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)

    The Rho factor is a ring-shaped motor protein made up of six subunits (or, in analogy to combustion engines, six "cylinders"). Such motor proteins (also known as hexameric...

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection TechnicalResonantNovember 15Rotary Firing in Ring-Shaped Protein

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection TechnicalResonantNovember 15Rotary Firing in Ring-Shaped

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection TechnicalResonantNovember 15Rotary Firing in Ring-ShapedRotary Firing

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection TechnicalResonantNovember 15Rotary Firing in Ring-ShapedRotary

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection TechnicalResonantNovember 15Rotary Firing in Ring-ShapedRotaryRotary

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Scienceand Requirements RecentlyElectronicResources ResourcesRobust,Roman SeawaterEnergy

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Scienceand Requirements RecentlyElectronicResources ResourcesRobust,Roman SeawaterEnergyRotary

  9. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection TechnicalResonantNovember 15Rotary Firing in

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection TechnicalResonantNovember 15Rotary Firing inRotary Firing in

  11. 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...

  12. Ring-shaped polariton lasing in pillar microcavities

    SciTech Connect (OSTI)

    Kalevich, V. K., E-mail: kalevich@solid.ioffe.ru; Afanasiev, M. M.; Lukoshkin, V. A.; Kavokin, K. V. [Spin Optics Laboratory, State University of Saint-Petersburg, 1, Ulianovskaya, 198504 St-Petersburg (Russian Federation); A.F. Ioffe Physico-Technical Institute, Russian Academy of Sciences, 26, Politechnicheskaya, 194021 St-Petersburg (Russian Federation); Tsintzos, S. I. [IESL-FORTH, P.O. Box 1527, 71110 Heraklion, Crete (Greece); Savvidis, P. G. [IESL-FORTH, P.O. Box 1527, 71110 Heraklion, Crete (Greece); Department of Materials Science and Technology, University of Crete, 71003 Heraklion, Crete (Greece); Kavokin, A. V. [Spin Optics Laboratory, State University of Saint-Petersburg, 1, Ulianovskaya, 198504 St-Petersburg (Russian Federation); Physics and Astronomy School, University of Southampton, Highfield, Southampton SO171BJ (United Kingdom)

    2014-03-07T23:59:59.000Z

    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.

  13. 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. [Physics Department, Technion, Haifa 32000 (Israel)] [Physics Department, Technion, Haifa 32000 (Israel)

    2013-05-15T23:59:59.000Z

    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.

  14. Observation of radio frequency ring-shaped hollow cathode discharge plasma with MgO and Al electrodes for plasma processing

    SciTech Connect (OSTI)

    Ohtsu, Yasunori, E-mail: ohtsuy@cc.saga-u.ac.jp; Matsumoto, Naoki [Department of Electrical and Electronic Engineering, Graduate School of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502 (Japan)

    2014-05-15T23:59:59.000Z

    Various high-density plasma sources have been proposed for plasma processing. Especially, the hollow cathode discharge is one of the powerful ones. In this work, radio-frequency (RF) driven ring-shaped hollow cathode discharges with high secondary-electron emission have been investigated, using an aluminum (Al) cathode, coated or not with magnesium oxide (MgO). The thickness of MgO thin film is approximately 200?nm. The RF discharge voltage for the coated cathode is almost the same as that for the uncoated one, in a wide range of Ar gas pressure, from 5.3 to 53.2?Pa. The results reveal that the plasma density has a peak at an Ar gas pressure of 10.6?Pa for both cathodes. The plasma density for the coated cathode is about 1.5–3 times higher than that for the uncoated one, at various gas pressures. To the contrary, the electron temperature for the coated cathode is lower than temperature obtained with the uncoated cathode, at various gas pressures. Radial profiles of electron saturation current, which is proportional to plasma flux, are also examined for a wide range of gas pressure. Radial profiles of electron temperature at various axial positions are almost uniform for both cathodes so that the diffusion process due to density gradient is dominant for plasma transport. The secondary electrons emitted from the coated cathode contribute to the improvement of the plasma flux radial profile obtained using the uncoated cathode.

  15. Wedding ring shaped excitation coil

    DOE Patents [OSTI]

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

    2001-01-01T23:59:59.000Z

    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.

  16. Proteins

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

    and Design Andrew Bradbury Protein Engineering Geoff Waldo Structural Biology Tom Terwilliger LANL Facilities and Resources * Protein Crystallography Station: Scientists at this...

  17. Proteins

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

    Get Expertise Cliff Unkefer Director, Protein Crystallography Station Email Tom Terwilliger Laboratory Fellow Email Andrew Bradbury Bioscience Group Leader Email Rebecca...

  18. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtectingSciTech Connect ProteinShop:

  19. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract ManagementDiscovering HowAnaDynamic Switching of theDynein Motor

  20. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract ManagementDiscovering HowAnaDynamic Switching of theDynein

  1. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA :Work with Jefferson Lab |NuclearDynamicreversedDynein

  2. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA :Work with Jefferson Lab

  3. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA :Work with Jefferson LabDynein Motor Domain Shows

  4. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA :Work with Jefferson LabDynein Motor Domain ShowsDynein

  5. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA :Work with Jefferson LabDynein Motor Domain

  6. Explaining species distribution patterns through hierarchical modeling

    E-Print Network [OSTI]

    Gelfand, Alan E.; Silander, John A., Jr.; Wu, Shanshan; Latimer, Andrew; Lewis, Paul O.; Rebelo, Anthony G.; Holder, Mark T.

    2006-01-01T23:59:59.000Z

    Bayesian Analysis (2006) 1, Number 1, pp. 41–92 Explaining Species Distribution Patterns through Hierarchical Modeling Alan E. Gelfand?, John A. Silander Jr†., Shanshan Wu‡, Andrew Latimer§, Paul O. Lewis¶, Anthony G. Rebelo? and Mark Holder..., spatial logistic re- gression, species range, species richness. 1 Introduction Ecologists increasingly use species distribution models to address theoretical and practi- cal issues including predicting the response of species to climate change (Midgley et...

  7. Type-IV Pilus Deformation Can Explain Retraction Behavior

    E-Print Network [OSTI]

    Ranajay Ghosh; Aloke Kumar; Ashkan Vaziri

    2014-09-18T23:59:59.000Z

    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

  8. Dissipative dark matter explains rotation curves

    E-Print Network [OSTI]

    Foot, R

    2015-01-01T23:59:59.000Z

    Dissipative dark matter, where dark matter particles interact with a massless (or very light) boson, is studied. Such dark matter can arise in simple hidden sector gauge models, including those featuring an unbroken $U(1)'$ gauge symmetry, leading to a dark photon. Previous work has shown that such models can not only explain the LSS and CMB, but potentially also dark matter phenomena on small scales, such as the inferred cored structure of dark matter halos. In this picture, dark matter halos of disk galaxies not only cool via dissipative interactions but are also heated via ordinary supernovae (facilitated by an assumed photon - dark photon kinetic mixing interaction). This interaction between the dark matter halo and ordinary baryons, a very special feature of these types of models, plays a critical role in governing the physical properties of the dark matter halo. Here, we further study the implications of this type of dissipative dark matter for disk galaxies. Building on earlier work, we develop a simpl...

  9. Towards Explaining the Speed of k-Means Bodo Manthey

    E-Print Network [OSTI]

    Al Hanbali, Ahmad

    Towards Explaining the Speed of k-Means Bodo Manthey University of Twente, Department of Applied Mathematics P. O. Box 217, 7500 AE Enschede, The Netherlands b.manthey@utwente.nl The k-means method exponential worst-case running-time. To explain the speed of the k-means method, a smoothed analysis has been

  10. The nanofluidics can explain ascent of water in tallest trees

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    The nanofluidics can explain ascent of water in tallest trees Henri Gouin Abstract. In Amazing, inhomogeneous liquid nanolayers wet the xylem walls of microtubes. The nanofluidic model of crude sap in tall

  11. Chelyabinsk meteorite explains unusual spectral properties of Baptistina Asteroid Family

    E-Print Network [OSTI]

    Bottke, William F.

    Chelyabinsk meteorite explains unusual spectral properties of Baptistina Asteroid Family Vishnu and compositional properties of Chelyabinsk meteorite to identify its pos- sible parent body in the main asteroid analysis confirms that the two lithologies of the Chelyabinsk mete- orite are extremely similar in modal

  12. 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

  13. 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

  14. Measuring and Explaining Electricity Price Changes in Restructured States

    SciTech Connect (OSTI)

    Fagan, Mark L.

    2006-06-15T23:59:59.000Z

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

  15. Dynamical Models Explaining Social Balance and Evolution of Cooperation

    E-Print Network [OSTI]

    De Leenheer, Patrick

    factions. Examples of such a split abound: revolutionaries versus an old regime, Republicans versus such factions emerge. An earlier model could explain the formation of such factions if reputations were assumed to split into two factions. In addition, the alternative model may lead to cooperation when faced

  16. 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

    2005-09-21T23:59:59.000Z

    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.

  17. A Pionic Hadron Explains the Muon Magnetic Moment Anomaly

    E-Print Network [OSTI]

    Rainer W. Schiel; John P. Ralston

    2007-10-01T23:59:59.000Z

    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.

  18. "OPERA superluminal neutrinos explained by spontaneous emission and stimulated absorption"

    E-Print Network [OSTI]

    Rafael Torrealba

    2011-12-05T23:59:59.000Z

    In this work it is shown, that for short 3ns neutrino pulses reported by OPERA, a relativistic shape deforming effect of the neutrino distribution function due to spontaneous emission, produces an earlier arrival of 65.8ns in agreement with the reported 62.1ns\\pm 3.7ns, with a RMS of 16.4ns explaining the apparent superluminal effect. It is also shown, that early arrival of long 10500ns neutrinos pulse to Gran Sasso, by 57.8ns with respect to the speed of light, could be explained by a shape deforming effect due to a combination of stimulated absorption and spontaneous emission, while traveling by the decay tunnel that acts as a LASER tube.

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

    E-Print Network [OSTI]

    Subenoy Chakraborty; Supriya Pan; Subhajit Saha

    2014-10-30T23:59:59.000Z

    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.

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

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

    Marques Tavares, Gustavo; Schmaltz, Martin

    2011-09-01T23:59:59.000Z

    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 small 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.

  1. Circuit architecture explains functional similarity of bacterial heat shock responses

    E-Print Network [OSTI]

    Inoue, Masayo; Trusina, Ala

    2012-01-01T23:59:59.000Z

    Heat shock response is a stress response to temperature changes and a consecutive increase in amounts of unfolded proteins. To restore homeostasis, cells upregulate chaperones facilitating protein folding by means of transcription factors (TF). We here investigate two heat shock systems: one characteristic to gram negative bacteria, mediated by transcriptional activator sigma32 in E. coli, and another characteristic to gram positive bacteria, mediated by transcriptional repressor HrcA in L. lactis. We construct simple mathematical model of the two systems focusing on the negative feedbacks, where free chaperons suppress sigma32 activation in the former, while they activate HrcA repression in the latter. We demonstrate that both systems, in spite of the difference at the TF regulation level, are capable of showing very similar heat shock dynamics. We find that differences in regulation impose distinct constrains on chaperone-TF binding affinities: the binding constant of free sigma32 to chaperon DnaK, known to...

  2. Heterogeneity of cells may explain allometric scaling of metabolic rate

    E-Print Network [OSTI]

    Takemoto, Kazuhiro

    2015-01-01T23:59:59.000Z

    The origin of allometric scaling of metabolic rate is a long-standing question in biology. Several models has been proposed for explaining the origin; however, they have advantages and disadvantages. In particular, previous models only demonstrate either two important observations for the allometric scaling: the variability of scaling exponents and predominance of 3/4-power law. Thus, these models have a dispute over their validity. In this study, we propose a simple geometry model, and show that a hypothesis that total surface area of cells determines metabolic rate can reproduce these two observations by combining two concepts: the impact of cell sizes on metabolic rate and fractal-like (hierarchical) organization. The proposed model both theoretically and numerically demonstrates the approximately 3/4-power law although several different biological strategies are considered. The model validity is confirmed using empirical data. Furthermore, the model suggests the importance of heterogeneity of cell size fo...

  3. Mesoscale symmetries explain dynamical equivalence of food webs

    E-Print Network [OSTI]

    Aufderheide, Helge; Gross, Thilo

    2012-01-01T23:59:59.000Z

    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.

  4. Explaining the Proton Radius Puzzle with Disformal Scalars

    E-Print Network [OSTI]

    Philippe Brax; Clare Burrage

    2014-07-15T23:59:59.000Z

    We analyse the consequences of a disformal interaction between a massless scalar and matter particles in the context of atomic physics. We focus on the displacement of the atomic energy levels that it induces, and in particular the change in the Lamb shift between the 2s and 2p states. We find that the correction to the Lamb shift depends on the mass of the fermion orbiting around the nucleus, implying a larger effect for muonic atoms. Taking the cut-off scale describing the effective scalar field theory close to the QCD scale, we find that the disformal interaction can account for the observed difference in the proton radius of muonic versus electronic Hydrogen. Explaining the proton radius puzzle is only possible when the scalar field is embedded in non-linear theories which alleviate constraints from collider and stellar physics. Short distance properties of the Galileon where non-perturbative effects in vacuum are present ensure that unitarity is preserved in high energy particle collisions. In matter, the chameleon mechanism alleviates the constraints on disformal interactions coming from the burning rates for stellar objects. We show how to combine these two properties in a single model which renders the proposed explanation of the proton radius puzzle viable.

  5. 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)

    2014-04-10T23:59:59.000Z

    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.

  6. 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 ...

  7. Protein Sequence, Structure, Stability and Functionality

    E-Print Network [OSTI]

    J. C. Phillips

    2008-02-25T23:59:59.000Z

    Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino acids, and protein scientists have long described protein-water interactions in terms of qualitative amino acid hydrophobicity scales. Here we examine several recent scales and argue plausibly (in terms of self-organized criticality) that one of them should be regarded as an absolute scale (within the protein universe), analogous to the dielectric scale of bond ionicity in inorganic octet compounds. Applications to repeat proteins (containing upwards of 900 amino acids) are successful, far beyond reasonable expectations, in all cases studied so far. While some of the results are obvious and can be obtained from the ex vitro spatial structures alone, many are hidden from plain view, and can be called phantom relations. As a byproduct, the network theory explains the exceptional functionality of leucine in zippers, heptads, and repeat consensus sites.

  8. Supplementary Protocol Here we provide details on the implementation of five analyses in Thunder, explaining

    E-Print Network [OSTI]

    Cai, Long

    , explaining for each the goal of the analysis, how it can be run from the Python shell (e.g. in iPython

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

    ScienceCinema (OSTI)

    Pleier,Marc-Andre

    2014-06-04T23:59:59.000Z

    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

    SciTech Connect (OSTI)

    Pleier,Marc-Andre

    2013-10-07T23:59:59.000Z

    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. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2012 BINF 731 Protein Engineering Protein Engineering Increase catalytic activity Change substrate binding site to increase specificity Change the thermal Engineering Protein Engineering #12;Protein Engineering Protein Engineering Protein Engineering Protein

  12. 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 the relationship between energy security and greenhouse gas emissions Larry Hughes and Nikita Sheth Abstract for explaining this relationship, based upon jurisdiction-specific data on energy supply, infrastructure

  13. Dynamics of cerebral blood flow regulation explained using a lumped parameter model

    E-Print Network [OSTI]

    Olufsen, Mette Sofie

    Dynamics of cerebral blood flow regulation explained using a lumped parameter model METTE S, and Harvard Medical School, Boston, Massachusetts 02131 Received 22 May 2001; accepted in final form 10 regulation explained using a lumped parameter model. Am J Physiol Regulatory Integra- tive Comp Physiol 282

  14. 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

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

    E-Print Network [OSTI]

    Brown, Cody McClain

    2013-08-31T23:59:59.000Z

    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...

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

    E-Print Network [OSTI]

    Montero, Juan-Pablo

    1998-01-01T23:59:59.000Z

    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 ...

  17. The role of involvement and commitment in explaining intention to engage in birding trips

    E-Print Network [OSTI]

    Kim, Seong-Seop

    1996-01-01T23:59:59.000Z

    -psychological involvement measures, and measures of commitment; (c) to ascertain how well Laurent and Kapferer's (1985) scale, Zaichkowsky's (1985) scale, a set of behavioral measures, and commitment nimures explain intention to go on birding trips; (4) to conceptualize...

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

    E-Print Network [OSTI]

    Goldman, Jasper, 1978-

    2003-01-01T23:59:59.000Z

    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 ...

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

    E-Print Network [OSTI]

    Daly, Sarah Zukerman

    2011-01-01T23:59:59.000Z

    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)? ...

  20. Constraints on adaptation: explaining deviation from optimal sex ratio using artificial neural networks

    E-Print Network [OSTI]

    West, Stuart

    Y Keywords: adaptation; artificial neural networks; evolutionary constraints; parasitoid; sex ratio by modelling information acquisition and processing using artificial neural networks (ANNs) evolving accordingConstraints on adaptation: explaining deviation from optimal sex ratio using artificial neural

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

    E-Print Network [OSTI]

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

    2005-01-01T23:59:59.000Z

    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, ...

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

    E-Print Network [OSTI]

    Welt, Cory

    2004-01-01T23:59:59.000Z

    (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 ...

  3. o Take courses for personal enrichment ONLY. o Other, please explain

    E-Print Network [OSTI]

    Rose, Michael R.

    o Take courses for personal enrichment ONLY. o Other, please explain: ACADEMIC PLANNING FORM courses related to my major for my personal enrichment. List below the TITLES of courses in which you wish

  4. To begin, could you explain the context from which this study emerged?

    E-Print Network [OSTI]

    Oliver, Douglas L.

    stay lean when kept on a high calorie diet. Similarly, Indy mice that lack the mouse homolog of Indy'm not dead yet) gene, encodes a Drosophila protein that is highly similar to a mammalian sodium cotransporter membrane protein that transports Krebs cycle intermediates across the cells of tissues involved

  5. Distinct quaternary structures of the AAA+ Lon protease control substrate degradation

    E-Print Network [OSTI]

    Vieux (Kloss), Ellen

    Lon is an ATPase associated with cellular activities (AAA+) protease that controls cell division in response to stress and also degrades misfolded and damaged proteins. Subunits of Lon are known to assemble into ring-shaped ...

  6. Shotgun protein sequencing.

    SciTech Connect (OSTI)

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

    2009-06-01T23:59:59.000Z

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

  7. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

    Informatics Structural Bioinformatics Computational Structural Biology Protein Engineering Protein Design Drug/ Proteins Alberts B, et al. Molecular Biology of the Cell. Proteins TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN Protein Science Biochemistry Biophysics Molecular Biology Crystallography NMR Spectroscopy Protein

  8. Protein-protein complexation in bioluminescence

    E-Print Network [OSTI]

    Zhijie, Liu

    systems of marine organisms, including bacteria, jellyfish and soft corals, with particular focus on methodology used to detect and characterize these interactions. In some bioluminescence systems, protein efficiency. In addition to luciferases many bioluminescence systems contain supplemental proteins which can

  9. Engineering and Characterization of a Superfolder Green Fluorescent Protein

    SciTech Connect (OSTI)

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

    2006-01-01T23:59:59.000Z

    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.

  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. 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 ...

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

    E-Print Network [OSTI]

    Better 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 portfolio of technology options that can provide abundant energy to power economic development and still

  13. ULO Course Learning Outcome Assessment Method Pedagogy 08-Explain how an external change to a

    E-Print Network [OSTI]

    Barrash, Warren

    as the addition of a solute to a material, or a phase change) affects the structure, proper- ties, processing and to a material (such as a change in tempera- ture, or an applied stress), and/or an internal change (suchENGR245 ULO Course Learning Outcome Assessment Method Pedagogy 08- Explain how an external change

  14. Can Habitat Alteration and Spring Angling Explain Largemouth Bass Nest Success?

    E-Print Network [OSTI]

    Micropterus spp. As keystone predators and valued sport fish in North American lakes, black basses MicropterusCan Habitat Alteration and Spring Angling Explain Largemouth Bass Nest Success? TYLER WAGNER, 13 Natural Resources Building, East Lansing, Michigan 48824, USA Abstract.--Largemouth bass

  15. Mechanisms of classical crystal growth theory explain quartz and silicate dissolution behavior

    E-Print Network [OSTI]

    Dove, Patricia M.

    Mechanisms of classical crystal growth theory explain quartz and silicate dissolution behavior processes was previously unknown for oxides or silicates, our mechanism-based findings are consistent, the geochemistry of earth systems is, in large part, controlled by the kinetics of silicate mineral dissolution

  16. Researcher Profile This cheatsheet will briefly explain how to utilise your Researcher Profile in IRMA.

    E-Print Network [OSTI]

    Researcher Profile This cheatsheet will briefly explain how to utilise your Researcher Profile Username (MAIS ID (Staff, Student or MAIS other number)) and MAIS Password. Researcher Profile 1) After straightaway, click on Home in the top right corner, then click on Researcher Profile. #12;Printed: 17 December

  17. 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

  18. 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

  19. The Mystery of Dos Bocas Reservoir, Puerto Rico: Explaining Extreme Spatial Heterogeneity in Largemouth Bass Distribution

    E-Print Network [OSTI]

    Cope, W. Gregory

    The Mystery of Dos Bocas Reservoir, Puerto Rico: Explaining Extreme Spatial Heterogeneity.--Dos Bocas Reservoir, Puerto Rico, has pronounced in-lake variability in fish distributions, especially composition between the two basins of Dos Bocas Reservoir, Puerto Rico; characterized by the absence of top

  20. 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

  1. Can R-parity violation explain the LSND data as well?

    E-Print Network [OSTI]

    Asmaa Abada; Gautam Bhattacharyya

    2000-09-15T23:59:59.000Z

    The recent Super-Kamiokande data now admit only one type of mass hierarchy in a framework with three active and one sterile neutrinos. We show that neutrino masses and mixings generated by R-parity-violating couplings, with values within their experimental upper limits, are capable of reproducing this hierarchy, explaining all neutrino data particularly after including the LSND results.

  2. Explaining the road accident risk: weather effects Ruth Bergel-Hayat1*

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1 Explaining the road accident risk: weather effects Ruth Bergel-Hayat1* , Mohammed Debbarh1 conditions and road accident risk at an aggregate level and on a monthly basis, in order to improve road accidents. Time series analysis models with explanatory variables that measure the weather quantitatively

  3. Protein Dynamics and Biocatalysis

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

    Protein Dynamics and Biocatalysis Protein Dynamics and Biocatalysis 1998 Annual Report Grand Challenge Projects biocatalysis.gif A model of the Michaelis complex for the TEM-1...

  4. Culex quinquefasciatus Storage Proteins

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

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

  5. Engineering novel fluorescent proteins

    E-Print Network [OSTI]

    Shaner, Nathan Christopher

    2006-01-01T23:59:59.000Z

    pellet by QIAprep spin column (Qiagen) and submitted for sequencing. Protein Productionpellets by QIAprep spin column (Qiagen) and submitted for sequencing. Protein production

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

    ScienceCinema (OSTI)

    Grossenbacher, John

    2013-05-28T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Grossenbacher, John

    2011-01-01T23:59:59.000Z

    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.

  8. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2012 BINF 731 Protein Engineering Protein Engineering Increase catalytic activity Change substrate binding site to increase specificity Change the thermal stability Increase proteins resistance to proteases Change codon composition Protein Engineering

  9. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

    Crystallography NMR Spectroscopy Protein Informatics Structural Bioinformatics Computational Structural Biology/ Proteins Alberts B, et al. Molecular Biology of the Cell. Proteins TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN Hartl F.U. et al., Nature, 2011 Proteins Protein Science Biochemistry Biophysics Molecular Biology

  10. 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)

    2010-07-20T23:59:59.000Z

    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.

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

    DOE Patents [OSTI]

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

    2010-02-23T23:59:59.000Z

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

  12. Fundamental constraints on the abundances of chemotaxis proteins

    E-Print Network [OSTI]

    Bitbol, Anne-Florence

    2015-01-01T23:59:59.000Z

    Flagellated bacteria, such as Escherichia coli, perform directed motion in gradients of concentration of attractants and repellents in a process called chemotaxis. The E. coli chemotaxis signaling pathway is a model for signal transduction, but it has unique features. We demonstrate that the need for fast signaling necessitates high abundances of the proteins involved in this pathway. We show that further constraints on the abundances of chemotaxis proteins arise from the requirements of self-assembly, both of flagellar motors and of chemoreceptor arrays. All these constraints are specific to chemotaxis, and published data confirm that chemotaxis proteins tend to be more highly expressed than their homologs in other pathways. Employing a chemotaxis pathway model, we show that the gain of the pathway at the level of the response regulator CheY increases with overall chemotaxis protein abundances. This may explain why, at least in one E. coli strain, the abundance of all chemotaxis proteins is higher in media w...

  13. 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.

    2015-03-12T23:59:59.000Z

    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

  14. Statistical mechanics problem sheet 3 1. Does an ideal gas satisfy the third law of thermodynamics? Explain.

    E-Print Network [OSTI]

    Dettmann, Carl

    ? Explain. 2. Give a rough estimate of the amount of molten salt required to store 10MWh of heat energy from

  15. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2009 BINF 731 Protein Engineering Protein Engineering Increase catalytic activity Change substrate binding site to increase specificity Change the thermal152S -1.08 1goj S152T 1.12 Protein Engineering Protein Engineering #12;Protein Engineering Protein

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

    Energy Savers [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 onYou are now leaving Energy.gov You are now leaving Energy.gov You are being directed off Energy.gov. Are you0 ARRA Newsletters 2010 ARRA Newsletters201416-17,Proposed8. EXPLAIN HOW YOU

  17. Citation advantage of Open Access articles likely explained by quality differential and media effects

    E-Print Network [OSTI]

    Philip M. Davis

    2007-01-16T23:59:59.000Z

    In a study of articles published in the Proceedings of the National Academy of Sciences, Gunther Eysenbach discovered a significant citation advantage for those articles made freely-available upon publication (Eysenbach 2006). While the author attempted to control for confounding factors that may have explained the citation differential, the study was unable to control for characteristics of the article that may have led some authors to pay the additional page charges ($1,000) for immediate OA status. OA articles published in PNAS were more than twice as likely to be featured on the front cover of the journal (3.3% vs. 1.4%), nearly twice as likely to be picked up by the media (15% vs. 8%) and when cited reached, on average, nearly twice as many news outlets as subscription-based articles (4.2 vs. 2.6). The citation advantage of Open Access articles in PNAS may likely be explained by a quality differential and the amplification of media effects.

  18. CAN A LONG NANOFLARE STORM EXPLAIN THE OBSERVED EMISSION MEASURE DISTRIBUTIONS IN ACTIVE REGION CORES?

    SciTech Connect (OSTI)

    Mulu-Moore, Fana M.; Winebarger, Amy R. [NASA Marshall Space Flight Center, VP 62, Huntsville, AL 35812 (United States); Warren, Harry P., E-mail: fanamariam.mulumoore@nasa.gov [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States)

    2011-11-20T23:59:59.000Z

    All theories that attempt to explain the heating of the high-temperature plasma observed in the solar corona are based on short bursts of energy. The intensities and velocities measured in the cores of quiescent active regions, however, can be steady over many hours of observation. One heating scenario that has been proposed to reconcile such observations with impulsive heating models is the 'long nanoflare storm', where short-duration heating events occur infrequently on many sub-resolution strands; the emission of the strands is then averaged together to explain the observed steady structures. In this Letter, we examine the emission measure distribution predicted for such a long nanoflare storm by modeling an arcade of strands in an active region core. Comparisons of the computed emission measure distributions with recent observations indicate that the long nanoflare storm scenario implies greater than five times more 1 MK emission than is actually observed for all plausible combinations of loop lengths, heating rates, and abundances. We conjecture that if the plasma had 'super coronal' abundances, the model may be able to match the observations at low temperatures.

  19. Destabilized bioluminescent proteins

    DOE Patents [OSTI]

    Allen, Michael S. (Knoxville, TN); Rakesh, Gupta (New Delhi, IN); Gary, Sayler S. (Blaine, TN)

    2007-07-31T23:59:59.000Z

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

  20. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    NONE

    1995-12-31T23:59:59.000Z

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

  2. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01T23:59:59.000Z

    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...

  3. EXPLAINING THE Sr AND Ba SCATTER IN EXTREMELY METAL-POOR STARS

    SciTech Connect (OSTI)

    Aoki, W.; Suda, T.; Boyd, R. N.; Kajino, T.; Famiano, M. A., E-mail: aoki.wako@nao.ac.jp, E-mail: takuma.suda@nao.ac.jp, E-mail: richard11boyde@comcast.net, E-mail: kajino@nao.ac.jp, E-mail: michael.famiano@wmich.edu [National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo 181-8588 (Japan)

    2013-03-20T23:59:59.000Z

    Compilations of abundances of strontium and barium in extremely metal-poor stars show that an apparent cutoff is observed for [Sr/Ba] at [Fe/H] < -3.6 and large fluctuations for [Fe/H] > -3.6 with a clear upper bound depending on metallicity. We study the factors that place upper limits on the logarithmic ratio [Sr/Ba]. A model is developed in which the collapses of type II supernovae are found to reproduce many of the features seen in the data. This model is consistent with galactic chemical evolution constraints of light-element enrichment in metal-poor stars. Effects of turbulence in an explosive site have also been simulated, and are found to be important in explaining the large scatter observed in the [Sr/Ba] data.

  4. The Dust Scattering Model Can Not Explain The Shallow X-ray Decay in GRB Afterglows

    E-Print Network [OSTI]

    Rong-Feng Shen; Richard Willingale; Pawan Kumar; Paul T. O'Brien; Phil A. Evans

    2009-03-02T23:59:59.000Z

    A dust scattering model was recently proposed to explain the shallow X-ray decay (plateau) observed prevalently in Gamma-Ray Burst (GRB) early afterglows. In this model the plateau is the scattered prompt X-ray emission by the dust located close (about 10 to a few hundred pc) to the GRB site. In this paper we carefully investigate the model and find that the scattered emission undergoes strong spectral softening with time, due to the model's essential ingredient that harder X-ray photons have smaller scattering angle thus arrive earlier, while softer photons suffer larger angle scattering and arrive later. The model predicts a significant change, i.e., $\\Delta \\b \\sim 2 - 3$, in the X-ray spectral index from the beginning of the plateau toward the end of the plateau, while the observed data shows close to zero softening during the plateau and the plateau-to-normal transition phase. The scattering model predicts a big difference between the harder X-ray light curve and the softer X-ray light curve, i.e., the plateau in harder X-rays ends much earlier than in softer X-rays. This feature is not seen in the data. The large scattering optical depths of the dust required by the model imply strong extinction in optical, $A_V \\gtrsim $ 10, which contradicts current findings of $A_V= 0.1 - 0.7$ from optical and X-ray afterglow observations. We conclude that the dust scattering model can not explain the X-ray plateaus.

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

    E-Print Network [OSTI]

    Fernández Suárez, Marta

    2008-01-01T23:59:59.000Z

    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 ...

  6. 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, George N.; Mead, David; Steinmetz, Eric J.; Michnick, Stephen W.

    2015-04-23T23:59:59.000Z

    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

  7. Inferring the Rate-Length Law of Protein Folding

    E-Print Network [OSTI]

    Lane, Thomas J

    2013-01-01T23:59:59.000Z

    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.

  8. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12T23:59:59.000Z

    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.

  9. Pressure cryocooling protein crystals

    DOE Patents [OSTI]

    Kim, Chae Un (Ithaca, NY); Gruner, Sol M. (Ithaca, NY)

    2011-10-04T23:59:59.000Z

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

  10. Self assembling proteins

    DOE Patents [OSTI]

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

    2004-06-29T23:59:59.000Z

    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.

  11. . DNA, RNA, Protein

    E-Print Network [OSTI]

    Yoo, SukIn

    1. , . DNA, RNA, Protein [1-4]. DNA . DNA A, T, G, C . DNA , DNA DNA . , DNA DNA . DNA DNA . , PCR , , DNA [5]. DNA DNA , DNA

  12. Approximate Mirror Symmetry in Heliospheric Plasma Flow Explains VOYAGER 2 Observations

    E-Print Network [OSTI]

    Grygorczuk, Jolanta; Grzedzielski, Stan

    2015-01-01T23:59:59.000Z

    The Sun and the undisturbed interstellar magnetic field and plasma velocity vectors (Bis,Vis) define a mirror symmetry plane of the flow at large heliospheric distances. We show that for the Bis direction defined by IBEX Ribbon center, the radial direction of Voyager 2 over the last decade, and the (thermal proton) plasma velocity measured by the spacecraft since 2010.5, are almost parallel to the (Bis,Vis)-plane, which coincides in practice with the Hydrogen Deflection Plane. These facts can be simply explained if approximate mirror symmetry is also maintained on the inner side of the heliopause. Such approximate symmetry is possible since the solar wind ram pressure is almost spherically symmetric and the plasma beta value in the inner heliosheath is high. In the proposed symmetry, the plasma flow speed measured by Voyager 2 in the inner heliosheath is expected to rotate more in the transverse than in the polar direction (explanation alternative to McComas & Schwadron (2014)), in evident agreement with ...

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

    E-Print Network [OSTI]

    Jacques Moret-Bailly

    2007-02-09T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Tchekhovskoy, Alexander

    2015-01-01T23:59:59.000Z

    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...

  15. Axion-like particles explain the unphysical redshift-dependence of AGN gamma-ray spectra

    E-Print Network [OSTI]

    Galanti, Giorgio; De Angelis, Alessandro; Bignami, Giovanni F

    2015-01-01T23:59:59.000Z

    Blazars are a class of AGN known to be powerful very-high-energy (VHE, 100 GeV - 100 TeV) celestial gamma-ray emitters. At the time of writing, 41 blazars, spread all over the sky and with known redshift in the range $0.0215 \\leq z \\leq 0.635$ have been observed in the VHE band by the Imaging Atmospheric Cherenkov Telescopes H.E.S.S., MAGIC and VERITAS. Thus, they represent an isotropic and relatively local extragalactic sample, unaffected by significant cosmological evolution. The blazar emitted spectra are well fitted by a power law with index $\\Gamma_{\\rm em}$. We show that the $\\Gamma_{\\rm em}$ distribution exhibits an unexpected and previously unnoticed unphysical redshift-dependence. We demonstrate that this result is not due to any selection effect. It is difficult to imagine an intrinsic mechanism which could lead to such a spectral variation, and so this result seriously challenges the conventional view. We propose that such a behaviour is explained by oscillations between the VHE gamma-rays and Axio...

  16. The Extended Bloch Representation of Quantum Mechanics. Explaining Superposition, Interference and Entanglement

    E-Print Network [OSTI]

    Diederik Aerts; Massimiliano Sassoli de Bianchi

    2015-04-19T23:59:59.000Z

    The extended Bloch representation of quantum mechanics was recently derived to offer a (hidden-measurement) solution to the measurement problem. In this article we use it to investigate the geometry of superposition and entangled states, explaining the interference effects, and the entanglement correlations, in terms of the different orientations that a state-vector can take within the generalized Bloch sphere. We also introduce a tensorial determination of the generators of SU(N), particularly suitable to describe multipartite systems, from the viewpoint of the sub-entities. We then use it to show that non-product states admit a general description in which the sub-entities can always remain in well-defined states, even when they are entangled. Therefore, the completed version of quantum mechanics provided by the extended Bloch representation, in which the density operators are also representative of pure states, allows to solve not only the well-known measurement problem, but also the lesser-known entanglement problem. This because we no longer need to give up the general physical principle saying that a composite entity exists, and therefore is in a pure state, if and only if its components also exist, and therefore are in well-defined pure states.

  17. Petrology of the Devonian gas-bearing shale along Lake Erie helps explain gas shows

    SciTech Connect (OSTI)

    Broadhead, R.F.; Potter, P.E.

    1980-11-01T23:59:59.000Z

    Comprehensive petrologic study of 136 thin sections of the Ohio Shale along Lake Erie, when combined with detailed stratigraphic study, helps explain the occurrence of its gas shows, most of which occur in the silty, greenish-gray, organic poor Chagrin Shale and Three Lick Bed. Both have thicker siltstone laminae and more siltstone beds than other members of the Ohio Shale and both units also contain more clayshales. The source of the gas in the Chagrin Shale and Three Lick Bed of the Ohio Shale is believed to be the bituminous-rich shales of the middle and lower parts of the underlying Huron Member of the Ohio Shale. Eleven petrographic types were recognized and extended descriptions are provided of the major ones - claystones, clayshales, mudshales, and bituminous shales plus laminated and unlaminated siltstones and very minor marlstones and sandstones. In addition three major types of lamination were identified and studied. Thirty-two shale samples were analyzed for organic carbon, whole rock hydrogen and whole rock nitrogen with a Perkin-Elmer 240 Elemental Analyzer and provided the data base for source rock evaluation of the Ohio Shale.

  18. Explaining Low Energy ?-ray Excess from the Galactic Centre using a Two Component Dark Matter Model

    E-Print Network [OSTI]

    Anirban Biswas

    2014-12-04T23:59:59.000Z

    Over the past few years, there has been a hint of the $\\gamma$-ray excess observed by the Fermi-LAT satellite borne telescope from the region surrounding the Galactic Centre at an energy range $\\sim 1$-$3$ GeV. The nature of this excess $\\gamma$-ray spectrum is found to be consistent with the $\\gamma$-ray emission expected from dark matter annihilation at the Galactic Centre while disfavouring other known astrophysical sources as the possible origin of this phenomena. It is also reported that the spectrum and morphology of this excess $\\gamma$-rays can well be explained by the dark matter particles having mass in the range $30\\sim 40$ GeV annihilating into ${\\rm b}$ $\\bar{\\rm b}$ final state with an annihilation cross section ${\\sigma {\\rm v}} \\sim 1.4 - 2.0\\times10^{-26}$ cm$^3/$s at the Galactic centre. In this work, we propose a two component dark matter model where two different types of dark matter particles namely a complex scalar and a Dirac fermion are considered. The stability of both the dark sector particles are maintained by virtue of an additional local U$(1)_{\\rm X}$ gauge symmetry. We find that our proposed scenario can provide a viable explanation besides satisfying all the existing relevant theoretical, experimental and observational bounds.

  19. "Bring it on": Explaining persistence in science at the intersection of identity and epistemology

    E-Print Network [OSTI]

    Conlin, Luke D; Gupta, Ayush; Elby, Andrew

    2015-01-01T23:59:59.000Z

    Research has documented a sharp decline in students' interest and persistence in science, starting in middle school, particularly among students from underrepresented populations. In working to address this problem, we can learn a great deal from positive examples of students getting excited about science, especially students who were previously disengaged. In this paper, we present a case study of Estevan, an 8th grade student who came into Ms. K's science class with a reputation as a potential "problem student," but left as a leader of the class, even making plans to pursue a career in science. Through analysis of interviews and classroom interactions, we show how Estevan's love of science can be partially explained by an alignment between his identity as a lover of challenges and his epistemology of science as involving the challenge of figuring things out for yourself. This alignment was possible in part because it was supported by his caring teacher, who attended to his ideas and constantly challenged hi...

  20. 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

  1. Peptidomimetics to mimic protein-protein interactions

    E-Print Network [OSTI]

    Xia, Zebin

    2005-08-29T23:59:59.000Z

    , minimization of each of several hundred conformers, and cut off. Experience with Insight II/Discover versus Quanta/CHARMm, and between Insight II/CHARMm versus Quanta/CHARMm has taught that the forcefield is the key factor in QMD studies. Protein A has been...

  2. Pervasive degeneracy and epistasis in a protein-protein interface

    E-Print Network [OSTI]

    Podgornaia, Anna Igorevna

    2014-01-01T23:59:59.000Z

    Signal transduction pathways rely on transient yet specific protein-protein interactions. How a limited set of amino acids can enforce cognate protein interactions while excluding undesired pairings remains poorly understood, ...

  3. Interfacial rheology of globular proteins

    E-Print Network [OSTI]

    Jaishankar, Aditya

    2011-01-01T23:59:59.000Z

    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 ...

  4. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

    Biology Crystallography NMR Spectroscopy Protein Informatics Structural Bioinformatics Computational Structural Biology Protein Engineering Protein Design Drug Design Molecular Modeling Proteomics Structural Weissig (Eds) Structural bioinformatics Hoboken, N.J. : Wiley-Liss, 2003. Jenny Gu, Philip Bourne (Eds

  5. Protein folding and cosmology

    E-Print Network [OSTI]

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

    1997-06-04T23:59:59.000Z

    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.

  6. 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)

    2001-07-03T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Neumaier, Arnold

    ­called protein folding problem. The static aspect is concerned with how to predict the folded (native, tertiary at solutions to the protein folding problem. Key words. protein folding, molecular mechanics, transition states. This so­called protein folding problem is one of the most challenging problems in current bio­ chemistry

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

    E-Print Network [OSTI]

    Neumaier, Arnold

    -called protein folding problem. The static aspect is concerned with how to predict the folded (native, tertiary at solutions to the protein folding problem. Key words. protein folding, molecular mechanics, transition states. This so-called protein folding problem is one of the most challenging problems in current bio- chemistry

  9. And if there was no need of dark energy to explain the acceleration of the expansion of the universe?

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    And if there was no need of dark energy to explain the acceleration of the expansion, only the hypothetical presence of dark energy is used in present theories. But, the dimensions the pressure p (calculated within the Friedmann model) and the force density is a simple derivation

  10. 1-4244-1243-9/07/$25.00 2007 IEEE Asking Internet Users to Explain Non-Use in Kyrgyzstan

    E-Print Network [OSTI]

    1-4244-1243-9/07/$25.00 ©2007 IEEE Asking Internet Users to Explain Non-Use in Kyrgyzstan Chad, and specifically Kyrgyzstan, Internet adoption seems to be tapering off well below saturation levels. Survey data picture of how to define Internet use in Kyrgyzstan, and why some people are adopting ICTs and why others

  11. "Our Fine Arts," explained the poet Paul Valry in 1928, "were instituted at a time very different

    E-Print Network [OSTI]

    Canales, Jimena

    "Our Fine Arts," explained the poet Paul Valéry in 1928, "were instituted at a time very different images or auditory ones, born and disappearing at the faintest gesture, almost by a sign." The poet, but the home-delivery service of "Sensible Reality" dreamt of by the poet has still not reached us. Valéry

  12. Being a Long-Living Software Mayor --the SimCity Metaphor to Explain the Challenges Behind Software Evolution

    E-Print Network [OSTI]

    Ducasse, Stéphane

    and that such a system can simply die. We propose to use the SimCity game as a metaphor to explain the challengesCity The goal of SimCity is to be a long-living mayor of a prosperous city. To be reelected the mayor should

  13. Hydrogen Fuel Cell Problems 1) Explain why the hydrogen fuel cell vehicle is not as efficient as the reported "tank

    E-Print Network [OSTI]

    Bowen, James D.

    Hydrogen Fuel Cell Problems 1) Explain why the hydrogen fuel cell vehicle is not as efficient of ethanol? A flex-fuel SUV has a 25 gallon tank. Its sustainably-minded owner has decided to use E85 ethanol? 1 yr/person/450pounds of corn * 461 pounds of corn = 1.02 yrs #12;Electric Vehicle Problems 1

  14. CO2 Concentration Global warming is a hot topic these days. One of the factors that may explain increases

    E-Print Network [OSTI]

    Carriquiry, Alicia

    CO2 Concentration Global warming is a hot topic these days. One of the factors that may explain increases in global temperatures is the amount of carbon dioxide (CO2) in the atmosphere. Is there a relationship between the amount of carbon dioxide in the atmosphere and global temperatures? Data Collection

  15. 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

  16. 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

  17. The unfolded-protein-response

    E-Print Network [OSTI]

    Walter, Peter

    proteins in the ER. At the restrictive temperature, see53mutants lack phosphomannomutaseThe unfolded- protein-response pathway in yeast The accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggers the increased production of several ER- resident proteins. This signalling

  18. 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

  19. 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

  20. Expression of Recombinant Proteins in Microalgae

    E-Print Network [OSTI]

    Mayfield, Stephen P.; Franklin, Scott E.

    2003-01-01T23:59:59.000Z

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

  1. Protein sequence databases Rolf Apweiler1,

    E-Print Network [OSTI]

    Information NREF non-redundant reference databases PDB Protein Data Bank PIR Protein Information Resource PIR

  2. [16) Green Fluorescent Protein Chimeras to Probe Protein-Protein Interactions

    E-Print Network [OSTI]

    Raines, Ronald T.

    [16) Green Fluorescent Protein Chimeras to Probe Protein-Protein Interactions By SANG-HYUN PARK of reproduction in any form reserved. 0076-6879/00 $30.00 #12;252 A B OTHER APPROACHES USING CHIMERAS c ~S65T GFPHDII M 66 .......... 4S,.!;. 31 ui' 14 ..... [lB) FIG. 1. Green fluorescent protein chimera. (A

  3. 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 Key words: artificial knot, chaperone, free energy landscape, knotted protein, protein folding

  4. Cellulose binding domain proteins

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

    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.

  5. Cellulose binding domain proteins

    DOE Patents [OSTI]

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

    1998-11-17T23:59:59.000Z

    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.

  6. Annotation Transfer Between Genomes: ProteinProtein Interologs and

    E-Print Network [OSTI]

    Gerstein, Mark

    , Drosophila melanogaster, and Helicobacter pylori, we find that protein­protein interactions can, and Helicobacter pylori, scientists have elucidated the functions of many of their gene products. Given

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

    E-Print Network [OSTI]

    Hosur, Raghavendra

    2012-01-01T23:59:59.000Z

    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 ...

  8. Potential of Mean Force for ProteinProtein Interaction Studies

    E-Print Network [OSTI]

    Luhua, Lai

    affinity and to discriminate between cor- rect and incorrect protein­protein interactions by running, such as rotational and translational entropy loss, hydrophobic and hydrophilic surface areas, the number of frozen

  9. 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 ...

  10. Dipolar response of hydrated proteins

    E-Print Network [OSTI]

    Dmitry V. Matyushov

    2011-08-12T23:59:59.000Z

    The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins. The effective dielectric constant of the solvated protein, representing the average dipole moment induced at the protein by a uniform external field, shows a remarkable variation among the proteins studied by numerical simulations. It changes from 0.5 for ubiquitin to 640 for cytochrome c. The former value implies a negative dipolar susceptibility of ubiquitin, that is a dia-electric dipolar response and negative dielectrophoresis. It means that a protein carrying an average dipole of ~240 D is expected to repel from the region of a stronger electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the protein dipole in the overall dipolar susceptibility. This phenomenon can be characterized as overscreening of protein's dipole by the hydration shell. In contrast to the neutral ubiquitin, charged proteins studied here show para-electric dipolar response and positive dielectrophoresis. The protein-water dipolar cross-correlations are long-ranged, extending approximately 2 nm from the protein surface into the bulk. The analysis of numerical simulations suggests that the polarization of the protein-water interface is strongly affected by the distribution of the protein surface charge. This component of the protein dipolar response gains in importance for high frequencies, above the protein Debye peak, when the response of the protein dipole becomes dynamically arrested. The interface response found in simulations suggests a possibility of a positive increment of the high-frequency dielectric constant of the solution compared to the dielectric constant of the solvent, in support of the observed THz absorbance of protein solutions.

  11. Protein Dynamics Hit the Big Screen

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

    Protein Dynamics Hit the Big Screen Protein Dynamics Hit the Big Screen Now playing at a supercomputer near you: proteins in action June 29, 2005 Contact: Dan Krotz,...

  12. Carbon Nanotube Templated Asembly of Protein. | EMSL

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

    Nanotube Templated Asembly of Protein. Carbon Nanotube Templated Asembly of Protein. Abstract: This paper describes a novel general strategy for fabricating protein-polyion...

  13. Convergent evolution of protein structure

    E-Print Network [OSTI]

    Fischer, Daniel

    , well-defined, three-dimensional (3-D) structure of a protein dictates the way in which it performs its bi- ological function. Knowing the 3-D structure of a pro- tein allows researchers to gain insight on the active site of the protein or on the way it interacts with small molecules and other proteins. Thus, 3-D

  14. 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

  15. 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

  16. 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

  17. Thermodynamics of protein folding: a random matrix formulation

    E-Print Network [OSTI]

    Pragya Shukla

    2010-10-16T23:59:59.000Z

    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.

  18. Protein subcellular localization assays using split fluorescent proteins

    DOE Patents [OSTI]

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

    2009-09-08T23:59:59.000Z

    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).

  19. IN VITRO GAS PRODUCTION OF CALIFORNIA FEEDSTUFFS Nov-03 (terminology explained at the bottom) (new samples in italics )

    E-Print Network [OSTI]

    Delany, Mary E.

    IN VITRO GAS PRODUCTION OF CALIFORNIA FEEDSTUFFS Nov-03 (terminology explained at the bottom) (new.6 226.0 114.4 11.34 Mean 109.3 199.4 90.2 215.6 106.3 11.90 Alfalfa Pellets 87.0 189.6 102.5 217.9 130.41 Cottonseed (fuzzy pellet) 37.9 54.6 16.7 85.0 47.1 8.53 Cottonseed (pima) 23.5 54.4 30.9 65.8 42.3 7.42 #12

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

    E-Print Network [OSTI]

    Allanach, Ben; Mondal, Subhadeep; Mitra, Manimala

    2014-01-01T23:59:59.000Z

    The recent CMS searches 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 an excess around $m_{eejj} \\sim 2$ TeV. In this work, we explain the reported CMS excess with R-parity violating supersymmetry (SUSY). We consider the resonant slepton and sneutrino production, followed by the three body decays of neutralino and chargino via R-parity violating coupling. These fit the excess for slepton and sneutrino masses around 2 TeV. This scenario can further be tested in neutrinoless double beta decay experiment ($0\

  1. Explaining the CMS eejj Excess With R?parity Violating Supersymmetry and Implications for Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Allanach, Ben; Biswas, Sanjoy; Mondal, Subhadeep; Mitra, Manimala

    2015-01-01T23:59:59.000Z

    IPPP/14/78, DCPT/14/156 Explaining the CMS eejj Excess With R?parity Violating Supersymmetry and Implications for Neutrinoless Double Beta Decay Ben Allanach,1 Sanjoy Biswas,2 Subhadeep Mondal,3 and Manimala Mitra4 1DAMTP, CMS, Wilberforce Road... production, followed by the three body decays of neutralino and chargino via R-parity violating coupling. These fit the excess for slepton and sneutrino masses around 2 TeV. This scenario can further be tested in neutrinoless double beta decay experiment (0...

  2. Can we explain AMS-02 antiproton and positron excesses simultaneously by nearby supernovae without pulsars nor dark matter?

    E-Print Network [OSTI]

    Kohri, Kazunori; Fujita, Yutaka; Yamazaki, Ryo

    2015-01-01T23:59:59.000Z

    We explain the excess of the antiproton fraction recently reported by the AMS-02 experiment by considering collisions between cosmic-ray protons accelerated by a local supernova remnant (SNR) and the surrounding dense cloud. The same "pp collisions" provide the right branching ratio to fit the observed positron excess simultaneously without a fine tuning. The supernova happened in relatively lower metalicity than the major cosmic-ray sources. The cutoff energy of electrons marks the supernova age of ~10^{5} years, while the antiproton excess may extend to higher energy. Both antiproton and positron fluxes are completely consistent with our predictions in Fujita, Kohri, Yamazaki and Ioka (2009).

  3. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01T23:59:59.000Z

    H. (2008). Understanding protein folding: small proteins inG. (1997). Theory of protein folding: the energy landscapeenergy landscape of protein folding: a synthesis. Proteins

  4. 10/14/09 2:35 PMMathematicians' Alternate Model of the Universe Explains Away the Need For Dark Energy | Popular Science Page 1 of 13http://www.popsci.com/military-aviation-amp-space/article/2009-09/mathematicians-seek-explain-away-dark-energy-universe

    E-Print Network [OSTI]

    Temple, Blake

    -09/mathematicians-seek-explain-away-dark-energy-universe Mathematicians' Alternate Model of the Universe Explains An alternative theory eliminates dark energy by placing Earth at the center of expansion Expanding Universe What;10/14/09 2:35 PMMathematicians' Alternate Model of the Universe Explains Away the Need For Dark Energy

  5. Sampling the conformation of protein surface residues for flexible protein docking

    E-Print Network [OSTI]

    Francis-Lyon, Patricia; Gu, Shengyin; Hass, Joel; Amenta, Nina; Koehl, Patrice

    2010-01-01T23:59:59.000Z

    References 1. Bonvin AM: Flexible protein-protein docking.Wolfson H: Principles of flexible protein-protein docking.R, Wolfson HJ: Geometry-based flexible and symmetric protein

  6. Mathematical methods for protein science

    SciTech Connect (OSTI)

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

    1997-12-31T23:59:59.000Z

    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.

  7. A randomized global optimization method for protein-protein docking

    E-Print Network [OSTI]

    2003-04-10T23:59:59.000Z

    e.g., the well known problem of protein folding), when dealing with docking some important modifications are necessary. In particular, when rigid docking is ...

  8. 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

    2015-01-01T23:59:59.000Z

    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...

  9. Explaining the CMS $eejj$ and $e \\slashed {p}_T jj$ Excess and Leptogenesis in Superstring Inspired $E_6$ Models

    E-Print Network [OSTI]

    Dhuria, Mansi; Rangarajan, Raghavan; Sarkar, Utpal

    2015-01-01T23:59:59.000Z

    We show that superstring inspired $E_6$ models can explain both the recently detected excess $eejj$ and $e \\slashed p_T jj$ signals at CMS, and also allow for leptogenesis. Working in a R-parity conserving low energy supersymmetric effective model, we show that the excess CMS events can be produced via the decay of exotic sleptons in alternative left-right symmetric models of $E_6$, which can also accommodate leptogenesis at a high scale. On the other hand, either the $eejj$ excess or the $e \\slashed p_T jj$ excess can be produced via the decays of right handed gauge bosons, but some of these scenarios may not accommodate letptogenesis as there will be strong $B-L$ violation at low energy, which, along with the anomalous fast electroweak $B+L$ violation, will wash out all baryon asymmetry. Baryogenesis below the electroweak scale may then need to be implemented in these models.

  10. 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

    2014-12-01T23:59:59.000Z

    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\

  11. 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.

    2006-01-01T23:59:59.000Z

    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.

  12. 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)

    2009-09-08T23:59:59.000Z

    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.

  13. Protein Flips Lipids Across Membranes

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

    used by these proteins to expel toxins from cells therefore represent key targets for the development of drugs designed to combat the growing problem of multidrug resistance....

  14. 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)

    2009-05-05T23:59:59.000Z

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

  15. Expression of multiple proteins in transgenic plants

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  16. 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)

    2013-03-29T23:59:59.000Z

    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.

  17. 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

  18. Cost Avoidance vs. Utility Bill Accounting - Explaining theDiscrepancy Between Guaranteed Savings in ESPC Projects and UtilityBills

    SciTech Connect (OSTI)

    Kumar, S.; Sartor, D.

    2005-08-15T23:59:59.000Z

    Federal agencies often ask if Energy Savings PerformanceContracts (ESPCs) result in the energy and cost savings projected duringthe project development phase. After investing in ESPCs, federal agenciesexpect a reduction in the total energy use and energy cost at the agencylevel. Such questions about the program are common when implementing anESPC project. But is this a fair or accurate perception? Moreimportantly, should the federal agencies evaluate the success or failureof ESPCs by comparing the utility costs before and after projectimplementation?In fact, ESPC contracts employ measurement andverification (M&V) protocols to measure and ensure kilowatt-hour orBTU savings at the project level. In most cases, the translation toenergy cost savings is not based on actual utility rate structure, but acontracted utility rate that takes the existing utility rate at the timethe contract is signed with a clause to escalate the utility rate by afixed percentage for the duration of the contract. Reporting mechanisms,which advertise these savings in dollars, may imply an impact to budgetsat a much higher level depending on actual utility rate structure. FEMPhas prepared the following analysis to explain why the utility billreduction may not materialize, demonstrate its larger implication onagency s energy reduction goals, and advocate setting the rightexpectations at the outset to preempt the often asked question why I amnot seeing the savings in my utility bill?

  19. 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

    2015-01-01T23:59:59.000Z

    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...

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

    E-Print Network [OSTI]

    Zhu, L; Kaback, HR; Dalbey, RE

    2013-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Amos, Joseph Edward

    2013-02-22T23:59:59.000Z

    cells begin to divide (Ebens et al. , 1993), suggesting the existence of a mechanism(s) to inactivate ana or bypass ana-mediated repression. Analysis of the sequence (474 amino acids, 55kD) shows that ana is a novel protein: it shows no obvious... system The S was actively used in the transhtion of the nascent proteins. When this film was compared to the marker, the size of the bands in each lane closely corresponds to the estimated size of ana- myc protein (-57kD). Next, the reticulocyte...

  2. Probing Single-Molecule Protein Conformational Dynamics. | EMSL

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

    Single-Molecule Protein Conformational Dynamics. Probing Single-Molecule Protein Conformational Dynamics. Abstract: Protein conformational fluctuations and dynamics, often...

  3. Optimized Null Model for Protein Structure Networks

    E-Print Network [OSTI]

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

    2009-01-01T23:59:59.000Z

    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

  4. A motion planning approach to protein folding

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

    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 three-dimensional structure...

  5. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01T23:59:59.000Z

    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 ...

  6. A motion planning approach to protein folding 

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

    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 ...

  7. GWIDD: Genome-wide protein docking database

    E-Print Network [OSTI]

    Kundrotas, Petras J.; Zhu, Zhengwei; Vasker, Ilya A.

    2009-11-09T23:59:59.000Z

    Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein–protein interactions on the genome scale...

  8. EVA: evaluation of protein structure prediction servers

    E-Print Network [OSTI]

    Sali, Andrej

    day, sequences of newly available protein structures in the Protein Data Bank (PDB) are sent performance of protein structure prediction servers through a battery of objective measures for prediction

  9. MODELING PROTEIN INTERACTIONS THROUGH STRUCTURE ALIGNMENT

    E-Print Network [OSTI]

    Sinha, Rohita

    2011-08-31T23:59:59.000Z

    Rapid accumulation of the experimental data on protein-protein complexes drives the paradigm shift in protein docking from "traditional" template free approaches to template based techniques. Homology docking algorithms ...

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

    E-Print Network [OSTI]

    Barakat, Nora Hisham

    2007-01-01T23:59:59.000Z

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

  11. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01T23:59:59.000Z

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

  12. Entropic stabilization of proteins and its proteomic consequences

    E-Print Network [OSTI]

    Igor N. Berezovsky; William W. Chen; Paul J. Choi; Eugene I. Shakhnovich

    2005-06-22T23:59:59.000Z

    We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in folded states of proteins. This finding suggests that Lysines would preferentially entropically stabilize the native state. Indeed we show in computational experiments that Arginine-to-Lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize that if evolution uses this physical mechanisms in its strategies of thermophilic adaptation then hyperthermostable organisms would have much greater content of Lysines in their proteomes than of comparable in size and similarly charged Arginines.. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias towards Arginine-to-Lysine replacement in hyperthermophilic organisms and overall much greater content of Lysines than Arginines in hyperthermophiles. This finding cannot be explained by GC compositional biases. Our study provides an example of how analysis of a delicate physical mechanism of thermostability helps to resolve a puzzle in comparative genomics as to why aminoacid compositions of hyperthermophilic proteomes are significantly biased towards Lysines but not Arginines

  13. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

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

    2010-07-18T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Bayro, Marvin J

    2010-01-01T23:59:59.000Z

    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. Assigning protein functions by comparative genome analysis protein phylogenetic profiles

    DOE Patents [OSTI]

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

    2003-05-13T23:59:59.000Z

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

  16. Adhesives from modified soy protein

    DOE Patents [OSTI]

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

    2008-08-26T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01T23:59:59.000Z

    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^{\

  18. Quantitative proteomics analysis of adsorbed plasma proteins...

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

    proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size Quantitative proteomics analysis of adsorbed plasma proteins...

  19. Automated Purification of Recombinant Proteins: Combining High...

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

    mapping protein interactions and other approaches of current functional genomics require not only purifying large numbers of proteins but also obtaining sufficient...

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

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

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

  1. Computational prediction and analysis of protein structure

    E-Print Network [OSTI]

    Meruelo, Alejandro Daniel

    2012-01-01T23:59:59.000Z

    I, and Bowie JU. Kink prediction in membrane proteins.Los Angeles Computational prediction and analysis of proteinOF THE DISSERTATION Computational prediction and analysis of

  2. 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, ...

  3. Fast events in protein folding

    SciTech Connect (OSTI)

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

    1996-04-01T23:59:59.000Z

    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.

  4. 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

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

    E-Print Network [OSTI]

    Stevenson, Calum

    2012-11-30T23:59:59.000Z

    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 ...

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

    DOE Patents [OSTI]

    Eisenberg, David (Los Angeles, CA); Marcotte, Edward M. (Los Angeles, CA); Pellegrini, Matteo (Sherman Oaks, CA); Thompson, Michael J. (Santa Monica, CA); Yeates, Todd O. (Agoura Hills, CA)

    2002-10-15T23:59:59.000Z

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

  7. Recombinant fluorescent protein microsphere calibration standard

    DOE Patents [OSTI]

    Nolan, John P. (Santa Fe, NM); Nolan, Rhiannon L. (Santa Fe, NM); Ruscetti, Teresa (Los Alamos, NM); Lehnert, Bruce E. (Los Alamos, NM)

    2001-01-01T23:59:59.000Z

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

  8. 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

  9. 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 The protein folding and protein design problems are addressed, using coarse-grained models with only two types

  10. How Hydrogen Bond Redundancy Affects Protein Flexibility

    E-Print Network [OSTI]

    Naomi Fox; Filip Jagodzinski; Jeanne Hardy; Ileana Streinu

    Modeling a Protein as a BodyBarHinge and Associated Graph Main Question: Stability in proteins is the resistance to denaturation, or unfolding. A protein that is highly stable has a high tolerance to bonds breaking before unfolding; an unstable protein has less tolerance. In this study, we focus on the question, how many hydrogen bonds

  11. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01T23:59:59.000Z

    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 ...

  12. Explaining the observed long coherence effects by 2D photon echo experiments in photosynthetic EET : Two-Component Phonon Spectrum model

    E-Print Network [OSTI]

    Singh, Navinder; Amritkar, R E

    2011-01-01T23:59:59.000Z

    We propose a simple stochastic model which successfully explains the long coherence effects observed in photosynthetic Excitation Energy Transport (EET) by 2D photon echo experiments of G. S. Engel et. al. (Nature, {\\bf 446} 782, (2007)). Our Two-Component Phonon Spectrum (TCPS) model is based upon the division of phonon degrees of freedom into a systematic component which is treated through polaron transformation and a stochastic component which is treated through dynamical disorder. This model successfully explains the observed long coherence upto $ \\sim 600 fsec$ in EET experiments.

  13. Explaining the observed long coherence effects by 2D photon echo experiments in photosynthetic EET : Two-Component Phonon Spectrum model

    E-Print Network [OSTI]

    Navinder Singh; V. M. Kenkre; R. E. Amritkar

    2011-12-16T23:59:59.000Z

    We propose a simple stochastic model which successfully explains the long coherence effects observed in photosynthetic Excitation Energy Transport (EET) by 2D photon echo experiments of G. S. Engel et. al. (Nature, {\\bf 446} 782, (2007)). Our Two-Component Phonon Spectrum (TCPS) model is based upon the division of phonon degrees of freedom into a systematic component which is treated through polaron transformation and a stochastic component which is treated through dynamical disorder. This model successfully explains the observed long coherence upto $ \\sim 600 fsec$ in EET experiments.

  14. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01T23:59:59.000Z

    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.

  15. SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION

    SciTech Connect (OSTI)

    JOHN C WALKER

    2011-11-01T23:59:59.000Z

    Protein phosphorylation and dephosphorylation play key roles in many aspects of plant biology, including control of cell division, pathways of carbon and nitrogen metabolism, pattern formation, hormonal responses, and abiotic and biotic responses to environmental signals. A Symposium on Plant Protein Phosphorylation was hosted on the Columbia campus of the University of Missouri from May 26-28, 2010. The symposium provided an interdisciplinary venue at which scholars studying protein modification, as it relates to a broad range of biological questions and using a variety of plant species, presented their research. It also provided a forum where current international challenges in studies related to protein phosphorylation could be examined. The symposium also stimulated research collaborations through interactions and networking among those in the research community and engaged students and early career investigators in studying issues in plant biology from an interdisciplinary perspective. The proposed symposium, which drew 165 researchers from 13 countries and 21 States, facilitated a rapid dissemination of acquired knowledge and technical expertise regarding protein phosphorylation in plants to a broad range of plant biologists worldwide.

  16. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01T23:59:59.000Z

    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.

  17. 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

  18. 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

  19. Prediction of Interface Residues in ProteinProtein Complexes by a Consensus Neural Network Method: Test

    E-Print Network [OSTI]

    Weston, Ken

    Prediction of Interface Residues in Protein­Protein Complexes by a Consensus Neural Network Method important information for predicting struc- tures of new protein complexes. This motivated us to develop the PPISP method for predicting inter- face residues in protein­protein complexes. In PPISP, sequence

  20. Protein folding in the ER.

    SciTech Connect (OSTI)

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

    1999-10-01T23:59:59.000Z

    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.

  1. A novel mechanism and kinetic model to explain enhanced xylose yields from dilute sulfuric acid compared to hydrothermal pretreatment of corn stover

    E-Print Network [OSTI]

    California at Riverside, University of

    A novel mechanism and kinetic model to explain enhanced xylose yields from dilute sulfuric acid stover Dilute sulfuric acid Hydrothermal pretreatment Kinetic model Xylose a b s t r a c t Pretreatment of corn stover in 0.5% sulfuric acid at 160 °C for 40 min realized a maximum monomeric plus oligomeric

  2. 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

  3. . . . 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

  4. be explained by the indirect aerosol cloud effect. The use of a parcel model to determine the cloud droplet number concentration

    E-Print Network [OSTI]

    Reiners, Peter W.

    cloud properties and their effect on the surface radiation budget: selected cases from FIRE ACE. Jbe explained by the indirect aerosol cloud effect. The use of a parcel model to determine the cloud droplet number concentration enables us to separate the effects of the cloud LWP and cloud droplet number

  5. Method for protein structure alignment

    DOE Patents [OSTI]

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

    2005-02-22T23:59:59.000Z

    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.

  6. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips LipidsProtein

  7. Supporting Information Protein structural dynamics of photoactive yellow protein in

    E-Print Network [OSTI]

    Ihee, Hyotcherl

    , Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic solvent heating. Although the heating mostly affects q region above 1.5 Å­1 the heating signal should, in the case of PYP, the solvent heating signal is much smaller than the contribution from the protein

  8. Method for voltage-gated protein fractionation

    DOE Patents [OSTI]

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

    2012-04-24T23:59:59.000Z

    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.

  9. Protein phase feeding of poultry

    E-Print Network [OSTI]

    Vest, Larry Rufus

    1966-01-01T23:59:59.000Z

    and together, to a corn-soybean diet for laying chickens. Poultry Sci, 33:1191-1197. Middendorf, D. F. , N. V. Helbacka and G. F. Combs, 1959. Ei'feet of protein levels and kelp ash on performance of laying hens. Poultry Sci. 38:1229. Miller, E. C. , M. L...

  10. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

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

    1998-02-17T23:59:59.000Z

    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.

  11. 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)

    1998-01-01T23:59:59.000Z

    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. ProteinProtein Docking with Backbone Flexibility Chu Wang, Philip Bradley and David Baker

    E-Print Network [OSTI]

    Baker, David

    Protein­Protein Docking with Backbone Flexibility Chu Wang, Philip Bradley and David Baker Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195

  13. The prediction of protein-protein interaction of A-thaliana and X-campestris pv. campestris based on protein domain and interolog approaches

    E-Print Network [OSTI]

    Kurubanjerdjit, N; Tsai, JJP; Sheu, CY; Ng, KL

    2013-01-01T23:59:59.000Z

    as the input for our prediction Browne F, Zhang HR, Wang HYtechniques: a review on the prediction of protein-proteinF, Zhang Z and Peng YL (2011) Prediction of protein-protein

  14. Contributions to the analysis of proteins

    E-Print Network [OSTI]

    Sharifi Sedeh, Reza

    2011-01-01T23:59:59.000Z

    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 ...

  15. Protein Thioester Synthesis Enabled by Sortase

    E-Print Network [OSTI]

    Ling, Jingjing

    Proteins containing a C-terminal thioester are important intermediates in semisynthesis. Currently there is one main method for the synthesis of protein thioesters that relies upon the use of engineered inteins. Here we ...

  16. Protein Identification Using Top-Down. | EMSL

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

    Identification Using Top-Down. Protein Identification Using Top-Down. Abstract: In the last two years, due to advances in protein separation and mass spectrometry, top-down mass...

  17. Evolutionary Approaches to Protein Engineering B. STEIPETEIPE

    E-Print Network [OSTI]

    Steipe, Boris

    Evolutionary Approaches to Protein Engineering B. STEIPETEIPE 1 Targets and Tasks for Protein Engineering . . . . . . . . . . . . . . . . . . 56 1.1 Folding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 1.1.1 Thermodynamic Stability . . . . . . . . . . . . . . . . . . . . . . . . . 57 1.1.2 Thermal

  18. Exact rotamer optimization for computational protein design

    E-Print Network [OSTI]

    Hong, Eun-Jong, 1975-

    2008-01-01T23:59:59.000Z

    The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a ...

  19. 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

  20. Biophysical characterization of protein folding and misfolding. 

    E-Print Network [OSTI]

    Schmittschmitt, Jason Peter

    2004-09-30T23:59:59.000Z

    The HPr proteins were characterized as folding by a two-state folding mechanism. Here, we present a comparison of the equilibrium and kinetic folding for the HPr protein from Bacillus subtilis, E coli and a key variant ...

  1. Global Optimization and Protein Structure Prediction

    E-Print Network [OSTI]

    Neumaier, Arnold

    The protein folding problem, i.e., the problem of how to predict the folded native, tertiary structure of the static protein folding problem only, ignoring the possible pathways of folding. The talk will have

  2. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01T23:59:59.000Z

    Intermediates can accelerate protein folding. Proceedings ofunifying mechanism for protein folding? [Review]. Trends incoordinate for protein folding. Journal of Chemical Physics

  3. The unfolded protein response during prostate cancer development

    E-Print Network [OSTI]

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

    2009-01-01T23:59:59.000Z

    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

  4. agouti related protein: Topics by E-print Network

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

    dietary of protein percentage on the nutrient fluxes across the gland and their relation- ship to milk production. Milk production, milk protein yield, and milk protein...

  5. Computational Modeling of Protein Interactions at Multiple Lengthscales

    E-Print Network [OSTI]

    Yap, Eng Hui

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Anderson, William David

    2007-01-01T23:59:59.000Z

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

  7. Structural and biological studies of bone morphogenetic protein-15

    E-Print Network [OSTI]

    McMahon, Heather Eileen

    2007-01-01T23:59:59.000Z

    homolog, GDF-9; both proteins lack the fourth of seventhe recombinant protein with this mutation lacks biologicallacks biological activity and, intriguingly, the mutant protein

  8. Iterative Information Model Development Protein sequence

    E-Print Network [OSTI]

    Protein Information Resource (PIR) Protein Science Team (11) Executive Team Members Dr. Winona Barker. Cecilia Arighi, Senior Protein Scientist, Research Assistant Professor Natalia Petrova, PhD StudentPIR Director Dr. Cathy Wu Professor PIR Director Dr. Cathy Wu Professor Bioinformatics Team (9) Executive Team

  9. 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

  10. 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

  11. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K. (Berkeley, CA)

    1997-01-01T23:59:59.000Z

    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.

  12. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, G.K.

    1997-04-29T23:59:59.000Z

    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.

  13. GREEN FLUORESCENT PROTEIN The green revolution

    E-Print Network [OSTI]

    Stearns, Tim

    GREEN FLUORESCENT PROTEIN The green revolution Green fluorescent protein allows gene expression a fluorescent product when expressed. Just such a molecule, green fluorescent protein (GFP), has recently green light when disturbed (often seen when riding in a boat at night). In Aequorea, the green

  14. On the Complexity of Protein Folding

    E-Print Network [OSTI]

    Pierluigi Crescenzi; Deborah Goldman; Christos Papadimitriou; Antonio Piccolboni; Mihalis Yannakakis

    We show that the protein folding problem in the two-dimensional H-P model is NP-complete. 1 Introduction Proteins are polymer chains consisting of monomers of twenty different kinds. Much of the genetic information in the DNA contains the sequence information of proteins, with three nucleotides

  15. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Hura, Greg

    2013-05-29T23:59:59.000Z

    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.

  16. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Greg Hura

    2010-01-08T23:59:59.000Z

    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.

  17. Protein Structures Revealed at Record Pace

    SciTech Connect (OSTI)

    Hura, Greg

    2009-01-01T23:59:59.000Z

    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.

  18. REGULATION OF TELOMERASE BY TELOMERIC PROTEINS

    E-Print Network [OSTI]

    de Lange, Titia

    REGULATION OF TELOMERASE BY TELOMERIC PROTEINS Agata Smogorzewska1 and Titia de Lange2 1 Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02115; email: asmogorzewska@partners.org 2, and Sm proteins in budding yeast). Telomerase is regulated in cis by proteins that bind to telomeric DNA

  19. Amphiphiles for protein solubilization and stabilization

    DOE Patents [OSTI]

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

    2012-09-11T23:59:59.000Z

    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.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Snow, Christopher

    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

  6. Protein Patterning with Programmable Surface Chemistry Chips

    E-Print Network [OSTI]

    step with different protein solution on a different heater. The micro-fabrication process consists-isopropylacrylamide, ppNIPAM) onto arrays of micro-fabricated metallic heaters. Activating a single heater causes proteins were used to demonstrate localized immobilization of proteins on the surface of coated micro-heater

  7. The effect of proteins from different sources on egg production and hatchability in the mature fowl

    E-Print Network [OSTI]

    Nowlin, Donald Henderson

    1954-01-01T23:59:59.000Z

    citrate were also commonly added to the diets. Osborne and Mendel provided roughage in the form of blotting paper on tne bottom of the cages ~ The chickens o these experiments suffered from "a peculiar leg weaknosss which was attributed to a lack... that hatchability could not bs maintained at high levels or even at the "norm" without the addition of some still unknown animal protein factors, even with vitamin BI2 in the diet, It has been extremely difficult to explain entirely on the basis of the vitamin...

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

    SciTech Connect (OSTI)

    Huang, David M.; Chandler, David

    2000-04-01T23:59:59.000Z

    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.

  9. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21T23:59:59.000Z

    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.

  10. Protein Information Resource Integrated Protein Informatics Resource for Genomic & Proteomic Research

    E-Print Network [OSTI]

    Research For four decades the Protein Information Resource (PIR) has provided databases and protein-1978]. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) i protein sequences for sequence tracking from: Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, Ref

  11. Protein Information Resource: A Community Resource for Expert Annotation of Protein Data

    E-Print Network [OSTI]

    -2195 The Protein Information Resource (PIR) provides protein databases and analysis tools to support research on molecular evolution, functional genomics, and computational biology. PIR, along with the Munich Information Center for Protein Sequences and the Japan International Protein Information Database, maintains the PIR

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

    E-Print Network [OSTI]

    Langmead, Christopher James

    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

  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. 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

  15. Extracellular secretion of recombinant proteins

    DOE Patents [OSTI]

    Linger, Jeffrey G.; Darzins, Aldis

    2014-07-22T23:59:59.000Z

    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.

  16. Impact of Charge Variation on the Encapsulation of Nanoparticles by Virus Coat Proteins

    E-Print Network [OSTI]

    Lin, Hsiang-Ku; Zandi, Roya

    2012-01-01T23:59:59.000Z

    Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work, Daniel et al. [ACS Nano 4 (2010), 3853-3860] found the encapsulation efficiency to sensitively depend on the interplay between the surface charge density of negatively charged gold nanoparticles and the number of positive charges on the RNA binding domains of the proteins. Surprisingly, these experiments reveal that despite the highly cooperative nature of the co-assembly at low pH, the efficiency of encapsulation is a gradual function of their surface charge density. We present a simple all-or-nothing mass action law combined with an electrostatic interaction model to explain the experiments. We find quantitative agreement with experimental observations, supporting the existence of a natural statistical charge distribution between nanoparticles.

  17. Impact of Charge Variation on the Encapsulation of Nanoparticles by Virus Coat Proteins

    E-Print Network [OSTI]

    Hsiang-Ku Lin; Paul van der Schoot; Roya Zandi

    2012-10-16T23:59:59.000Z

    Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work, Daniel et al. [ACS Nano 4 (2010), 3853-3860] found the encapsulation efficiency to sensitively depend on the interplay between the surface charge density of negatively charged gold nanoparticles and the number of positive charges on the RNA binding domains of the proteins. Surprisingly, these experiments reveal that despite the highly cooperative nature of the co-assembly at low pH, the efficiency of encapsulation is a gradual function of their surface charge density. We present a simple all-or-nothing mass action law combined with an electrostatic interaction model to explain the experiments. We find quantitative agreement with experimental observations, supporting the existence of a natural statistical charge distribution between nanoparticles.

  18. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)IntegratedSpeedingTechnical News,Program90803

  19. Computational and experimental investigations of forces in protein folding

    E-Print Network [OSTI]

    Schell, David Andrew

    2005-02-17T23:59:59.000Z

    in protein folding is essential to the understanding and treatment of protein misfolding diseases. When proteins fold, a significant amount of surface area is buried in the protein interior. It has long been known that burial of hydrophobic surface area...

  20. 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

  1. Soliton concepts and the protein structure

    E-Print Network [OSTI]

    Andrei Krokhotin; Antti J. Niemi; Xubiao Peng

    2011-09-18T23:59:59.000Z

    Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion, from a relatively small number of components. Here we propose to identify the modular building blocks of proteins with the dark soliton solution of a generalized discrete nonlinear Schrodinger equation. For this we show that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop specific parameters and we identify their possible values in Protein Data Bank. We show that with a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop, we cover over 90% of all proteins with experimental accuracy. We also present two examples that describe how the loop library can be employed both to model and to analyze the structure of folded proteins.

  2. Protein Identification Using Top-Down

    SciTech Connect (OSTI)

    Liu, Xiaowen; Sirotkin, Yakov; Shen, Yufeng; Anderson, Gordon A.; Tsai, Yi-Hsuan S.; Ting, Ying S.; Goodlett, David R.; Smith, Richard D.; Bafna, Vineet; Pevzner, Pavel A.

    2012-06-01T23:59:59.000Z

    In the last two years, due to advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications (PTMs). We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark MS-Align+ along with PIITA, ProSightPTM and SEQUEST, which were previously used for top-down MS/MS database searches. We demonstrate that MS-Align+ and PIITA significantly increase the number of identified proteins as compared to ProSightPTM and SEQUEST.

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

    DOE Patents [OSTI]

    Laible, Philip D; Hanson, Deborah K

    2013-06-04T23:59:59.000Z

    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.

  4. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips Lipids Across

  5. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips Lipids

  6. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips

  7. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    National Laboratory Stone and Webster The Boeing Company University of Illinois University of Wisconsin #12 accessible and up to date. A steady stream of about 150 visitors per week log on to the FIRE web site since

  8. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Laboratory Stone and Webster The Boeing Company University of Illinois University of Wisconsin #12;NSO to date. A steady stream of about 150 visitors per week log on to the FIRE web site since the site

  9. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Laboratory Stone and Webster The Boeing Company University of Illinois University of Wisconsin #12;NSO visitors per week logs on to the FIRE web site since the site was initiated in early July, 1999. #12

  10. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Princeton Plasma Physics Laboratory Sandia National Laboratory Stone and Webster The Boeing Company on FIRE and fusion science accessible and up to date. A steady stream of about 150 visitors per week log

  11. Laboratories to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Technical Issues Divertor and PFCs Disruptions Vac Vessel Nuclear Heating Remote Handling Incorporate with some new methods of remote participation to improve future workshops. Remote particpants, please send as next step. · NRC Interim Report identified "integrated physics of a self-heated plasma" as one

  12. 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

    2006-02-17T23:59:59.000Z

    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.

  13. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

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

    2006-07-27T23:59:59.000Z

    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.

  14. DIRECT INTERACTION OF ROTAVIRUS NON STRUCTURAL PROTEIN 4 WITH HEAT SHOCK PROTEIN 56 PROTEIN 

    E-Print Network [OSTI]

    Moon, Soon Young

    2012-05-04T23:59:59.000Z

    growth on a plate. Also when URA3 is activated, yeast convert 5FOA (5 fluorooratic acid) to 5 fluorouracil, which is toxic. Thus stronger the interaction of two proteins, less growth is observed in 5FOA plate. When lacZ is activated, yeast will express...: SC that lacks leu, trp, and histamine (his) but contains 3AT (We tested three concentrations, 12.5mM, 50mM and 100 mM), SC that lacks leu, trp, and uracil (ura), SC that lacks leu, trp, but contains 0.2% 5 fluoroorotic acid (5FOA), and Yeast...

  15. Studies involving low protein broiler diets

    E-Print Network [OSTI]

    Parkin, David Palmer

    1971-01-01T23:59:59.000Z

    STUDIES INVOLVING L(% PROTEIN BROILER DIETS A Thesis by David Palmer Parkin Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirement for the degree of MASTER OF SCIENCE May 1971 Major Subject...: Poultry Science STUDIES INVOLVING LS& PROTEIN BROILER DIETS A Thesis by David Palmer Parkin Approved as to style and content by: (Chairman of Commit e) ead of. Departmen Me er) (Member) (Memb ) May 1971 ABSTRACT Studies Involving Low Protein...

  16. 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)

  17. Class II virus membrane fusion proteins

    SciTech Connect (OSTI)

    Kielian, Margaret [Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461 (United States)]. E-mail: kielian@aecom.yu.edu

    2006-01-05T23:59:59.000Z

    Enveloped animal viruses fuse their membrane with a host cell membrane, thus delivering the virus genetic material into the cytoplasm and initiating infection. This critical membrane fusion reaction is mediated by a virus transmembrane protein known as the fusion protein, which inserts its hydrophobic fusion peptide into the cell membrane and refolds to drive the fusion reaction. This review describes recent advances in our understanding of the structure and function of the class II fusion proteins of the alphaviruses and flaviviruses. Inhibition of the fusion protein refolding reaction confirms its importance in fusion and suggests new antiviral strategies for these medically important viruses.

  18. Amyloid Deposits: Protection Against Toxic Protein Species?

    E-Print Network [OSTI]

    Lindquist, Susan

    Neurodegenerative diseases ranging from Alzheimer’s disease and polyglutamine diseases to transmissible spongiform encephalopathies are associated with the aggregation and accumulation of misfolded proteins. In several ...

  19. Protein Structure Suggests Role as Molecular Adapter

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

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

  20. Top-to-Bottom Protein Characterization | EMSL

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

    protein mixtures using an integrated strategy-including using EMSL's 12-Tesla Fourier-Transform Ion Cyclotron Resonance mass spectrometer-reduces the total amount of...

  1. Knots and Swelling in Protein Folding

    E-Print Network [OSTI]

    Martin Lundgren; Antti J. Niemi

    2009-06-26T23:59:59.000Z

    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.

  2. The thermodynamics of protein aggregation reactions may underpin the enhanced metabolic efficiency associated with heterosis, some balancing selection, and the evolution of ploidy levels

    E-Print Network [OSTI]

    Ginn, Brian R

    2015-01-01T23:59:59.000Z

    Identifying the physical basis of heterosis (or hybrid vigor) has remained elusive despite over a hundred years of research on the subject. The three main theories of heterosis are dominance theory, overdominance theory, and epistasis theory. Kacser and Burns (1981) identified the molecular basis of dominance, which has greatly enhanced our understanding of its importance to heterosis. This paper aims to explain how overdominance, and some features of epistasis, can similarly emerge from the molecular dynamics of proteins. Possessing multiple alleles at a gene locus results in the synthesis of different allozymes at reduced concentrations. This in turn reduces the rate at which each allozyme forms soluble oligomers, which are toxic and must be degraded, because allozymes co-aggregate at low efficiencies. The model developed in this paper will be used to explain how heterozygosity can impact the metabolic efficiency of an organism. It can also explain why the viabilities of some inbred lines seem to decline ra...

  3. Protein activation of a ribozyme: the role of bacterial RNase P protein

    E-Print Network [OSTI]

    Pace, Norman

    Protein activation of a ribozyme: the role of bacterial RNase P protein Amy H Buck1 , Andrew B Dalby2 , Alexander W Poole2,3 , Alexei V Kazantsev2 and Norman R Pace2, * 1 Department of Chemistry

  4. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database.

    E-Print Network [OSTI]

    Bickerton, George R; Higueruelo, Alicia P; Blundell, Tom L

    2011-07-29T23:59:59.000Z

    to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified...

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

    E-Print Network [OSTI]

    Fu, Hailong

    2010-07-14T23:59:59.000Z

    for increasing protein stability. Finally, using a combination of eight previously identified stabilizing mutations; we successfully designed two RNase Sa variants (7S, 8S) that have both much higher Tms and conformational stabilities than wild-type protein over...

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

    SciTech Connect (OSTI)

    B Wallace; R Janes

    2011-12-31T23:59:59.000Z

    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. 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

  8. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-08-13T23:59:59.000Z

    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.

  9. Multiscale Approach to Protein Engineering in Bioluminescence

    E-Print Network [OSTI]

    Maryland at College Park, University of

    ) Molecular Dynamics (protein) Reduced Modeling (protein/DLSA) #12;Hybrid Quantum Mechanical/Molecular LEVEL TISSUE LEVEL CELLULAR LEVEL SUBCELLULAR LEVEL MOLECULAR LEVEL ATOMIC LEVEL Multiscale in Biology state First excited electronic state Wavelength Absorbance Excitation of DLSA #12;Wavelength 560nm 605

  10. MP 33200 EZQ Protein Quantitation Kit

    E-Print Network [OSTI]

    Lebendiker, Mario

    . After spotting the samples, completing the protocol takes only about 1 hour. The protein concentration Standards 1.1 Make a stock solution of ovalbumin. The ovalbumin (Com- ponent D) supplied with the kit can be used to make protein standards for the assay. To make a 10 mg/mL stock solution, add 200 µL of buffer

  11. RESEARCH ARTICLES Protein Domain Movements: Detection

    E-Print Network [OSTI]

    Wriggers, Willy

    by anonymous ftp to ftp.ks.uiuc.edu in the directory pub/hingefind or on the World Wide Web at URLftp:1­14, 1997. 1997 Wiley-Liss, Inc. Key words: protein architecture; hinge-bend- ing; lactoferrin; hexokinase flexibil- ity to a wide spectrum of biochemical function in catalysis, regulation, protein assembly

  12. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

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

    1990-08-23T23:59:59.000Z

    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.

  13. 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

  14. Mining Protein Contact Maps Jingjing Hu

    E-Print Network [OSTI]

    Bystroff, Chris

    Mining Protein Contact Maps Jingjing Hu , Xiaolan Shen , Yu Shao ¡ , Chris Bystroff matrix of pairwise, inter-residue contacts, or "contact map". The contact map provides a host of use- ful information about the protein's structure. In this paper we de- scribe how data mining can be used to extract

  15. Production of Therapeutic Proteins in Plants

    E-Print Network [OSTI]

    Bradford, Kent

    responses are often proteins. While short peptide chains (containing fewer than 30 amino acids) can be syn facilities will fall far short of demand, as aug- menting cell culture facilities requires large investments in buildings and equip- ment. Recently, transgenic (i.e., plants engineered to produce specific proteins) plant

  16. 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

  17. The chemical properties and biological significance of gossypol protein complexes

    E-Print Network [OSTI]

    Baliga, Bantval Prabhakara

    1956-01-01T23:59:59.000Z

    ................................. 2 III. REVIEW OF LITERATURE ......................... 4 1. Cottonseed Proteins ....................... 4 2. Evaluation of Proteins ................... 5 5. The Pigments of Cottonseed.............. 11 4. The Physiological Significance of Free...-Protein Complexes . 59 5. Chemical Analysis of Cottonseed Meal and Gossypol-Protein Complexes .......... 59 4. Biological Evaluation ..................... 44 5. Enzymatic Hydrolysis of Gossypol-Protein Complexes............................. 46 6. Bibliography...

  18. 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

  19. A newly discovered protein export machine in malaria parasites

    E-Print Network [OSTI]

    Arnold, Jonathan

    associated with protein translocons), a novel protein termed PTEX150 and a known parasite protein, exported importance, the mechanism of protein export is not known although export initially requires proteins to enter,3,14 , but homology searches for relatives of known members of translocon systems have failed to predict its identity

  20. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01T23:59:59.000Z

    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,...

  1. 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.

    2003-01-01T23:59:59.000Z

    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.

  2. Instability of GGL domain-containing RGS proteins in mice lacking the G protein -subunit G 5

    E-Print Network [OSTI]

    Wensel, Theodore G.

    Instability of GGL domain-containing RGS proteins in mice lacking the G protein -subunit G 5 Ching, Houston, TX 77030 Contributed by Melvin I. Simon, March 28, 2003 RGS (regulator of G protein signaling) proteins containing the G protein -like (GGL) domain (RGS6, RGS7, RGS9, and RGS11) inter- act

  3. 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 New Crystal Structures Lift Fog around Protein Folding Print Wednesday, 25 July 2012 00:00 Nature's proteins set a high bar...

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

    E-Print Network [OSTI]

    Landman, Allison Simone

    2009-01-01T23:59:59.000Z

    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 ...

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

    E-Print Network [OSTI]

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

    2011-01-01T23:59:59.000Z

    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. 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

  7. Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation

    E-Print Network [OSTI]

    Baer, Christina Elizabeth

    2010-01-01T23:59:59.000Z

    in pathways that lack scaffolding proteins that restrictC- spine, as this apo-protein lacks the ligand adenosinethe Mtb kinome as this protein lacks the Arg preceding the

  8. RACK1, A Multifaceted Scaffolding Protein: Structure and Function

    E-Print Network [OSTI]

    Adams, David R; Ron, Dorit; Kiely, Patrick A

    2011-01-01T23:59:59.000Z

    B-C turn. Thus, RACK1 proteins lack the GH motif in the D-Aways. WD-repeat proteins themselves lack any enzy- maticlocation and protein partnerships may be modulated. The lack

  9. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01T23:59:59.000Z

    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

  10. 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

  11. 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

  12. Preparation of white sunflower protein isolates

    E-Print Network [OSTI]

    Wen, Hwei-Mei

    1982-01-01T23:59:59.000Z

    plant. 25 Flow chart of procedures used in Run VI for separation of non-storage and storage fraction of sunflower protein isolate in the pilot plant 26 10 Flow chart of procedures used in Run VII for separation of non-storage and storage fraction... of sunflower protein isolate in the pilot plant 27 Flow chart of procedures used in Run VIII for separation of non-storage and storage fraction of sunflower protein isolate in the pilot plant 29 12 Influence of NaBH4 concentration on the color (Hunter L...

  13. Introducing Protein Folding Using Simple Models

    E-Print Network [OSTI]

    D. Thirumalai; D. K. Klimov

    2001-01-04T23:59:59.000Z

    We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use of lattice models to understand the selection of the limited set of viable protein folds; (ii) the relationship between structure and sequence spaces; (iii) the application of lattice models for studying folding mechanisms (topological frustration, kinetic partitioning mechanism). Classification of folding scenarios based on the intrinsic thermodynamic properties of a sequence (namely, the collapse and folding transition temperatures) is outlined. A brief discussion of random heteropolymer model is also presented.

  14. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01T23:59:59.000Z

    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.

  15. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein FlipsProteinProtein

  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

    2012-01-01T23:59:59.000Z

    Page 10 of 16 protein folding and the lack of predictabilitythe lack of intrinsic folding properties of the protein (lack trxB and gor and cannot efficiently re- duce oxidized proteins.

  17. Hybrid Protein Model (HPM) : a method to compact protein 3D-structure information and physicochemical properties

    E-Print Network [OSTI]

    Boyer, Edmond

    Hybrid Protein Model (HPM) : a method to compact protein 3D-structure information of the Seventh International Symposium on String Processing Information R #12;Hybrid Protein Model (HPM

  18. accurate protein identification: Topics by E-print Network

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

    and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional...

  19. Probing the Dynamics of a Protein Hydrophobic Core by Deutron...

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

    Dynamics of a Protein Hydrophobic Core by Deutron Solid-State Nuclear Magnetic Resonance Spectroscopy . Probing the Dynamics of a Protein Hydrophobic Core by Deutron Solid-State...

  20. Dual spatial maps of transcript and protein abundance in the...

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

    Dual spatial maps of transcript and protein abundance in the mouse brain. Dual spatial maps of transcript and protein abundance in the mouse brain. Abstract: Integrating...

  1. Mapping protein abundance patterns in the brain using voxelation...

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

    protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry. Mapping protein abundance patterns in the brain using voxelation...

  2. Topological Analysis of Protein Co-Abundance Networks Identifies...

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

    Topological Analysis of Protein Co-Abundance Networks Identifies Novel Host Targets Important for HCV Infection and Pathogenesis Topological Analysis of Protein Co-Abundance...

  3. Improving NMR Protein Structure Quality by Rosetta Refinement...

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

    NMR Protein Structure Quality by Rosetta Refinement: A Molecular Replacement Study. Improving NMR Protein Structure Quality by Rosetta Refinement: A Molecular Replacement Study....

  4. Targeted Protein Degradation by Salmonella under Phagosome-Mimicking...

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

    Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Targeted Protein Degradation by Salmonella under Phagosome-Mimicking...

  5. Identification of a putative protein profile associating with...

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

    a putative protein profile associating with tamoxifen therapy resistance in breast cancer. Identification of a putative protein profile associating with tamoxifen therapy...

  6. Enrichment of Functional Redox Reactive Proteins and Identification...

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

    Redox Reactive Proteins and Identification by Mass Spectrometry Results in Several Terminal Fe(III) Enrichment of Functional Redox Reactive Proteins and Identification by Mass...

  7. adhesion plaque protein: Topics by E-print Network

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

    film, and exhibit ultralow protein adsorption and cell attachment with the coating. This "stealth" or "non 14 Mechanistic studies on zymogen-activator and adhesion proteins (ZAAP)...

  8. adhesive protein inspired: Topics by E-print Network

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

    film, and exhibit ultralow protein adsorption and cell attachment with the coating. This "stealth" or "non 16 Mechanistic studies on zymogen-activator and adhesion proteins (ZAAP)...

  9. adhesion modification protein: Topics by E-print Network

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

    film, and exhibit ultralow protein adsorption and cell attachment with the coating. This "stealth" or "non 14 DOI: 10.1002asia.200800427 Chemical Modification of Proteins at...

  10. adhesion protein neuroligin: Topics by E-print Network

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

    film, and exhibit ultralow protein adsorption and cell attachment with the coating. This "stealth" or "non 14 Mechanistic studies on zymogen-activator and adhesion proteins (ZAAP)...

  11. astrovirus coat protein: Topics by E-print Network

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

    Marcus A. 71 Patterning Proteins and Cells Using Two-Dimensional Arrays of Colloids Materials Science Websites Summary: Patterning Proteins and Cells Using Two-Dimensional...

  12. Atomic structure of nitrate-binding protein crucial for photosynthetic...

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

    structure of nitrate-binding protein crucial for photosynthetic productivity. Atomic structure of nitrate-binding protein crucial for photosynthetic productivity. Abstract:...

  13. Mycobacterium tuberculosis Ser/Thr protein kinase B mediates...

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

    Mycobacterium tuberculosis SerThr protein kinase B mediates an oxygen-dependent replication switch. Mycobacterium tuberculosis SerThr protein kinase B mediates an...

  14. Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma...

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

    Mass Abstract: The detection of low-abundance protein disease biomarkers from human blood poses significant challenges due to the high dynamic range of protein concentrations...

  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. 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

  17. automated protein structure: Topics by E-print Network

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

    functions are not yet prediction on protein structures. 1 Introduction 1.1 Structural Genomics With the sequencing of the human Brutlag, Doug 4 Automated prediction of protein...

  18. Application of proteomics in the discovery of candidate protein...

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

    proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program Application of proteomics in the discovery of candidate protein...

  19. Identification of soybean proteins from a single cell type: The...

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

    soybean proteins from a single cell type: The root hair. Identification of soybean proteins from a single cell type: The root hair. Abstract: Root hairs are a terminally...

  20. 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.

    2009-06-01T23:59:59.000Z

    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.

  1. Are dust shell models well-suited to explain interferometric data of late-type stars in the near-infrared?

    E-Print Network [OSTI]

    P. Schuller; P. Salomé; G. Perrin; B. Mennesson; G. Niccolini; P. de Laverny; S. Ridgway; V. Coudé du Foresto; W. A. Traub; .

    2004-01-22T23:59:59.000Z

    Recently available near-infrared interferometric data on late-type stars show a strong increase of diameter for asymptotic giant branch (AGB) stars between the K (2.0 - 2.4 \\mu m) and L (3.4 - 4.1 \\mu m) bands. Aiming at an explanation of these findings, we chose the objects \\alpha Orionis (Betelgeuse), SW Virginis, and R Leonis, which are of different spectral types and stages of evolution, and which are surrounded by circumstellar envelopes with different optical thicknesses. For these stars, we compared observations with spherically symmetric dust shell models. Photometric and 11 \\mu m interferometric data were also taken into account to further constrain the models. -- [...] -- We conclude that AGB models comprising a photosphere and dust shell, although consistent with SED data and also interferometric data in K and at 11 \\mu m, cannot explain the visibility data in L; an additional source of model opacity, possibly related to a gas component, is needed in L to be consistent with the visibility data.

  2. 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)

    2013-10-01T23:59:59.000Z

    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.

  3. CLP-based protein fragment assembly

    E-Print Network [OSTI]

    Palu', Alessandro Dal; Fogolari, Federico; Pontelli, Enrico; 10.1017/S1471068410000372

    2010-01-01T23:59:59.000Z

    The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.

  4. 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...

  5. Prion protein in health and disease

    E-Print Network [OSTI]

    Steele, Andrew D., Ph. D. Massachusetts Institute of Technology

    2008-01-01T23:59:59.000Z

    The prion protein (PrP) is a conserved glycoprotein tethered to cell membranes by a glycosylphosphatidylinositol anchor. In mammals, PrP is expressed in many tissues, most abundantly in brain, heart, and muscle. Importantly, ...

  6. Structural and Energetic Heterogeneity in Protein Folding

    E-Print Network [OSTI]

    Steven S. Plotkin; Jose N. Onuchic

    2000-09-27T23:59:59.000Z

    A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native stability, as well as entropic heterogeneity intrinsic to the topology of the native structure are both investigated as to their impact on the folding free energy landscape and resulting folding mechanism. Given a minimally frustrated protein, both structural and energetic heterogeneity lower the thermodynamic barrier to folding, and designing in sufficient heterogeneity can eliminate the barrier at the folding transition temperature. Sequences with different distributions of stability throughout the protein and correspondingly different folding mechanisms may still be good folders to the same structure. This theoretical framework allows for a systematic study of the coupled effects of energetics and topology in protein folding, and provides interpretations and predictions for future experiments which may investigate these effects.

  7. STATISTICAL CHARACTERIZATION OF PROTEIN ENSEMBLES Diego Rother

    E-Print Network [OSTI]

    Minnesota, University of

    framework and apply it to artificial data and protein ensembles obtained from molecular dynamics simulations the space of conformations in agreement with NMR observations [1] . 1 Department of Electrical and Computer

  8. Exploring the mechanisms of fibrillar protein aggregation 

    E-Print Network [OSTI]

    Ryan, Morris

    2013-11-28T23:59:59.000Z

    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...

  9. 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

  10. Energetics of protein charge transfer and photosynthesis

    E-Print Network [OSTI]

    Matyushov, Dmitry

    Energetics of protein charge transfer and photosynthesis Dmitry Matyushov Arizona State scheme is to snap a proton from solution! #12; Bacterial photosynthesis e 0.25 eV lost in two

  11. Purification of recombinant proteins with magnetic nanoclusters

    E-Print Network [OSTI]

    Ditsch, Andre (Andre Paul)

    2005-01-01T23:59:59.000Z

    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 ...

  12. Telomere-associated proteins in Arabidopsis thaliana

    E-Print Network [OSTI]

    Surovtseva, Yulia V.

    2009-05-15T23:59:59.000Z

    . Telomere functions are mediated by a large array of telomere-associated proteins. Mutations in telomere-related genes cause immediate telomere dysfunction, activation of DNA damage response, and accumulation of end-to-end chromosome fusions. In addition...

  13. Photovoltaic devices using photosynthetic protein complexes

    E-Print Network [OSTI]

    Das, Rupa, 1980-

    2004-01-01T23:59:59.000Z

    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 ...

  14. Ensemble modeling of [beta]-sheet proteins

    E-Print Network [OSTI]

    O'Donnell, Charles William

    2011-01-01T23:59:59.000Z

    Our ability to characterize protein structure and dynamics is vastly outpaced by the speed of modern genetic sequencing, creating a growing divide between our knowledge of biological sequence and structure. Structural ...

  15. Genetic analysis of protein N-Glycosylation 

    E-Print Network [OSTI]

    Huffman, Jennifer Elizabeth

    2014-11-28T23:59:59.000Z

    The majority of human proteins are post-translationally modified by covalent addition of one or more complex oligosaccharides (glycans). Alterations in glycosylation processing are associated with numerous diseases and ...

  16. Orpinomyces xylanase proteins and coding sequences

    DOE Patents [OSTI]

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

    1998-10-20T23:59:59.000Z

    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.

  17. Biomimetic materials for protein storage and transport

    DOE Patents [OSTI]

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

    2012-05-01T23:59:59.000Z

    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.

  18. Characterisation of endogenous KRAB zinc finger proteins 

    E-Print Network [OSTI]

    Crawford, Catherine

    2009-01-01T23:59:59.000Z

    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 ...

  19. 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)

    2012-01-17T23:59:59.000Z

    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.

  20. 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)

    2009-01-27T23:59:59.000Z

    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.

  1. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26T23:59:59.000Z

    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^{\

  2. 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)

    2013-12-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Kolhoff, Arend J., E-mail: akolhoff@eia.nl [Netherlands Commission for Environmental Assessment, P.O. Box 2345, 3500 GH Utrecht (Netherlands); Driessen, Peter P.J., E-mail: p.driessen@uu.nl [Copernicus Institute of Sustainable Development, Utrecht University, P.O. Box 80115, 3508 TC (Netherlands); Runhaar, Hens A.C., E-mail: h.a.c.runhaar@uu.nl [Copernicus Institute of Sustainable Development, Utrecht University, P.O. Box 80115, 3508 TC (Netherlands)

    2013-01-15T23:59:59.000Z

    Actors in the field of international development co-operation supporting the development of EIA legislation in developing countries often do not achieve the results envisaged. The performance of EIA in these countries often remains weak. One reason, we assume, is that often those actors support the establishment of overly ambitious EIA legislation that cannot achieve its objectives in the light of constraining contexts. To provide more effective support we need to better understand the enabling and constraining contextual factors that influence the development of EIA legislation and to which support actors should align itself. In this article a new analysis framework for classifying, characterizing and explaining the development of EIA legislation is described, measured in terms of ambition levels. Ambitions are defined as intentions the EIA authorities aim to fulfill, expressed in formal EIA legislation. Three country cases, Yemen, Georgia and Ghana are used to illustrate the usefulness of our framework and as a first test to refine the framework. We have formulated the following five hypotheses that complement and refine our analysis framework. One, EIA legislation may develop multilinearly in terms of ambition levels. Two, ambitions in EIA legislation seem to be influenced to a great extent by the power and capacity of, on the one hand, the environmental authorities supporting EIA and, on the other hand, the sector authorities hindering the development of EIA. Three, the political system is the most important context factor influencing the rules of policy-making and the power of the different actors involved. Four, the importance of context factors on the development of ambitions is dependent on the phase of EIA system development. Five, some ambitions seem to be influenced by particular factors; for instance the ambitions for the object of study seem to be influenced by the level of environmental awareness of the sector ministries and parliament. The analysis framework may also assist actors involved in the development of EIA legislation in setting ambitions for EIA legislation that are feasible within the context in which it will be developed and implemented. Application of a country-specific EIA model would seem to be the preferred model to develop EIA legislation because by taking capacities of actors and context factors as a starting point, it offers more potential to well-performing EIA systems. - Highlights: Black-Right-Pointing-Pointer EIA systems develop from less to high ambitious and sometimes vice versa. Black-Right-Pointing-Pointer Ambitions in EIA legislation are determined by the capacity of environment- and sector authority. Black-Right-Pointing-Pointer The political system is the most important context factor explaining the ambitions of an EIA system. Black-Right-Pointing-Pointer An analysis framework developed to measure EIA system ambitions might help to setambitions.

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

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01T23:59:59.000Z

    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.

  5. 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

  6. Folding simulations of small proteins Seung-Yeon Kima

    E-Print Network [OSTI]

    Lee, Jooyoung

    Abstract Understanding how a protein folds is a long-standing challenge in modern science. We have used-native conformations are carried out for each protein. In all cases, proteins fold into their native-like conformations, ~108 Monte Carlo steps). D 2004 Elsevier B.V. All rights reserved. Keywords: Protein folding; Computer

  7. Optik Giriim Grntleme -Molekler konformasyon ve protein dizin lmlerine uygulamalar

    E-Print Network [OSTI]

    yapabildik [1]. Ayrica polimer yüzeylerin konformasyonunda olan deiiklikleri ve DNA-protein komplekslerinin

  8. Membrane Proteins DOI: 10.1002/anie.201107343

    E-Print Network [OSTI]

    Wallace, Mark

    is hampered by a lack of high-throughput methods for their study. Membrane proteins remain such challengingMembrane Proteins DOI: 10.1002/anie.201107343 Quantification of Membrane Protein Inhibition. Wallace* Despite the importance of membrane proteins as drug targets the discovery of new compounds

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

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

    DOE Patents [OSTI]

    Mayfield, Stephen P. (Cardiff, CA)

    2010-03-16T23:59:59.000Z

    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.

  16. 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)

    2008-05-06T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Powers, Robert

    of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally of various genomics efforts has been a vast growth in putative protein sequences that lack any experimental identified in various proteomes.2,4­6 Structural genomics is augmenting the functional assignment

  18. Calculations of the binding affinities of protein-protein complexes with the fast multipole method

    E-Print Network [OSTI]

    Song, Xueyu

    Calculations of the binding affinities of protein-protein complexes with the fast multipole method the boundary element method in combination with the fast multipole method. The residue level model with the fast multipole method allows us to efficiently investigate how the mutations on the active site

  19. 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 methods can be broadly classified into two categories, that is, template-based1­6 and taxonomy- based.7­13 In recent years, the taxonomy-based method has attracted great attention due to its encouraging performance

  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. DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

    E-Print Network [OSTI]

    Vajda, Sandor

    DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking Gwo-Yu Chuang,* Dima As the Reference State (DARS) is a simple and natural approach to the construction of structure directly in docking calculations. We investigated the performance of various DARS versions for docking

  2. 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

  3. Ribosomal Proteins S5 and L6: High-resolution Crystal Structures and Roles in Protein Synthesis and

    E-Print Network [OSTI]

    Ramakrishnan, Venki

    Ribosomal Proteins S5 and L6: High-resolution Crystal Structures and Roles in Protein Synthesis proteins and characterize these mutations. The S5 protein, from the small ribosomal unit, is associated propose that the C-terminal half of S5, which contains the accuracy mutations, organizes RNA structures

  4. Protein Science (1997), 6:347-354.Cambridge University Press. Printed in the USA. Copyright 0 1997The Protein Society

    E-Print Network [OSTI]

    Baker, David

    -limiting step in protein folding JEFFREY A. RANK' AND DAVID BAKER2 `Department of Physics, University to the barrier to protein foldinghnfolding. Importantly for the simulation of protein folding without explicit. Keywords: hydrophobic interaction; potential of mean force; protein folding The hydrophobic interaction

  5. Computational Flow Chart for Indentifying Hit Molecules for a Target Protein Protein-Ligand (PL) complex as input

    E-Print Network [OSTI]

    Jayaram, Bhyravabotla

    Computational Flow Chart for Indentifying Hit Molecules for a Target Protein Case A Protein Predict Binding Energy of the PL Complex Scanning single molecule uploaded Scanning million molecules calculated parameters of the protein Predict binding energy of the new molecule for the same protein

  6. Protein Expression and PuriWcation 36 (2004) 207216 www.elsevier.com/locate/yprep

    E-Print Network [OSTI]

    Yciency of spontaneous protein folding. 2004 Elsevier Inc. All rights reserved. Keywords: Fusion protein; Aggregation; Protein folding; Electrostatic repulsion Protein production and characterization has been greatly aggregation during the protein folding process [4]. Polypeptide aggregation during overexpression therefore

  7. A comparative study of HPr proteins from extremophilic organisms

    E-Print Network [OSTI]

    Syed Ali, Abbas Razvi

    2006-04-12T23:59:59.000Z

    . Sequence, in turn, defines structure as studied in the field of protein folding. Sequence is also the variable which organisms change as they evolve to adapt their proteins to the environments they inhabit. The sequence... associated with protein folding and ?G, the free energy of protein stabilization. Proteins from thermophiles alter their sequence in a way such that it optimizes the interactions holding their conformations together; these optimizations...

  8. Prion protein induced signaling cascades in monocytes

    SciTech Connect (OSTI)

    Krebs, Bjarne [Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Muenchen (Germany); Dorner-Ciossek, Cornelia [CNS Research III, Boehringer Ingelheim Pharma GmbH and Co KG, Biberach/Riss (Germany); Schmalzbauer, Ruediger [Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich (Germany); Vassallo, Neville [Department of Physiology and Biochemistry, University of Malta, Msida (Malta); Herms, Jochen [Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich (Germany); Kretzschmar, Hans A. [Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich (Germany)]. E-mail: Hans.Kretzschmar@med.uni-muenchen.de

    2006-02-03T23:59:59.000Z

    Prion proteins play a central role in transmission and pathogenesis of transmissible spongiform encephalopathies. The cellular prion protein (PrP{sup C}), whose physiological function remains elusive, is anchored to the surface of a variety of cell types including neurons and cells of the lymphoreticular system. In this study, we investigated the response of a mouse monocyte/macrophage cell line to exposure with PrP{sup C} fusion proteins synthesized with a human Fc-tag. PrP{sup C} fusion proteins showed an attachment to the surface of monocyte/macrophages in nanomolar concentrations. This was accompanied by an increase of cellular tyrosine phosphorylation as a result of activated signaling pathways. Detailed investigations exhibited activation of downstream pathways through a stimulation with PrP fusion proteins, which include phosphorylation of ERK{sub 1,2} and Akt kinase. Macrophages opsonize and present antigenic structures, contact lymphocytes, and deliver cytokines. The findings reported here may become the basis of understanding the molecular function of PrP{sup C} in monocytes and macrophages.

  9. Human Cementum Protein 1 induces expression of bone and cementum proteins by human gingival fibroblasts

    SciTech Connect (OSTI)

    Carmona-Rodriguez, Bruno [Laboratorio de Biologia Celular y Molecular, Facultad de Odontologia, UNAM, Cd. Universitaria, Coyoacan, Mexico, D.F. 04510 (Mexico); Alvarez-Perez, Marco Antonio [Laboratorio de Biologia Celular y Molecular, Facultad de Odontologia, UNAM, Cd. Universitaria, Coyoacan, Mexico, D.F. 04510 (Mexico); Narayanan, A. Sampath [Department of Pathology, School of Medicine, UW, Seattle (United States); Zeichner-David, Margarita [Center for Craniofacial Molecular Biology, School of Dentistry, USC, Los Angeles (United States); Reyes-Gasga, Jose [Instituto de Fisica, UNAM (Mexico); Molina-Guarneros, Juan [Facultad de Medicina, UNAM (Mexico); Garcia-Hernandez, Ana Lilia [Laboratorio de Biologia Celular y Molecular, Facultad de Odontologia, UNAM, Cd. Universitaria, Coyoacan, Mexico, D.F. 04510 (Mexico); Suarez-Franco, Jose Luis [Laboratorio de Biologia Celular y Molecular, Facultad de Odontologia, UNAM, Cd. Universitaria, Coyoacan, Mexico, D.F. 04510 (Mexico); Chavarria, Ivet Gil [Laboratorio de Biologia Celular y Molecular, Facultad de Odontologia, UNAM, Cd. Universitaria, Coyoacan, Mexico, D.F. 04510 (Mexico); Villarreal-Ramirez, Eduardo [Laboratorio de Biologia Celular y Molecular, Facultad de Odontologia, UNAM, Cd. Universitaria, Coyoacan, Mexico, D.F. 04510 (Mexico); Arzate, Higinio [Laboratorio de Biologia Celular y Molecular, Facultad de Odontologia, UNAM, Cd. Universitaria, Coyoacan, Mexico, D.F. 04510 (Mexico)]. E-mail: harzate@servidor.unam.mx

    2007-07-06T23:59:59.000Z

    We recently presented evidence showing that a human cementoblastoma-derived protein, named Cementum Protein 1 (CEMP1) may play a role as a local regulator of cementoblast differentiation and cementum-matrix mineralization. This protein was shown to be expressed by cementoblasts and progenitor cells localized in the periodontal ligament. In this study we demonstrate that transfection of CEMP1 into human gingival fibroblasts (HGF) induces mineralization and expression of bone and cementum-matrix proteins. The transfected HGF cells had higher alkaline phosphatase activity and proliferation rate and they expressed genes for alkaline phosphatase, bone sialoprotein, osteocalcin, osteopontin, the transcription factor Runx2/Cbfa1, and cementum attachment protein (CAP). They also produced biological-type hydroxyapatite. These findings indicate that the CEMP1 might participate in differentiation and mineralization of nonosteogenic cells, and that it might have a potential function in cementum and bone formation.

  10. Differential stoichiometry among core ribosomal proteins

    E-Print Network [OSTI]

    Nikolai Slavov; Sefan Semrau; Edoardo Airoldi; Bogdan Budnik; Alexander van Oudenaarden

    2015-04-15T23:59:59.000Z

    Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its deregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs), some experiments suggest a more variable composition. Testing such variability requires direct and precise quantification of RPs. We used mass-spectrometry to directly quantify RPs across monosomes and polysomes of mouse embryonic stem cells (ESC) and budding yeast. Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes. Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.

  11. Compositions and methods for improved protein production

    DOE Patents [OSTI]

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

    2012-07-10T23:59:59.000Z

    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.

  12. Bayesian Nonparametric Methods for Protein Structure Prediction

    E-Print Network [OSTI]

    Lennox, Kristin Patricia

    2011-10-21T23:59:59.000Z

    prior into our nonparametric density estimate and find that this significantly improves per- formance for protein loop prediction. The final piece of our structure prediction strategy is to connect side-chain locations to our torsion angle... FIGURE Page 1 Diagram of protein backbone, including and angles, whole po- sitions, and half positions. At the ith residue, the angle describes the torsion around the bond Ni-C i, measuring the angle between the Ci 1-Ni and the C i-Ci bonds, while...

  13. Proteotronics: Electronic devices based on proteins

    E-Print Network [OSTI]

    E. Alfinito; L. Reggiani; J. Pousset

    2014-05-15T23:59:59.000Z

    The convergent interests of different scientific disciplines, from biochemistry to electronics, toward the investigation of protein electrical properties, has promoted the development of a novel bailiwick, the so called proteotronics. The main aim of proteotronics is to propose and achieve innovative electronic devices, based on the selective action of specific proteins. This paper gives a sketch of the fields of applications of proteotronics, by using as significant example the detection of a specific odorant molecule carried out by an olfactory receptor. The experiment is briefly reviewed and its theoretical interpretation given. Further experiments are envisioned and expected results discussed in the perspective of an experimental validation.

  14. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17T23:59:59.000Z

    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.

  15. Protein synthesis driven by dynamical stochastic transcription

    E-Print Network [OSTI]

    Guilherme C. P. Innocentini; Michael Forger; Fernando Antoneli

    2014-12-23T23:59:59.000Z

    In this letter we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics of protein density is governed by a random differential equation. The coupling between the two processes is given by a stochastic perturbation whose statistics satisfies the master equations. In this approach, from the knowledge of the analytical time dependent distribution of mRNA number, we are able to calculate the dynamics of the probability density of the protein population.

  16. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  17. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting your personalSedimentProteinProtein

  18. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein FlipsProtein Instability

  19. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein FlipsProtein

  20. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProteinThreading Method |Protein

  1. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProteinThreading MethodProtein

  2. Protein shake-up | ornl.gov

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProteinThreadingProtein shake-up

  3. Functional characterization of acyl-CoA binding protein (ACBP) and oxysterol binding protein-related proteins (ORPS) from Cryptosporidium parvum

    E-Print Network [OSTI]

    Zeng, Bin

    2009-05-15T23:59:59.000Z

    with the parasitophorous vacuole membrane (PVM), which implies that this protein may be involved in lipid remodelling in the PVM, or in the transport of fatty acids across the membrane. We also identified two distinct oxysterol binding protein (OSBP)-related proteins (ORPs...

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

    E-Print Network [OSTI]

    Slavoff, Sarah Ann

    2010-01-01T23:59:59.000Z

    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 ...

  5. Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example

    E-Print Network [OSTI]

    Alibes, Andreu

    Quite often a single or a combination of protein mutations is linked to specific diseases. However, distinguishing from sequence information which mutations have real effects in the protein’s function is not trivial. Protein ...

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

    E-Print Network [OSTI]

    Shang, Yue

    2007-09-17T23:59:59.000Z

    .4 by Pichia expresion system. Detected by commasie blue staining. Column was eluted with six 1 ml aliquots of imadazole. A total of 25 ul of each elution was loaded on the gel. E1 is the first elution through which has the most protein detected. 20kDa E6... E5 E4 E3 E2 E1 31 15kDa E7 E6 E5 E4 E3 E2 E1 Figure 10. Hypothetical protein MG 10424.4 purified from P. pastoris. Column was eluted six times and protein started to come out from the first...

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

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-12-28T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Simmons, Walter

    2013-01-01T23:59:59.000Z

    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...

  9. 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

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

    E-Print Network [OSTI]

    Powers, Robert

    analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we,2). These databases constitute the extent of our knowledge related to genomics, prote- omics, metabolomics, and structural genomics. Most serve as data warehouses with simple interfaces for data retrieval (3). To address

  11. Protein Data Bank Project at Rutgers University

    SciTech Connect (OSTI)

    Berman, Helen

    2002-07-18T23:59:59.000Z

    The central activities of the Protein Data Base continue to be the collection, archiving and distribution of high quality structural data to the scientific community on a timely basis. The systems that have been developed for doing this has become increasingly reliable and stable. We have completed the inventory of magnetic and paper media that was received from Brookhaven National Laboratory.

  12. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

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

    1998-01-13T23:59:59.000Z

    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.

  13. Protein Models Comparator Scalable Bioinformatics Computing on

    E-Print Network [OSTI]

    Krasnogor, Natalio

    of parameters of energy functions used in template-free modelling and refinement. Although many protein Engine cloud platform and is a showcase of how the emerging PaaS (Platform as a Service) technology could, the predicted structure is compared against the target native structure. This type of evaluation is performed

  14. COMMUNICATION Protein Chemistry at Membrane Interfaces

    E-Print Network [OSTI]

    White, Stephen

    of hydrophobic (ÁGHÈ) and electrostatic (ÁGES) free energies. If these are simply addi- tive, then the observed free energy of binding (ÁGobs) will be given by ÁGobs ÁGHÈ ÁGES, where ÁGHÈ À sNPANP and ÁGES z suggest that hydrophobic and electrostatic binding free energies of proteins at membrane interfaces

  15. 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

  16. Towards a Molecular Understanding of Protein Solubility

    E-Print Network [OSTI]

    Kramer, Ryan 1984-

    2011-05-31T23:59:59.000Z

    be used to obtain comparative solubility measurements, and they fall into three broad classes: salts, long-chain polymers, and organic solvents. Our group has used a model protein, RNase Sa, to create 20 variants that differ by the residues at a single...

  17. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11T23:59:59.000Z

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

  18. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

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

  19. Elucidating Amyloid -Protein Folding and Assembly: A

    E-Print Network [OSTI]

    Stanley, H. Eugene

    for a comprehensive review). A fibrils are the principal protein component of the extracellular deposits (amyloid that A 42 forms fibrils at significantly higher rates than does A 40. Importantly, A 42 self-association. A fibrils are formed by a small number of stacked, extended, ribbon-like -sheets, each of which is formed

  20. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13T23:59:59.000Z

    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.

  1. Histone H1 proteins in Chlamydomonas reinhardtii

    E-Print Network [OSTI]

    Salinger, Andrew Paul

    1994-01-01T23:59:59.000Z

    compared to histones collected from pea leaf nuclei. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of 5% perchloric acid (PCA) extracts of isolated C. reinhardtii nuclei revealed two Hl proteins (Hia and Hlb) along with an H2B...

  2. Neurofilament Proteins in Avian Auditory Hair Cells

    E-Print Network [OSTI]

    Rubel, Edwin

    Neurofilament Proteins in Avian Auditory Hair Cells ELIZABETH C. OESTERLE,* DIANA I. LURIE avian inner ear by using immunocytochemical techniques. NF-M was detected in auditory hair cells and VIIIth cranial nerve neurons. NF-M-positive hair cells are first detected at embryonic day 11 (E11

  3. Metal-directed protein self-assembly

    E-Print Network [OSTI]

    Salgado. Eric N.

    2010-01-01T23:59:59.000Z

    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

  4. 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)

    2014-03-15T23:59:59.000Z

    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.

  5. Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry

    SciTech Connect (OSTI)

    Zhang, Haizhen; Tang, Xiaoting; Munske, Gerhard R.; Tolic, Nikola; Anderson, Gordon A.; Bruce, James E.

    2009-03-01T23:59:59.000Z

    We present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno/affinity purifications. The strategy consists of: (i) chemical cross-linking reaction: intact cell labeling with a novel class of chemical cross-linkers, protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by 2D-LC/MS/MS; and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. The primary advantage of the PIR approach and distinction from current technology is that protein interactions together with topologies are detected in native biological systems by stabilizing protein complexes with new covalent bonds while the proteins are present in the original cellular environment. Thus, weak or transient interactions or interactions that require properly folded, localized, or membrane-bound proteins can be labeled and identified through the PIR approach. This strategy was applied to S. oneidensis bacterial cells and initial studies resulted in identification of a set of protein-protein interactions and their contact/binding regions. Furthermore, most identified interactions involved membrane proteins, suggesting the PIR approach is particularly suited for studies of membrane protein-protein interactions, an area under-represented with current widely-used approaches.

  6. Corn Storage Protein - A Molecular Genetic Model

    SciTech Connect (OSTI)

    Messing, Joachim [Rutgers, The State University of New Jersey

    2013-05-31T23:59:59.000Z

    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.

  7. Belgian energy and protein feeding standards for growing and fattening cattle

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    ). 2. Protein Crude protein and digestible crude protein are used to express the protein requirements the liveweight range of 200 - 350 kg, a digestible crude protein content of 10.3 per cent (11.2 per cent crude was not depressed. Between 350 and 480 kg 10.3 per cent digestible crude protein (11.2 per cent crude protein

  8. THE ENTEROHEMORRHAGIC ESCHERICHIA COLI EFFECTOR PROTEIN NLEF BINDS MAMMALIAN HOST PROTEINS

    E-Print Network [OSTI]

    Olsen, Rachel Lee

    2012-12-31T23:59:59.000Z

    The extracellular human pathogens enterohemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC) and the related mouse pathogen Citrobacter rodentium inject type III secretion system (T3SS) effector proteins to ...

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

    E-Print Network [OSTI]

    Tovchigrechko, Andrey; Vakser, Ilya A.

    2006-07-01T23:59:59.000Z

    -based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320...

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

    E-Print Network [OSTI]

    Mukherjee, Srayanta

    2011-12-31T23:59:59.000Z

    approach using TM-score as the objective function. However, the traditional NW dynamic programming was redesigned to prevent the cross alignment of chains during the structure alignment process. Driven by the knowledge obtained from MM-align that protein...

  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.

    2007-01-01T23:59:59.000Z

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

    E-Print Network [OSTI]

    Ruvinsky, Anatoly M.; Vakser, Ilya A.

    2008-09-01T23:59:59.000Z

    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...

  13. The roles of protein disulfide-isomerase associated 6 and alpha-B crystallin in chaperone-mediated cardioprotection /

    E-Print Network [OSTI]

    Vekich, John Alan

    2013-01-01T23:59:59.000Z

    Protein Folding ..5 A. Protein Folding in the EndoplasmicBraakman I, Bulleid NJ. Protein folding and modification in

  14. Consistent blind protein structure generation from NMR chemical shift data

    E-Print Network [OSTI]

    Baker, David

    Consistent blind protein structure generation from NMR chemical shift data Yang Shen*, Oliver Lange been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 k

  15. 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

  16. DB-PABP: a database of polyanion-binding proteins

    E-Print Network [OSTI]

    Fang, Jianwen; Dong, Yinghua; Slamat-Miller, Nazila; Middaugh, C. Russell

    2007-10-04T23:59:59.000Z

    The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many...

  17. The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

    E-Print Network [OSTI]

    Dixit, Anshuman; Verkhivker, Gennady M.

    2011-10-06T23:59:59.000Z

    The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present ...

  18. A Complete Microfluidic Screening Platform for Rational Protein Crystallization

    E-Print Network [OSTI]

    Hansen, Carl L.

    A Complete Microfluidic Screening Platform for Rational Protein Crystallization Billy T. C. Lau integration, and low reagent consumption, microfluidic devices have emerged as viable technologies for protein crystallization. Current microfluidic crystallization technologies have focused on two separate strategies: one

  19. Rapid and Efficient Protein Digestion using Trypsin Coated Magnetic...

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

    were carried out on a single model protein, a five protein mixture, and a whole mouse brain proteome, and also compared for digestion at atmospheric pressure and 37 ºC for...

  20. autoinducer-2 processing protein: Topics by E-print Network

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

    of two fatty acids and a hydrophilic group provided by a phosphoric acid ester... Perez Hernandez, Gabriela 2005-08-29 82 Winter 2011 Evaluating Protein-Protein Docking Web...

  1. Structure and function of Pseudomonas aeruginosa protein PA1324 (21170)

    E-Print Network [OSTI]

    Powers, Robert

    Northwest National Laboratory, Biological Sciences Division, Northeast Structural Genomics Consortium and Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056 Received 12 June 2008 aeruginosa PA1324; NMR; functional genomics; NMR high-throughput screens; protein-ligand binding; protein

  2. Optimizing a global alignment of protein interaction networks

    E-Print Network [OSTI]

    Ma, C.-Y.

    Motivation: The global alignment of protein interaction networks is a widely studied problem. It is an important first step in understanding the relationship between the proteins in different species and identifying ...

  3. Computational approaches for identifying inhibitors of protein interactions 

    E-Print Network [OSTI]

    Mehio, Wissam

    2011-06-27T23:59:59.000Z

    Inter-molecular interaction is at the heart of biological function. Proteins can interact with ligands, peptides, small molecules, and other proteins to serve their structural or functional purpose. With advances in ...

  4. activation protein expression: Topics by E-print Network

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

    the relative rates of protein synthesis 98 Reduced 293T cell susceptibility to acrolein due to aldose reductase-like-1 protein expression CiteSeer Summary: Acrolein is a...

  5. A genetic bistable switch utilizing nonlinear protein degradation

    E-Print Network [OSTI]

    Huang, Daniel; Holtz, William J; Maharbiz, Michel M

    2012-01-01T23:59:59.000Z

    T: Nonlinear protein degradation and the function of geneticRT: Evolution of the ssrA degradation tag in Mycoplasma:AD: Inducible protein degradation in Bacillus subtilis using

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

    E-Print Network [OSTI]

    Schubert, Christian Reinhold

    2009-01-01T23:59:59.000Z

    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 ...

  7. Protein-DNA interaction, random walks and polymer statistics

    E-Print Network [OSTI]

    Slutsky, Michael

    2005-01-01T23:59:59.000Z

    In Part I of the thesis, a general physical framework describing the kinetics of protein- DNA interaction is developed. Recognition and binding of specific sites on DNA by proteins is central for many cellular functions ...

  8. Function of the anterior gradient protein family in cancer 

    E-Print Network [OSTI]

    Fourtouna, Argyro

    2009-01-01T23:59:59.000Z

    Proteomic technologies verified Anterior Gradient 2, AGR-2, as a protein over-expressed in human cancers, including breast, prostate and oesophagus cancers, with the ability to inhibit the tumour suppressor protein p53. AGR-2 gene is a hormone...

  9. Synthesis of Proteins with Homogenous Chemical and Posttranslational Modifications

    E-Print Network [OSTI]

    Wu, Bo

    2014-06-19T23:59:59.000Z

    Genetic encoding non-canonical amino acids (NCAAs) is a facile approach to synthesize proteins with homogenous modifications. In my graduate study, I demonstrated the application of this approach in the synthesis of a variety of proteins with site...

  10. Lipid-dependent regulation of the unfolded protein response

    E-Print Network [OSTI]

    Volmer, Romain; Ron, David

    2014-12-25T23:59:59.000Z

    Protein folding homeostasis in the lumen of the endoplasmic reticulum is defended by signal transduction pathways that are activated by an imbalance between unfolded proteins and chaperones (so called ER stress). Collectively referred...

  11. arabinogalactan protein distribution: Topics by E-print Network

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

    or a computer farm. Michael Cahill; Sean Cahill; Kevin Cahill 2001-08-14 92 Protein evolution CiteSeer Summary: On the origin of proteins A series of mistakes over the past...

  12. Experimental and Computational Studies on Protein Folding, Misfolding and Stability

    E-Print Network [OSTI]

    Wei, Yun

    2010-07-14T23:59:59.000Z

    Proteins need fold to perform their biological function. Thus, understanding how proteins fold could be the key to understanding life. In the first study, the stability and structure of several !-hairpin peptide variants derived from the C...

  13. Why are MD simulated protein folding times wrong? Dmitry Nerukh

    E-Print Network [OSTI]

    Nerukh, Dmitry

    Why are MD simulated protein folding times wrong? Dmitry Nerukh Unilever Centre for Molecular.ac.uk The question of significant deviations of protein folding times simulated using molecular dynamics from

  14. Protein Folding Simulation in CCP Luca Bortolussi1

    E-Print Network [OSTI]

    Bortolussi, Luca

    Protein Folding Simulation in CCP Luca Bortolussi1 , Alessandro Dal Pal`u1 , Agostino Dovier1 as the protein folding. This problem is fundamental for biological and pharmaceutical research. Currently

  15. Rational design of additives for inhibition of protein aggregation

    E-Print Network [OSTI]

    Shukla, Diwakar

    2011-01-01T23:59:59.000Z

    Protein based therapeutics hold great promise in the treatment of human diseases and disorders and subsequently, they have become the fastest growing sector of new drugs being developed. Proteins are, however, inherently ...

  16. acid binding proteins: Topics by E-print Network

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

    The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

  17. acidbinding protein concentration: Topics by E-print Network

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

    The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

  18. acid sensitive protein: Topics by E-print Network

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

    The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Protein structures uncovered Amino acids are molecules and are...

  19. A comparative study of HPr proteins from extremophilic organisms 

    E-Print Network [OSTI]

    Syed Ali, Abbas Razvi

    2006-04-12T23:59:59.000Z

    A thermodynamic study of five homologous HPr proteins derived from organisms inhabiting diverse environments has been undertaken. The aim of this study was to further our understanding of protein stabilization in extremes ...

  20. How the Membrane Protein AmtB Transports Ammonia

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

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

  1. Self-assembly of globular protein-polymer diblock copolymers

    E-Print Network [OSTI]

    Thomas, Carla S. (Carla Stephanie)

    2014-01-01T23:59:59.000Z

    Self-assembly of protein-polymer block copolymers provides a simple bottom-up approach towards protein nanopatteming for the fabrication of more effective and efficient bioelectronic and biocatalytic devices. Changes in ...

  2. Fragile X mental retardation protein and synaptic plasticity

    E-Print Network [OSTI]

    Sidorov, Michael Samuel

    Loss of the translational repressor FMRP causes Fragile X syndrome. In healthy neurons, FMRP modulates the local translation of numerous synaptic proteins. Synthesis of these proteins is required for the maintenance and ...

  3. E-Print Network 3.0 - a-binding protein acbp6 Sample Search Results

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

    Biology and Medicine 3 Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding Summary: kinetics using FRET with acyl-CoA binding protein. In protein folding,...

  4. E-Print Network 3.0 - auxilin-like j-domain protein Sample Search...

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

    conserved family of ubiquitous molecular chaperones that play essential roles in protein folding... Bcl-2 BAP : BiP-Associated Proteins ; proteins associes BiP CFTR : Cystic...

  5. E-Print Network 3.0 - a-3 proteins weakly Sample Search Results

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

    structures of proteins are the support... focuses to understand the mechanisms of protein folding and stability. Furthermore, protein ... Source: Ecole Polytechnique, Centre de...

  6. E-Print Network 3.0 - ankyrin-repeat membrane protein Sample...

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

    10 Stabilizing IB by "Consensus" Design Diego U. Ferreiro1,3 Summary: Keywords: protein folding; ankyrin repeat protein; NF-B; transcription factor; repeat protein...

  7. E-Print Network 3.0 - ankyrin protein networks Sample Search...

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

    >> 21 Stabilizing IB by "Consensus" Design Diego U. Ferreiro1,3 Summary: Keywords: protein folding; ankyrin repeat protein; NF-B; transcription factor; repeat protein...

  8. Redox Characterization of Proteins Involved in the Mitochondrial Intermembrane Space Pathway

    E-Print Network [OSTI]

    Neal, Sonya Elina

    2013-01-01T23:59:59.000Z

    Bardwell. 1999. Oxidative protein folding is driven by theRedox regulation of protein folding in the mitochondrial2008. Disulfide-linked protein folding pathways. Annu. Rev.

  9. Facilitation of protein 3-D structure determination using enhanced peptide amide deuterium exchange mass spectrometry (DXMS)

    E-Print Network [OSTI]

    Pantazatos, Dennis Peter

    2006-01-01T23:59:59.000Z

    hydrophobic interaction in protein folding. Proc Natl Acad1999;28:1-27. 15. Protein Folding, Dynamics, and StructuralHydrogen exchange and protein folding. Curr. Opin. Struct.

  10. Signatures of the protein folding pathway in two-dimensional ultraviolet spectroscopy

    E-Print Network [OSTI]

    Jiang, J; Lai, Z; Wang, J; Mukamel, S

    2014-01-01T23:59:59.000Z

    2) Dobson, C. M. Protein Folding and Misfolding. Naturethe Complexity of Protein Folding. Curr. Opin. Struct. Biol.Signatures of the Protein Folding Pathway in Two-Dimensional

  11. Microfluidic advantage : novel techniques for protein folding and oxygen control in cell cultures

    E-Print Network [OSTI]

    Polinkovsky, Mark E.; Polinkovsky, Mark E.

    2012-01-01T23:59:59.000Z

    Novel Techniques for Protein Folding and Oxygen Control inTemperature Jump System to Study Fast Protein FoldingNovel Techniques for Protein Folding and Oxygen Control in

  12. Carbon-deuterium bonds as an infrared probe of protein dynamics, local electrostatics and folding

    E-Print Network [OSTI]

    Sagle, Laura B.

    2006-01-01T23:59:59.000Z

    and Englander, W. S. , Protein Folding: A Stepwise AssemblyEnglander, S. W. , Protein Folding Intermediates – NativeR. L. , How Does Protein Folding Get Started? Trends

  13. MORPH-PRO: a novel algorithm and web server for protein morphing

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    PA: Pathways to a protein folding intermediate observed in amotion planning to study protein folding pathways. J ComputGo N: Studies on protein folding, unfolding and fluctuations

  14. Single proteins that serve linked functions in intracellular and extracellular microenvironments

    E-Print Network [OSTI]

    Radisky, Derek C.

    2009-01-01T23:59:59.000Z

    listed above, these proteins lack exocytosis-targetingthe cell. These proteins often lack defined secretory signalthe lack of an exocytosis signal sequence in proteins with

  15. alpha-tocopherol transfer protein: Topics by E-print Network

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

    proteins often evolve Nachman, Michael 4 Density Functional Theory for Protein Transfer Free Energy CERN Preprints Summary: We cast the problem of protein transfer free energy...

  16. Energy landscapes for protein folding, binding, and aggregation : simple funnels and beyond

    E-Print Network [OSTI]

    Cho, Samuel Sung-Il

    2007-01-01T23:59:59.000Z

    coordinates capture protein folding on smooth landscapes.in the Prediction of Protein Folding Kinetics. Proc. Natl.Landscapes for Protein Folding, Binding, and Aggregation:

  17. A multi-objective evolutionary approach to the protein structure prediction problem

    E-Print Network [OSTI]

    -objective optimization; Pareto front; protein folding; protein structure prediction; multi-objective evolutionary and of growing biological polymers with specific material properties. Protein folding (PF) has

  18. The cardiokine story unfolds: ischemic stress-induced protein secretion

    E-Print Network [OSTI]

    Glembotski, Christopher

    on secreted proteins to mount a response designed to resist stress-induced damage. This review examines

  19. RACK1, A Multifaceted Scaffolding Protein: Structure and Function

    E-Print Network [OSTI]

    Adams, David R; Ron, Dorit; Kiely, Patrick A

    2011-01-01T23:59:59.000Z

    protein interacts with Helicobacter pylori VacA cytotoxin:16 (HPV 16) [213] and Helicobacter pylori [214]. There are

  20. Utilization of oilseed proteins in precooked breakfast sausage

    E-Print Network [OSTI]

    Harward, Eugene Rees

    1979-01-01T23:59:59.000Z

    Committee: Dr. R. N. Terrell Dr. G. C. Smith Three separate but interrelated experiments were conducted to determine the effects of oilseed protein products on the physical, sensory and chemical properties of precooked breakfast links. Three types... links (control and protein-added) were made in which vary- ing levels of raw meat were replaced with an equivalent weight of soy or cottonseed proteins which were calculated to contain approximately 16% protein on a hydrated basis. In Experiment 1...