determined biological task, in the sense that they gather one or a few protein species out of the hundreds of different ones that a cell membrane may contain. By analyzing the balance between mixing entropy and protein affinities, we propose that such protein sorting in distinct domains can be explained without appealing to pre-existing lipidic micro-phase separations, as in the lipid raft scenario. We show that the proposed scenario is compatible with known physical interactions between membrane proteins, even if thousands of different species coexist.

  18. Stabilization of Proteins against Aggregation

    E-Print Network [OSTI]

    Baynes, Brian M.

    Proteins degrade in vitro by a variety of routes, the most common of which is aggregation. In order to develop protein formulations that will limit aggregation, researchers use heuristic, experimental screening procedures. ...

  19. 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.

  20. IFITM Proteins Restrict Viral Membrane Hemifusion

    E-Print Network [OSTI]

    2013-01-01

    M (2008) HIV-1 accessory proteins–ensuring viral survival intransmembrane genes and proteins. J Interferon Cytokine Reset al. (2009) The IFITM proteins mediate cellular resistance

  1. Hydrogen Bond Shaping of Membrane Protein Structure

    E-Print Network [OSTI]

    Cao, Zheng

    2013-01-01

    Bowie JU (2011) Membrane protein folding: how important areRadford SE (2000) Protein folding mechanisms: new methodset al. (2003) Membrane protein folding: beyond the two stage

  2. Creating a Journal Article Record This user guide will explain how to enter a Journal Article into IRMA.

    E-Print Network [OSTI]

    Creating a Journal Article Record This user guide will explain how to enter a Journal Article" to log into IRMA CREATING A JOURNAL ARTICLE RECORD: 1) After logging on, you should see something like entering a new Publication record. 4) In the Publication Output field, click to choose Journal. Have a look

  3. Two-dimensional model problem to explain counter-rotating vortex pair formation in a transverse jet

    E-Print Network [OSTI]

    Mahesh, Krishnan

    Two-dimensional model problem to explain counter-rotating vortex pair formation in a transverse jet A two-dimensional model problem is used to study the evolution of the cross section of a transverse jet and the counter-rotating vortex pair CVP . The solution to the model problem shows deformation of the jet similar

  4. Petaflop Computing for Protein Folding

    E-Print Network [OSTI]

    Izaguirre, Jesús A.

    "SIAM01p 2000/12/4 page 1 Petaflop Computing for Protein Folding Shannon K. Kuntz, Richard C. Murphy, Michael T. Niemier, Jesus Izaguirre, and Peter M. Kogge 1 Introduction Protein Folding the protein folding problem, while Silicon Graphics has been continually working to produce more powerful

  5. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    Theoretical Perspectives on Protein Folding D. Thirumalai,1 Edward P. O'Brien,2 Greg Morrison,3 Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions remains to be done to solve the protein folding problem in the broadest sense. 159 Annu.Rev.Biophys.2010

  6. Fluorescent Protein Applications in Microscopy

    E-Print Network [OSTI]

    Straight, Aaron

    . The Identification of Green Fluorescent Protein III. Formation of the GFP Chromophore IV. The Structure of GFP V environment. II. The Identification of Green Fluorescent Protein The isolation of green fluorescent protein of Aequorea, Shimomura et al. noted that the lumines- cence from aequorin was blue rather than the green

  7. Protein subcellular localization assays using split fluorescent proteins

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)

    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).

  8. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

    H. (2008). Understanding protein folding: small proteins inmultiple pathways of protein folding. Chem Biol 2, 255-60.Polymer principles and protein folding. Protein Sci 8, 1166-

  9. Mathematical methods for protein science

    SciTech Connect (OSTI)

    Hart, W.; Istrail, S.; Atkins, J. [Sandia National Labs., Albuquerque, NM (United States)

    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.

  10. Self-organized periodicity of protein clusters in growing bacteria

    E-Print Network [OSTI]

    Hui Wang; Ned S. Wingreen; Ranjan Mukhopadhyay

    2008-08-06

    Chemotaxis receptors in E. coli form clusters at the cell poles and also laterally along the cell body, and this clustering plays an important role in signal transduction. Recently, experiments using flourrescence imaging have shown that, during cell growth, lateral clusters form at positions approximately periodically spaced along the cell body. In this paper, we demonstrate within a lattice model that such spatial organization could arise spontaneously from a stochastic nucleation mechanism. The same mechanism may explain the recent observation of periodic aggregates of misfolded proteins in E. coli.

  11. Thermodynamics of protein folding: a random matrix formulation

    E-Print Network [OSTI]

    Pragya Shukla

    2010-10-16

    The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows however that the evolution of the statistical measures e.g Gibbs free energy, heat capacity, entropy is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies.

  12. Navigation strategies of motor proteins on decorated tracks

    E-Print Network [OSTI]

    Bertalan, Zsolt; La Porta, Caterina A M; Zapperi, Stefano

    2015-01-01

    Motor proteins display widely different stepping patterns as they move on microtubule tracks, from the deterministic linear or helical motion performed by the protein kinesin to the uncoordinated random steps made by dynein. How these different strategies produce an efficient navigation system needed to ensure correct cellular functioning is still unclear. Here, we show by numerical simulations that deterministic and random motor steps yield different outcomes when random obstacles decorate the microtubule tracks: kinesin moves faster on clean tracks but its motion is strongly hindered on decorated tracks, while dynein is slower on clean tracks but more efficient in avoiding obstacles. Further simulations indicate that dynein's advantage on decorated tracks is due to its ability to step backwards. Our results explain how different navigation strategies are employed by the cell to optimize motor driven cargo transport.

  13. Navigation strategies of motor proteins on decorated tracks

    E-Print Network [OSTI]

    Zsolt Bertalan; Zoe Budrikis; Caterina A. M. La Porta; Stefano Zapperi

    2015-09-08

    Motor proteins display widely different stepping patterns as they move on microtubule tracks, from the deterministic linear or helical motion performed by the protein kinesin to the uncoordinated random steps made by dynein. How these different strategies produce an efficient navigation system needed to ensure correct cellular functioning is still unclear. Here, we show by numerical simulations that deterministic and random motor steps yield different outcomes when random obstacles decorate the microtubule tracks: kinesin moves faster on clean tracks but its motion is strongly hindered on decorated tracks, while dynein is slower on clean tracks but more efficient in avoiding obstacles. Further simulations indicate that dynein's advantage on decorated tracks is due to its ability to step backwards. Our results explain how different navigation strategies are employed by the cell to optimize motor driven cargo transport.

  14. Formation of S0 galaxies through mergers: Explaining angular momentum and concentration change from spirals to S0s

    E-Print Network [OSTI]

    Querejeta, Miguel; Tapia, Trinidad; Borlaff, Alejandro; van de Ven, Glenn; Lyubenova, Mariya; Martig, Marie; Falcón-Barroso, Jesús; Méndez-Abreu, Jairo

    2015-01-01

    The CALIFA team has recently found that the stellar angular momentum and concentration of late-type spiral galaxies are incompatible with those of lenticular galaxies (S0s), concluding that fading alone cannot satisfactorily explain the evolution from spirals into S0s. Here we explore whether major mergers can provide an alternative way to transform spirals into S0s by analysing the spiral-spiral major mergers from the GalMer database that lead to realistic, relaxed S0-like galaxies. We find that the change in stellar angular momentum and concentration can explain the differences in the $\\lambda_\\mathrm{Re}$--$R_{90}/R_{50}$ plane found by the CALIFA team. Major mergers thus offer a feasible explanation for the transformation of spirals into S0s.

  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. How a Vicinal Layer of Solvent Modulates the Dynamics of Proteins

    E-Print Network [OSTI]

    C. Atilgan; A. O. Aykut; A. R. Atilgan

    2007-07-11

    The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.

  17. Protein Flips Lipids Across Membranes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Across Membranes Print Wednesday, 26 October 2005 00:00 Found ubiquitously in both bacteria and humans, membrane proteins of the adenosine triphosphate (ATP)-binding cassette...

  18. High throughput protein production screening

    DOE Patents [OSTI]

    Beernink, Peter T. (Walnut Creek, CA); Coleman, Matthew A. (Oakland, CA); Segelke, Brent W. (San Ramon, CA)

    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.

  19. Protein Flips Lipids Across Membranes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen ProteinProteinProtein

  20. Aquaporin-9 Protein Is the Primary Route of Hepatocyte Glycerol Uptake for Glycerol Gluconeogenesis in Mice*S

    E-Print Network [OSTI]

    de Groot, Bert

    Aquaporin-9 Protein Is the Primary Route of Hepatocyte Glycerol Uptake for Glycerol Gluconeogenesis glycerol uptake for gluconeogenesis. Significance: Aquaporin-9 may be a drug target in diabetes treatment of hepatocyte glycerol uptake for gluconeogenesis and thereby explain the previously observed, alleviated

  1. Noise in protein expression scales with natural protein abundance

    E-Print Network [OSTI]

    Paulsson, Johan

    Noise in protein expression scales with natural protein abundance Arren Bar-Even1, Johan Paulsson2,3, Narendra Maheshri4, Miri Carmi1, Erin O'Shea4, Yitzhak Pilpel1 & Naama Barkai1,5 Noise in gene expression-specific regulation. Studies of individual promoters have suggested different dominating noise sources, raising

  2. Prediction protein--protein interaction sites heterocomplexes with neural networks

    E-Print Network [OSTI]

    Pazos, Florencio

    Prediction protein--protein interaction sites heterocomplexes with neural networks Piero Fariselli neural network based system, which a cross validation proce­ dure and allows correct detection 73 face. However neural networks trained a reduced representation of interacting patch sequence profile su

  3. Protein detection system

    DOE Patents [OSTI]

    Fruetel, Julie A. (Livermore, CA); Fiechtner, Gregory J. (Bethesda, MD); Kliner, Dahv A. V. (San Ramon, CA); McIlroy, Andrew (Livermore, CA)

    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.

  4. Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled...

    Office of Scientific and Technical Information (OSTI)

    Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor Crystallogenesis Citation Details In-Document Search Title: Modified T4 Lysozyme Fusion Proteins...

  5. Bond rupture mechanism enables to explain in block asymmetry of elaxation, force-velocity curve and the path of energy dissipation in muscle

    E-Print Network [OSTI]

    Eugene V. Rosenfeld

    2015-07-22

    Bond rupture mechanism enables to explain in block asymmetry of elaxation, force-velocity curve and the path of energy dissipation in muscle

  6. Explaining Soft Law

    E-Print Network [OSTI]

    Guzman, Andrew T.; Meyer, Timothy L.

    2009-01-01

    the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996their stockpiles of nuclear weapons. If Russia subsequently

  7. Explaining Soft Law

    E-Print Network [OSTI]

    Guzman, Andrew; Meyer, Timothy L.

    2010-01-01

    the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996their stockpiles of nuclear weapons. If Russia subsequently

  8. Explaining Charter School Effectiveness

    E-Print Network [OSTI]

    Angrist, Joshua

    Lottery estimates suggest Massachusetts' urban charter schools boost achievement well beyond that of traditional urban public schools students, while nonurban charters reduce achievement from a higher baseline. The fact ...

  9. Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation

    E-Print Network [OSTI]

    van Dijk, Erik; Knowles, Tuomas; Frenkel, Daan; Abeln, Sanne

    2015-01-01

    The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.

  10. Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation

    E-Print Network [OSTI]

    Erik van Dijk; Patrick Varilly; Tuomas Knowles; Daan Frenkel; Sanne Abeln

    2015-11-25

    The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.

  11. Water at interface with proteins

    E-Print Network [OSTI]

    Giancarlo Franzese; Valentino Bianco; Svilen Iskrov

    2010-12-07

    Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of the hydration water and the dynamics of protein. These works have generated a large amount of data whose interpretation is debated. New experiments measure the dynamics of water at low temperature on the surface of proteins, finding a qualitative change (crossover) that might be related to the slowing down and stop of the protein's activity (protein glass transition), possibly relevant for the safe preservation of organic material at low temperature. To better understand the experimental data several scenarios have been discussed. Here, we review these experiments and discuss their interpretations in relation with the anomalous properties of water. We summarize the results for the thermodynamics and dynamics of supercooled water at an interface. We consider also the effect of water on protein stability, making a step in the direction of understanding, by means of Monte Carlo simulations and theoretical calculations, how the interplay of water cooperativity and hydrogen bonds interfacial strengthening affects the protein cold denaturation.

  12. Expression of multiple proteins in transgenic plants

    DOE Patents [OSTI]

    Vierstra, Richard D. (Madison, WI); Walker, Joseph M. (Madison, WI)

    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.

  13. Introduction to Grid computing Protein folding

    E-Print Network [OSTI]

    Boyar, Joan

    Introduction to Grid computing Protein folding Protein folding is an extremely hot topic in medical research these days, unfortunately protein folding is extremely computationally demanding and requires a huge supercomputer to fold even the simplest proteins. Luckily the task of calculating protein foldings

  14. Fusion Protein Products Screen Purify Detect Cleave

    E-Print Network [OSTI]

    Lebendiker, Mario

    Fusion Protein Products · Screen · Purify · Detect · Cleave Fusion Protein Products · Screen researchers look to plasmid vectors to express fusion proteins, they find themselves in need of methods proteins is also included for those fusion proteins that may have an inaccessible tag. Pierce offers a host

  15. An investigation into the role of protein-ligand interactions on obligate and transient protein-protein interactions 

    E-Print Network [OSTI]

    Quinlan, Robert Jason

    2005-02-17

    Protein-ligand and protein-protein interactions are critical to cellular function. Most cellular metabolic and signal tranduction pathways are influenced by these interactions, consequently molecular level understanding ...

  16. Structural Studies of Proteins Involved in Diseases of Protein Deposition and a Protein Involved in Nitrogenase Assembly

    E-Print Network [OSTI]

    Phillips, Aaron Hale

    2010-01-01

    the product of NIFB protein. J. Biol. Chem. , 1994.Cleavage of structural proteins during the assembly of theof Escherichia coli NusA with protein N of phage lambda.

  17. YidC protein, a molecular chaperone for LacY protein folding via the SecYEG protein machinery

    E-Print Network [OSTI]

    Zhu, L; Kaback, HR; Dalbey, RE

    2013-01-01

    GroEL-GroES- mediated protein folding. Chem. Rev. 106, 1917–of chaperone-mediated protein folding in the cytosol. Nat.that impair membrane protein folding and generate a membrane

  18. 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...

  19. Studying the protein expression in human B lymphoblastoid cells exposed to 1.8-GHz (GSM) radiofrequency radiation (RFR) with protein microarray

    SciTech Connect (OSTI)

    Zhijian, Chen [Department of Environmental and Occupational Health, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, Zhejiang (China) [Department of Environmental and Occupational Health, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, Zhejiang (China); Institute of Environmental Health, Medical College, Zhejiang University, Hangzhou 310058, Zhejiang (China); Xiaoxue, Li [Institute of Environmental Health, Medical College, Zhejiang University, Hangzhou 310058, Zhejiang (China)] [Institute of Environmental Health, Medical College, Zhejiang University, Hangzhou 310058, Zhejiang (China); Wei, Zheng [Zhejiang International Travel Healthcare Center, 230 Zhonghezhong Road, Hangzhou 310003 (China)] [Zhejiang International Travel Healthcare Center, 230 Zhonghezhong Road, Hangzhou 310003 (China); Yezhen, Lu; Jianlin, Lou; Deqiang, Lu; Shijie, Chen; Lifen, Jin [Institute of Environmental Health, Medical College, Zhejiang University, Hangzhou 310058, Zhejiang (China)] [Institute of Environmental Health, Medical College, Zhejiang University, Hangzhou 310058, Zhejiang (China); Jiliang, He, E-mail: he_jiliang@hotmail.com [Institute of Environmental Health, Medical College, Zhejiang University, Hangzhou 310058, Zhejiang (China)] [Institute of Environmental Health, Medical College, Zhejiang University, Hangzhou 310058, Zhejiang (China)

    2013-03-29

    Highlights: ? Protein microarray shows the differential expression of 27 proteins induced by RFR. ? RPA32 related to DNA repair is down-regulated in Western blot. ? p73 related to cell genome stability and apoptosis is up-regulated in Western blot. -- Abstract: In the present study, the protein microarray was used to investigate the protein expression in human B-cell lymphoblastoid cells intermittently exposed to 1.8-GHz GSM radiofrequency radiation (RFR) at the specific absorption rate (SAR) of 2.0 W/kg for 24 h. The differential expression of 27 proteins was found, which were related to DNA damage repair, apoptosis, oncogenesis, cell cycle and proliferation (ratio >1.5-fold, P < 0.05). The results validated with Western blot assay indicated that the expression of RPA32 was significantly down-regulated (P < 0.05) while the expression of p73 was significantly up-regulated in RFR exposure group (P < 0.05). Because of the crucial roles of those proteins in DNA repair and cell apoptosis, the results of present investigation may explain the biological effects of RFR on DNA damage/repair and cell apoptosis.

  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. WELCOME TO THE PHYSICS LABORATORY! Physics is the human attempt to explain our world. The success of that attempt is evident in the

    E-Print Network [OSTI]

    Minnesota, University of

    general concepts of physics. You should always be prepared to explain your ideas or actions to othersINTRO - 1 WELCOME TO THE PHYSICS LABORATORY! Physics is the human attempt to explain our world, and computers. You have already developed your own physical perception of the world around you. Some of those

  2. WELCOME TO THE PHYSICS LABORATORY! Physics is our human attempt to explain the workings of the world. The success of that attempt is

    E-Print Network [OSTI]

    Minnesota, University of

    general concepts of physics. You should always be prepared to explain your ideas or actions to othersINTRO - 1 WELCOME TO THE PHYSICS LABORATORY! Physics is our human attempt to explain the workings, automobiles, televisions, and computers. You have already developed your own physical theories to understand

  3. WELCOME TO THE PHYSICS LABORATORY! Physics is our human attempt to explain the workings of the world. The success of that attempt is

    E-Print Network [OSTI]

    Minnesota, University of

    general concepts of physics. You should always be prepared to explain your ideas or actions to othersINTRO -1 WELCOME TO THE PHYSICS LABORATORY! Physics is our human attempt to explain the workings, cars, and computers. You have already developed your own physical theories to understand the world

  4. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

    D. Thirumalai; Edward P. O'Brien; Greg Morrison; Changbong Hyeon

    2010-07-18

    Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The experimental data and theoretical methods have revealed the multifaceted character of proteins. Proteins exhibit universal features that can be determined using only the number of amino acid residues (N) and polymer concepts. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and time scales of folding are to a large extent determined by N. The consequences of finite N especially on how individual residues order upon folding depends on the topology of the folded states. Such intricate details can be predicted using the Molecular Transfer Model that combines simulations with measured transfer free energies of protein building blocks from water to the desired concentration of the denaturant. By watching one molecule fold at a time, using single molecule methods, the validity of the theoretically anticipated heterogeneity in the folding routes, and the N-dependent time scales for the three stages in the approach to the native state have been established. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the "protein folding problem" in the broadest sense.

  5. A survey of integral ?-helical membrane proteins

    E-Print Network [OSTI]

    2009-01-01

    opti- mum eukaryotic integral membrane proteins forLarge-scale identi?cation of yeast integral membrane protein009-9069-8 A survey of integral a-helical membrane proteins

  6. Protein Interactions in Regulation and Assembly 

    E-Print Network [OSTI]

    Hsiao, Hao-Ching

    2015-03-17

    The objectives of this work include: validation of yeast-based assays, investigation of protein-protein interactions in the regulatory role of an intrinsically disordered protein, Ultrabithorax (Ubx), and exploration of possible application of Ubx...

  7. A survey of integral ?-helical membrane proteins

    E-Print Network [OSTI]

    2009-01-01

    cation of all human G-protein coupled receptors. However, avon Heijne G (2007) Membrane protein structure: predictionH (2007) Locating proteins in the cell using TargetP,

  8. A motion planning approach to protein folding 

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30

    Protein folding is considered to be one of the grand challenge problems in biology. Protein folding refers to how a protein's amino acid sequence, under certain physiological conditions, folds into a stable close-packed ...

  9. Optimized Null Model for Protein Structure Networks

    E-Print Network [OSTI]

    Milenkovic, Tijana; Filippis, Ioannis; Lappe, Michael; Przulj, Natasa

    2009-01-01

    play a key role in protein folding. Phys Rev E Stat Nonlinstages in non-two-state protein folding. J Mol Biol 357(5):determinants of protein folding. PNAS 12. Soyer A, Chomilier

  10. A Novel Topology for Representing Protein Folds

    E-Print Network [OSTI]

    Segal, Mark R

    2009-01-01

    1993). Cooperativity in protein-folding kinetics. Proc NatlVoelz VA. (2007). The protein folding problem: when will itMS, Weikl TR. (2008). The protein folding problem. Annu Rev

  11. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01

    Knowing how sequence information dictates the formation of protein structure is critical for accurate prediction of structure, for de novo protein design, and for understanding protein folding and misfolding. Based on ...

  12. Towards a Molecular Understanding of Protein Solubility 

    E-Print Network [OSTI]

    Kramer, Ryan 1984-

    2011-05-31

    Protein solubility is a problem for many protein chemists including structural biologists and those developing protein pharmaceuticals. Knowledge of how intrinsic factors influence solubility is limited due to the difficulty ...

  13. An Integrated Docking Pipeline for the Prediction of Large-Scale Protein-Protein Interactions

    E-Print Network [OSTI]

    An Integrated Docking Pipeline for the Prediction of Large-Scale Protein-Protein Interactions Xin. In this study, we developed a protein-protein docking pipeline (PPDP) that integrates a variety of state studies. In this study, we developed a protein-protein docking pipeline by integrat

  14. Protein MAS NMR methodology and structural analysis of protein assemblies

    E-Print Network [OSTI]

    Bayro, Marvin J

    2010-01-01

    Methodological developments and applications of solid-state magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy, with particular emphasis on the analysis of protein structure, are described in this thesis. ...

  15. Optimal contact map alignment of protein–protein interfaces

    E-Print Network [OSTI]

    Pulim, Vinay

    The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous ...

  16. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

    W. A. (2004). The protein folding 'speed limit'. CurrentG. (1997). Theory of protein folding: the energy landscapeenergy landscape of protein folding: a synthesis. Proteins

  17. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

    Stochastic Dynamics on a Protein Folding Energy Landscape .and J. N. Onuchic. Protein folding funnels: kinetic pathwaysthe energy landscape of protein folding. Proteins: Struct.

  18. Combining in vivo and in silico screening for protein stability

    E-Print Network [OSTI]

    Barakat, Nora Hisham

    2007-01-01

    Implications for the Protein Folding Code". Biochemistry 44(Proteolytic selection for protein folding using filamentousin vivo screening for protein folding and increased protein

  19. Effective potentials for Folding Proteins

    E-Print Network [OSTI]

    Nan-yow Chen; Zheng-Yao Su; Chung-Yu Mou

    2006-01-28

    A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.

  20. Adhesives from modified soy protein

    DOE Patents [OSTI]

    Sun, Susan (Manhattan, KS); Wang, Donghai (Manhattan, KS); Zhong, Zhikai (Manhattan, KS); Yang, Guang (Shanghai, CN)

    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.

  1. Protein Flips Lipids Across Membranes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen ProteinProtein Flips

  2. Protein Flips Lipids Across Membranes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen ProteinProtein

  3. Elastic energy of proteins and the stages of protein folding

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01

    We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable parameters are fitted to data from the computer simulation of the folding of a set of proteins using the CSAW (conditioned self-avoiding walk) model. The elastic energy gives rise to scaling relations of the form $R_{g}\\sim N^{\

  4. Explaining a CMS $eejj$ Excess With $\\mathcal{R}-$parity Violating Supersymmetry and Implications for Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Ben Allanach; Sanjoy Biswas; Subhadeep Mondal; Manimala Mitra

    2014-12-01

    A recent CMS search for the right handed gauge boson $W_R$ reports an interesting deviation from the Standard Model. The search has been conducted in the $eejj$ channel and has shown a 2.8$\\sigma$ excess around $m_{eejj} \\sim 2$ TeV. In this work, we explain the reported CMS excess with R-parity violating supersymmetry (SUSY). We consider resonant selectron and sneutrino production, followed by the three body decays of the neutralino and chargino via an $\\mathcal{R}-$parity violating coupling. We fit the excess for slepton masses around 2 TeV. The scenario can further be tested in neutrinoless double beta decay ($0\

  5. Vibronic coupling explains the ultrafast carotenoid-to-bacteriochlorophyll energy transfer in natural and artificial light harvesters

    E-Print Network [OSTI]

    Perlík, Václav; Cranston, Laura J; Cogdell, Richard J; Lincoln, Craig N; Savolainen, Janne; Šanda, František; Man?al, Tomáš; Hauer, Jürgen

    2015-01-01

    The initial energy transfer in photosynthesis occurs between the light-harvesting pigments and on ultrafast timescales. We analyze the carotenoid to bacteriochlorophyll energy transfer in LH2 Marichromatium purpuratum as well as in an artificial light-harvesting dyad system by using transient grating and two-dimensional electronic spectroscopy with 10 fs time resolution. We find that F\\"orster-type models reproduce the experimentally observed 60 fs transfer times, but overestimate coupling constants, which leads to a disagreement with both linear absorption and electronic 2D-spectra. We show that a vibronic model, which treats carotenoid vibrations on both electronic ground and excited state as part of the system's Hamiltonian, reproduces all measured quantities. Importantly, the vibronic model presented here can explain the fast energy transfer rates with only moderate coupling constants, which are in agreement with structure based calculations. Counterintuitively, the vibrational levels on the carotenoid el...

  6. Formation of the Galactic bulge from a two-component stellar disk: Explaining cylindrical rotation and vertical metallicity gradient

    E-Print Network [OSTI]

    Bekki, Kenji

    2011-01-01

    Recent observational studies have revealed that the Galactic bulge has cylindrical rotation and a steeper vertical metallicity gradient. We adopt two representative models for the bulge formation and thereby investigate whether the two models can explain both the observed cylindrical rotation and vertical metallicity gradient in a self-consistent manner. One is the "pure disk scenario" (PDS) in which the bulge is formed from a pure thin stellar disk through spontaneous bar instability. The other is the "two-component disk scenario" (TCDS) in which the bulge is formed from a disk composed of thin and thick disks through bar instability. Our numerical simulations show that although PDS can reproduce the cylindrical rotation, it shows a rather flatter vertical metallicity gradient that is inconsistent with observations. The derived flatter metallicity gradient is due to the vertical mixing of stars with different initial metallicities by the stellar bar. This result implies that the bulge can not be simply forme...

  7. Search for: "protein folding" | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    protein folding" Find + Advanced Search Advanced Search All Fields: "protein folding" Title: Full Text: Bibliographic Data: Creator Author: Name Name ORCID Search Authors...

  8. Extracellular Proteins Promote Zinc Sulfide Aggregation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Extracellular Proteins Promote Zinc Sulfide Aggregation Extracellular Proteins Promote Zinc Sulfide Aggregation Print Wednesday, 26 September 2007 00:00 Researchers from the ALS,...

  9. Protein shake-up | ornl.gov

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein shake-up Researchers use neutron scattering and supercomputing to study shape of a protein involved in cancer ORNL researchers are using neutrons and modeling to better...

  10. Validating Computer-Designed Proteins for Vaccines

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    flexibility in their scaffold protein structure, allowing the computationally modeled protein to "virtually" fold in many different ways around the epitope. They then used...

  11. 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:...

  12. ARTIFICIAL NEURAL NETWORKS IN PROTEIN

    E-Print Network [OSTI]

    . It is possible that the more ideal solution to protein secondary structure prediction is an advanced ensemble, -sheets, and random coils as a result of hydrogen bonds (secondary structure). These secondary structures

  13. Topological Solitons and Folded Proteins

    E-Print Network [OSTI]

    M. N. Chernodub; Shuangwei Hu; Antti J. Niemi

    2010-03-23

    We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by assembling the solitons together, one after another. We present a simple theoretical model that realizes our proposal and apply it to a number of biologically active proteins including 1VII, 2RB8, 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to construct solitons that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 0.7 Angstrom or less for the central alpha-carbons, i.e. within the limits of current experimental accuracy.

  14. Order, disorder, and protein aggregation

    E-Print Network [OSTI]

    Gurry, Thomas

    2015-01-01

    Protein aggregation underlies a number of human diseases. Most notably, it occurs widely in neurodegenerative diseases, including Alzheimer's and Parkinson's. At the molecular level, neurotoxicity is thought to originate ...

  15. Protein Folding Sculpting Evolutionary Change

    E-Print Network [OSTI]

    Lindquist, Susan

    Our work suggests that the forces that govern protein folding exert a profound effect on how genotypes are translated into phenotypes and that this in turn has strong effects on evolutionary processes. Molecular chaperones, ...

  16. 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.

  17. Prediction of protein function using protein-protein interaction data Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen

    E-Print Network [OSTI]

    Chen, Ting

    prediction based on protein interaction data. The supplementary data is available at httpPrediction of protein function using protein-protein interaction data Minghua Deng, Kui Zhang of Biological Sciences University of Southern California 1042 West 36th Place Los Angeles, CA 90089-1113 Tel

  18. Interaction of membrane-spanning proteins with peripheral and lipid-anchored membrane proteins: perspectives from protein lipid interactions (Review)

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    Interaction of membrane-spanning proteins with peripheral and lipid-anchored membrane proteins: perspectives from protein ± lipid interactions (Review) D. Marsh{*, L. I. HorvaÂth{, M. J. Swamy}, S ± protein interactions in double-reconstituted systems involving both integral and peripheral or lipid

  19. The Discrete Frenet Frame, Inflection Point Solitons And Curve Visualization with Applications to Folded Proteins

    E-Print Network [OSTI]

    Shuangwei Hu; Martin Lundgren; Antti J. Niemi

    2011-02-28

    We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three dimensional space. Our approach is based on the concept of an intrinsically discrete curve, which enables us to more effectively describe curves that in the limit where the length of line segments vanishes approach fractal structures in lieu of continuous curves. We verify that in the case of differentiable curves the continuum limit of our discrete equation does reproduce the generalized Frenet equation. As an application we consider folded proteins, their Hausdorff dimension is known to be fractal. We explain how to employ the orientation of $C_\\beta$ carbons of amino acids along a protein backbone to introduce a preferred framing along the backbone. By analyzing the experimentally resolved fold geometries in the Protein Data Bank we observe that this $C_\\beta$ framing relates intimately to the discrete Frenet framing. We also explain how inflection points can be located in the loops, and clarify their distinctive r\\^ole in determining the loop structure of foldel proteins.

  20. Protein-protein interactions of the cold shock protein CspE of salmonella typhimurium 

    E-Print Network [OSTI]

    Gwynne, Peter John

    2015-06-29

    Despite their name, a number of the cold shock proteins are expressed during normal growth, and not just during cold shock, in several species. The function of these constitutively expressed CspA paralogues is unclear. ...

  1. Database mining studies on protein-peptide and protein-protein interactions 

    E-Print Network [OSTI]

    Stevenson, Calum

    2012-11-30

    A major area of interest is the identification of proteins that play a role in hormone dependent cancers and in collaboration with the MRC Centre for Reproductive Health we studied the gonadotropin releasing hormone ...

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

    SciTech Connect (OSTI)

    Pykäläinen, Anette; Boczkowska, Malgorzata; Zhao, Hongxia; Saarikangas, Juha; Rebowski, Grzegorz; Jansen, Maurice; Hakanen, Janne; Koskela, Essi V.; Peränen, 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.

  3. 272 Dispatch Protein folding: Chaperones get Hip

    E-Print Network [OSTI]

    Craig, Elizabeth A

    272 Dispatch Protein folding: Chaperones get Hip Thomas Ziegelhoffer, Jill L. Johnson and Elizabeth the complexity of the Hsp70 `chaperone machine' that mediates early steps of protein folding in cells. Address of protein folding and translocation through their ability to recognize non-native conformations of proteins

  4. Proteins Wriggle Michael Cahill,* Sean Cahill,

    E-Print Network [OSTI]

    Cahill, Kevin

    Proteins Wriggle Michael Cahill,* Sean Cahill, and Kevin Cahill *School of Medicine, Uniformed strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model, when proteins fold under

  5. EVA: evaluation of protein structure prediction servers

    E-Print Network [OSTI]

    Sali, Andrej

    10027, USA, 5 Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, Madrid

  6. Protein-Folding Dynamics: Overview of Molecular

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Protein-Folding Dynamics: Overview of Molecular Simulation Techniques Harold A. Scheraga, Mey folding in silico. Although just a few years ago the dynamic be- havior of a protein molecule could models of proteins now make it possible to study protein- folding pathways from completely unfolded

  7. Protein Misfolding, Genetics, and Disease Anika Nagpal

    E-Print Network [OSTI]

    Brutlag, Doug

    of misfolding may be key to understanding how many bodily processes go awry, and how the protein folding system. 1 Dobson, Christopher M. "Principles of Protein Folding, Misfolding on the mechanism of protein folding. One which is backed up by much evidence is that a protein folds

  8. Deflagrations in hybrid CONe white dwarfs: a route to explain the faint Type Iax supernova 2008ha

    E-Print Network [OSTI]

    Kromer, M; Pakmor, R; Ruiter, A J; Hillebrandt, W; Marquardt, K S; Roepke, F K; Seitenzahl, I R; Sim, S A; Taubenberger, S

    2015-01-01

    Stellar evolution models predict the existence of hybrid white dwarfs (WDs) with a carbon-oxygen core surrounded by an oxygen-neon mantle. Being born with masses ~1.1 Msun, hybrid WDs in a binary system may easily approach the Chandrasekhar mass (MCh) by accretion and give rise to a thermonuclear explosion. Here, we investigate an off-centre deflagration in a near-MCh hybrid WD under the assumption that nuclear burning only occurs in carbon-rich material. Performing hydrodynamics simulations of the explosion and detailed nucleosynthesis post-processing calculations, we find that only 0.014 Msun of material is ejected while the remainder of the mass stays bound. The ejecta consist predominantly of iron-group elements, O, C, Si and S. We also calculate synthetic observables for our model and find reasonable agreement with the faint Type Iax SN 2008ha. This shows for the first time that deflagrations in near-MCh WDs can in principle explain the observed diversity of Type Iax supernovae. Leaving behind a near-MCh...

  9. 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.

  10. 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.

  11. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01

    We construct a phenomenological effective field theory model that describes the universality class of biologically active single-strand proteins. The model allows both for an explicit construction of native state protein conformations, and a dynamical description of protein folding and unfolding processes. The model reveals a connection between homochirality and protein collapse, and enables the theoretical investigation of various other aspects of protein folding even in the case of very long polypeptide chains where other methods are not available.

  12. 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.

  13. Exploiting Elements of Transcriptional Machinery to Enhance Protein Stability

    E-Print Network [OSTI]

    Love, John J.

    Exploiting Elements of Transcriptional Machinery to Enhance Protein Stability Nora H. Barakat Ltd. All rights reserved. *Corresponding author Keywords: protein design; protein stability of protein design aspires to engineer proteins of specific function. Function is correlated directly

  14. Small Molecule Screen Reveals Regulation of Survival Motor Neuron Protein Abundance by Ras Proteins

    E-Print Network [OSTI]

    Stockwell, Brent R.

    Small Molecule Screen Reveals Regulation of Survival Motor Neuron Protein Abundance by Ras Proteins States *S Supporting Information ABSTRACT: Small molecule modulators of protein activity have proven invaluable in the study of protein function and regulation. While inhibitors of protein activity

  15. Topological Aspects of DNA Function and Protein Folding 533 Identifying knots in proteins

    E-Print Network [OSTI]

    Bigelow, Stephen

    Topological Aspects of DNA Function and Protein Folding 533 Identifying knots in proteins Kenneth C proteins. How these knotted proteins fold and finding the evolutionary advantage provided by these knots are among some of the key questions currently being studied in the protein folding field. The detection

  16. Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and

    E-Print Network [OSTI]

    Bruck, Jehoshua (Shuki)

    Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling to preventing crosstalk among related signaling path- ways, scaffold proteins might facilitate signal cases, such as mitogen-activated protein kinase (MAPK) cascades, scaffold proteins are necessary

  17. Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

    E-Print Network [OSTI]

    Yang, Sichun

    Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective simulation pipeline to study protein-protein association from an energy landscape perspective. First of MD simulations and a simplified CG protein model with an emphasis on the energy landscape aspects

  18. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01

    The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how energy from diverse small sources can drive a complex molecule to a unique state. We explore the possibility that the missing factor is in the geometry. A comparison of folding with other physical phenomena, together with analytic modeling of a molecule, led us to analyze the physics of optical caustic formation and of folding behavior side-by-side. The physics of folding and caustics is ostensibly very different but there are several strong parallels. This comparison emphasizes the mathematical similarity and also identifies differences. Since the 1970's, the physics of optical caustics has been developed to a very high degree of mathematical sophistication using catastrophe theory. That kind of quantitative application of catastrophe theory has not previously been applied ...

  19. 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.

  20. 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.

  1. Protein Flips Lipids Across Membranes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen Protein

  2. Method for voltage-gated protein fractionation

    DOE Patents [OSTI]

    Hatch, Anson (Tracy, CA); Singh, Anup K. (Danville, CA)

    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.

  3. Design of protein-protein interaction specificity using computational methods and experimental library screening

    E-Print Network [OSTI]

    Chen, Tsan-Chou Scott

    2012-01-01

    Computational design of protein-protein interaction specificity is a powerful tool to examine and expand our understanding about how protein sequence determines interaction specificity. It also has many applications in ...

  4. UNDERSTANDING FORCES THAT CONTRIBUTE TO PROTEIN STABILITY: APPLICATION FOR INCREASING PROTEIN STABILITY 

    E-Print Network [OSTI]

    Fu, Hailong

    2010-07-14

    The aim of this study is to further our understanding of the forces that contribute to protein stability and to investigate how site-directed mutagenesis might be used for increasing protein stability. Eleven proteins ...

  5. Exploring Key Orientations of Small Molecules to Disrupt Protein-protein Interactions 

    E-Print Network [OSTI]

    Ko, Eunhwa

    2012-07-16

    Protein-protein interactions (PPIs) are attractive targets because of their therapeutic potential. One approach to design small molecules that can disrupt the PPIs is to use structural information of proteins. With this ...

  6. 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.

  7. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    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.

  8. Ezrin-anchored Protein Kinase A Coordinates Phosphorylation-dependent Disassembly of a NHERF1

    E-Print Network [OSTI]

    Scott, John D.

    complexes (6). Ancillary protein- protein interactions proceed through the EBD and ERM adapter proteins

  9. Contributions to the analysis of proteins

    E-Print Network [OSTI]

    Sharifi Sedeh, Reza

    2011-01-01

    Proteins are essential to organisms and play a central role in almost every biological process. The analysis of the conformational dynamics and mechanics of proteins using numerical methods, such as normal mode analysis ...

  10. Lanthanide-tagged proteins – An illuminating partnership

    E-Print Network [OSTI]

    Imperiali, Barbara

    Lanthanide-tagged proteins are valuable for exploiting the unique properties of Ln ions for investigating protein structure, function, and dynamics. Introduction of the Ln into the target is accomplished via chemical ...

  11. The Logic Linking Protein Acetylation and Metabolism

    E-Print Network [OSTI]

    Guarente, Leonard Pershing

    Protein acetylation now rivals phosphorylation in frequency of occurrence but is incompletely understood. A picture is presented in which protein acetylation is linked to available energy via the NAD-dependent deacetylases. ...

  12. Topology to geometry in protein folding: -Lactoglobulin

    E-Print Network [OSTI]

    Berry, R. Stephen

    Topology to geometry in protein folding: -Lactoglobulin Ariel Ferna´ndez* , Andre´s Colubri , and R angles and at the -carbon atoms of the peptide backbone dominate protein folding. Next in importance

  13. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    view, ALS-linked mutant SOD1 genes all code for structurally unstable forms of the SOD protein. Inevitably some of these unstable SOD proteins lose their normal folding enough...

  14. Metal-directed protein self-assembly

    E-Print Network [OSTI]

    Salgado. Eric N.

    2010-01-01

    F. A. 2010. Evolution of metal selectivity in templatedR. J. , Tezcan, F. A. 2010. Metal-Directed Protein Self-B. , Tezcan, F. A. 2010. Metal templated design of protein

  15. Protein-Folding Landscapes in Multi-Chain Systems

    E-Print Network [OSTI]

    Cellmer, Troy; Bratko, Dusan; Prausnitz, John M.; Blanch, Harvey

    2005-01-01

    a common approach to studying protein folding in isolationto investigate protein folding in the presence of multipleProtein-Folding Landscapes in Multi-Chain Systems Major

  16. Protein-folding via divide-and-conquer optimization

    E-Print Network [OSTI]

    Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

    2004-01-01

    Protein-folding vianumerical optimization Protein folding via divide-and-premise brings the protein-folding problem into the realm of

  17. Vertebrate Membrane Proteins: Structure, Function, and Insights from Biophysical Approaches

    E-Print Network [OSTI]

    Palczewski, Krzysztof

    Vertebrate Membrane Proteins: Structure, Function, and Insights from Biophysical Approaches DANIEL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 B. Membrane proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 III. Interactions of proteins with membranes

  18. Elucidating amyloid ?-protein folding and assembly: A multidisciplinary approach

    E-Print Network [OSTI]

    2006-01-01

    dynamics approach to protein folding and aggregation.study of amyloid ?-protein folding and oligomerization.nucleation of amyloid ?-protein folding. Proc. Natl. Acad.

  19. Computational Modeling of Protein Interactions at Multiple Lengthscales

    E-Print Network [OSTI]

    Yap, Eng Hui

    2010-01-01

    A. , Dominant Forces in Protein Folding. Biochemistry 1990,Hydrophobic Effect in Protein Folding and Other NoncovalentD. , Solvation Energy in Protein Folding and Binding. Nature

  20. The unfolded protein response during prostate cancer development

    E-Print Network [OSTI]

    So, Alex Yick-Lun; Fuente, Erwin; Walter, Peter; Shuman, Marc; Bernales, Sebastián

    2009-01-01

    chaperones to enhance protein folding and genes that mediatesurvival by adjusting ER protein folding capacity but ifmaintain fidelity in ER protein folding and assembly. The

  1. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

    unifying mechanism for protein folding? [Review]. Trends incoordinate for protein folding. Journal of Chemical PhysicsIntermediates can accelerate protein folding. Proceedings of

  2. Conformational dynamics of interleukin-1beta and protein- membrane interactions

    E-Print Network [OSTI]

    Anderson, William David

    2007-01-01

    et al. (1995). "Protein folding intermediates: native-statethe equilibrium protein folding pathway: structure-basedEnglander, S. W. (2000). "Protein folding intermediates and

  3. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

    Stochastic Dynamics on a Protein Folding Energy Landscape .and J. N. Onuchic. Protein folding funnels: kinetic pathwaysand T. Head-Gordon. Protein folding by distributed computing

  4. Can 3-D models explain the observed fractions of fossil and non-fossil carbon in and near Mexico City?

    SciTech Connect (OSTI)

    Hodzic, Alma; Jimenez, Jose L.; Prevot, A. S. H.; Szidat, S.; Fast, Jerome D.; Madronich, Sasha

    2010-11-25

    Abstract. A 3-D chemistry-transport model has been applied to the Mexico City metropolitan area to investigate the origin of elevated levels of non-fossil (NF) carbonaceous aerosols observed in this highly urbanized region. High time resolution measurements of the fine aerosol concentration and composition, and 12 or 24 h integrated 14C measurements of aerosol modern carbon have been performed in and near Mexico City during the March 2006 MILAGRO field experiment. The non-fossil carbon fraction (fNF), which is lower than the measured modern fraction (fM) due to the elevated 14C in the atmosphere caused by nuclear bomb testing, is estimated from the measured fM and the source-dependent information on modern carbon enrichment. The fNF contained in PM1 total carbon analyzed by a US team (f TC NF ) ranged from 0.37 to 0.67 at the downtown location, and from 0.50 to 0.86 at the suburban site. Substantially lower values (i.e. 0.24–0.49) were found for PM10 filters downtown by an independent set of measurements (Swiss team), which are inconsistent with the modeled and known differences between the size ranges, suggesting higher than expected uncertainties in the measurement techniques of 14C. An increase in the non-fossil organic carbon (OC) fraction (f OC NF ) by 0.10–0.15 was observed for both sets of filters during periods with enhanced wildfire activity in comparison to periods when fires were suppressed by rain, which is consistent with the wildfire impacts estimated with other methods. Model results show that the relatively high fraction of nonfossil carbon found in Mexico City seems to arise from the combination in about equal proportions of regional biogenic SOA, biomass burning POA and SOA, as well as non-fossil urban POA and SOA. Predicted spatial and temporal variations for f OC NF are similar to those in the measurements between the urban vs. suburban sites, and high-fire vs. low-fire periods. The absolute modeled values of f OC NF are consistent with the Swiss dataset but lower than the US dataset. Resolving the 14C measurement discrepancies is necessary for further progress in model evaluation. The model simulations that included secondary organic aerosol (SOA) formation from semi-volatile and intermediate volatility (S/IVOC) vapors showed improved closure for the total OA mass compared to simulations which only included SOA from VOCs, providing a more realistic basis to evaluate the fNF predictions. f OC NF urban sources of modern carbon are important in reducing or removing the difference in fNF between model and measurements, even though they are often neglected on the interpretation of 14C datasets. An underprediction of biomass burning POA by the model during some mornings also explains a part of the model-measurement differences. The fNF of urban POA and SOA precursors is an important parameter that needs to be better constrained by measurements. Performing faster ( 3 h) 14C measurements in future campaigns is critical to further progress in this area. To our knowledge this is the first time that radiocarbon measurements are used together with aerosol mass spectrometer (AMS) organic components to assess the performance of a regional model for organic aerosols.

  5. Membrane Protein Crystallization in Lipidic Mesophases. Hosting...

    Office of Scientific and Technical Information (OSTI)

    CATIONS; CRYSTALLIZATION; CRYSTALLOGRAPHY; CRYSTALS; HOST; LIPIDS; MEMBRANE PROTEINS; MEMBRANES; NUCLEAR MAGNETIC RESONANCE; PEPTIDES; RANGE; SHAPE; SIZE Word Cloud More...

  6. Bayesian Nonparametric Methods for Protein Structure Prediction 

    E-Print Network [OSTI]

    Lennox, Kristin Patricia

    2011-10-21

    . We use our method to address the bioinformatics question of what distributions should be used when sampling to generate new candidate models for a protein?s structure, a matter of considerable interest to the structure prediction community. Recall... structure predictions by incorporating information about closely related ?template? protein structures into searches of protein conformation space. This is accomplished by generating density estimates on conformation space via various simpli- fications...

  7. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K. (Berkeley, CA)

    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.

  8. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Devadas, Srinivas

    Simultaneous Alignment and Folding of Protein Sequences J´er^ome Waldisp¨uhl1,2 , Charles W. O techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu. 1 Introduction The consensus fold of two proteins is their common minimum energy structure, given

  9. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Will, Sebastian

    Simultaneous Alignment and Folding of Protein Sequences J´er^ome Waldisp¨uhl1,2 , Charles W. O-homology proteins. In this work, we present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is poly- nomial in time

  10. 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.

  11. Intracellular Signaling by the Unfolded Protein

    E-Print Network [OSTI]

    Mullins, Dyche

    reticulum stress, signal transduction, organelle homeostasis, protein folding, regulated mRNA splicing triggers an exten- sive transcriptional response, which adjusts the ER protein folding capacity according to reestablish homeostasis in the cell's protein folding capacity or--if this cannot be achieved-- commit cells

  12. UNCORRECTED 3 Protein folding: Then and now

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    UNCORRECTED PROOF 1 2 Review 3 Protein folding: Then and now 4 Yiwen Chen 1 , Feng Ding 1 , Huifen 8 9 Abstract 10 Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how 11 a protein folds has now become vital

  13. Approximate Inference and Protein-Folding

    E-Print Network [OSTI]

    Weiss, Yair

    Approximate Inference and Protein-Folding Chen Yanover and Yair Weiss School of Computer Science Side-chain prediction is an important subtask in the protein-folding problem. We show that #12;nding algorithms, including a widely used protein-folding software (SCWRL). 1 Introduction Inference in graphical

  14. On Hydrophobicity and Conformational Specificity in Proteins

    E-Print Network [OSTI]

    Sandelin, Erik

    On Hydrophobicity and Conformational Specificity in Proteins Erik Sandelin1 2 Stockholm of monomeric globular single domain proteins. We find that the total fraction of hydrophobic residues is roughly constant and has no discernible dependence on protein size. This results in a decrease

  15. Amphiphiles for protein solubilization and stabilization

    DOE Patents [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.

  16. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Atomistic Protein Folding Simulations on the Submillisecond Time Scale Using Worldwide Distributed Abstract: Atomistic simulations of protein folding have the potential to be a great complement. Biopolymers 68: 91­109, 2003 Keywords: atomistic protein folding; microsecond time scale; computer hardware

  17. Disulfide-Linked Protein Folding Pathways

    E-Print Network [OSTI]

    Bardwell, James

    Disulfide-Linked Protein Folding Pathways Bharath S. Mamathambika1,3 and James C. Bardwell2,3, 1 of protein folding is difficult because it involves the identification and characterization of folding to protein folding in vitro and in vivo. 211 Click here for quick links to Annual Reviews content online

  18. STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS

    E-Print Network [OSTI]

    Dinner, Aaron

    STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS AARON R. DINNER New Chemistry Laboratory for Protein Folding: Advances in Chemical Physics, Volume 120. Edited by Richard A. Friesner. Series Editors Experimental and theoretical studies have led to the emergence of a unified general mechanism for protein

  19. EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS

    E-Print Network [OSTI]

    Guibas, Leonidas J.

    EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS D. RUSSEL and L. GUIBAS Computer of secondary and tertiary structures as the protein folds. 1 Introduction There has been extensive work understanding of protein folding by studying their ensemble behaviors. Most currently used methods

  20. 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.

  1. Protein folding: not just another optimization

    E-Print Network [OSTI]

    Karplus, Kevin

    Protein folding: not just another optimization problem Kevin Karplus karplus of California, Santa Cruz protein-folding: not just opt ­ p.1/68 #12;Outline of Talk What is Bioinformatics initio" methods Contact prediction protein-folding: not just opt ­ p.2/68 #12;What is Bioinformatics

  2. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Hura, Greg

    2013-05-29

    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.

  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. 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.

  5. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21

    We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three dimensional conformation from a contact map and the Monte Carlo dynamics in contact map space. We then discuss two approximations to the free energy of the contact maps and a method to derive energy parameters based on perceptron learning. Finally we present results, first for predictions based on threading and then for energy minimization of crambin and of a set of 6 immunoglobulins. The main result is that we proved that the two simple approximations we studied for the free energy are not suitable for protein folding. Perspectives are discussed in the last section.

  6. 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.

  7. Topological Aspects of DNA Function and Protein Folding 523 Knotting pathways in proteins

    E-Print Network [OSTI]

    Bigelow, Stephen

    Topological Aspects of DNA Function and Protein Folding 523 Knotting pathways in proteins Joanna I Road, Santa Barbara, CA 93106, U.S.A. Abstract Most proteins, in order to perform their biological function, have to fold to a compact native state. The increasing number of knotted and slipknotted proteins

  8. Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design

    E-Print Network [OSTI]

    Powers, Robert

    Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design and accurate functional as- signment of novel proteins is increasing in impor- tance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally

  9. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Studying submicrosecond protein folding

    E-Print Network [OSTI]

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Studying submicrosecond protein folding kinetics INTRODUCTION To understand the intrinsic principles of protein folding, the events in the folding process have to be systematically explored from small to large time scales. Tradi- tional methods for triggering protein folding

  10. Structural Context of Exons in Protein Domains: Implications for Protein Modelling and Design

    E-Print Network [OSTI]

    Moreira, Bruno Contreras

    Structural Context of Exons in Protein Domains: Implications for Protein Modelling and Design Bruno structures taken from the Protein Data Bank. A first analysis of this set of proteins shows that intron boundaries prefer to be in non-regular secondary structure elements, while avoiding a-helices and b

  11. Membrane protein folding on the example of outer membrane protein A of Escherichia coli

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    Membrane protein folding on the example of outer membrane protein A of Escherichia coli J. H and mechanisms by which membrane proteins insert and fold into a biomem- brane have mostly been studiedA that involves at least three struc- turally distinct folding intermediates. Key words. Membrane protein folding

  12. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving taxonomy-based protein fold

    E-Print Network [OSTI]

    Chen, Xin

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving taxonomy-based protein fold recognition INTRODUCTION Protein fold recognition from amino acid sequences is one of the funda- mental problems in structural bioinformatics, as fold information could facilitate the identification of a protein's tertiary

  13. Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis

    E-Print Network [OSTI]

    Dinner, Aaron

    Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis Aaron R. Dinner1- turing conditions are commonly employed to study the mechanism by which a protein folds to its native of determining the mechanism by which a protein folds would be to use an accurate high-resolution model

  14. Detecting Protein-Protein Interaction Decoys using Fast Free Energy Calculations

    E-Print Network [OSTI]

    Detecting Protein-Protein Interaction Decoys using Fast Free Energy Calculations Christopher James, Generalized Belief Propagation, Free Energy, Protein- Protein Interactions #12;Abstract We present a physics for a given complex, and Generalized Belief Propa- gation to perform the free energy calculation. Our method

  15. SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm

    E-Print Network [OSTI]

    Lobstein, Julie; Emrich, Charlie A; Jeans, Chris; Faulkner, Melinda; Riggs, Paul; Berkmen, Mehmet

    2012-01-01

    Schein CH: Optimizing protein folding to the native state inJ, Terwilliger TC: Rapid protein-folding assay using greenbuilding bridges in protein folding. Trends Biochem Sci

  16. SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm

    E-Print Network [OSTI]

    Lobstein, Julie; Emrich, Charlie A; Jeans, Chris; Faulkner, Melinda; Riggs, Paul; Berkmen, Mehmet

    2012-01-01

    B strains, PR helped with the protein purification and MBacquisition through eukaryotic protein evolution. Mol Biol2. Reuters: The therapeutic proteins outlook to 2007: An

  17. . . . they took twenty-seven eight-by-ten color glossy photographs with circles and arrows and a paragraph on the back of each one explaining what each

    E-Print Network [OSTI]

    Palmeri, Thomas

    and a paragraph on the back of each one explaining what each one was to be used as evidence against us. --from systems. A basic modus operandi of cognitive science is to "carve things up at the joints" (c.f., Fodor

  18. may also explain the larger extent of quiet Sun spicules1,2 mode power and granular flows are stronger by up to 50% and

    E-Print Network [OSTI]

    Johnson, Peter D.

    may also explain the larger extent of quiet Sun spicules1,2 where p- mode power and granular flows 2004; doi:10.1038/nature02749. 1. Beckers, J. M. Solar spicules. Sol. Phys. 3, 367­433 (1968). 2. Beckers, J. M. Solar spicules. Annu. Rev. Astron. Astrophys. 10, 73­100 (1972). 3. Sterling, A. C. Solar

  19. arXiv:1205.6074v1[physics.bio-ph]28May2012 Mesoscale symmetries explain dynamical equivalence of food webs

    E-Print Network [OSTI]

    arXiv:1205.6074v1[physics.bio-ph]28May2012 Mesoscale symmetries explain dynamical equivalence is to identify mesoscale structures that have distinct dynamical implications. In this paper we present show that this equivalence is rooted in mesoscale symmetries that exist in these webs. Certain

  20. Friedman Web Site Student Cheat Sheet This document explains the different ways you can interact, while logged in, to the Friedman web site.

    E-Print Network [OSTI]

    Dennett, Daniel

    1 Friedman Web Site Student Cheat Sheet This document explains the different ways you can interact, while logged in, to the Friedman web site. Contents Friedman Web Site Student Cheat Sheet page on the Friedman web site and click on the white text Login in the red footer. In the next screen

  1. This booklet explains how hydropower is a part of the nation's energy base and how the U.S. Army Corps of Engineers helps develop this

    E-Print Network [OSTI]

    US Army Corps of Engineers

    #12;This booklet explains how hydropower is a part of the nation's energy base and how the U by building and operating hydropower plants in connection with its large multiple-purpose dams. Hydroelectric Hydropower Our supply of fossil fuel is limited; we still buy a substantial portion of the oil we use from

  2. Env. Sci 310/550 --Stella or Vensim? Both Stella and Vensim are excellent programs for dynamic modeling, and both are explained and used in Modeling

    E-Print Network [OSTI]

    Ford, Andrew

    Env. Sci 310/550 -- Stella or Vensim? Both Stella and Vensim are excellent programs for dynamic modeling, and both are explained and used in Modeling the Environment: 2nd Edition. You can select either program for this course. Previous students' experiences may help you decide which software is best for you

  3. VPN for Android (4.x) at TU Delft This manual explains how to connect your Android device (Android 4.x -ARM and Intel Android) to

    E-Print Network [OSTI]

    van Vliet, Lucas J.

    VPN for Android (4.x) at TU Delft This manual explains how to connect your Android device (Android 4.x - ARM and Intel Android) to the TU Delft VPN-servers. Note this manual is as is, officially there is no support for Android devices at TU Delft. We recommend to install Anyconnect ICS+, a Cisco VPN Client

  4. Amplitude saturation of MEMS resonators explained by autoparametric resonance This article has been downloaded from IOPscience. Please scroll down to see the full text article.

    E-Print Network [OSTI]

    Hulshof, Joost

    Amplitude saturation of MEMS resonators explained by autoparametric resonance This article has been. Microeng. 20 (2010) 105012 (15pp) doi:10.1088/0960-1317/20/10/105012 Amplitude saturation of MEMS This paper describes a phenomenon that limits the power handling of MEMS resonators. It is observed

  5. A mycological assessment of highly digestible protein sorghum lines. 

    E-Print Network [OSTI]

    Portillo, Ostilio Rolando

    2009-05-15

    The improved protein digestibility of the highly digestible protein (HD) sorghum lines is attributed to the invaginated shape of the endosperm protein bodies that provides better proteolytic access to the kafirins containing protein bodies. Recent...

  6. Protein folding using contact maps Michele Vendruscolo and Eytan Domany

    E-Print Network [OSTI]

    Domany, Eytan

    Protein folding using contact maps Michele Vendruscolo and Eytan Domany Department of Physics 26 I. INTRODUCTION Computational approaches to protein folding are divided into two main categories protein fold prediction. Contact maps are a particularly manageable representation of protein structure

  7. 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.

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

    DOE Patents [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.

  9. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

    P. Faccioli; M. Sega; F. Pederiva; H. Orland

    2006-07-27

    We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy between thermal and quantum diffusion: by writing the solution of the Fokker-Planck equation for the time-evolution of a protein in a viscous heat-bath in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is applied to the folding of the Villin Headpiece Subdomain, in the framework of a Go-model. We have found that, in this model, the transition occurs through an initial collapsing phase driven by the starting coil configuration and a later rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This method is completely general, does not require the prior knowledge of any reaction coordinate and represents an efficient tool to perfom ab-initio simulations of the entire folding process with available computers.

  10. Soft Matter Perspective on Protein Crystal Assembly

    E-Print Network [OSTI]

    Diana Fusco; Patrick Charbonneau

    2015-07-10

    Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter physics to understand colloidal assembly offer some insights into the problem of crystallizing proteins. This topical review describes the various analogies that have been made between proteins and colloids in that context. We highlight the explanatory power of patchy particle models, but also the challenges of providing guidance for crystallizing specific proteins. We conclude with a presentation of possible future research directions. This article is intended for soft matter scientists interested in protein crystallization as a self-assembly problem, and as an introduction to the pertinent physics literature for protein scientists more generally.

  11. Quantifying protein diffusion and capture on filaments

    E-Print Network [OSTI]

    Emanuel Reithmann; Louis Reese; Erwin Frey

    2015-03-03

    The functional relevance of regulating proteins is often limited to specific binding sites such as the ends of microtubules or actin-filaments. A localization of proteins on these functional sites is of great importance. We present a quantitative theory for a diffusion and capture process, where proteins diffuse on a filament and stop diffusing when reaching the filament's end. It is found that end-association after one-dimensional diffusion is the main source for tip-localization of such proteins. As a consequence, diffusion and capture is highly efficient in enhancing the reaction velocity of enzymatic reactions, where proteins and filament ends are to each other as enzyme and substrate. We show that the reaction velocity can effectively be described within a Michaelis-Menten framework. Together one-dimensional diffusion and capture beats the (three-dimensional) Smoluchowski diffusion limit for the rate of protein association to filament ends.

  12. Quantifying protein diffusion and capture on filaments

    E-Print Network [OSTI]

    Reithmann, Emanuel; Frey, Erwin

    2015-01-01

    The functional relevance of regulating proteins is often limited to specific binding sites such as the ends of microtubules or actin-filaments. A localization of proteins on these functional sites is of great importance. We present a quantitative theory for a diffusion and capture process, where proteins diffuse on a filament and stop diffusing when reaching the filament's end. It is found that end-association after one-dimensional diffusion is the main source for tip-localization of such proteins. As a consequence, diffusion and capture is highly efficient in enhancing the reaction velocity of enzymatic reactions, where proteins and filament ends are to each other as enzyme and substrate. We show that the reaction velocity can effectively be described within a Michaelis-Menten framework. Together one-dimensional diffusion and capture beats the (three-dimensional) Smoluchowski diffusion limit for the rate of protein association to filament ends.

  13. 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.

  14. Protein Dynamics Hit the Big Screen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    synthesize adenosine triphosphate (ATP), the fuel that powers many biomolecular motors. "Proteins are very complex molecules with thousands of atoms, but they don't come...

  15. A rational route to probing membrane proteins

    E-Print Network [OSTI]

    Keating, Amy E.

    A recent report describes the design of short peptides that bind specifically to transmembrane regions of integrins, providing an exciting tool for probing the biology of membrane proteins.

  16. Extracellular Proteins Promote Zinc Sulfide Aggregation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Extracellular Proteins Promote Zinc Sulfide Aggregation Print Researchers from the ALS, Berkeley Lab's National Center for Electron Microscopy (NCEM), and Lawrence Livermore...

  17. Hydrogen Bond Shaping of Membrane Protein Structure

    E-Print Network [OSTI]

    Cao, Zheng

    2013-01-01

    2 1.3. HYDROGEN BOND STRENGTHAND EQUILIBRIUM HYDROGEN / DEUTERIUM FRACTIONATION4 1.4. MEASUING HYDROGEN BOND STRENGTH IN A MEMBRANE PROTEIN

  18. Knots and Swelling in Protein Folding

    E-Print Network [OSTI]

    Martin Lundgren; Antti J. Niemi

    2009-06-26

    Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic activities and enhance binding. Moreover, knotted proteins may even have some substantial biomedical significance in relation to illnesses such as Parkinson's disease. But to a large extent the biological role of knots remains a conundrum. In particular, there is no explanation why knotted proteins are so scarce. Here we argue that knots are relatively rare because they tend to cause swelling in proteins that are too short, and presently short proteins are over-represented in the Protein Data Bank (PDB). Using Monte Carlo simulations we predict that the figure-8 knot leads to the most compact protein configuration when the number of amino acids is in the range of 200-600. For the existence of the simplest knot, the trefoil, we estimate a theoretical upper bound of 300-400 amino acids, in line with the available PDB data.

  19. 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.

  20. 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)

  1. Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies

    E-Print Network [OSTI]

    Kim, Do-Nyun

    The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis ...

  2. STRUCTURAL MODELING OF PROTEIN-PROTEIN INTERACTIONS USING MULTIPLE-CHAIN THREADING AND FRAGMENT ASSEMBLY

    E-Print Network [OSTI]

    Mukherjee, Srayanta

    2011-12-31

    Since its birth, the study of protein structures has made progress with leaps and bounds. However, owing to the expenses and difficulties involved, the number of protein structures has not been able to catch up with the ...

  3. Integration of On-Line Protein Digestion, Peptide Separation, and Protein Identification Using

    E-Print Network [OSTI]

    Zare, Richard N.

    Integration of On-Line Protein Digestion, Peptide Separation, and Protein Identification Using promotes penetra- tion of large molecular proteins into the column. The immobilized pepsin-digested electrophoresis column to a mass spectrometer. The on-line digestion of insulin chain and lysozyme provides

  4. Coupling between motor proteins determines dynamic behaviors of motor protein assemblies

    E-Print Network [OSTI]

    Coupling between motor proteins determines dynamic behaviors of motor protein assemblies Jonathan W of intracellular cargos by multiple microtubule motor proteins is believed to be a common and significant phenomenon in vivo, yet signatures of the microscopic dynamics of multiple motor systems are only now

  5. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Protein structure mining using

    E-Print Network [OSTI]

    Srinivasan, N.

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Protein structure mining using a structural alphabet to structure prediction and validation. Mining of information from this huge amount of data plays a crucial evaluation of a new structure mining method called PB-ALIGN. It is based on the encod- ing of protein

  6. 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.

  7. specificity of genomics-based protein-function prediction, although whether specific experimental testing of protein

    E-Print Network [OSTI]

    Lässig, Michael

    specificity of genomics-based protein-function prediction, although whether specific experimental interactome. Proc. Natl. Acad. Sci. U. S. A. 98, 4569­4574 9 Dwight, S.S. et al. (2002) Saccharomyces Genome for predicting protein­protein interactions from genomic data. Science 302, 449­453 17 Troyanskaya, O.G. et al

  8. Introduction to current and future protein therapeutics: A protein engineering perspective

    SciTech Connect (OSTI)

    Carter, Paul J., E-mail: pjc@gene.com

    2011-05-15

    Protein therapeutics and its enabling sister discipline, protein engineering, have emerged since the early 1980s. The first protein therapeutics were recombinant versions of natural proteins. Proteins purposefully modified to increase their clinical potential soon followed with enhancements derived from protein or glycoengineering, Fc fusion or conjugation to polyethylene glycol. Antibody-based drugs subsequently arose as the largest and fastest growing class of protein therapeutics. The rationale for developing better protein therapeutics with enhanced efficacy, greater safety, reduced immunogenicity or improved delivery comes from the convergence of clinical, scientific, technological and commercial drivers that have identified unmet needs and provided strategies to address them. Future protein drugs seem likely to be more extensively engineered to improve their performance, e.g., antibodies and Fc fusion proteins with enhanced effector functions or extended half-life. Two old concepts for improving antibodies, namely antibody-drug conjugates and bispecific antibodies, have advanced to the cusp of clinical success. As for newer protein therapeutic platform technologies, several engineered protein scaffolds are in early clinical development and offer differences and some potential advantages over antibodies.

  9. In Vitro Transport of a Fluorescent Nuclear Protein and Exclusion of Non-Nuclear Proteins

    E-Print Network [OSTI]

    Forbes, Douglass

    In Vitro Transport of a Fluorescent Nuclear Protein and Exclusion of Non-Nuclear Proteins Donald D microscopic assay for nuclear transport. The assay uses an extract of Xenopus eggs, normal or synthetic nuclei, and a fluorescently labeled nuclear protein, nucleoplasmin. This in vitro system accurately mimics in vivo nuclear

  10. Original article PROFESS: a PROtein Function, Evolution,

    E-Print Network [OSTI]

    Powers, Robert

    Original article PROFESS: a PROtein Function, Evolution, Structure and Sequence database Thomas introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift

  11. Experimental Observation of Bonding Electrons in Proteins*

    E-Print Network [OSTI]

    Experimental Observation of Bonding Electrons in Proteins* (Received for publication, April 15 enables bonding details of electron distributions in proteins to be revealed experimentally for the first time. We move one step closer to imaging directly the fine details of the electronic structure on which

  12. Protein Interactions in Regulation and Assembly 

    E-Print Network [OSTI]

    Hsiao, Hao-Ching

    2015-03-17

    , which interact with other proteins, as well as characterization of cell behaviors on biomaterials formed by self-assemble Ubx proteins will be discussed in this dissertation. Figure 1.12 Ubx fibers accommodate cells regardless of the cell type. Ubx...

  13. Chemistry & Biology Conversion of Red Fluorescent Protein

    E-Print Network [OSTI]

    Verkhusha, Vladislav V.

    resonance energy transfer applications. INTRODUCTION Green fluorescent protein (GFP) from Aequoria victoria for multicolor and lifetime imaging, as well as the outstanding donor for green fluorescent proteins in Fo¨ rster green fluorescent probes, such as TagGFP or EGFP (Shaner et al., 2005). The improvement

  14. 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.

  15. MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY

    E-Print Network [OSTI]

    Quake, Stephen R.

    MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY Thesis by Megan J. Anderson In Partial of this project. #12;iv I would also like to thank all of the microfluidic foundry technicians who provided me laboratories to produce high-quality protein crystals, the use of microfluidic technology for structural

  16. Biophysical characterization of protein folding and misfolding. 

    E-Print Network [OSTI]

    Schmittschmitt, Jason Peter

    2004-09-30

    here amyloid fibril formation for these proteins as a function of pH. The pH at maximal fibril formation correlates with the pH dependence of protein solubility, but not with stability, for these variants. Additionally, we show that the pH at maximal...

  17. Thermodynamics of Protein Folding Erik Sandelin

    E-Print Network [OSTI]

    Sandelin, Erik

    Thermodynamics of Protein Folding and Design Erik Sandelin Department of Theoretical Physics Lund Sölvegatan 14A 223 62 LUND September 2000 Erik Sandelin Thermodynamics of Protein Folding and Design sequence-independent local interactions which are found to strongly influence the thermodynamics

  18. PIC : Protein Interaction Calculator HELP AND GUIDELINES

    E-Print Network [OSTI]

    Srinivasan, N.

    PIC : Protein Interaction Calculator HELP AND GUIDELINES CONTENTS 1. Overview 2. Method 3. Input 4 (PIC) is a server which, given the coordinate set of threedimensional structure of a protein colored by PIC programmes can be downloaded and conveniently displayed with structural viewers

  19. Solvent dramatically affects protein structure refinement

    E-Print Network [OSTI]

    Summa, Christopher M.

    Solvent dramatically affects protein structure refinement Gaurav Chopraa , Christopher M. Summab, fold and function in aqueous solution in vivo and in vitro. In this work, we study the role of solvent explicit and implicit solvent were performed on a set of 75 native proteins to test the various energy

  20. Mismatch String Kernels for SVM Protein Classification

    E-Print Network [OSTI]

    Noble, William Stafford

    machines (SVMs) in a discriminative approach to the protein classification problem. These kernels measure efficiently using a mismatch tree data structure and report experiments on a benchmark SCOP dataset, where we savings. 1 Introduction A fundamental problem in computational biology is the classification of proteins

  1. Rotary protein motors George Oster1

    E-Print Network [OSTI]

    Oster, George

    unambiguously iden- tified as rotary engines: the bacterial flagellar motor and the two motors that constituteRotary protein motors George Oster1 and Hongyun Wang2 1 Depts Molecular and Cellular Biology review the current understanding of how these protein motors convert their energy supply into a rotary

  2. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01

    Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the exclusive dominant mechanism of protein folding, and attributes the structural transition from one characteristic state to another to energy barriers. Conversely, the concept of kinetic stability overemphasizes dominant mechanisms that are related to kinetic factors. This article explores the stability condition of protein structures from the viewpoint of meso-science, paying attention to the compromise in the competition between minimum free energy and other dominant mechanisms. Based on our study of complex systems, we propose that protein folding is a meso-scale, dissipative, nonlinear and non-equilibrium process that is dominated by the compromise between free energy and other dominant mechanisms such as environmental factors. Consequently, a protein shows dynamic structures,...

  3. Can Contact Potentials Reliably Predict Stability of Proteins?

    E-Print Network [OSTI]

    Khatun, Jainab

    ; protein stability; mutation; protein folding; protein design*Corresponding author Introduction and structure, a problem known as the protein folding problem.1 ­ 8 Conversely, identifying amino acid sequences Despite recent remark- able successes in protein folding in silico,21 ­ 24 the folding time-scales of most

  4. Protein Folding Challenge and Theoretical Computer Science Somenath Biswas

    E-Print Network [OSTI]

    Biswas, Somenath

    Protein Folding Challenge and Theoretical Computer Science Somenath Biswas Department of Computer the chain of amino acids that defines a protein. The protein folding problem is: given a sequence of amino to use an efficient algorithm to carry out protein folding. The atoms in a protein molecule attract each

  5. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-08-13

    The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how energy from diverse small sources can drive a complex molecule to a unique state. We explore the possibility that the missing factor is in the geometry. A comparison of folding with other physical phenomena, together with analytic modeling of a molecule, led us to analyze the physics of optical caustic formation and of folding behavior side-by-side. The physics of folding and caustics is ostensibly very different but there are several strong parallels. This comparison emphasizes the mathematical similarity and also identifies differences. Since the 1970's, the physics of optical caustics has been developed to a very high degree of mathematical sophistication using catastrophe theory. That kind of quantitative application of catastrophe theory has not previously been applied to folding nor have the points of similarity with optics been identified or exploited. A putative underlying physical link between caustics and folding is a torsion wave of non-constant wave speed, propagating on the dihedral angles and $\\Psi$ found in an analytical model of the molecule. Regardless of whether we have correctly identified an underlying link, the analogy between caustic formation and folding is strong and the parallels (and differences) in the physics are useful.

  6. 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.

  7. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Colloquium at Princeton Plasma Physics Laboratory March 8, 2000 http://fire.pppl.gov A Next Step Option Institute of Technology Oak Ridge National Laboratory Princeton Plasma Physics Laboratory Sandia National: SOFT/Fr Sep 98 IAEA/Ja Oct 98 APS-DPP Nov 98 FPA Jan 99 APEX/UCLA Feb 99 APS Cent Mar 99 IGNITOR May 99

  8. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Physics Workshop Princeton Plasma Physics Laboratory May 1, 2000 http://fire.pppl.gov A Next Step Option Institute of Technology Oak Ridge National Laboratory Princeton Plasma Physics Laboratory Sandia National: SOFT/Fr Sep 98 IAEA/Ja Oct 98 APS-DPP Nov 98 FPA Jan 99 APEX/UCLA Feb 99 APS Cent Mar 99 IGNITOR May 99

  9. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    has benefited from the prior design and R&D activities on BPX, TPX and ITER. Advanced Energy Systems/FIRE Community Involvement (FY-99) A Proactive NSO/FIRE Outreach Program has been undertaken to solicit comments and suggestions from the community on the next step. · Presentations have been made and comments received from

  10. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    &D activities on BPX, TPX and ITER. Advanced Energy Systems Argonne National Laboratory Bechtel Technology University of Illinois University of Wisconsin #12;NSO/FIRE Community Involvement (FY-99) A Proactive NSO/FIRE Outreach Program has been undertaken to solicit comments and suggestions from the community on the next

  11. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    for Technology. FIRE has benefited from the prior design and R&D activities on BPX, TPX and ITER. Advanced Energy;NSO/FIRE Community Involvement (FY-99) A Proactive NSO/FIRE Outreach Program has been undertaken to solicit comments and suggestions from the community on the next step. · Presentations have been made

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  13. 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...

  14. Micro-algae come of age as a platform for recombinant protein production

    E-Print Network [OSTI]

    Specht, Elizabeth; Miyake-Stoner, Shigeki; Mayfield, Stephen

    2010-01-01

    in therapeutic protein production in algae Expression levelrecombinant protein production Elizabeth Specht • Shigekirecombinant protein production in Chlamydomonas, including

  15. Development of anomalous diffusion among crowding proteins

    E-Print Network [OSTI]

    Margaret R. Horton; Felix Höfling; Joachim O. Rädler; Thomas Franosch

    2010-03-19

    In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to anomalous transport, though the nature of the onset of this behavior is still under debate and difficult to investigate experimentally. Here, we present a systematic study where proteins bound to supported lipid membranes diffuse freely in two dimensions, but are increasingly hindered by the presence of other like proteins. In our model system, the surface coverage of the protein avidin on the lipid bilayer is well controlled by varying the concentration of biotinylated lipid anchors. Using fluorescence correlation spectroscopy (FCS), we measure the time correlation function over long times and convert it to the mean-square displacement of the diffusing proteins. Our approach allows for high precision data and a clear distinction between anomalous and normal diffusion. It enables us to investigate the onset of anomalous diffusion, which takes place when the area coverage of membrane proteins increases beyond approximately 5%. This transition region exhibits pronounced spatial heterogeneities. Increasing the packing fraction further, transport becomes more and more anomalous, manifested in a decrease of the exponent of subdiffusion.

  16. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

    and the mechanism of protein folding. Ann Rev Biochem 1982;Baldwin RL. How does protein folding get started? TRENDS inNucleation mechanisms in protein folding. Current Opinion in

  17. Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding

    E-Print Network [OSTI]

    Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding Intermediate, the results show that protein folding intermediates are ensembles of different structural forms direct experi- mental evidence in support of a basic tenet of energy landscape theory for protein folding

  18. Intrinsically Disordered Proteins May Select Partners by Fold 

    E-Print Network [OSTI]

    Gonzalez, Kim 1988-

    2010-12-08

    Intrinsically disordered proteins lack a rigid structure due to their simple amino acid sequence. Because of their multiple roles, disordered proteins often account for a majority of proteins known to be associated with various diseases...

  19. Molecular Characterization of a Novel Class of DNA Binding Proteins

    E-Print Network [OSTI]

    Spears, Tatsinda Verity

    2010-01-01

    1a virion reveals 21 proteins. J. Gen. Virol. 90:359-365.2c virion structural proteins. J. Gen. Virol. 88:2194-7.2c virion structural proteins. J. Gen. Virol. 88:2194-2197.

  20. Quantifying internal friction in unfolded and intrinsically disordered proteins with

    E-Print Network [OSTI]

    Bigelow, Stephen

    Quantifying internal friction in unfolded and intrinsically disordered proteins with single reflects the "roughness" of the energy land- scape, plays an important role for proteins by modulating spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins

  1. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

    a unifying mechanism for protein folding? [Review]. TrendsOn the transition coordinate for protein folding. Journal ofMonoclonal Antibodies. Protein Science 6(1), 99-108. Strang,

  2. Functional Delivery of Proteins Using Engineered Degradable Polymeric Nanocapsules

    E-Print Network [OSTI]

    Biswas, Anuradha

    2013-01-01

    Baca, Q.J. & Golan, D.E. Protein therapeutics: a summary andK.A. & Dowdy, S.F. Protein transduction: unrestrictedBundell, K.R. & Lindsay, M.A. Protein transduction domains:

  3. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

    C. Are there pathways for protein folding? Journal de Chimieand the mechanism of protein folding. Ann Rev Biochem 1982;Baldwin RL. How does protein folding get started? TRENDS in

  4. THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES

    E-Print Network [OSTI]

    Sosnick, Tobin R.

    THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES FOR DELINEATION ............................................................................................................ 1 1.1 Why study protein folding .............................................................................. 3 1.2.1 How fast should a protein fold ........................................................... 3

  5. Trends in template/fragment-free protein structure prediction

    E-Print Network [OSTI]

    Zhou, Yaoqi; Duan, Yong; Yang, Yuedong; Faraggi, Eshel; Lei, Hongxing

    2011-01-01

    1998) Pathways to a protein folding intermediate observed instudy of all-atom protein folding and structure predic-JD, Dill KA (2007) Protein folding by zipping and assembly.

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    protein inhibitor of EBV-associated cancer, and can now be used to design proteins to fight other infectious agents and cancers. Some viruses plan for this, and produce proteins...

  7. Mutations that suppress the thermosensitivity of green fluorescent protein

    E-Print Network [OSTI]

    Haseloff, Jim

    Mutations that suppress the thermosensitivity of green fluorescent protein Kirby R. Siemering*, Ralph Golbik, Richard Sever* and Jim Haseloff* Background: The green fluorescent protein (GFP temperatures. Background The green fluorescent protein (GFP) from the bio- luminescent jellyfish Aequorea

  8. Predicting Protein Folding Kinetics via Temporal Logic Model Checking: Extended

    E-Print Network [OSTI]

    Langmead, Christopher James

    Predicting Protein Folding Kinetics via Temporal Logic Model Checking: Extended Abstract Abstract. We present a novel approach for predicting protein folding kinetics using techniques from checking. We tested our method on 19 test proteins. The quantitative predictions regarding folding rates

  9. Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

    E-Print Network [OSTI]

    Baker, David

    Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping Michael D. Tyka1 Keywords: Rosetta; alternative conformations; protein mobility; structure prediction; validation What through analysis of detailed protein energy landscapes generated by large-scale, native- enhanced sampling

  10. Pocket protein family function in mesenchymal tissue development and tumorigenesis

    E-Print Network [OSTI]

    Landman, Allison Simone

    2009-01-01

    pRB is a member of the pocket protein family, which includes the closely related proteins p107 and p130. The pocket proteins are critical regulators of the cell cycle and function to restrain proliferation by controlling ...

  11. Functionality and Protein-Water Interactions

    E-Print Network [OSTI]

    J. C. Phillips

    2008-03-02

    The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess water-induced medium-range order that is sometimes similar, but can also be complementary, to structural order. Study of these hitherto "phantom" order parameters promises far-reaching incremental improvements in the theory of protein dynamics. A by-product of the theory is an independent evaluation of the reliability of different hydrophobicity scales.

  12. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01

    A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially assumed to be nonlinear and represented by the Sine-Gordon equation, while the nonlinear external bosonic sources is represented by $\\phi^4$ interaction. It is argued that the nonlinear source induces the folding pathway in a different way than the previous work with initially linear backbone. Also, the nonlinearity of protein backbone decreases the folding speed.

  13. Protein Structure Suggests Role as Molecular Adapter

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big ScreenProteinThreadingProtein

  14. Metalloprotein and redox protein design are rapidly advancing toward the chemical synthesis of novel proteins that have

    E-Print Network [OSTI]

    Gibney, Brian R.

    485 Metalloprotein and redox protein design are rapidly advancing toward the chemical synthesis of novel proteins that have predictable structures and functions. Current data demonstrate a breadth and combinatorial strategies. These sophisticated synthetic analogs of natural proteins constructively test our

  15. New Crystal Structures Lift Fog around Protein Folding

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  16. Robust, High-Throughput Analysis of Protein Structures

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  17. Robust, High-Throughput Analysis of Protein Structures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Robust, High-Throughput Analysis of Protein Structures Robust, High-Throughput Analysis of Protein Structures Print Wednesday, 28 October 2009 00:00 Scientists have developed a...

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

    Office of Scientific and Technical Information (OSTI)

    to G protein-coupled receptors The use of molecular replacement in solving the structures of G protein-coupled receptors is discussed, with specific examples being described...

  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. Crystallizing Membrane Proteins in Lipidic Mesophases. A Host...

    Office of Scientific and Technical Information (OSTI)

    Crystallizing Membrane Proteins in Lipidic Mesophases. A Host Lipid Screen Citation Details In-Document Search Title: Crystallizing Membrane Proteins in Lipidic Mesophases. A Host...

  1. Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios

    E-Print Network [OSTI]

    Berry, R. Stephen

    Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios Ariel Ferna presents a method to portray protein folding dynamics at a coarse resolution, based on a pattern

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    homologous protein kinases found in normal, healthy cells. It has been widely used to fight colon cancers and chronic myeloid leukemia. The protein kinase Abl is involved in...

  3. How is the balance between protein synthesis and degradation achieved?

    E-Print Network [OSTI]

    Rothman, Stephen

    2010-01-01

    as: Rothman, How is the balance between protein synthesisAccess Research How is the balance between protein synthesisstate concentrations. Balance between them is achieved

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

    Broader source: All U.S. Department of Energy (DOE) Office 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...

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

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Wednesday, 03 December 2014 00:00 Immortality is...

  6. Body shape regulation by Tweedle family proteins in Drosophila melanogaster

    E-Print Network [OSTI]

    Guan, Xiao

    2006-01-01

    of TwdlF-RFP fusion protein in young ?rst in- starTwdlD-RFP fusion protein in young ?rst in- star larvae. tt:

  7. Biomimetic materials for protein storage and transport

    DOE Patents [OSTI]

    Firestone, Millicent A. (Elmhurst, IL); Laible, Philip D. (Villa Park, IL)

    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.

  8. Simultaneous alignment and folding of protein sequences

    E-Print Network [OSTI]

    Waldispuhl, Jerome

    Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first ...

  9. Exploring the mechanisms of fibrillar protein aggregation 

    E-Print Network [OSTI]

    Ryan, Morris

    2013-11-28

    conditions, pointing to possible in vivo strategies for controlling cytotoxicity. I probe the structural nature of the transition by performing small angle neutron scattering. Secondly, I study the formation of amyloid-like brils from the protein ovalbumin. I...

  10. IDENTIFYING CANDIDATE PROTEIN FOR REMOVAL OF ENVIRONMENTALLY

    E-Print Network [OSTI]

    Uppsala Universitet

    IDENTIFYING CANDIDATE PROTEIN FOR REMOVAL OF ENVIRONMENTALLY HAZARDOUS SUBSTANCES Pharem Biotech products and technologies for removing environmental hazardous substances in our everyday life. The products can be applied in areas from the private customer up to the global corporate perspective

  11. Characterisation of endogenous KRAB zinc finger proteins 

    E-Print Network [OSTI]

    Crawford, Catherine

    2009-01-01

    The Krüppel-associated box (KRAB) zinc finger protein (ZFP) genes comprise one of the largest gene families in the mammalian genome, encoding transcription factors with an N-terminal KRAB domain and C-terminal zinc ...

  12. Validating Computer-Designed Proteins for Vaccines

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  13. Validating Computer-Designed Proteins for Vaccines

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    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 a...

  14. Mapping the Protein Universe | Argonne National Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office 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...

  15. Histone H1 proteins in Chlamydomonas reinhardtii 

    E-Print Network [OSTI]

    Salinger, Andrew Paul

    1994-01-01

    The Hl proteins of the unicellular green alga Chlamydomonas reinhardtii were extracted from isolated nuclei, fractionated by two-dimensional electrophoresis, and analyzed by peptide mapping and N-terminal sequencing. C. reinhardtli histones were...

  16. Purification of recombinant proteins with magnetic nanoclusters

    E-Print Network [OSTI]

    Ditsch, Andre (Andre Paul)

    2005-01-01

    This thesis focused on the development and analysis of a new class of magnetic fluids for recovery of recombinant proteins from fermentation broth. Magnetic fluids are colloidally stable dispersions of magnetic nanoclusters ...

  17. Selenomethionine Biotransformation and Incorporation into Proteins

    E-Print Network [OSTI]

    Hopkins, William A.

    Selenomethionine Biotransformation and Incorporation into Proteins along a Simulated Terrestrial mass spectrometry to investigate biotransformations of selenomethionine along a simulated terrestrial in the environment. Given the richness of biochemical pathways through which Se ma

  18. Protein Scaffolding for Small Molecule Catalysts

    SciTech Connect (OSTI)

    Baker, David [Univ. of Washington, Seattle, WA (United States)

    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.

  19. Photovoltaic devices using photosynthetic protein complexes

    E-Print Network [OSTI]

    Das, Rupa, 1980-

    2004-01-01

    Photosynthetic proteins have been used as an active material in design of organic solar cells. Traditional organic solar cells have the limitation of not being able to absorb light in the visible-NIR region of the solar ...

  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. Positive modulator of bone morphogenic protein-2

    DOE Patents [OSTI]

    Zamora, Paul O. (Gaithersburg, MD); Pena, Louis A. (Poquott, NY); Lin, Xinhua (Plainview, NY); Takahashi, Kazuyuki (Germantown, MD)

    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.

  2. Complement Evasion by S. aureus Surface Proteins 

    E-Print Network [OSTI]

    Kang, Mingsong

    2014-08-28

    ‘Collagen Hug' model ............................................................ 31 Figure 14 Fg-binding MSCRAMMs bind to different sites of fibrinogen ...................... 34 Figure 15 Domain orgnazation of Sdr protein family.... ............................................................... 89 Figure 29 Biacore analysis of the interactions between C3 or C3 small components and the recombinant Bbp or SdrE proteins ..................................................... 90 Figure 30 Bbp doesn’t share binding sites on C3b with factor...

  3. Exo-endo cellulase fusion protein

    DOE Patents [OSTI]

    Bower, Benjamin S. (Palo Alto, CA); Larenas, Edmund A. (Palo Alto, CA); Mitchinson, Colin (Palo Alto, CA)

    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.

  4. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26

    In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure from random coil. The process involves an intricate interplay between global geometry and local structure, and each protein seems to present special problems. We introduce CSAW (conditioned self-avoiding walk), a model of protein folding that combines the features of self-avoiding walk (SAW) and the Monte Carlo method. In this model, the unfolded protein chain is treated as a random coil described by SAW. Folding is induced by hydrophobic forces and other interactions, such as hydrogen bonding, which can be taken into account by imposing conditions on SAW. Conceptually, the mathematical basis is a generalized Langevin equation. To illustrate the flexibility and capabilities of the model, we consider several examples, including helix formation, elastic properties, and the transition in the folding of myoglobin. From the CSAW simulation and physical arguments, we find a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. The elastic energy gives rise to scaling laws $R_{g}\\sim N^{\

  5. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

    E-Print Network [OSTI]

    Jain, Ajay N.

    2009-01-01

    in docking: improved pose prediction through protein pocketacceptable results in pose prediction have been generallyoptimization requires accurate pose prediction for novel

  6. Split green fluorescent protein as a modular binding partner for protein crystallization

    SciTech Connect (OSTI)

    Nguyen, Hau B. [Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545 (United States); Hung, Li-Wei [Los Alamos National Laboratory, MS D454, Los Alamos, NM 87545 (United States); Yeates, Todd O. [University of California, PO Box 951569, Los Angeles, CA 90095 (United States); Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov; Waldo, Geoffrey S., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545 (United States)

    2013-12-01

    A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP ?-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was tested by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization.

  7. 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.

  8. Cellular mechanisms of membrane protein folding William R Skach

    E-Print Network [OSTI]

    Cai, Long

    Cellular mechanisms of membrane protein folding William R Skach The membrane protein­folding. This Perspective will focus on emerging evidence that the RTC functions as a protein-folding machine that restricts. The process of polytopic (multispanning) membrane protein folding can be viewed as a series of sequential

  9. Adaptive dimensionality reduction of stochastic differential equations for protein dynamics

    E-Print Network [OSTI]

    Izaguirre, Jesús A.

    . Understanding protein motion or dynamics is critical to solving problems as diverse as protein folding into a significant sampling problem for all but the most elementary of systems. While small proteins fold or have bond vibrations are on the order of femtoseconds (10-15 sec) while proteins fold on a time

  10. Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics

    E-Print Network [OSTI]

    Weng, Zhiping

    Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics Rong Chen1 A comprehensive docking study was performed on 27 distinct protein-protein com- plexes. For 13 test systems space without any knowledge of the binding sites was performed for all proteins except nine antibodies

  11. DNA topology confers sequence specificity to nonspecific architectural proteins

    E-Print Network [OSTI]

    Swigon, David

    DNA topology confers sequence specificity to nonspecific architectural proteins Juan Weia , Luke proteins into tightly organized 3D struc- tures. The bacterial heat-unstable (HU) protein builds up. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which

  12. Evolutionary Monte Carlo for protein folding simulations Faming Lianga)

    E-Print Network [OSTI]

    Liang, Faming

    Evolutionary Monte Carlo for protein folding simulations Faming Lianga) Department of Statistics to simulations of protein folding on simple lattice models, and to finding the ground state of a protein. In all structures in protein folding. The numerical results show that it is drastically superior to other methods

  13. Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics

    E-Print Network [OSTI]

    Santiago, Juan G.

    Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics David E. Hertzog with numerical simulations to minimize the mixing time of a microfluidic mixer developed for protein folding reported continuous flow mixer for protein folding. Fast events in protein folding often occur

  14. DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS

    E-Print Network [OSTI]

    Langmead, Christopher James

    DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS Arvind Ramanathan Lane a spatio-temporal analysis of protein folding pathways. We applied our method to folding simulations of how a protein folds into its functionally relevant conformations. Protein folding pathways span over

  15. Steiner Minimal Trees, Twist Angles, and the Protein Folding Problem

    E-Print Network [OSTI]

    Smith, J. MacGregor

    Steiner Minimal Trees, Twist Angles, and the Protein Folding Problem J. MacGregor Smith, Yunho Jang. These properties should be ultimately useful in the ab ini- tio protein folding prediction. Proteins 2007;66:889­ 902. VVC 2006 Wiley-Liss, Inc. Key words: Steiner trees; twist angles; protein fold- ing; side chain

  16. FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin ABSTRACT A discrete classical mechanics (DCM of the genetic code. A DCM model for protein folding allows a set of folding nuclei to be derived for each. A PROTEIN FOLDING MODEL Let us consider the following protein folding model. A chemical group of mass m

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

    DOE Patents [OSTI]

    Mayfield, Stephen P. (Cardiff, CA)

    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.

  18. Directional interactions and cooperativity between mechanosensitive membrane proteins

    E-Print Network [OSTI]

    Christoph A. Haselwandter; Rob Phillips

    2013-05-24

    While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we explore the relation between the shape of membrane proteins and the cooperative function of membrane proteins induced by membrane-mediated elastic interactions. For the experimental model system of mechanosensitive ion channels we find that the sign and strength of elastic interactions depend on the protein shape, yielding distinct cooperative gating curves for distinct protein orientations. Our approach predicts how directional elastic interactions affect the molecular structure, organization, and biological function of proteins in crowded membranes.

  19. Structural determination of intact proteins using mass spectrometry

    DOE Patents [OSTI]

    Kruppa, Gary (San Francisco, CA); Schoeniger, Joseph S. (Oakland, CA); Young, Malin M. (Livermore, CA)

    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.

  20. Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches

    E-Print Network [OSTI]

    Schwarz, Ulrich

    proteins according to the known experimental structures of the protein complexes. In the computer are modulated by molecular features of the systems under consideration. Moreover it allows us to assess and lifetimes. Examples of such complexes are ribosomes, poly- merases, spliceosomes, nuclear pore complexes

  1. Identifying Modulators of Protein-Protein Interactions Using Photonic Crystal Biosensors James T. Heeres

    E-Print Network [OSTI]

    Cunningham, Brian

    Identifying Modulators of Protein-Protein Interactions Using Photonic Crystal Biosensors James T or untagged version of the cognate partner. This assay, based on photonic crystal (PC) biosensor technology or fluorescence measurements. PC biosensors are surface structures comprised of a subwavelength polymer grating

  2. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving NMR protein structure quality

    E-Print Network [OSTI]

    Baker, David

    of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 5 conformational sampling and/or a superior force field, was capable of find- ing alternative low energy protein, New Jersey INTRODUCTION The use of nuclear magnetic resonance (NMR) spec- troscopy-derived protein

  3. Metal ions and protein aggregation: the case fo Prion protein and -amyloids

    E-Print Network [OSTI]

    Morante, Silvia

    Metal ions and protein aggregation: the case fo Prion protein and -amyloids Silvia Morante community, is the structural rôle played by metals in intra-molecular and inter-molecular interactions. Metals are essential elements for many of the fundamental activities of cells. Storing, metabolism

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

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    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

  5. BRIEF COMMUNICATION Protein-Polymer Grafts via a Soy Protein Derived Macro-RAFT

    E-Print Network [OSTI]

    Bong, Dennis

    BRIEF COMMUNICATION Protein-Polymer Grafts via a Soy Protein Derived Macro-RAFT Chain Transfer Methodology to produce materials derived from renewable resources is of great importance in decreasing both of renewable resource derived materials are enabling from economic, environmental, industrial and basic science

  6. Universality of Vibrational Spectra of Globular Proteins

    E-Print Network [OSTI]

    Na, Hyuntae; ben-Avraham, Daniel

    2015-01-01

    It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e., regardless of the protein in question it closely follows one universal curve. The present study, including 135 proteins analyzed with a full atomic empirical potential (CHARMM22) and using the full complement of all atoms Cartesian degrees of freedom, goes far beyond confirming previous claims of universality, finding that universality holds even in the high-frequency range (300- 4000 1/cm), where peaks and turns in the density of states are faithfully reproduced from one protein to the next. We also characterize fluctuations of the spectral density from the average, paving the way to a meaningful discussion of rare, unusual spectra and the structural reasons for the deviations in such "outlier" proteins. Since the method used for the derivation of the vibrational modes (potential energy formulation, set of degrees of freedom employed, etc.) has a dramatic effect on the spectral density, another signific...

  7. 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, evaporation rate can be controlled or adjusted in this method during the crystallization process to favor either nucleation or growing processes for optimizing crystallization process. The protein crystals gotten by this method were experimentally proven to possess high x-ray diffraction qualities. Finally, we crystallized human lactate dehydrogenase 1 (H4) complexed with NADH and determined its structure by x-ray crystallography. The structure of LDH/NADH displays a significantly different structural feature, compared with LDH/NADH/inhibitor ternary complex structure, that subunits in LDH/NADH complex show open conformation or two conformations on the active site while the subunits in LDH/NADH/inhibitor are all in close conformation. Multiple LDH/NADH crystals were obtained and used for x-ray diffraction experiments. Difference in subunit conformation was observed among the structures independently solved from multiple individual LDH/NADH crystals. Structural differences observed among crystals suggest the existence of multiple conformers in solution.

  8. Abstract--Fusion proteins are an important class of proteins with diverse applications in biotechnology. They consist of 2 or

    E-Print Network [OSTI]

    Abstract-- Fusion proteins are an important class of proteins with diverse applications the conformational space of fusion proteins conferred by the flexible linkers is important to predicting its behavior. In this paper, we introduce a modeling tool called FPMOD (Fusion Protein MODeller) which samples

  9. PROTEINS: Structure, Function, and Genetics 42:332-344 Q00I\\ Protein Structural Domainss Analysis of the SDee Domains

    E-Print Network [OSTI]

    Barton, Geoffrey J.

    PROTEINS: Structure, Function, and Genetics 42:332-344 Q00I\\ Protein Structural Domainss Analysis-dimensional structures in the Protein Data Bank (pDB). The database includes definitions for complex, multiple- segment. For the November lggg release, 7,995 PDB entries contained t9,767 protein chains and gave rise to 18r89Gdomains

  10. Protein Engineering vol.7 no.9 pp. 1059-1068, 1994 The protein threading problem with sequence amino acid

    E-Print Network [OSTI]

    Lathrop, Richard H.

    that the direct protein folding problem is NP-complete by providing the corresponding proof for the 'inverse' protein folding problem. It provides a theoretical basis for understanding algorithms currently in use algorithms. Key words: contact potentials/inverse protein folding/NP-com- plete/protein structure prediction

  11. Comparison between Protein-Polyethylene Glycol (PEG) Interactions and the Effect of PEG on Protein-Protein Interactions Using the Liquid-Liquid Phase Transition

    E-Print Network [OSTI]

    Benedek, George B.

    Comparison between Protein-Polyethylene Glycol (PEG) Interactions and the Effect of PEG on Protein transitions is the required presence of additives such as polyethylene glycol (PEG). To investigate

  12. Cotranslational folding of deeply knotted proteins

    E-Print Network [OSTI]

    Chwastyk, Mateusz

    2015-01-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

  13. Protein search for multiple targets on DNA

    E-Print Network [OSTI]

    Martin Lange; Maria Kochugaeva; Anatoly B. Kolomeisky

    2015-08-03

    Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic approach that takes into account most relevant physical-chemical processes and leads to fully analytical description of all dynamic properties. Specifically, systems with two and three targets have been explicitly investigated. It is found that multiple targets in most cases accelerate the search in comparison with a single target situation. However, the acceleration is not always proportional to the number of targets. Surprisingly, there are even situations when it takes longer to find one of the multiple targets in comparison with the single target. It depends on the spatial position of the targets, distances between them, average scanning lengths of protein molecules on DNA, and the total DNA lengths. Physical-chemical explanations of observed results are presented. Our predictions are compared with experimental observations as well as with results from a continuum theory for the protein search. Extensive Monte Carlo computer simulations fully support our theoretical calculations.

  14. Compositions and methods for improved protein production

    DOE Patents [OSTI]

    Bodie, Elizabeth A. (San Carlos, CA); Kim, Steve (San Francisco, CA)

    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.

  15. Compositions and methods for improved protein production

    SciTech Connect (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.

  16. Facilitated diffusion of proteins on chromatin

    E-Print Network [OSTI]

    O. Benichou; C. Chevalier; B. Meyer; R. Voituriez

    2011-01-26

    We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor, and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.

  17. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17

    We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as hydrogen bonding, which can be taken into account by imposing conditions on SAW. The resulting model is termed CSAW (conditioned self-avoiding walk. Conceptually, the mathematical basis is a generalized Langevin equation. In practice, the model is implemented on a computer by combining SAW and Monte Carlo. To illustrate the flexibility and capabilities of the model, we consider a number of examples, including folding pathways, elastic properties, helix formation, and collective modes.

  18. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

    Campisi, Judith (Berkeley, CA); Kim, Sahn-Ho (Albany, CA)

    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.

  19. Protein Dynamics Hit the Big Screen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen Protein Dynamics Hit

  20. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big ScreenProtein Instability and

  1. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big ScreenProtein Instability

  2. Protein Structure Suggests Role as Molecular Adapter

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big ScreenProteinThreading

  3. Protein Structure Suggests Role as Molecular Adapter

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the BigProtein Structure Suggests

  4. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-Rich MatricesstudentsProjectsPropertymaterials |ProteinProtein

  5. The Biological Big Bang: The First Oceans of Primordial Planets at 2-8 Million Years Explain Hoyle/Wickramasinghe Cometary Panspermia

    E-Print Network [OSTI]

    Gibson, Carl H

    2011-01-01

    Hydrogravitional-dynamics (HGD) cosmology of Gibson/Schild 1996 predicts that the primordial H-He^4 gas of big bang nucleosynthesis became proto-globular-star-cluster clumps of Earth-mass planets at 300 Kyr. The first stars formed from mergers of these 3000 K gas planets. Chemicals C, N, O, Fe etc. created by stars and supernovae then seeded many of the reducing hydrogen gas planets with oxides to give them hot water oceans with metallic iron-nickel cores. Water oceans at critical temperature 647 K then hosted the first organic chemistry and the first life, distributed to the 10^80 planets of the cosmological big bang by comets produced by the new (HGD) planet-merger star formation mechanism. The biological big bang scenario occurs between 2 Myr when liquid oceans condensed and 8 Myr when they froze. HGD cosmology explains, very naturally, the Hoyle/Wickramasinghe concept of cometary panspermia by giving a vast, hot, nourishing, cosmological primordial soup for abiogenesis, and the means for transmitting the ...

  6. Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

    SciTech Connect (OSTI)

    Svintradze, David V. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Peterson, Darrell L. [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Collazo-Santiago, Evys A.; Lewis, Janina P. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Wright, H. Tonie, E-mail: xrdproc@vcu.edu [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Virginia Commonwealth University, Richmond, VA 23298-0566 (United States)

    2013-10-01

    Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.

  7. 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.

  8. Enzyme-mediated labeling of proteins and protein-protein interactions in vitro and in living cells

    E-Print Network [OSTI]

    Slavoff, Sarah Ann

    2010-01-01

    The E. coli biotin ligase enzyme, BirA, has been previously used by the Ting research group for site-specific labeling of peptide-tagged cell surface proteins. We sought to expand the utility of biotin ligase-mediated ...

  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. Predicting Protein Secondary and Supersecondary Structure

    E-Print Network [OSTI]

    Singh, Mona

    N C H H C O i-1 i+1 i Peptide bond FIGURE 29.1: Proteins are polymers of amino acids. Each amino the amino group, carboxyl group, and side chain are attached is called the alpha carbon (C). Two amino acids i - 1 and i are linked linearly through a peptide bond between the carboxyl group of amino acid i

  11. Protein Structure Modeling With MODELLER Narayanan Eswar$

    E-Print Network [OSTI]

    Sali, Andrej

    of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar se- quence and the template(s); (iii) building a model based on the alignment with the cho- sen user intervention and within minutes on a desktop computer. Apart from model building, MODELLER can

  12. Energy use by biological protein transport pathways

    E-Print Network [OSTI]

    Economou, Tassos

    Energy use by biological protein transport pathways Nathan N. Alder1 and Steven M. Theg2 1 of metabolic energy, using the free energy of ATP and GTP hydrolysis and/or a transmembrane protonmotive force provided insights into the mechanisms of energy transduction, force generation and energy use by different

  13. Assembly mechanism of recombinant spider silk proteins

    E-Print Network [OSTI]

    engineered and recombinantly produced spider dragline silk proteins eADF3 (engineered Araneus diadematus and identification of the essential parameters of dragline silk assembly. Changes in ionic conditions and pH result of these results, we propose a model for dragline silk aggregation and early steps of fiber assembly

  14. Chemistry & Biology Red Fluorescent Protein with Reversibly

    E-Print Network [OSTI]

    Verkhusha, Vladislav V.

    to the photoswitchable absor- bance, rsTagRFP can be used as an acceptor for a photochromic Fo¨ rster resonance energy-OFF photoswitching of the rsTagRFP acceptor. INTRODUCTION Green fluorescent protein (GFP) from Aequorea victoriaTFP0.7 (Henderson et al., 2007), green Dronpa (Ando et al., 2004) and its derivatives (Ando et al

  15. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13

    The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.

  16. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

    Alex Hansen; Mogens H. Jensen; Kim Sneppen; Giovanni Zocchi

    1998-01-13

    We argue that the first order folding transitions of proteins observed at physiological chemical conditions end in a critical point for a given temperature and chemical potential of the surrounding water. We investigate this critical point using a hierarchical Hamiltonian and determine its universality class. This class differs qualitatively from those of other known models.

  17. Metal-directed protein self-assembly

    E-Print Network [OSTI]

    Salgado. Eric N.

    2010-01-01

    of a Metal-Templated Protein Tetramer Introduction ThoroughRIDC-2 4 Zn-mediated RIDC-2 tetramer viii Zn 4 : C82 RIDC-1mediated C82 RIDC-1 2,BMB tetramer Zn 4 : C82 RIDC-1 2,BMH

  18. January, 2003 1 The Protein Space

    E-Print Network [OSTI]

    Linial, Michal

    roadmap in ProtoClass Biological examples THE PURPOSE: New superfamilies for SG ProTarget - ranked list of hypothetical proteins. 7-15% (*), 15-20% (**). #12;January, 2003 17 ProtoClass Road-Maps A horizontal view provides `distances' between clusters. Those are the basis for creating Road-Maps. We test the biological

  19. Frequent Subsequence-Based Protein Localization

    E-Print Network [OSTI]

    Zaiane, Osmar R.

    using frequent subsequences of amino acids: one based on support vector machines (SVM), one based and the experimental results show that our methods perform better than the existing approaches based on amino acid cell. All proteins are composed of linear sequences of smaller molecules called amino acids

  20. Flavors of Protein Disorder Slobodan Vucetic,1

    E-Print Network [OSTI]

    Vucetic, Slobodan

    variously characterized proteins with long (>30 amino acids) disordered regions, 3 flavors, called V, C, and S flavors were distinguishable by amino acid compositions, sequence locations, and biological function do not fold because of an atypical amino acid composition was suggested more than 20 years ago.8

  1. Using qualitative uncertainty in protein topology prediction

    E-Print Network [OSTI]

    Parsons, Simon

    contain at least 10 amino acids. Because these constraints are derived from aggregate properties of a col, which consists of a list of the amino acids that make up the protein, through the secondary structure, which is a description of the way that the amino acids are grouped together into substructures

  2. Therapeutic Protein and Glycoprotein Production, Optimization, and Analysis Methods

    E-Print Network [OSTI]

    Toumi, Melinda L.

    2010-05-31

    studied in this dissertation, so more detail is included about these proteins. Human growth hormone (hGH) is an endogenous 22 kDa protein that is critical to proper growth and metabolism.16 The hGH protein is nonglycosylated in the most abundant form... studied in this dissertation, so more detail is included about these proteins. Human growth hormone (hGH) is an endogenous 22 kDa protein that is critical to proper growth and metabolism.16 The hGH protein is nonglycosylated in the most abundant form...

  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. 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 academia and industry, progress in plant research and new crop development could accelerate and benefit the public.

  5. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Refinement of protein termini in

    E-Print Network [OSTI]

    Lee, Jooyoung

    Science, Soongsil University, Seoul 156-743, Republic of Korea INTRODUCTION The proportion of proteins that template-based modeling can generate reasonably accurate models is rapidly increasing due to the continuous

  6. Protein-Protein Interactions of the Human Iron Sulfur Cluster Biosynthesis Complex 

    E-Print Network [OSTI]

    Levy, Michaella J

    2014-06-05

    footprinting experiments where the SD, SDU, and SDUF complexes were exposed to different does of synchrotron radiation (generating hydroxyl radicals) and the resulting modified proteins were proteolytically digested and analyzed by MALDI mass spectrometry...

  7. Analysis of secreted proteins of Magnaporthe grisea and the search for protein effectors 

    E-Print Network [OSTI]

    Shang, Yue

    2007-09-17

    Magnaporthe grisea is a notorious pathogenic fungus that causes rice blast disease worldwide. Proteins secreted by the fungus are likely candidates for being effectors that are potentially recognized by determinants of ...

  8. A structural and energetic description of protein-protein interactions in atomic detail 

    E-Print Network [OSTI]

    Fischer, Tiffany Brink

    2007-04-25

    interactions, we focus on QContacts� identification of atomic contacts in a protein interface compared against the current methods. Initially, we investigated in detail the differences between QContacts, radial cutoff and Change in Solvent Accessible...

  9. Design and synthesis of probes for detection of protein-protein interaction and RNA localization

    E-Print Network [OSTI]

    Ryan, Jeremy Adam

    2005-01-01

    The use of the ketone biotin - benzophenone-biotin hydrazide system for detecting the formation of cyan fluorescent protein and NF-kappaB p50 dimers was assessed. A series of benzophenone-based probes were synthesized and ...

  10. GRAMM-X public web server for protein-protein docking

    E-Print Network [OSTI]

    Tovchigrechko, Andrey; Vakser, Ilya A.

    2006-07-01

    Protein docking software GRAMM-X and its web interface (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx) extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge...

  11. 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. Several proteins have identical Zn(II) affinities to GGG. That is, little, if any, of their Zn(II) binding energy is required to fold the protein, whereas some have affinities weakened by up to 5.7 kcal/mol; i.e., the Zn(II) binding energy is being used to fold the protein.

  12. The Principle of Stationary Action in Biophysics: Stability in Protein Folding

    E-Print Network [OSTI]

    Simmons, Walter

    2013-01-01

    Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action principle can be applied directly to study the stability of biological processes. The action principle in classical physics starts with the first variation of the action and leads immediately to the equations of motion. The second variation of the action leads in a natural way to powerful theorems that provide quantitative treatment of stability and focusing and also explain how some very complex processes can behave as though some seemingly important forces drop out. We first apply these ideas to the non-equilibrium states involved in two-state folding. We treat torsional waves and use the action principle to talk about critical points in the dynamics. For some proteins the theory resembles TST. We reach several quantitative and qualitative conclusions. Besides giving an e...

  13. Toward a Theory on the Stability of Protein Folding: Challenges for Folding Models

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-12-28

    We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the progress from the random coil to the native state. In this paper we explore the stability of folding using established methods from physics and mathematics. Our result is a preliminary theory of the physics of folding. We suggest some tests of these ideas using folding simulations. We begin by supposing that folding events are related in some way to mechanical waves on the molecule. We adopt an analytical approach to the physics which was pioneered by M.V. Berry, (in another context), based upon mathematics developed mainly by R. Thom and V.I. Arnold. We find that the stability of the folding process can be understood in terms of structures known as caustics, which occur in many kinds of wave phenomena. The picture that emerges is that natural selection has given us a set of protein molecules which have mechanical waves that propagate according to several mathematically specific restrictions. Successful simulations of folding can be used to test and constrain these wave motions. With some additional assumptions the theory explains or is consistent with a number of experimental facts about folding. We emphasize that this wave-based approach is fundamentally different from energy-based approaches.

  14. Chasing Funnels on Protein-Protein Energy Landscapes at Different Resolutions

    E-Print Network [OSTI]

    Ruvinsky, Anatoly M.; Vakser, Ilya A.

    2008-09-01

    landscape determines structure, kinetics, and thermodynamics of macromolecule complexes. The major characteristics of the landscapes—the folding/binding funnel, the ruggedness of the terrain, etc.—are important for inter- preting protein folding... University, which led to a better understanding of the landscape changes. The study was supported by National Institutes of Health grant R01 GM074255. REFERENCES 1. Onuchic, J. N., and P. G. Wolynes. 2004. Theory of protein folding. Curr. Opin. Struct. Biol...

  15. Cytosolic Sensing of Bacterial Flagellin: A Tale of Two Proteins

    E-Print Network [OSTI]

    Lightfield, Karla

    2010-01-01

    McDonald C, Nunez G (2005) NOD-LRR proteins: role in host-Inohara N, Nunez G (2001) The NOD: a signaling module that14. Inohara N, Nunez G (2003) NODs: intracellular proteins

  16. HARMONY: a server for the assessment of protein structures

    E-Print Network [OSTI]

    Srinivasan, N.

    HARMONY: a server for the assessment of protein structures G. Pugalenthi, K. Shameer, N. Srinivasan structure validation is an important step in computationalmodelingandstructuredetermination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (f

  17. Studies on the nucleocapsid protein of infectious bronchitis virus 

    E-Print Network [OSTI]

    Jayaram, Jyothi

    2005-08-29

    Because phosphorylation of the infectious bronchitis virus (IBV) nucleocapsid (N) protein may regulate its multiple roles in viral replication, the dynamics of N phosphorylation were examined. In the infected cell, N was the only viral protein...

  18. Energetics of [alpha]-helix formation in peptides and proteins

    E-Print Network [OSTI]

    Schubert, Christian Reinhold

    2009-01-01

    This thesis focuses on the energetics of !-helix formation in peptides and proteins. The [alpha]-helix is the most prevalent type of secondary structure found in proteins, and has arguably dominated our thinking about ...

  19. Biophysical and structural characterisation of protein-peptide interactions 

    E-Print Network [OSTI]

    Brown, Peter N.

    2010-01-01

    Proliferating cell nuclear antigen (PCNA) is an essential protein in the cell. It is involved in transcription and many types of DNA repair and replication. Homologues of this protein are found in all orders of life. The ...

  20. Protein Helical Topology Prediction Using Mixed-Integer Linear Programming

    E-Print Network [OSTI]

    Singh, Jaswinder Pal

    Allister Department of Chemical Engineering Princeton University The protein folding problem represents one enhances the ASTRO-FOLD protein folding approach of Klepeis and Floudas (2003), which finds the structure