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)

    AAA+ and RecA. Rho belongs to the RecA family, which is most common in bacteria. AAA+ motors are predominantly found in eukaryotes, including humans, as well as some human...

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassive Solar HomePromisingStories »SubmitterJ. NorbyN.Rocks RocksEnergy

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassive Solar HomePromisingStories »SubmitterJ. NorbyN.Rocks RocksEnergyRotary

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0 Resource ProgramEnergyMaterials: SulfurRosenbaum s Proposal

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0 Resource ProgramEnergyMaterials: SulfurRosenbaum s ProposalRotary

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0 Resource ProgramEnergyMaterials: SulfurRosenbaum s

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0 Resource ProgramEnergyMaterials: SulfurRosenbaum sRotary Firing

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0 Resource ProgramEnergyMaterials: SulfurRosenbaum sRotary

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0 Resource ProgramEnergyMaterials: SulfurRosenbaum sRotaryRotary

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0 Resource ProgramEnergyMaterials: SulfurRosenbaum

  11. Study of CMOS APS Responsivity Enhancement: Ring-Shaped Photodiode

    E-Print Network [OSTI]

    Study of CMOS APS Responsivity Enhancement: Ring-Shaped Photodiode Tatiana Danov, Igor Shcherback obtained from various ring-shaped pixel photodiodes with different inner radius, implemented in a standard illumination. We show that the photodiodes with a small ring-opening exhibit better sensitivity in the blue

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

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

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

  13. 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 1.53 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. ALSNews Vol. 308

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

    In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure...

  17. Proteins

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

    Bioscience: Bioenergy, Biosecurity, and Health Proteins Protein Engineering, Structure, and Function Los Alamos scientists seek a comprehensive understanding of the structure...

  18. Proteins

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

    Scientists manipulate and mimic proteins for use in creating solutions for medicine, sustainable energy, and more Read caption + Los Alamos National Laboratory graduate...

  19. 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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedlesAdvanced Photon Source The SuperpowerrelatedProteins

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed NewcatalystNeutron scattering characterizes dynamics in polymer

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed NewcatalystNeutron scattering characterizes dynamics in polymerDynein Motor Domain

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed NewcatalystNeutron scattering characterizes dynamics in polymerDynein Motor

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed NewcatalystNeutron scattering characterizes dynamics in polymerDynein MotorDynein

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed NewcatalystNeutron scattering characterizes dynamics in polymerDynein

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to UserProduct:Directives Templates8.Siftingnanocrystals forDynein Motor

  6. 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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to UserProduct:Directives Templates8.Siftingnanocrystals forDynein

  7. The Subsumptive Constraints Account of why explaining "why?" helps learning

    E-Print Network [OSTI]

    Williams, Joseph Jay

    2013-01-01T23:59:59.000Z

    2010). Why does explaining help learning? Insight from anand development .. 8 1.3. Why does explaining why? helpof why explaining why? helps learning by Joseph Jay

  8. Physics of Intrinsic Plasma Rotation Explained for the First...

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

    Physics of Intrinsic Plasma Rotation Explained for First Time Physics of Intrinsic Plasma Rotation Explained for First Time Key understanding for modeling future fusion reactors...

  9. 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...

  10. Power, policy and war : explaining the Iran-Iraq War.

    E-Print Network [OSTI]

    Donovan, Jerome Denis

    2008-01-01T23:59:59.000Z

    ??The failure of traditional analytical tools in successfully predicting the end of the Cold War has seen a series of competing methods seeking to explain (more)

  11. A discontinuity of the background explains the Pioneer anomaly

    E-Print Network [OSTI]

    Frederic Henry-Couannier

    2007-03-02T23:59:59.000Z

    The Pioneer anomaly is explained very simply if we assume that somewhere between us and the aircraft, the scale factor has undergone a discrete jump from an expansion a(t) regime to a contraction 1/a(t) regime

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

    E-Print Network [OSTI]

    Kotchen, Matthew J.

    EXPLAINING THE PRICE OF VOLUNTARY CARBON OFFSETS MARC N. CONTE Stanford University, Stanford, CA of voluntary carbon offsets. We estimate hedonic price functions using a variety of provider- and project-profit or not-for-profit. Keywords: Voluntary carbon offsets; hedonic price method. 1. Introduction

  13. Nuclear Physics Explained in Simple Terms Ernest M. Henley

    E-Print Network [OSTI]

    Garcia, Alejandro

    Nuclear Physics Explained in Simple Terms Ernest M. Henley University of Washington Alejandro Garc challenges that the human mind has ever undertaken. Nuclear physics is a mature science, more than one be understood. We wrote this book to address the curiosity of the lay person with respect to nuclear physics

  14. 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

  15. www.kostic.niu.edu Energy Everywhere Explained

    E-Print Network [OSTI]

    Kostic, Milivoje M.

    www.kostic.niu.edu Energy Everywhere Explained: Importance of Energy Conservation and Renewable ..." One hour of solar energy falling on Earth could power the World for a year Slide 9www and Alternative Energy Resources Prof. M. Kostic Mechanical Engineering NORTHERN ILLINOIS UNIVERSITY NIU SET House

  16. Phosphor: Explaining Transitions in the User Interface Using Afterglow Effects

    E-Print Network [OSTI]

    Hunt, Galen

    Phosphor: Explaining Transitions in the User Interface Using Afterglow Effects Patrick Baudisch, especially in situations where users did not need an explanation. We propose a different approach. Phosphor in retrospect. Manipulating a phosphor slider, for example, leaves an afterglow that illustrates how the knob

  17. Continued on next page A letter explaining the 2005 HVAC

    E-Print Network [OSTI]

    Continued on next page A letter explaining the 2005 HVAC Change-out to consumers is available this bulletin, or downloaded from the 2005 HVAC Change out Information website at: www.energy.ca.gov/title24 duct sealing requirements for HVAC change-outs in existing homes become effective October 1, 2005

  18. 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

  19. "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.

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

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data CenterFranconia, Virginia: Energy ResourcesLoadingPenobscot County, Maine:PlugNumberOfArraProjectTypeTopic2GrossGenYes, Please Explain Jump

  1. 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.

  2. E-Print Network 3.0 - agent networks explaining Sample Search...

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

    and Information Sciences 2 Tutorial Eight 1. Explain the addressing scheme used in Mobile IP? Summary: IP? Explain your answer. Is it necessary for a foreign agent to...

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

    E-Print Network [OSTI]

    Ahmad, Sajjad

    Mick Jagger Explains High Crude Oil Prices How can Mick Jagger of The Rolling Stones help explain the current high crude oil price? It does not relate to Mick' short stint at the London School of Economics, the oil industry operates on the same principle, at least in the short run. The industry relies on proven

  4. 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 ...

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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...

  10. 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)? ...

  11. 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

  12. Manipulating and Visualizing Proteins

    E-Print Network [OSTI]

    Simon, Horst D.

    2003-01-01T23:59:59.000Z

    to unravel the protein folding problem, which refers toand adaptable to different protein folding methodologies. Ifinterface. Clearly, protein-folding research will have far-

  13. Total 100pts 1.Please use brief statements to explain the following terms in engineering

    E-Print Network [OSTI]

    Huang, Haimei

    is loaded and supported as shown in the following.Determine a. The reactions at supports4 B, and C. (6%) bTotal 100pts 1.Please use brief statements to explain the following terms in engineering mechanics is simply supported and carries a uniformly distributed load of 5 kN/m over the fill length of the beam

  14. 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

  15. Tutorial Eight 1. Explain the addressing scheme used in Mobile IP?

    E-Print Network [OSTI]

    Hamey, Len

    COMP 347 Tutorial Eight Mobile IP 1. Explain the addressing scheme used in Mobile IP? 2. One simple method to implement mobility is to let the mobile host change its address as it goes to the new network with this approach? 3. What role does a mobile host, a home agent and a foreign agent play in mobile IP protocol? 4

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

    E-Print Network [OSTI]

    Barthelat, Francois

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

  17. 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 ...

  18. Au#sm Explained: Synergis#c Poisoning from Aluminum and Glyphosate

    E-Print Network [OSTI]

    Seneff, Stephanie

    Au#sm Explained: Synergis#c Poisoning from Aluminum and Glyphosate Stephanie #12;Outline · Glyphosate and AuOsm · Aluminum, glyphosate, sulfate and the pineal gland ­ Sunlight Deficiency ­ SynergisOc Effects of Glyphosate and Aluminum

  19. Can The Natario Warp Drive Explain The OPERA Superluminal Neutrino At CERN??

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Can The Natario Warp Drive Explain The OPERA Superluminal Neutrino At CERN?? Fernando Loup of the micro Warp Drive:Microscopical particle-sized Warp Bubbles carrying inside sub-atomic particles Universe after the Big Bang and they used the Alcubierre Warp Drive geometry in their mathematical model

  20. Can selection on nest size from nest predation explain the latitudinal gradient in clutch size?

    E-Print Network [OSTI]

    Martin, Thomas E.

    Can selection on nest size from nest predation explain the latitudinal gradient in clutch size. 2. The nest size hypothesis posits that higher nest predation in the tropics favours selection for smaller nests and thereby constrains clutch size by shrinking available space for eggs and/or nestlings

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

    E-Print Network [OSTI]

    Hughes, Larry

    ERG/200806 A graphical technique for explaining the relationship between energy security and the differences between energy security and greenhouse gas emissions. This paper presents a graphical technique. This paper presents a graphical technique for illustrating the relationship between energy security

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. Discover protein sequence signatures from protein-protein interaction data

    E-Print Network [OSTI]

    Fang, Jianwen; Haasl, R. J.; Dong, Yinghua; Lushington, Gerald H.

    2005-11-23T23:59:59.000Z

    Background: The development of high-throughput technologies such as yeast two- hybrid systems and mass spectrometry technologies has made it possible to generate large protein-protein interaction ( PPI) datasets. Mining ...

  8. 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.

  9. 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

  10. 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...

  11. 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.

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

    E-Print Network [OSTI]

    Luca Maccione

    2013-01-24T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Maccione, Luca

    2012-01-01T23:59:59.000Z

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

  14. Protein Design Zhilei Chen

    E-Print Network [OSTI]

    Zhao, Huimin

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

  15. 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

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. "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...

  3. 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 ...

  4. Enriched Protein-Protein Interactions from Biomedical Text

    E-Print Network [OSTI]

    Edinburgh, University of

    Enriched Protein-Protein Interactions from Biomedical Text Barry Haddow, Michael Matthews from Biomedical Text #12;Overview The TXM Project Protein-Protein Interactions Enriched Protein Protein-Protein Interactions from Biomedical Text #12;Project Information Text Mining Programme funded (3

  5. 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

  6. Optimization Approaches to Protein Folding.

    E-Print Network [OSTI]

    Yoon, Hyun-suk

    2006-01-01T23:59:59.000Z

    ??This research shows optimization approaches to protein folding. The protein folding problem is to predict the compact three dimensional structure of a protein based on (more)

  7. 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.

  8. Protein-protein interactions as a tool for site-specific labeling of proteins

    E-Print Network [OSTI]

    Jager, M; Michalet, X; Weiss, Shimon

    2005-01-01T23:59:59.000Z

    Single- molecule protein folding: Diffusion fluorescence1995. Catalysis of a protein folding reaction: Mechanisticfree-energy surface for protein folding with single-molecule

  9. 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...

  10. 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.

  11. Enzymatic Digestion in Aqueous-Organic Solvents: A Mass Spectrometry-Based Approach in Monitoring Protein Conformation Changes

    E-Print Network [OSTI]

    Tuvilla, Mavreen Rose

    2013-05-08T23:59:59.000Z

    has a lesser impact compared to methanol and ethanol. This may explain why relative to ethanol and methanol, there are fewer digest fragment ions. On the other hand, it is a denaturant thus promoting more digest fragment ions relative to water... of Proteins???????????????????? 9 Cytochrome C???????????????????. 9 Green Fluorescent Protein??????????????.. 11 2. MATERIALS AND METHODS????????????????. 16 Materials...

  12. 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.

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

    E-Print Network [OSTI]

    Fernndez Surez, 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 ...

  14. 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.

  15. "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 Valry 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. Valry

  16. A fluid approach to HIV A readable anthropological account of social networks in South Africa and Uganda explains differences in

    E-Print Network [OSTI]

    Cai, Long

    and Uganda explains differences in the spread of sexually transmitted diseases in those countries, finds, but it was a "ritualistic act of cleansing and strengthening", says Thornton. Uganda's HIV story offers a more pleasant in its fight against the virus. Uganda reduced HIV prevalence by two- thirds during the 1990s. Causes

  17. 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

  18. 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

  19. 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 as the reported "tank to wheel" efficiencies would suggest. Hydrogen must be produced, stored, and transported to heat and leaking of hydrogen in the atmosphere. Additionally it takes power to produce hydrogen

  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. 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 ...

  3. Protein folding and cosmology

    E-Print Network [OSTI]

    Gonzlez-Diz, P F

    1997-01-01T23:59:59.000Z

    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.

  4. 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.

  5. Cotton and Protein Interactions

    SciTech Connect (OSTI)

    Goheen, Steven C.; Edwards, J. V.; Rayburn, Alfred R.; Gaither, Kari A.; Castro, Nathan J.

    2006-06-30T23:59:59.000Z

    The adsorbent properties of important wound fluid proteins and cotton cellulose are reviewed. This review focuses on the adsorption of albumin to cotton-based wound dressings and some chemically modified derivatives targeted for chronic wounds. Adsorption of elastase in the presence of albumin was examined as a model to understand the interactive properties of these wound fluid components with cotton fibers. In the chronic non-healing wound, elastase appears to be over-expressed, and it digests tissue and growth factors, interfering with the normal healing process. Albumin is the most prevalent protein in wound fluid, and in highly to moderately exudative wounds, it may bind significantly to the fibers of wound dressings. Thus, the relative binding properties of both elastase and albumin to wound dressing fibers are of interest in the design of more effective wound dressings. The present work examines the binding of albumin to two different derivatives of cotton, and quantifies the elastase binding to the same derivatives following exposure of albumin to the fiber surface. An HPLC adsorption technique was employed coupled with a colorimetric enzyme assay to quantify the relative binding properties of albumin and elastase to cotton. The results of wound protein binding are discussed in relation to the porosity and surface chemistry interactions of cotton and wound proteins. Studies are directed to understanding the implications of protein adsorption phenomena in terms of fiber-protein models that have implications for rationally designing dressings for chronic wounds.

  6. Discrete Applied Mathematics 127 (2003) 145161 The algorithmics of folding proteins on lattices

    E-Print Network [OSTI]

    Istrail, Sorin

    2003-01-01T23:59:59.000Z

    Institute of Science, Bangalore 560 012, India bStrand Genomics Pvt Ltd. India cKombinatorische Geometrie and biologists have found that folding proteins to their minimum energy conformations is a challenging unsolved optimization problem. Computational complexity theory has been useful in explaining, at least partially

  7. 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.

  8. Explaining Soft Law

    E-Print Network [OSTI]

    Guzman, Andrew T.; Meyer, Timothy L.

    2009-01-01T23:59:59.000Z

    practices and are also soft law. The Nuclear Suppliers Grouplaw whose pedigree is unquestioned. Similarly, in the Nuclearlaw and nonlaw suggests. If states have a Legality of the Threat or Use of Nuclear

  9. Explaining Soft Law

    E-Print Network [OSTI]

    Guzman, Andrew; Meyer, Timothy L.

    2010-01-01T23:59:59.000Z

    practices and are also soft law. The Nuclear Suppliers Grouplaw whose pedigree is unquestioned. Similarly, in the Nuclearlaw cannot exist as a coherent category must hold the view that what Legality of the Threat or Use of Nuclear

  10. 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

  11. 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\

  12. Dark matter conversion as a source of boost factor for explaining the cosmic ray positron and electron excesses

    E-Print Network [OSTI]

    Ze-Peng Liu; Yue-Liang Wu; Yu-Feng Zhou

    2011-12-17T23:59:59.000Z

    In interacting multi-component dark matter (DM) models, if the DM components are nearly degenerate in mass and the interactions between them are strong enough, the relatively heavy DM components can be converted into lighter ones at late time after the thermal decoupling. Consequently, the relic density of the lightest DM component can be considerably enhanced at late time. This may contribute to an alternative source of boost factor required to explain the positron and electron excesses reported by the recent DM indirect search experiments such as PAMELA, Fermi-LAT and HESS etc..

  13. 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

  14. 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

  15. 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

  16. 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

  17. Protein sequence databases Rolf Apweiler1,

    E-Print Network [OSTI]

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

  18. 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

  19. [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

  20. 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\

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. Stabilized polyacrylic saccharide protein conjugates

    DOE Patents [OSTI]

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

    1996-02-20T23:59:59.000Z

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

  8. A Novel Topology for Representing Protein Folds

    E-Print Network [OSTI]

    Segal, Mark R

    2009-01-01T23:59:59.000Z

    J. (2008). Predicting protein folding rates from geometric1993). Cooperativity in protein-folding kinetics. Proc NatlVoelz VA. (2007). The protein folding problem: when will it

  9. Hydration dynamics near a model protein surface

    E-Print Network [OSTI]

    Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

    2003-01-01T23:59:59.000Z

    AE, Onuchic JN. 2002. Protein folding mediated by solvation:of hydration forces in protein folding. Journal of Physicalthe broader context of protein folding and function and as

  10. 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,...

  11. 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

  12. 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

  13. 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

  14. Challenging Proteins Principles and Methods

    E-Print Network [OSTI]

    Jacobsen, Steve

    .............................................................................................................................................................12 Small-scale expression screening of histidine-tagged membrane proteins from E. coli lysates Gel Filtration Principles and Methods 18-1022-18 Recombinant Protein Purification Handbook Principles and Methods 18-1142-75 Protein Purification Handbook 18-1132-29 Hydrophobic Interaction and Reversed Phase

  15. 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).

  16. 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...

  17. Protein domain organisation: adding order

    E-Print Network [OSTI]

    Kummerfeld, Sarah K; Teichmann, Sarah A

    2009-01-29T23:59:59.000Z

    4 81811 membrane_organization_and_biogenesis 4 81811 vesicle-mediated_transport 4 81811 intracellular_protein_transport 4 54117 immune_response 3 54117 negative_regulation_of_cell_proliferation 3 54117 signal_transducer_activity 3 50715 ligase... -type_endopeptidase_activity 4 69055 binding 3 52788 identical_protein_binding 4 54585 nucleoside-triphosphatase_activity 3 54585 ATPase_activity 3 54585 protein_transport 3 54585 caspase_activation 3 54585 unfolded_protein_response 3 54585 magnesium_ion_binding 3 54585 protein...

  18. 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.

  19. 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

  20. Protein Dynamics and Biocatalysis

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProtein

  1. 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.

  2. 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.

  3. Protein detection system

    DOE Patents [OSTI]

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

    2009-05-05T23:59:59.000Z

    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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. This factsheet explains what international students in the Netherlands must do to be properly insured. For some students, this means that they are obliged to take

    E-Print Network [OSTI]

    van Suijlekom, Walter

    This factsheet explains what international students in the Netherlands must do to be properly internship, your stay in the Netherlands is classified as not being solely for study purposes. As an employee is irrelevant. (2) People under the age of 30, who are in the Netherlands solely for study purposes do not need

  9. 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

  10. 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, 1917of chaperone-mediated protein folding in the cytosol. Nat.that impair membrane protein folding and generate a membrane

  11. 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

  12. 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.

  13. 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. ...

  14. 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

  15. 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

  16. 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 proteinprotein interactions on the genome scale...

  17. Metal-directed protein self-assembly

    E-Print Network [OSTI]

    Salgado. Eric N.

    2010-01-01T23:59:59.000Z

    Metal-Directed Protein Self- Assembly. Acc. Chem. Res. 43,Metal-directed protein self-assembly. Acc. Chem. Res. 43,Metal- mediated self-assembly of protein superstructures:

  18. 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 ...

  19. 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...

  20. 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 ...

  1. 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.

  2. Protein crystallography with spallation neutrons

    SciTech Connect (OSTI)

    Langan, P. (Paul); Schoenborn, Benno P.

    2003-01-01T23:59:59.000Z

    proteins and oriented molecular complexes. With spallation neutrons and their time dependent wavelength structure, one can select data with an optimal wavelength bandwidth and cover the whole Laue spectrum as time (wavelength) resolved diffraction data. This optimizes data quality with best peak to background ratios and provides spatial and energy resolution to eliminate peak overlaps. Such a Protein Crystallography Station (PCS) has been built and tested at Los Alamos Neutron Science Center. A partially coupled moderator is used to increase flux and data are collected by a Cylindrical He3 detector covering 120' with 200mm height. The PCS is described along with examples of data collected from a number of proteins.

  3. 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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProteinProteinProtein

  4. 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^{\

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

    E-Print Network [OSTI]

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

  6. 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

  7. 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.

  8. 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...

  9. 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

  10. 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...

  11. 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, ...

  12. 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.

  13. 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 ...

  14. 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 ...

  15. 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

  16. 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

  17. Thermodynamics of Protein Folding Erik Sandelin

    E-Print Network [OSTI]

    Sandelin, Erik

    Thermodynamics of Protein Folding and Design Erik Sandelin Department of Theoretical Physics Lund Sölvegatan 14A 223 62 LUND September 2000 Erik Sandelin Thermodynamics of Protein Folding and Design The protein folding and protein design problems are addressed, using coarse-grained models with only two types

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Protein phase feeding of poultry

    E-Print Network [OSTI]

    Vest, Larry Rufus

    1966-01-01T23:59:59.000Z

    PROTEIN PHASE FEEDING OF POULTRY A Thesis By Larry Rufus Vest Submitted to the Graduate College of the Texas AM University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE January 1966 Major Subject Poultry... Science PROTEIN PHASE FEEDING OF POULTRY A Thesis Larry Rufus Vest Approved as to style and content by: man o o x tee par e em e e er January 1966 ACKNOWLEDGE MENTS Tbe author wishes to express his sincere gratitude and deep appreciation to Dr...

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProteinProtein Flips

  7. 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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProteinProtein

  8. 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

  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 to date. A steady stream of about 150 visitors per week log on to the FIRE web site since the site

  10. 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

  11. 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

  12. 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

  13. 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.

  14. GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

    E-Print Network [OSTI]

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

    2012-07-11T23:59:59.000Z

    Protein-protein interactions are a key component of life processes. The knowledge of the three-dimensional structure of these interactions is important for understanding protein function. Genome-Wide Docking Database ...

  15. 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.

  16. 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.

  17. protein structure communications 1. Introduction

    E-Print Network [OSTI]

    Tsai, Ming-Daw

    protein structure communications 1. Introduction Phospholipases A2 (PLA2s) are widely distributed metabolism, signal transduction and eicosanoid production (Dennis, 1997 ). PLA2 enzymes are characterized PLA2s (80-110 kDa) are present in many cell types and are involved in phospholipid metabolism

  18. Engineering native and artificial heme c containing proteins for biochemical applications and studies of protein folding.

    E-Print Network [OSTI]

    Asher, Wesley B. (1984 - ); Bren, Kara

    2012-01-01T23:59:59.000Z

    ??Heme c containing proteins are known for their intense colors and essential functions in nature. These proteins contain heme that is covalently bound to the (more)

  19. 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

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

    E-Print Network [OSTI]

    Amos, Joseph Edward

    2013-02-22T23:59:59.000Z

    of a Cell Cycle Regulator. (April 2001) Joseph Edward Amos Department of Biochemistry Texas A&M University Fellows Advisor: Dr. Sumana Datta Department of Biochemistry and Biophysics The role of anachronism (ana) protein in stem cell division...-157. 29 Vita Name: Joseph Edward Amos Permanent Address: 114 Stephanie Dr. Palestine, TX 75801 Educational Background: Texas A & M University Bachelor of Science Biochemistry, May 2001 Fall 1998-Spring 2001 Kilgore College Summer 1997-Fall 1998...

  1. 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.

  2. 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 ...

  3. 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 ...

  4. 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

  5. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    SciTech Connect (OSTI)

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01T23:59:59.000Z

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

  6. 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.

  7. 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...

  8. 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

  9. 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

  10. Struts, springs and crumple zones: protein structures under force

    E-Print Network [OSTI]

    Dill, Jesse

    2012-01-01T23:59:59.000Z

    molecule studies of protein folding using atomic Observation of Active Protein Folding Using Lock-?molecule studies of protein folding. Annual Review

  11. Computational Modeling of Protein Interactions at Multiple Lengthscales

    E-Print Network [OSTI]

    Yap, Eng Hui

    2010-01-01T23:59:59.000Z

    barrier mechanism in protein folding. Journal of MolecularH. , Early events in protein folding explored by rapidthe kinetics of protein folding. Methods 2004, 34, (1), 15-

  12. Protein-Folding Landscapes in Multi-Chain Systems

    E-Print Network [OSTI]

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

    2005-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

    2004-01-01T23:59:59.000Z

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

  14. The unfolded protein response during prostate cancer development

    E-Print Network [OSTI]

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

    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

  15. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01T23:59:59.000Z

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

  16. Protein folding and diffusion: from in vitro to live cells.

    E-Print Network [OSTI]

    Guo, Minghao

    2014-01-01T23:59:59.000Z

    ??Protein folding landscapes and protein-protein interaction landscapes are subject to modulation by many factors inside living cells: crowding, electrostatics, hydrophobic interactions, and even hydrodynamic phenomena. (more)

  17. 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.

  18. 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

  19. 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

  20. Solvent dramatically affects protein structure refinement

    E-Print Network [OSTI]

    Summa, Christopher M.

    Solvent dramatically affects protein structure refinement Gaurav Chopraa , Christopher M. Summab structure), also known as the protein structure refinement problem. It has been shown that improve- ment in protein structure refinement. Molecular dynamics in explicit sol- vent and energy minimization in both

  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. 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.

  3. Amphiphiles for protein solubilization and stabilization

    DOE Patents [OSTI]

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

    2014-11-04T23:59:59.000Z

    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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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

  12. How Nature Fine Tunes Protein Stability

    E-Print Network [OSTI]

    Wickstrom, Megan

    2007-07-14T23:59:59.000Z

    finding was that the burial of charged groups also increased with increasing size from less than 25% in the small proteins to over 50% in the larger proteins. This suggests that burying charged groups in the interior of the protein is the primary strategy...

  13. 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

  14. 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

  15. 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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassive Solar HomePromising Science for PlutoniumAbout Us / OurBioscience: Bioenergy,

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

    E-Print Network [OSTI]

    Powers, Robert

    of various genomics efforts has been a vast growth in putative protein sequences that lack any experimental there are numerous examples of proteins with similar folds that lack any significant sequence homology.8Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

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

  3. Review Protein Folding and Misfolding on Surfaces

    E-Print Network [OSTI]

    Massimo Stefani

    2008-01-01T23:59:59.000Z

    Abstract: Protein folding, misfolding and aggregation, as well as the way misfolded and aggregated proteins affects cell viability are emerging as key themes in molecular and structural biology and in molecular medicine. Recent advances in the knowledge of the biophysical basis of protein folding have led to propose the energy landscape theory which provides a consistent framework to better understand how a protein folds rapidly and efficiently to the compact, biologically active structure. The increased knowledge on protein folding has highlighted its strict relation to protein misfolding and aggregation, either process being in close competition with the other, both relying on the same physicochemical basis. The theory has also provided information to better understand the structural and environmental factors affecting protein folding resulting in protein misfolding and aggregation into ordered or disordered polymeric assemblies. Among these, particular importance is given to the effects of surfaces. The latter, in some cases make possible rapid and efficient protein folding but most often recruit proteins/peptides increasing their local concentration thus favouring misfolding and accelerating the rate of nucleation. It is also emerging that surfaces can modify the path of protein misfolding and aggregation generating oligomers and polymers structurally different from those arising in the bulk solution and endowed with different physical properties and cytotoxicities.

  4. 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

  5. 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...

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. CONNNECT TO WiFi USING PROXY SETTINGS (MAC) This guide explains how to set up a modern Apple Mac (running OSX 10.3 or higher) to connect to the internet,

    E-Print Network [OSTI]

    Mottram, Nigel

    CONNNECT TO WiFi USING PROXY SETTINGS (MAC) This guide explains how to set up a modern Apple Mac Apple on the left of the menu bar. 2. Click on `System Preferences'. 3. Click on `Network'. 4. A window

  11. The Biochemical Investigation and Isolation of Small Molecule Inhibitors for Two Essential Proteins of Mycobacterium tuberculosis H37Rv: IspD and Wag31

    E-Print Network [OSTI]

    Joseph, Sonia

    2014-06-12T23:59:59.000Z

    residues that made it more flexible and may help explain the difference in the reaction kinetics between the two homologs. 1.3 Wag31 DivIVA family of proteins The DivIVA protein is highly conserved in gram positive bacteria. It is a cell division.... It is known that DivIVA localization at the poles is due to its recognition of the spherical inward curve of these cells near the poles compared to the remaining portion (which maintains a cylindrical curve which is less sharp). Furthermore, it has been...

  12. 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...

  13. 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.

  14. 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)

  15. Simulating Temperature Jumps for Protein Folding Studies.

    E-Print Network [OSTI]

    Kim, Seonah

    2007-01-01T23:59:59.000Z

    ??Protein folding is described as a dynamic process of an ensemble of molecules reaching well-defined three dimensional structures to achieve biological activity from linear amino (more)

  16. Controlling membrane protein folding using photoresponsive surfactant.

    E-Print Network [OSTI]

    Chang, Chia Hao

    2012-01-01T23:59:59.000Z

    ??Membrane proteins perform a number of roles in biological function. Membrane lipids can self assembly into numerous different phases in aqueous solution, including micelles, vesicles (more)

  17. 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.

  18. Brownian Dynamics Simulation of Protein Solutions: Structural...

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

    for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe...

  19. 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

  20. 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

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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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,...

  9. 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...

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. Cotranslational protein folding with L-systems

    E-Print Network [OSTI]

    Gemma B. Danks; Susan Stepney; Leo S. D. Caves

    Abstract. A protein molecule adopts a specific 3D structure, necessary for its function in the cell, through a process of folding. Modelling the folding process and predicting the final fold from the unique amino acid sequence remain challenging problems. We have previously described the application of L-systems, parallel rewriting rules, to modelling protein folding using two complementary approaches: a physics-based approach, using calculations of interatomic forces, and a knowledge-based approach, using data from fragments of known protein structures. Here we describe a model combining these two approaches creating an adaptive stochastic open L-systems model of protein folding. L-systems were originally developed to model growth and development. Here we also describe extensions of our L-systems models to investigate cotranslational protein folding, i.e. folding during protein biosynthesis on the ribosome, which is increasingly thought to play an important role. We demonstrate that cotranslational folding fits very naturally into the L-systems framework. Key words: Cotranslational protein folding, L-systems 1

  16. 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

  17. 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

  18. 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.

  19. Septin Self-Assembly: Plasticity and Protein Scaffolding

    E-Print Network [OSTI]

    Garcia, III, Galo

    2012-01-01T23:59:59.000Z

    Septin Self-Assembly: Plasticity and Protein Scaffolding BySpring 2012 Septin Self-Assembly: Plasticity and ProteinIII Abstract Septin Self-Assembly: Plasticity and Protein

  20. 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

  1. 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

  2. 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

  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. 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

  5. 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 ...

  6. 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...

  7. 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.

  8. 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.

  9. Dye-Doped Silica Nanoparticle Labels/Protein Microarray for Detection...

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

    Dye-Doped Silica Nanoparticle LabelsProtein Microarray for Detection of Protein Biomarkers. Dye-Doped Silica Nanoparticle LabelsProtein Microarray for Detection of Protein...

  10. 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.

  11. 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...

  12. 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)...

  13. 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)...

  14. 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...

  15. 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)...

  16. 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...

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

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

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

  18. 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...

  19. 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:...

  20. Amino acid treatment enhances protein recovery from sediment...

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

    treatment enhances protein recovery from sediment and soils for metaproteomic studies . Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic...

  1. Nanosized Optoelectronic Devices Based on Photoactivated Proteins Alice Dimonte,*,

    E-Print Network [OSTI]

    De Micheli, Giovanni

    Nanosized Optoelectronic Devices Based on Photoactivated Proteins Alice Dimonte,*, Stefano Frache gold electrodes have been used to develop optoelectronic devices based on photoactive proteins

  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. Antibody-free PRISM-SRM for multiplexed protein quantification...

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

    free PRISM-SRM for multiplexed protein quantification: Is this the new competition for immunoassays in bioanalysis? Antibody-free PRISM-SRM for multiplexed protein quantification:...

  4. Shotgun Proteomics Identifies Proteins Specific for Acute Renal...

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

    was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have...

  5. 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...

  6. 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...

  7. 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

  8. 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...

  9. 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...

  10. 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...

  11. A Hybrid Approach to Protein Differential Expression in Mass...

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

    Hybrid Approach to Protein Differential Expression in Mass Spectrometry-Based Proteomics. A Hybrid Approach to Protein Differential Expression in Mass Spectrometry-Based...

  12. 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....

  13. 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...

  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. Enhanced sampling and applications in protein folding.

    E-Print Network [OSTI]

    Zhang, Cheng

    2013-01-01T23:59:59.000Z

    ??We show that a single-copy tempering method is useful in protein-folding simulations of large scale and high accuracy (explicit solvent, atomic representation, and physics-based potential). (more)

  16. 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 ...

  17. 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.

  18. 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

  19. 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...

  20. 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.

  1. 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, ...

  2. 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.

  3. 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...

  4. 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 ...

  5. 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.

  6. 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^{\

  7. Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA

    E-Print Network [OSTI]

    Simona Cocco; John F. Marko; Remi Monasson

    2014-05-26T23:59:59.000Z

    Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the depen- dence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive 'rezipping' of the solution-phase protein onto DNA sites liberated by 'unzipping' of the originally bound protein; (2) that a model in which solution-phase proteins bind non-specifically to DNA can describe experiments on exchanges between the non specific DNA- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.

  8. 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.

  9. 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

  10. INTRODUCTION Proteins must mature to their native confor-

    E-Print Network [OSTI]

    Hebert, Daniel N.

    -Linked Carbohydrates Act as Lumenal Maturation and Quality Control Protein Tags Robert Daniels, Sherri Svedine

  11. Guide to Red Fluorescent Proteins and Biosensors for Flow Cytometry

    E-Print Network [OSTI]

    Verkhusha, Vladislav V.

    CHAPTER 17 Guide to Red Fluorescent Proteins and Biosensors for Flow Cytometry Kiryl D. PiatkevichH Stability of Fluorescence F. Optimization of Nucleotide and Amino Acid Sequences III. Modern Advanced Red-Shifted FPs A. Orange Fluorescent Proteins B. Red Fluorescent Proteins C. Far-Red Fluorescent Proteins IV

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

    E-Print Network [OSTI]

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

  13. Distribution of Protein Folds in the Three Superkingdoms of Life

    E-Print Network [OSTI]

    Distribution of Protein Folds in the Three Superkingdoms of Life Yuri I. Wolf,1,4 Steven E. Brenner Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois 60611 USA A sensitive protein-fold to protein kinases, -propellers and TIM-barrels. The observed diversity of protein folds in different

  14. Introduction Protein secretion is an essential process in prokaryotes and

    E-Print Network [OSTI]

    Cheng, Chi-Hing Christina

    Introduction Protein secretion is an essential process in prokaryotes and eukaryotes (Matlack et al., 1998). Protein synthesis takes place in the cytoplasm, therefore secretion requires one protein not understood. Protein translocation across biological membranes is dependent on temperature and membrane lipid

  15. 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

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. Protein folding in crowded environments and living cells.

    E-Print Network [OSTI]

    Dhar, Apratim

    2011-01-01T23:59:59.000Z

    ??Biomolecular dynamics and stability are predominantly investigated in vitro, and extrapolated to explain function in the living cell. In this thesis, we attempt to bridge (more)

  4. Evaluation of enzymatic modification of peanut protein isolate

    E-Print Network [OSTI]

    Hostetler, Marsha Kay

    1979-01-01T23:59:59.000Z

    of peanut protein ingredients . . . 2 Amino acid compositions of peanut protein isolate and casein . 3 Protein solubility of trypsin-hyd?olyzed peanut protein isolate 4 Protein solubility of chymotrypsin-hydrolyzed peanut protein isolate . 5 Protein... Acids Al anine Aspartic acid Cystine Glutamic acid Glycine Proline Serine Tyrosine 13. 1 3. 4 3. 4 6. 6 2. 9 0. 9 5. 5 2. 3 4. 3 3. 9 12. 5 22. 7 4. 0 4. 7 4. 9 4. 4 3. 8 2. 3 6. 1 10. 8 6. 8 2. 9 5. 5 4. 4 1. 2 6. 6 2...

  5. 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.

  6. Structure and expression of a novel compact myelin protein Small VCP-interacting protein (SVIP)

    SciTech Connect (OSTI)

    Wu, Jiawen [Department of Neurology, Vanderbilt University School of Medicine (United States)] [Department of Neurology, Vanderbilt University School of Medicine (United States); Peng, Dungeng [Department of Biochemistry, Vanderbilt University School of Medicine (United States)] [Department of Biochemistry, Vanderbilt University School of Medicine (United States); Voehler, Markus [Center for Structural Biology, Vanderbilt University (United States)] [Center for Structural Biology, Vanderbilt University (United States); Sanders, Charles R. [Department of Biochemistry, Vanderbilt University School of Medicine (United States) [Department of Biochemistry, Vanderbilt University School of Medicine (United States); Center for Structural Biology, Vanderbilt University (United States); Li, Jun, E-mail: jun.li.2@vanderbilt.edu [Department of Neurology, Vanderbilt University School of Medicine (United States) [Department of Neurology, Vanderbilt University School of Medicine (United States); Tennessee Valley Healthcare System (TVHS) Nashville VA (United States)

    2013-10-11T23:59:59.000Z

    Highlights: SVIP (small p97/VCP-interacting protein) co-localizes with myelin basic protein (MBP) in compact myelin. We determined that SVIP is an intrinsically disordered protein (IDP). The helical content of SVIP increases dramatically during its interaction with negatively charged lipid membrane. This study provides structural insight into interactions between SVIP and myelin membranes. -- Abstract: SVIP (small p97/VCP-interacting protein) was initially identified as one of many cofactors regulating the valosin containing protein (VCP), an AAA+ ATPase involved in endoplasmic-reticulum-associated protein degradation (ERAD). Our previous study showed that SVIP is expressed exclusively in the nervous system. In the present study, SVIP and VCP were seen to be co-localized in neuronal cell bodies. Interestingly, we also observed that SVIP co-localizes with myelin basic protein (MBP) in compact myelin, where VCP was absent. Furthermore, using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopic measurements, we determined that SVIP is an intrinsically disordered protein (IDP). However, upon binding to the surface of membranes containing a net negative charge, the helical content of SVIP increases dramatically. These findings provide structural insight into interactions between SVIP and myelin membranes.

  7. 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

  8. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS PROTS: A fragment based protein

    E-Print Network [OSTI]

    Zhang, Yang

    which live at elevated temperatures as high as 1138C.5 Thus, the proteins produced by thermophiles and practically.1­8 Protein-based drugs have become increasingly attractive because of their high efficiency at higher temperature, which can lead to more efficient industrial processes because chemical reactions

  9. 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.

  10. 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

  11. Allosteric Effects of RuvA Protein, ATP, and DNA on RuvB Protein-Mediated ATP Hydrolysis

    E-Print Network [OSTI]

    Cox, Michael M.

    Allosteric Effects of RuvA Protein, ATP, and DNA on RuvB Protein-Mediated ATP Hydrolysis Paul E ABSTRACT: A detailed characterization of RuvB protein-mediated ATP hydrolysis in the presence of RuvA protein has provided (a) the steady-state kinetic parameters of ATP hydrolysis within a RuvAB complex

  12. 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

  13. 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

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

    E-Print Network [OSTI]

    Annunziata, Onofrio

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

  15. 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.

  16. 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.

  17. 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.

  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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassive Solar HomePromising Science for PlutoniumAbout Us / Our ProgramsProteinProtein

  19. Protein Dynamics Hit the Big Screen

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProtein BridgesProtein

  20. 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 ...

  1. Specific inhibition of protein synthesis in the rabbit reticulocyte lysate by two types of oligoribonucleotides

    SciTech Connect (OSTI)

    Wagner, T.; Gross, M.; Sigler, P.B.

    1986-05-01T23:59:59.000Z

    The oligonucleotides AUG, AUGG and AUGA, i.e. homologues of the initiation codon, are recognized as initiation sites by the protein synthetic machinery of the reticulocyte lysate. They induce the accumulation of inactive initiation complexes (80S x AUG x Met-tRNA/sub 1//sup Met/) and thereby deprive the system of active ribosomes. The only dinucleotide that inhibits protein synthesis is CA. CA and all trinucleotides of the form XCA and CAX (where X=U, C,A or G) block chain elongation at a level of 10/sup -5/M. Interestingly, inhibition by XCA is transient, while that by CAX becomes progressively greater with time. This phenomenon can be explained by a 3'exonucleolytic activity in the lysate. Upon 3'terminal cleavage the XCA trinucleotides will lose the inhibitory CA, whereas CAX trinucleotides will simply be converted to CA, the specific inhibitor. This has been confirmed experimentally, since CC(/sup 3/H)A is completely hydrolyzed to CpC and p(/sup 3/H)A after 15 minutes of incubation. The mode of action of CA, while unclear, may be mediated by its similarity to the 3'-terminus of tRNA.

  2. 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...

  3. 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.

  4. Response of Penaeus vannamei to dietary protein level, protein source and polyculture

    E-Print Network [OSTI]

    Smith, Linda Louise

    1988-01-01T23:59:59.000Z

    experiments. Growth and survival were evaluated over 30- day experiments; and, apparent protein, lipid and total d 1et digestibilit1es were measured over a 3-day period immediately following each growth experiment. In monoculture, feeds containing var 1ed... related to handling stress. Apparent protein (78. 7-85. 8 %%d), lipid (45. 1-64. 8 4) and total diet digestibilities (43. 9-58. 4X) were similar among the three sizes of P. vannamei and were unrelated to protein-source ratio. In polyculture, either 6...

  5. Energy use by biological protein transport pathways

    E-Print Network [OSTI]

    Economou, Tassos

    residing within energy-conserving membranes use transmembrane ion gradients to drive substrate transport receptors impart specificity to a targeting route, and transport across or into the membrane is typicallyEnergy use by biological protein transport pathways Nathan N. Alder1 and Steven M. Theg2 1

  6. 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

  7. Supplemental Data Degradation-Mediated Protein

    E-Print Network [OSTI]

    Gardner, Rich

    Supplemental Data Degradation-Mediated Protein Quality Control in the Nucleus Richard G. Gardner:FITC) and DAPI (UV-2E/C) were from Chroma Technology Corp (Brattleboro, Vermont). Images were captured were assayed on YEPD plates containing 0.01­0.3% MMS or EMS. UV sensitivity was assayed by plating 400

  8. PROTEIN INTERACTIONS AND DISEASE MARICEL KANN

    E-Print Network [OSTI]

    Radivojac, Predrag

    and illnesses, including AIDS, cancer, and Alzheimer's disease. The goal of this session is to discuss interaction data to identify active pathways re- lated to HIV pathogenesis. A functional analysis for successful inference of protein interactions. Chen et al. developed a framework to mine disease

  9. Materials and Methods Protein expression and purification

    E-Print Network [OSTI]

    Joshua-Tor, Leemor

    Materials and Methods Protein expression and purification The Full length Argonaute gene from protease system was a generous gift from Dr. Chris Lima. PfAgo was further purified with a heating step with #12;the program CNS (S7) against the SHARP amplitudes. Water molecules were added conservatively (for

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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

  15. Using protein design algorithms to understand the molecular basis of disease caused by proteinDNA 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 proteins function is not trivial. Protein ...

  16. 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.

  17. 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.

  18. 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.

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

    E-Print Network [OSTI]

    Ryan, Jeremy Adam

    2005-01-01T23:59:59.000Z

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

  20. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Role of partial protein unfolding in

    E-Print Network [OSTI]

    Mallela, Krishna M. G.

    Cl, guanidinium chloride; HX, hydrogen exchange; NMR, nuclear magnetic resonance; SEC, size exclusion- tein formulations,11 as an anesthetic,12 as a membrane fluidizer,13 as a heat shock protein inducer,14

  1. 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.

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

    E-Print Network [OSTI]

    Fu, Hailong

    2010-07-14T23:59:59.000Z

    Page 1 Ribbon diagram showing the structure of VHP and VlsE ......................... 12 2 Far-UV CD spectra for VHP and VlsE ...................................................... 13 3 Energy diagrams for protein folding reaction... interactions, hydrogen bonding and hydrophobic effect. The stabilizing effects of these interactions are largely opposed by the major destabilizing force, which is the conformational entropy loss upon protein folding. Other forces, such as electrostatic...

  3. 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

    Herman B. Scholthof Wayne K. Versaw Head of Department, Dennis C. Gross May 2007 Major Subject: Plant Pathology ABSTRACT Analysis of Secreted Proteins of Magnaporthe grisea and the Search for Protein Efectors... parents, Ying Ma and Delong Shang, who supported me through the chalenges of graduate life. v ACKNOWLEDGMENTS I would like to thank my commite chair, Dr. Daniel Ebbole, who has been an outstanding both mentor and advisor. He taught me a lot...

  4. 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...

  5. 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 ...

  6. 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 C for...

  7. 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 ...

  8. Protein quality control in the mammalian endoplasmic reticulum

    E-Print Network [OSTI]

    Klemm, Elizabeth J. (Elizabeth Joanna)

    2011-01-01T23:59:59.000Z

    Quality control is an important part of protein biogenesis. Aberrant proteins must be destroyed before they aggregate and cause deleterious effects. Failure to do so can result in cell death or malfunction and, ultimately, ...

  9. 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...

  10. The effects of shared peptides on protein quantitation in label...

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

    The effects of shared peptides on protein quantitation in label-free proteomics by LCMSMS . The effects of shared peptides on protein quantitation in label-free proteomics by LC...

  11. 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...

  12. 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...

  13. 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...

  14. Small-Molecule Control of Protein Degradation Using Split Adaptors

    E-Print Network [OSTI]

    Davis, Joseph H.

    Targeted intracellular degradation provides a method to study the biological function of proteins and has numerous applications in biotechnology. One promising approach uses adaptor proteins to target substrates with ...

  15. 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

  16. 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

  17. 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

  18. 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 ...

  19. 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

  20. Quantitative analysis of cell surface membrane proteins using...

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

    the quantification of membrane proteome changes, enriched membrane protein samples from wild-type and mutant cells (generated from deletion of a type II secretion protein, GspD)...

  1. Thermal unfolding dynamics of proteins probed by nonlinear infrared spectroscopy

    E-Print Network [OSTI]

    Chung, Hoi Sung

    2007-01-01T23:59:59.000Z

    This thesis presents spectroscopic approaches to study the thermal unfolding dynamics of proteins. The spectroscopic tool is nonlinear infrared (IR) spectroscopy of the protein amide I band. Among various nonlinear IR ...

  2. Production and Functional Analysis of Recombinant Bovine Morphogenic Protein 15

    E-Print Network [OSTI]

    Burns, Gregory Willis

    2013-11-21T23:59:59.000Z

    dorsomorphin, a selective bone morphogenic protein receptor I inhibitor, demonstrated the purified proteins served as BMP15-like agonists. To examine the impact of our purified, bovine-specific peptides on oocyte maturation, cumulus oocyte complexes were...

  3. 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...

  4. 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 ...

  5. 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...

  6. 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...

  7. Activity-based protein profiling of secreted cellulolytic enzyme...

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

    based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30 Activity-based protein profiling of secreted cellulolytic...

  8. A comparative study of HPr proteins from extremophilic organisms

    E-Print Network [OSTI]

    Syed Ali, Abbas Razvi

    2006-04-12T23:59:59.000Z

    of the proteins were derived from moderate thermophiles (Streptococcus thermophilus and Bacillus staerothermophilus) and two from haloalkaliphilic organisms (Bacillus halodurans and Oceanobacillus iheyensis); these proteins were compared with HPr from...

  9. 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

  10. CARES Helps Explain Secondary Organic Aerosols

    SciTech Connect (OSTI)

    Zaveri, Rahul

    2014-03-28T23:59:59.000Z

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

  11. CARES Helps Explain Secondary Organic Aerosols

    ScienceCinema (OSTI)

    Zaveri, Rahul

    2014-06-02T23:59:59.000Z

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

  12. Explaining Africa agricultural and food trade deficits

    E-Print Network [OSTI]

    0.8 percent per year. Food consumption on per capita basis grew only at about 1 percent per year of food consumption and imports per capita is consistent with the weak economic growth and unchanged the highest net food imports per capita (USD 185 per year in real terms), they had ample means to pay

  13. In the crosshairs : explaining violence against civilians

    E-Print Network [OSTI]

    Heger, Lindsay L.

    2010-01-01T23:59:59.000Z

    of the time and the PKK (Kurdistan Workers Party in Turkey)separatist groups like the Kurdistan Workers Party attackJemaah Islamiya (JI) Kach Kurdistan Workers' Party (PKK)

  14. Laboratories are Needed to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Princeton Plasma Physics Laboratory Sandia National Laboratory Stone and Webster The Boeing Company stream of about 150 visitors per week log on to the FIRE web site since the site was initiated in early

  15. Laboratories are Needed to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    National Laboratory Stone and Webster The Boeing Company University of Illinois University of Wisconsin #12 10,000 visitors from around the world have logged on to the FIRE web site since the site

  16. Explaining the Price of Voluntary Carbon Offsets

    E-Print Network [OSTI]

    Conte, Marc N.; Kotchen, Matthew

    2009-01-01T23:59:59.000Z

    Energy and Sustainable Development, Stanford Univer- sity. Figure 1: Histogram of carbon offset prices (

  17. Do Disaster Expectations Explain Household Portfolios?

    E-Print Network [OSTI]

    Alan, Sule

    durable ex- penditure information; and ?nally, the Panel Study of Income Dynamics (1983-1994) that allows me to calibrate group speci?c income process parameters. Limited het- 3 erogeneity in all parameters is allowed for by estimating the structural... innovations to excess return to be correlated with innovations to per- manent or transitory income in normal market times. Allowing for such a correlation is straightforward and would reduce the ex-ante disaster probability and disaster size needed to match...

  18. Explaining the Price of Voluntary Carbon Offsets

    E-Print Network [OSTI]

    Conte, Marc N.; Kotchen, Matthew

    2009-01-01T23:59:59.000Z

    on fuel efficiency, hydropower, fuel substitution, solarbiomass methane, wind, hydropower, solar, and other. 8 OECDtypes of biomass methane, hydropower, so- lar, and wind. All

  19. Argonne explains nuclear recycling in 4 minutes

    ScienceCinema (OSTI)

    None

    2013-04-19T23:59:59.000Z

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

  20. 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

    , and its lower right at 34?20.5 S, 19?16.5 E, with total area of 4,456 km2. It comprises a rectangular area including the Kogelberg Biosphere Reserve and beyond, extending 41m east and 107m north from Cape Hangklip. The region is shown in Figure 1.... The survey paper of Guisan and Zimmerman (2000) provides discussion and extensive referencing. Let log ( p(k)i 1 ? p(k)i ) = wi??k + ?k + ?i, (5) where wi is a vector of grid cell level characteristics, and the ?ks are species level coefficients associated...

  1. Laboratories are Needed to Explore, Explain VLBACHANDRA

    E-Print Network [OSTI]

    Georgia Institute of Technology Idaho National Engineering Laboratory Lawrence Livermore National to Two DEMOs Fourth Phase Scientific Feasibility Burning Demo Engineering Base Electric Power Feasibility Three Large Tokamaks Tokamak Experimental Reactor LHD, W 7X JT-60 U JET TFTR Scientific Foundation

  2. Argonne explains nuclear recycling in 4 minutes

    SciTech Connect (OSTI)

    None

    2012-01-01T23:59:59.000Z

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

  3. Explaining the Price of Voluntary Carbon Offsets

    E-Print Network [OSTI]

    Conte, Marc N.; Kotchen, Matthew

    2009-01-01T23:59:59.000Z

    Greenhouse Gas Initiative (RGGI) of 10 Northeastern and Mid-32, partici- pants in the RGGI are allowed to offset up to

  4. The NIH rDNA Guidelines Explained

    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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2 andThe Molecular Bond: OctoberOptimizationPMEMD TheNIH

  5. NDA Explained | National Nuclear Security Administration

    National Nuclear Security Administration (NNSA)

    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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary) "ofEarlyEnergyDepartment ofDepartment ofofOxfordVeterans | NationalSafeguardsLongAdministration AboutNDA

  6. Our Science Explained | The Ames Laboratory

    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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recoveryLaboratorySpeedingOptimizing I/O performanceOther ResourcesDustyMarchOur

  7. Framework for a Protein Ontology Darren A. Natale1

    E-Print Network [OSTI]

    development of PRO, illustrated using human proteins from the TGF-beta signaling pathway (http://pir

  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

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

  9. 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

  10. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

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

    2010-05-25T23:59:59.000Z

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

  11. 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

  12. E-Print Network 3.0 - active core protein Sample Search Results

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

    protein with extension pc0741 conserved hypothetical protein pc0743... the Evolutionary History of Chlamydiae" (Horn et al.) Supporting Online Material 2 protein sequence...

  13. ATP Competitive Protein Kinase C Inhibitors Demonstrate Distinct State-Dependent Inhibition

    E-Print Network [OSTI]

    Smith, Ida M.; Hoshi, Naoto

    2011-01-01T23:59:59.000Z

    ATP Competitive Protein Kinase C Inhibitors Demonstratepreviously reported that some ATP competitive protein kinaseSmith IM, Hoshi N (2011) ATP Competitive Protein Kinase C

  14. E-Print Network 3.0 - abnormal protein bands Sample Search Results

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

    protein bands Search Powered by Explorit Topic List Advanced Search Sample search results for: abnormal protein bands Page: << < 1 2 3 4 5 > >> 1 An Introduction to Protein...

  15. 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 thecatalyzes oxidative protein folding in mitochondria. Naturecarriers in oxidative protein folding. International journal

  16. 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

  17. Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins

    E-Print Network [OSTI]

    Laurence, T A; Kong, X X; Jager, M; Weiss, S

    2005-01-01T23:59:59.000Z

    polyelec- trolytes and protein folding in particular, standsdynamics ? protein folding ? single-molecule ?uorescencestructure and dynamics. Protein folding is the most spec-

  18. The unfolded protein response : integrating stress signals from the endoplasmic reticulum to the nucleolus

    E-Print Network [OSTI]

    DuRose, Jenny Bratlien

    2008-01-01T23:59:59.000Z

    for monitoring the protein-folding environment of the ER andconditions that disrupted protein folding in the ER, andinterfering with ER protein folding induces the expression

  19. 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

  20. 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.

  1. Beyond the native state: Exploring the role of partially folded conformations on the protein energy landscape

    E-Print Network [OSTI]

    Connell, Katelyn Blair

    2010-01-01T23:59:59.000Z

    L. & Englander, S. W. (1995). Protein folding intermediates:Unifying features in protein- folding mechanisms. Proc Natlintermediate state in protein folding by a hydrophobic

  2. Effect of single-point sequence alterations on the aggregation propensity of a model protein

    E-Print Network [OSTI]

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

    2005-01-01T23:59:59.000Z

    effect on both protein folding and its aggregationstudied sequences, improves protein folding rates, foldingmechanisms implicated in protein folding as opposed to

  3. 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...

  4. 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,...

  5. 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...

  6. 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...

  7. E-Print Network 3.0 - age-induced protein modifications Sample...

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

    organisms Lack of post- translational modifications Endotoxins... eukaryotic protein folding and modification machinery Protein ExpressionProtein Expression 12;2 Rapid...

  8. E-Print Network 3.0 - accelerates protein gain Sample Search...

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

    state of the protein leading... of Protein Engineering Techniques to Elucidate Protein Folding Pathways. In P. Michael Conn, editor: Progress... : 978-0-12-374595-8 ...

  9. 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...

  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. 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:

  13. A Proteomic Study of Protein Tyrosine Nitration

    E-Print Network [OSTI]

    Hong, Sung Jung

    2008-08-28T23:59:59.000Z

    chromatography mass spectrometry 2.2 Introduction Creatine kinase (CK) is a 37 kDa protein expressed in high energy demanding tissues such as heart, skeletal muscle and brain. CK plays an important role in energy metabolism by effectively catalyzing...: Reactive oxygen species - RNS: Reactive nitrogen species - CK: Creatine Kinase - HPLC-ESI-MS/MS: High performance liquid chromatography-electrospray ionization tandem mass spectrometry. - 3-NY: 3-nitrotyrosine - NO: nitrogen monoxide - ONOO...

  14. Rigidity Analysis for Modeling Protein Motion

    E-Print Network [OSTI]

    Thomas, Shawna L.

    2010-07-14T23:59:59.000Z

    . ............................... 128 XIII Comparison of average relative exchange rate for both EX RS and EX CS between the entire protein and the experimentally defined folding core. ................................ 154 xii TABLE Page XIV Comparison between rigidityscores, cluster... exchange rates from rigidity scores and cluster scores to experimental data. ................... 131 50 Visual comparison of simulated exchange rates to experimental data. 149 51 Minimal variance thresholds (dashed lines) to cluster EX RS for Tendamistat...

  15. Rapid Protein Structure Detection and Assignment using Residual Dipolar Couplings

    E-Print Network [OSTI]

    Rapid Protein Structure Detection and Assignment using Residual Dipolar Couplings Michael A substructures by exploiting the orientational constraint of residual dipolar coupling (RDC). PEPMORPH reverses: We have tested PEPMORPH on a variety of real proteins deposited in the Protein Data Base (PDB), using

  16. Refolding of recombinant proteins Eliana De Bernardez Clark

    E-Print Network [OSTI]

    Lebendiker, Mario

    in in vitro protein folding. New additives to prevent aggregation have been added to a growing list. A wealth of literature on the role of chaperones and foldases in in vivo protein folding has triggered the development the formation of inclusion bodies was first observed almost two decades ago, existing protein folding protocols

  17. Phosphorylation in Synechocystis 1 PHOSPHORYLATION OF PHYCOBILISOME LINKER PROTEINS

    E-Print Network [OSTI]

    Paris-Sud XI, Universit de

    -NADPH reductase and the linker proteins of the phycobilisome antenna. Using mutants that lack specific setPhosphorylation in Synechocystis 1 JBC PHOSPHORYLATION OF PHYCOBILISOME LINKER PROTEINS@botanik.biologie.uni-muenchen.de The controversial issue of protein phosphorylation from the photosynthetic apparatus of Synechocystis sp. PCC 6803

  18. The variable and conserved interfaces of modeled olfactory receptor proteins

    E-Print Network [OSTI]

    Church, George M.

    of the odorants' contact residues in OR proteins remained unavailable. Due to the lack of X-ray crystallographicThe variable and conserved interfaces of modeled olfactory receptor proteins YITZHAK PILPEL models of other G-protein-coupled receptors, allows us to analyze the OR amino acid variability patterns

  19. Combinatorial Problems on Strings with Applications to Protein Folding

    E-Print Network [OSTI]

    Newman, Alantha

    Combinatorial Problems on Strings with Applications to Protein Folding Alantha Newman MIT San Jose, CA 95120, USA ruhl@almaden.ibm.com Abstract We consider the problem of protein folding in linear time. 1 Introduction We consider the problem of protein folding in the HP model on the three

  20. Protein Folding Simulation by Two-Stage Optimization

    E-Print Network [OSTI]

    Will, Sebastian

    Protein Folding Simulation by Two-Stage Optimization A. Dayem Ullah1 , L. Kapsokalivas1 , M. Mann2 propose a two-stage optimization approach for protein folding simulation in the FCC lattice, inspired from procedure based on simulated annealing alone. 1 Introduction The question of how proteins fold and whether

  1. Protein folding with stochastic L-systems Gemma Danks1

    E-Print Network [OSTI]

    Stepney, Susan

    Protein folding with stochastic L-systems Gemma Danks1 , Susan Stepney1 and Leo Caves1 1 University-like structures. Models of protein folding vary in complexity and the amount of prior knowledge they contain). The energy landscape theory of protein folding (Onuchic et al., 1997) predicts a rugged funnel-like energy

  2. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

    Schultz, Peter G. (La Jolla, CA); Wang, Lei (San Diego, CA)

    2009-04-28T23:59:59.000Z

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

  3. Self-assembled lipid and membrane protein polyhedral nanoparticles

    E-Print Network [OSTI]

    Stowell, Michael

    Self-assembled lipid and membrane protein polyhedral nanoparticles Tamara Bastaa,1 , Hsin-Jui Wub,1 for review January 28, 2012) We demonstrate that membrane proteins and phospholipids can self-assemble for the self-assembly of lipids and membrane proteins into closed polyhedral structures that can potentially

  4. Fra superledere over polymerer til proteiner: Hvis man vil fremstille

    E-Print Network [OSTI]

    Fra superledere over polymerer til proteiner: Hvis man vil fremstille tyndfilm af komplicerede tyndfilm af organiske materialer, som består af store og komplicerede molekyler: Polymerer, proteiner, antistoffer og DNA. Tyndfilm af polymerer er interessante i sensorer, fordi bestemte polymerer eller proteiner

  5. Comprehensive Superfamily and Function Classification of Protein Sequences

    E-Print Network [OSTI]

    on the basis of end-to-end similarity and domain architecture. The protein superfamily organization of the PIR-International Protein Sequence Database (PIR-PSD) is the only comprehensive protein classification system that is based are facilitated by the PIR Annotation and Similarity Database, which includes a pre- computed FASTA Database

  6. Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding

    E-Print Network [OSTI]

    Michalet, Xavier

    Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding David E. Hertzog,, Xavier a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 µs and sample) measurements of single-stranded DNA. We also demon- strate the feasibility of measuring fast protein folding

  7. Polymer Collapse, Protein Folding, and the Percolation Threshold

    E-Print Network [OSTI]

    Meirovitch, Hagai

    Polymer Collapse, Protein Folding, and the Percolation Threshold HAGAI MEIROVITCH University (Macromolecules 1989, 22, 3986­3997) to study protein folding, where H and P are the hydrophobic and polar amino; computer simulation; collapse transition; protein folding Introduction The behavior of dilute polymer

  8. Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives

    E-Print Network [OSTI]

    Janke, Wolfhard

    8 Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives Michael Bachmann applications. In this lecture, we focus on the anal- ysis of mesoscopic models for protein folding, aggregation for a more universal description of the notoriously difficult problem of protein fold- ing. In this approach

  9. Author's personal copy Protein folding in confined and crowded environments

    E-Print Network [OSTI]

    Weston, Ken

    Author's personal copy Review Protein folding in confined and crowded environments Huan-Xiang Zhou protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize

  10. COMMUNICATION First Principles Prediction of Protein Folding Rates

    E-Print Network [OSTI]

    Goddard III, William A.

    COMMUNICATION First Principles Prediction of Protein Folding Rates Derek A. Debe and William A studies have demonstrated that many small, single-domain proteins fold via simple two-state kinetics. We. # 1999 Academic Press Keywords: protein folding; kinetics; diffusion; fold topology; nucleation

  11. John von Neumann Institute for Computing Monte Carlo Protein Folding

    E-Print Network [OSTI]

    Hsu, Hsiao-Ping

    John von Neumann Institute for Computing Monte Carlo Protein Folding: Simulations of Met://www.fz-juelich.de/nic-series/volume20 #12;#12;Monte Carlo Protein Folding: Simulations of Met-Enkephalin with Solvent-Accessible Area difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular

  12. Predicting Protein Folding Mohammed J. Zaki, Vinay Nadimpally, Deb

    E-Print Network [OSTI]

    Zaki, Mohammed Javeed

    Predicting Protein Folding Pathways Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff 1. Predicting Protein Folding Pathways Summary. A structured folding pathway, which is a time ordered sequence of folding events, plays an important role in the protein folding process and hence

  13. Nonlinear dynamics of secondary protein folding Natalia G. Berloff

    E-Print Network [OSTI]

    Nonlinear dynamics of secondary protein folding Natalia G. Berloff Department of Applied field varies. Pacs: 87.15.-v, 87.15By, 05.45.-a, 41.20Jb Keywords: Folding pathway, protein folding interaction and hydrophobic effects. The most common shapes of the protein folding are alpha () and beta

  14. Protein folding: Then and now Yiwen Chen 1

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    Review Protein folding: Then and now Yiwen Chen 1 , Feng Ding 1 , Huifen Nie 1 , Adrian W decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally

  15. Protein folding by zipping and assembly S. Banu Ozkan*

    E-Print Network [OSTI]

    Southern California, University of

    Protein folding by zipping and assembly S. Banu Ozkan* , G. Albert Wu* , John D. Chodera, CA, May 2, 2007 (received for review April 13, 2006) How do proteins fold so quickly? Some denatured proteins fold to their native structures in only microseconds, on average, implying that there is a folding

  16. Author's personal copy Protein folding: Then and now

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    Author's personal copy Review Protein folding: Then and now Yiwen Chen 1 , Feng Ding 1 , Huifen Nie Available online 8 June 2007 Abstract Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital

  17. Multi-Agent Simulation of Protein Folding Luca Bortolussi1

    E-Print Network [OSTI]

    Bortolussi, Luca

    Multi-Agent Simulation of Protein Folding Luca Bortolussi1 , Agostino Dovier1 , and Federico residues) is known. The process for reaching this state is known as the protein fold- ing. This problem the feasibility and the power of the method. Keywords: Computational Biology, Agent-Based Technologies, Protein

  18. COMMUNICATION Are Residues in a Protein Folding Nucleus

    E-Print Network [OSTI]

    Dai, Yang

    COMMUNICATION Are Residues in a Protein Folding Nucleus Evolutionarily Conserved? Yan Yuan Tseng is the hallmark of life. It is important to understand how protein folding and evolution influence each other in protein folding nucleus as measured by experi- mental f-value and selection pressure as measured by v

  19. MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix

    E-Print Network [OSTI]

    Dix, Daniel B.

    MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix Department of Mathematics University of South Carolina Abstract. We present an elementary introduction to the protein folding problem directed toward, and biological problem, protein folding can also be precisely formulated as a set of mathematics problems. We

  20. Polypeptide chain collapse and protein folding Jayant B. Udgaonkar

    E-Print Network [OSTI]

    Review Polypeptide chain collapse and protein folding Jayant B. Udgaonkar National Centre is an integral component of a protein folding reaction. In this review, exper- imental characterization solvent [2]. A distinctive physical feature of any protein folding reaction is the greater than 3-fold

  1. MICROFLUIDIC DEVICE FOR SUPER-FAST EVALUATION OF MEMBRANE PROTEIN

    E-Print Network [OSTI]

    Stowell, Michael

    MICROFLUIDIC DEVICE FOR SUPER-FAST EVALUATION OF MEMBRANE PROTEIN CRYSTALLIZATION Hsin-Jui Wu1- throughput membraneless microfluidic device to fast produce the reconstitution of membrane protein in microfluidic channel can be completed in seconds to form protein/lipid particles under multiple conditions

  2. Serodiagnosis of avian infectious bronchitis virus using recombinant nucleocapsid protein

    E-Print Network [OSTI]

    Ndifuna, Abdul-El-Nuru

    1996-01-01T23:59:59.000Z

    A diagnostic immunoaassay using recombinant nucleocapsid protein to detect antibodies to I13V was designed. The nucleocapsid protein was expressed from an expression plasmid, Qiagen pQE8, in E. coli as a fusion protein that was purified on NI...

  3. Early Events in Protein Folding Explored by Rapid Mixing Methods

    E-Print Network [OSTI]

    Roder, Heinrich

    15 Early Events in Protein Folding Explored by Rapid Mixing Methods Heinrich Roder, Kosuke Maki for Understanding Protein Folding As with any complex reaction, time-resolved data are essential for elucidating the mechanism of protein folding. Even in cases where the whole process of folding occurs in a single step

  4. Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao

    E-Print Network [OSTI]

    Bystroff, Chris

    Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao Dept of Biology Rensselaer Polytechnic Institute, Troy, NY. e-mail:{bystrc, shaoy}@rpi.edu Summary Proteins fold through a series of intermediate states called a pathway. Protein folding pathways have been modeled using either simulations

  5. www.activemotif.comwww.activemotif.com Protein Purification

    E-Print Network [OSTI]

    Lebendiker, Mario

    , mammalian cells, yeast, and bacteria. For fast, small-scale purification of 6xHis-tagged proteins Binding, medium-scale purification of 6xHis-tagged proteins Binding capacity: 900 µg/column (45 nmol @ ~20 kwww.activemotif.comwww.activemotif.com Ni-TEDTM Protein Purification Active Motif 5431-C Avenida

  6. MICROPROTEOMICS: ANALYSIS OF PROTEIN DIVERSITY IN SMALL SAMPLES

    E-Print Network [OSTI]

    MICROPROTEOMICS: ANALYSIS OF PROTEIN DIVERSITY IN SMALL SAMPLES Howard B. Gutstein,1 * Jeffrey S.interscience.wiley.com) DOI 10.1002/mas.20161 Proteomics, the large-scale study of protein expression in organisms, offers be expressed by the genetic material of an organism. Advancements in protein extraction, purification

  7. Mini review Practical considerations in refolding proteins from inclusion bodies

    E-Print Network [OSTI]

    Lebendiker, Mario

    , removal of the denaturant, and assistance of refolding by small molecule additives. We will review key concentration, and (3) the effect of small molecule additives on refolding and aggregation of the proteins. ?- nomic sequence database, on a rapid, large-scale pro- duction of recombinant proteins. The proteins thus

  8. Overview of facility usage Protein Technology Core Facility

    E-Print Network [OSTI]

    Udgaonkar, Jayant B.

    performedFig9: Projects delivered Protein technology core has been successful as a small scale player expression and optimal purification is imperative for protein biology research groups in academia as well and technical guidance at all steps to optimize expression and purification to generate the protein of interest

  9. Automated Discovery of Structural Signatures of Protein Fold and Function

    E-Print Network [OSTI]

    Muggleton, Stephen H.

    Automated Discovery of Structural Signatures of Protein Fold and Function Marcel Turcotte1 sys- tematically for protein fold signatures, we have explored the use of Inductive Logic Programming fold. The work showed that signatures of protein folds exist, about half of rules discov- ered

  10. Diffusion of a protein in configuration space

    SciTech Connect (OSTI)

    Garcia, A.E.; Blumenfeld, R.; Hummer, G.; Sobehart, J.

    1995-09-01T23:59:59.000Z

    Simulations of biomolecular dynamics are commonly interpreted in terms of harmonic or quasi-harmonic models for the dynamics of the system. These models assume that biomolecules exhibit oscillations around a single energy minimum. However, spectroscopic data on myoglobin suggest that proteins sample multiple minima. Transitions between minima reveal a broad distribution of energy barriers. This behavior has been observed in other biomolecular systems. To elucidate the nature of protein dynamics the authors have studied a 1.2ns molecular dynamics trajectory of crambin in aqueous solution. This trajectory samples multiple local energy minima. Transitions between minima involve collective motions of amino acids over long distances. The authors show that nonlinear motions are responsible for most of the atomic fluctuations of the protein. These atomic fluctuations are not well described by large motions of individual atoms or a small group of atoms, but rather by concerted motions of many atoms. These nonlinear motions describe transitions between different basins of attraction. The signature of these motions manifests in local and global structural variables. A method for extracting Molecule Optimal Dynamic Coordinates (MODC) is presented.

  11. Nucleic acids encoding human trithorax protein

    DOE Patents [OSTI]

    Evans, Glen A. (Encinitas, CA); Djabali, Malek (Marseilles, FR); Selleri, Licia (Del Mar, CA); Parry, Pauline (San Diego, CA)

    2001-01-01T23:59:59.000Z

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

  12. Simple Models of the Protein Folding Problem

    E-Print Network [OSTI]

    Chao Tang

    1999-12-26T23:59:59.000Z

    The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I will give an introduction to the problem, and then focus on some recent work concerning the so-called ``designability principle''. The designability of a structure is measured by the number of sequences that have that structure as their unique ground state. Structures differ drastically in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures 1) possess ``proteinlike'' secondary structures and motifs, 2) are thermodynamically more stable, and 3) fold faster than other structures. These results suggest that protein structures are selected in nature because they are readily designed and stable against mutations, and that such selection simultaneously leads to thermodynamic stability and foldability. According to this picture, a key to the protein folding problem is to understand the emergence and the properties of the highly designable structures.

  13. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

    E-Print Network [OSTI]

    Liu, Shiyong; Vakser, Ilya A.

    2011-07-11T23:59:59.000Z

    Background: Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve ...

  14. Effect of dietary protein quality on fractional rates of muscle protein synthesis and catabolism in the rat

    E-Print Network [OSTI]

    Roeder, Richard Anthony

    1979-01-01T23:59:59.000Z

    EFFECT OF DIETARY PROTEIN QUALITY ON FRACTIONAL RATES OF MUSCLE PROTEIN SYNTHESIS AND CATABOLISM IN THE RAT A Thesis by RICHARD ANTHONY ROEDER Submitted to the Graduate College of Texas A8cM University in partial fulfillment... of the requirement for the degree of MASTER OF SCIENCE August 1979 Major Subject: Animal Nutrition EFFECT OF DIETARY PROTEIN QUALITY ON FRACTIONAL RATES OF MUSCLE PROTEIN SYNTHESIS AND CATABOLISM IN THE RAT A Thesis by RICHARD ANTHONY ROEDER Approved...

  15. A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants

    E-Print Network [OSTI]

    Li, Yunqi; Middaugh, C. Russell; Fang, Jianwen

    2010-01-28T23:59:59.000Z

    . Clearly, a key step in such approaches is the development of reliable methods for estimating the relative stability of possible mutants to identify favorable mutations. Such methods may also help better understand the protein- folding problem since... the ultimate outcome of protein folding is a native structure with the lowest free energy among many possible structures of a protein. A common approach to study the thermostability of proteins is to perform comparative studies of the sequences and...

  16. Protein Science (2000), 9: 197-200. Cambridge University Press. Printed in the USA. Copyright 2000 The Protein Society

    E-Print Network [OSTI]

    Levitt, Michael

    on the history of proteins classified in the SCOP structure database, we expect that only about a quarter this question. The SCOP database (Murzin et al., 1995) organizes proteins according to their structural on a protein sequence identical or nearly identical to one already in the database, perhaps with some mutations

  17. Energy Landscape and Transition State of Protein-Protein Association Ramzi Alsallaq and Huan-Xiang Zhou

    E-Print Network [OSTI]

    Weston, Ken

    Energy Landscape and Transition State of Protein-Protein Association Ramzi Alsallaq and Huan as well as the transition state for association. The energy landscape is funnel-like, with the deep well and rotational freedom. Echoing the protein folding process, we have previously proposed a transition state

  18. PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear

    E-Print Network [OSTI]

    Shorter, James

    accuracy with a lower false positive rate. All materials are freely available to the scientific community and protein identification and can help reduce the number of false positive resulPILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass

  19. Abstract The Tat protein-export system serves to trans-locate folded proteins, often containing redox cofactors,

    E-Print Network [OSTI]

    Palmer, Tracy

    - location by the Sec system proceeds by a `threading' mechanism in which the essentially unfolded substrate-bound respiratory complexes by the Tat protein-transport system Received: 27 February 2002 / Revised: 16 April 2002Abstract The Tat protein-export system serves to trans- locate folded proteins, often containing

  20. Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins

    E-Print Network [OSTI]

    D. K. Klimov; D. Thirumalai

    1998-04-22T23:59:59.000Z

    We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real proteins. We show that larger values of $\\Omega_{c}$ resembling those seen in proteins are obtained in lattice models with side chains (LMSC). The enhanced cooperativity in LMSC is due to the possibility of denser packing of side chains in the interior of the model protein. We also establish that $\\Omega_{c}$ correlates extremely well with (\\sigma = (T_{\\theta} -T_{f} )/T_{\\theta}), where (T_{\\theta}) and (T_{f}) are collapse and folding transition temperatures, respectively. These theoretical ideas are used to analyze folding transitions in various real proteins. The values of $\\Omega _{c}$ extracted from experiments show a correlation with $\\sigma $. We conclude that the degree of cooperativity can be expressed in terms of the single parameter $\\sigma $, which can be estimated from experimental data.