National Library of Energy BETA

Sample records for monochromatic protein crystallography

  1. Protein crystallography prescreen kit

    DOE Patents [OSTI]

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

    2007-10-02

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

  2. 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

  3. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

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

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; Chowdhury, Shatabdi Roy; Basu, Shibom; Boutet, Sébastien; Fromme, Petra; White, Thomas A.; Barty, Anton; Spence, John C. H.; et al

    2015-08-04

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is shown enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals deliveredmore »by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.« less

  4. Serial Femtosecond Crystallography of G Protein-Coupled Receptors

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

    Liu, Liu

    2013-10-23

    Serial femtosecond crystallography data on microcrystals of 5-HT2B receptor bound to ergotamine grown in lipidic cubic phase.

  5. Cryogenic Neutron Protein Crystallography: routine methods and potential benefits

    SciTech Connect (OSTI)

    Weiss, Kevin L [ORNL; Tomanicek, Stephen J [ORNL; NG, Joseph D [ORNL

    2014-01-01

    The use of cryocooling in neutron diffraction has been hampered by several technical challenges such as the need for specialized equipment and techniques. Recently we have developed and deployed equipment and strategies that allow for routine neutron data collection on cryocooled crystals using off the shelf components. This system has several advantages, compared to a closed displex cooling system such as fast cooling coupled with easier crystal mounting and centering. The ability to routinely collect cryogenic neutron data for analysis will significantly broaden the range of scientific questions that can be examined by neutron protein crystallography. Cryogenic neutron data collection for macromolecules has recently become available at the new Biological Diffractometer BIODIFF at FRM II and the Macromolecular Diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge National Laboratory. To evaluate the benefits of a cryocooled neutron structure we collected a full neutron data set on the BIODIFF instrument on a Toho-1 lactamase structure at 100K.

  6. Weighting Features to Recognize 3D Patterns of Electron Density in X-ray Protein Crystallography

    E-Print Network [OSTI]

    Ioerger, Thomas R.

    Weighting Features to Recognize 3D Patterns of Electron Density in X-ray Protein Crystallography features to recognize 3D patterns of electron density to determine protein structures. We present SLIDER, Texas A&M University 2 Department of Biochemistry & Biophysics, Texas A&M University 1 {kgopal

  7. Bent Diamond Crystals and Multilayer Based Optics at the new 5-Station Protein Crystallography Beamline 'Cassiopeia' at MAX-lab

    SciTech Connect (OSTI)

    Mammen, Christian B.; Als-Nielsen, Jens; Ursby, Thomas; Thunnissen, Marjolein

    2004-05-12

    A new 5-station beamline for protein crystallography is being commissioned at the Swedish synchrotron light source MAX-II at Lund University. Of the 2K/{gamma} = 14 mrad horizontal wiggler fan, the central 2 mrad are used and split in three parts. The central 1 mrad will be used for a station optimized for MAD experiments and on each side of the central fan, from 0.5 mrad to 1 mrad, there are two fixed energy stations using different energies of the same part of the beam. These, in total five stations, can be used simultaneously and independently for diffraction data collection. The two upstream monochromators for the side stations are meridionally bent asymmetric diamond(111) crystals in Laue transmission geometry. The monochromators for the downstream side stations are bent Ge(111) crystals in asymmetric Bragg reflection geometry. Curved multilayer mirrors inserted in the monochromatic beams provide focusing in the vertical plane. The first side station is under commissioning, and a preliminary test protein data set has been collected.

  8. SIBYLS - A SAXS and protein crystallography beamline at the ALS

    SciTech Connect (OSTI)

    Trame, Christine; MacDowell, Alastair A.; Celestre, Richard S.; Padmore, Howard A.; Cambie, Daniella; Domning, Edward E.; Duarte, Robert M.; Kelez, Nicholas; Plate, David W.; Holton, James M.; Frankel, Kenneth; Tsutakawa, Susan; Tsuruta, Hiro; Tainer, John A.; Cooper, Priscilla K.

    2003-08-22

    The new Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the Advanced Light Source will be dedicated to Macromolecular Crystallography (PX) and Small Angle X-ray Scattering (SAXS). SAXS will provide structural information of macromolecules in solutions and will complement high resolution PX studies on the same systems but in a crystalline state. The x-ray source is one of the 5 Tesla superbend dipoles recently installed at the ALS that allows for a hard x-ray program to be developed on the relatively low energy Advanced Light Source (ALS) ring (1.9 GeV). The beamline is equipped with fast interchangeable monochromator elements, consisting of either a pair of single Si(111) crystals for crystallography, or a pair of multilayers for the SAXS mode data collection (E/{Delta}E {approx} 1/110). Flux rates with Si(111) crystals for PX are measured as 2 x 10{sup 11} hv/sec/400 mA through a 100 {micro}m pinhole at 12.4 KeV. For SAXS the flux is up to 3 x 10{sup 13} photons/sec at 10 KeV with all apertures open when using the multilayer monochromator elements. The performance characteristics of this unique beamline will be described.

  9. A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography

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

    Bunker, Richard D.; Mandal, Kalyaneswar; Bashiri, Ghader; Chaston, Jessica J.; Pentelute, Bradley L.; Lott, J. Shaun; Kent, Stephen B. H.; Baker, Edward N.

    2015-04-07

    Racemic protein crystallography was used to determine the X-ray structure of the predicted Mycobacterium tuberculosis protein Rv1738, which had been completely recalcitrant to crystallization in its natural L-form. Native chemical ligation was used to synthesize both L-protein and D-protein enantiomers of Rv1738. Crystallization of the racemic {D-protein + L-protein} mixture was immediately successful. The resulting crystals diffracted to high resolution and also enabled facile structure determination because of the quantized phases of the data from centrosymmetric crystals. The X-ray structure of Rv1738 revealed striking similarity with bacterial hibernation factors, despite minimal sequence similarity. As a result, we predict that Rv1738,more »which is highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome.« less

  10. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source

    SciTech Connect (OSTI)

    MacDowell, Alastair A.; Celestre, Richard S.; Howells, Malcolm; McKinney, Wayne; Krupnick, James; Cambie, Daniella; Domning, Edward E; Duarte, Robert M.; Kelez, Nicholas; Plate, David W.; Cork, Carl W.; Earnest, Thomas N.; Dickert, Jeffery; Meigs, George; Ralston, Corie; Holton, James M.; Alber, Thomas; Berger, James M.; Agard, David A.; Padmore, Howard A.

    2004-08-01

    At the Advanced Light Source (ALS), three protein crystallography (PX) beamlines have been built that use as a source one of the three 6 Tesla single pole superconducting bending magnets (superbends) that were recently installed in the ring. The use of such single pole superconducting bend magnets enables the development of a hard x-ray program on a relatively low energy 1.9 GeV ring without taking up insertion device straight sections. The source is of relatively low power, but due to the small electron beam emittance, it has high brightness. X-ray optics are required to preserve the brightness and to match the illumination requirements for protein crystallography. This was achieved by means of a collimating premirror bent to a plane parabola, a double crystal monochromator followed by a toroidal mirror that focuses in the horizontal direction with a 2:1 demagnification. This optical arrangement partially balances aberrations from the collimating and toroidal mirrors such that a tight focused spot size is achieved. The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described.

  11. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

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

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques -Philippe

    2015-04-25

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore »resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

  12. Protein crystallography: From X-ray diffraction spots to a three dimensional image

    SciTech Connect (OSTI)

    Terwilliger, T.C.; Berendzen, J.

    1998-02-25

    Proteins are remarkable molecular machines that are essential for life. They can do many things ranging from the precise control of blood clotting to synthesizing complex organic compounds. Pictures of protein molecules are in high demand in biotechnology because they are important for applications such as drug discovery and for engineering enzymes for commercial use. X-ray crystallography is the most common method for determining the three-dimensional structures of protein molecules. When a crystal of a protein is placed in an X-ray beam, scattering of X-rays off the ordered molecules produces a diffraction pattern that can be measured on a position-sensitive CCD or image-plate detector. Protein crystals typically contain thousands of atoms and the diffraction data are generally measured to relatively low resolution. Consequently the direct methods approaches generally cannot be applied. Instead, if the crystal is modified by adding metal atoms at specific sites or by tuning the wavelength of the X-rays to cross an absorption edge of a metal atom in the crystal, then the information from these additional measurements is sufficient to first identify the /locations of the metal atoms. This information is then used along with the diffraction data to make a three-dimensional picture of electron densities. This picture can be used to determine the position of most or all of the atoms in the protein.

  13. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

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

    van Thor, Jasper J.; Madsen, Anders

    2015-01-01

    In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/?I) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ?F,more »in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

  14. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

    SciTech Connect (OSTI)

    van Thor, Jasper J.; Madsen, Anders

    2015-01-01

    In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/?I) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ?F, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.

  15. CCD(charge-coupled device)-based synchrotron x-ray detector for protein crystallography: Performance projected from an experiment

    SciTech Connect (OSTI)

    Strauss, M.G.; Naday, I.; Sherman, I.S.; Kraimer, M.R.; Westbrook, E.M.

    1986-01-01

    The intense x radiation from a synchrotron source could, with a suitable detector, provide a complete set of diffraction images from a protein crystal before the crystal is damaged by radiation (2 to 3 min). An area detector consisting of a 40 mm dia. x-ray fluorescing phosphor, coupled with an image intensifier and lens to a CCD image sensor, was developed to determine the effectiveness of such a detector in protein crystallography. The detector was used in an experiment with a rotating anode x-ray generator. Diffraction patterns from a lysozyme crystal obtained with this detector are compared to those obtained with film. The two images appear to be virtually identical. The flux of 10/sup 4/ x-ray photons/s was observed on the detector at the rotating anode generator. At the 6-GeV synchrotron being designed at Argonne, the flux on an 80 x 80 mm/sup 2/ detector is expected to be >10/sup 9/ photons/s. The projected design of such a synchrotron detector shows that a diffraction-peak count >10/sup 6/ could be obtained in approx.0.5 s. With an additional approx.0.5 s readout time of a 512 x 512 pixel CCD, the data acquisition time per frame would be approx.1 s so that ninety 1/sup 0/ diffraction images could be obtained, with approximately 1% precision, in less than 3 min.

  16. DIRECT CORRELATION OF PROTEIN STRUCTURE AND FUNCTION USING HIGH-PRESSURE X-RAY CRYSTALLOGRAPHY

    E-Print Network [OSTI]

    Gruner, Sol M.

    protein Citrine as a model system under high-pressure perturbation. Citrine has been compressed by high Buz Michael Barstow, Ph. D. Cornell University 2009 A protein molecule is an intricate system whose is used to refer to my co-authors: Nozomi Ando, Chae Un Kim, and my advisor, Sol Gruner, to whom I owe

  17. Automated High Throughput Drug Target Crystallography

    SciTech Connect (OSTI)

    Rupp, B

    2005-02-18

    The molecular structures of drug target proteins and receptors form the basis for 'rational' or structure guided drug design. The majority of target structures are experimentally determined by protein X-ray crystallography, which as evolved into a highly automated, high throughput drug discovery and screening tool. Process automation has accelerated tasks from parallel protein expression, fully automated crystallization, and rapid data collection to highly efficient structure determination methods. A thoroughly designed automation technology platform supported by a powerful informatics infrastructure forms the basis for optimal workflow implementation and the data mining and analysis tools to generate new leads from experimental protein drug target structures.

  18. Johann Deisenhofer, Crystallography, and Proteins

    Office of Scientific and Technical Information (OSTI)

    2011. with acknowledgment of APS at ANL Crystal Structure of the Catalytic Portion of Human HMG-CoA Reductase with acknowledgment of APS at ANL and NSLS at BNL Crystal...

  19. Johann Deisenhofer, Crystallography, and Proteins

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

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  20. Diamondoid Monolayers as Monochromatic Electron Source

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

    at the ALS to reveal an intriguing feature: monochromatized electron emission from a self-assembled monolayer of diamondoids. This discovery has immediately attracted the...

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

    Office of Scientific and Technical Information (OSTI)

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

  2. SMB, Macromolecular Crystallography

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

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  3. Nanostructure, Chemistry and Crystallography of Iron Nitride...

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

    Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic Materials by Ultra-High-Resolution Electron Microscopy and Related Methods Nanostructure, Chemistry and...

  4. A novel inert crystal delivery medium for serial femtosecond crystallography

    SciTech Connect (OSTI)

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; Hunter, Mark S.; Koglin, Jason E.; Kupitz, Christopher; Nelson, Garrett; Subramanian, Ganesh; White, Thomas A.; Zhao, Yun; Zook, James; Boutet, Sébastien; Cherezov, Vadim; Spence, John C. H.; Fromme, Raimund; Weierstall, Uwe; Fromme, Petra

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

  5. A novel inert crystal delivery medium for serial femtosecond crystallography

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

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; et al

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, themore »structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.« less

  6. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

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

    Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; et al

    2015-08-18

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore »Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

  7. Lipidic phase membrane protein serial femtosecond crystallography

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

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  8. Using Two-Dimensional Colloidal Crystals to Understand Crystallography

    E-Print Network [OSTI]

    Loening, Niko

    Using Two-Dimensional Colloidal Crystals to Understand Crystallography Instructor Notes Geometric). #12;Using Two-Dimensional Colloidal Crystals to Understand Crystallography Instructions for Students the patterns that result from the diffraction of electromagnetic radiation by a crystal provides structural

  9. Monochromatic and random wave breaking at blocking points

    E-Print Network [OSTI]

    Kirby, James T.

    ; published 4 July 2002. [1] In this paper we study the energy dissipation due to current-limited waveMonochromatic and random wave breaking at blocking points Arun Chawla Center for Coastal and Land and Technology, Portland, Oregon, USA James T. Kirby Center for Applied Coastal Research, University of Delaware

  10. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

    SciTech Connect (OSTI)

    Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; Pai, E. F.; Pearson, A. R.; Olson, J. S.; Anfinrud, P. A.; Ernst, O. P.; Miller, R. J. Dwayne

    2015-08-18

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.

  11. Theoretical crystallography with the Advanced Visualization System

    SciTech Connect (OSTI)

    Younkin, C.R.; Thornton, E.N.; Nicholas, J.B.; Jones, D.R.; Hess, A.C.

    1993-05-01

    Space is an Application Visualization System (AVS) graphics module designed for crystallographic and molecular research. The program can handle molecules, two-dimensional periodic systems, and three-dimensional periodic systems, all referred to in the paper as models. Using several methods, the user can select atoms, groups of atoms, or entire molecules. Selections can be moved, copied, deleted, and merged. An important feature of Space is the crystallography component. The program allows the user to generate the unit cell from the asymmetric unit, manipulate the unit cell, and replicate it in three dimensions. Space includes the Buerger reduction algorithm which determines the asymmetric unit and the space group of highest symmetry of an input unit cell. Space also allows the user to display planes in the lattice based on Miller indices, and to cleave the crystal to expose the surface. The user can display important precalculated volumetric data in Space, such as electron densities and electrostatic surfaces. With a variety of methods, Space can compute the electrostatic potential of any chemical system based on input point charges.

  12. The Development of the GCPCC Protein Crystallography Beamline at CAMD

    E-Print Network [OSTI]

    Phillips, George N. Jr.

    ) monochromator and a focusing toroidal mirror. Built off of the CAMD 7 T superconducting, energy-shifting wiggler. The radiation source for this beamline is a 7 T superconducting, energy-shifting wiggler at the Center of the flux produced by the superconducting side poles relative to the central pole is 16% at 7 keV, 3 % at 12

  13. Serial femtosecond crystallography of soluble proteins in lipidic...

    Office of Scientific and Technical Information (OSTI)

    are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector....

  14. Account / Revue Use of polynuclear metal clusters in protein crystallography

    E-Print Network [OSTI]

    (2005). © 2005 Académie des sciences. Published by Elsevier SAS. All rights reserved. Résumé L/ 1631-0748/$ - see front matter © 2005 Académie des sciences. Published by Elsevier SAS. All rights; accepted after revision 8 November 2004 Available online 14 July 2005 Abstract Application of polynuclear

  15. Serial femtosecond crystallography of soluble proteins in lipidic cubic

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail. (Conference) |Janka,FerraraTechnologies (Conference)

  16. Serial femtosecond crystallography of soluble proteins in lipidic cubic

    Office of Scientific and Technical Information (OSTI)

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  17. Combining Electron Crystallography and X-ray Crystallography to Study the MlotiK1 Cyclic Nucleotide-Regulated Potassium Channel

    SciTech Connect (OSTI)

    Clayton, G.; Aller, S; Wang, J; Unger, V; Morais-Cabral, J

    2009-01-01

    We have recently reported the X-ray structure of the cyclic nucleotide-regulated potassium channel, MlotiK1. Here we describe the application of both electron and X-ray crystallography to obtain high quality crystals. We suggest that the combined application of these techniques provides a useful strategy for membrane protein structure determination. We also present negative stain projection and cryo-data projection maps. These maps provide new insights about the properties of the MlotiK1 channel. In particular, a comparison of a 9 {angstrom} cryo-data projection with calculated model maps strongly suggests that there is a very weak interaction between the pore and the S1-S4 domains of this 6 TM tetrameric cation channel and that the S1-S4 domains can adopt multiple orientations relative to the pore.

  18. Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin

    E-Print Network [OSTI]

    Ramakrishnan, Venki

    determined by x-ray crystallography except at very high resolution. The scattering of neutrons by hydrogenEnhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin Fong and structurally, direct visu- alization of them by using crystallography is difficult. Neutron crys- tallography

  19. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

    SciTech Connect (OSTI)

    Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

    2013-05-01

    New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.

  20. Method and apparatus for producing monochromatic radiography with a bent Laue crystal

    SciTech Connect (OSTI)

    2000-03-14

    A method and apparatus are disclosed for producing a monochromatic beam. A plurality of beams are generated from a polyenergetic source. The beams are then transmitted through a bent crystal, preferably a bent Laue crystal, having a non-cylindrical shape. A position of the bent crystal is rocked with respect to the polyenergetic source until a plurality of divergent monochromatic beams are emitted from the bent crystal.

  1. Method and apparatus for producing monochromatic radiography with a bent laue crystal

    DOE Patents [OSTI]

    Zhong, Zhong (Apt. I 1131 Chaping 700 E. Loop Rd., Stony Brook, NY 11790); Chapman, Leroy Dean (4 Vermont Cir., Bolingbrook, IL 60440); Thomlinson, William C. (32 E. Masem, East Patchogue, NY 11772)

    2000-03-14

    A method and apparatus for producing a monochromatic beam. A plurality of beams are generated from a polyenergetic source. The beams are then transmitted through a bent crystal, preferably a bent Laue crystal, having a non-cylindrical shape. A position of the bent crystal is rocked with respect to the polyenergetic source until a plurality of divergent monochromatic beams are emitted from the bent crystal.

  2. Proteins

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

    Proteins Protein Engineering, Structure, and Function Los Alamos scientists seek a comprehensive understanding of the structure and function of proteins which can lead to a...

  3. A mirror for lab-based quasi-monochromatic parallel x-rays

    SciTech Connect (OSTI)

    Nguyen, Thanhhai; Lu, Xun; Lee, Chang Jun; Jeon, Insu; Jung, Jin-Ho; Jin, Gye-Hwan; Kim, Sung Youb

    2014-09-15

    A multilayered parabolic mirror with six W/Al bilayers was designed and fabricated to generate monochromatic parallel x-rays using a lab-based x-ray source. Using this mirror, curved bright bands were obtained in x-ray images as reflected x-rays. The parallelism of the reflected x-rays was investigated using the shape of the bands. The intensity and monochromatic characteristics of the reflected x-rays were evaluated through measurements of the x-ray spectra in the band. High intensity, nearly monochromatic, and parallel x-rays, which can be used for high resolution x-ray microscopes and local radiation therapy systems, were obtained.

  4. Proteins

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

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

  5. Hyperfine Interactions 125 (2000) 328 3 Monochromatization of synchrotron radiation for nuclear

    E-Print Network [OSTI]

    Jackson, Jennifer M.

    2000-01-01

    Hyperfine Interactions 125 (2000) 3­28 3 Monochromatization of synchrotron radiation for nuclear­30 keV is presented for applications involving nuclear resonant scattering. The relevant relationships for a variety of nuclear resonances in this energy range. 1. Introduction Synchrotron radiation sources have

  6. Monte Carlo Characterization of a Pulsed Laser-Wakefield Driven Monochromatic

    E-Print Network [OSTI]

    Umstadter, Donald

    Monte Carlo Characterization of a Pulsed Laser-Wakefield Driven Monochromatic X-Ray Source S. D facility at the University of Nebraska- Lincoln (UNL) is a 100-TW, 30-fs pulsed Ti:sapphire laser system. Diocles is routinely used to accelerate electron beams by means of laser-wakefield acceleration, which

  7. Development of lanthanide-binding tags (LBTs) as powerful and versatile peptides for use in studies of proteins and protein interactions

    E-Print Network [OSTI]

    Martin, Langdon James

    2008-01-01

    To determine the function of proteins of interest, chemical biologists employ their full panoply of techniques, including X-ray crystallography and NMR spectroscopy for structural information, and luminescence spectroscopy ...

  8. Research on a logarithmically bent Laue crystal analyzer for X-ray monochromatic backlight imaging

    SciTech Connect (OSTI)

    Wu, Yufen; Xiao, Shali; Lu, Jian; Liu, Lifeng; Yang, Qingguo; Huang, Xianbin

    2013-07-15

    A new logarithmically bent Laue imaging crystal analyzer (LBLICA) was proposed to obtain the monochromatic image of plasmas and exhibited a great potential for application in the Inertial Confinement Fusion experiment over a large field of view (FOV) and with a high spatial resolution. The imaging geometry of the LBLICA has been discussed. According to the Bragg condition and the equation of the logarithmic spiral, the key image parameters of the crystal analyzer, including the system magnification, the spatial resolution, and the FOV, have been analyzed theoretically. An experiment has been performed with a Cu target X-ray tube as a backlighter to backlight a mesh grid consisting of 50-?m Cu wires, and the monochromatic image of the grid has been obtained with a spatial resolution of approximately 30 ?m.

  9. High-resolution monochromatic x-ray imaging system based on spherically bent crystals

    SciTech Connect (OSTI)

    Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C.M.; Seely, J.; Feldman, U.; Holland, G.

    1998-08-01

    We have developed an improved x-ray imaging system based on spherically curve crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser. A spherically curved quartz crystal (2d=6.687 {Angstrom}, R=200 mm) has been used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the x-ray optical system is 1.7 {mu}m in selected places and 2{endash}3 {mu}m over a larger area. Time-resolved backlit monochromatic images of polystyrene planar targets driven by the Nike facility have been obtained with a spatial resolution of 2.5 {mu}m in selected places and 5 {mu}m over the focal spot of the Nike laser. {copyright} 1998 Optical Society of America

  10. High resolution monochromatic X-ray imaging system based on spherically bent crystals

    SciTech Connect (OSTI)

    Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C. M.; Seely, J.; Feldman, U.; Holland, G.

    1997-05-05

    We have developed a new X-ray imaging system based on spherically curved crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser. The imaging system is used for plasma diagnostics of the main target and for characterization of potential backlighters. A spherically curved quartz crystal (2d=6.687 A, R=200 mm) is used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the X-ray optical system is 3-4 {mu}m. Time resolved backlit monochromatic images of CH planar targets driven by the Nike facility have been obtained with 6-7 {mu}m spatial resolution.

  11. High resolution monochromatic X-ray imaging system based on spherically bent crystals

    SciTech Connect (OSTI)

    Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C.M.; Seely, J.; Feldman, U.; Holland, G.

    1997-05-01

    We have developed a new X-ray imaging system based on spherically curved crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser [1,2]. The imaging system is used for plasma diagnostics of the main target and for characterization of potential backlighters. A spherically curved quartz crystal (2d=6.687{Angstrom}, R=200mm) is used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the X-ray optical system is 3{endash}4 {mu}m. Time resolved backlit monochromatic images of CH planar targets driven by the Nike facility have been obtained with 6{endash}7 {mu}m spatial resolution. {copyright} {ital 1997 American Institute of Physics.}

  12. The Effect of the LISA Response Function on Observations of Monochromatic Sources

    E-Print Network [OSTI]

    Vecchio, A

    2004-01-01

    The Laser Interferometer Space Antenna (LISA) is expected to provide the largest observational sample of binary systems of faint sub-solar mass compact objects, in particular white-dwarfs, whose radiation is monochromatic over most of the LISA observational window. Current astrophysical estimates suggest that the instrument will be able to resolve about 10000 such systems, with a large fraction of them at frequencies above 3 mHz, where the wavelength of gravitational waves becomes comparable to or shorter than the LISA arm-length. This affects the structure of the so-called LISA transfer function which cannot be treated as constant in this frequency range: it introduces characteristic phase and amplitude modulations that depend on the source location in the sky and the emission frequency. Here we investigate the effect of the LISA transfer function on detection and parameter estimation for monochromatic sources. For signal detection we show that filters constructed by approximating the transfer function as a ...

  13. Light trapping for emission from a photovoltaic cell under normally incident monochromatic illumination

    SciTech Connect (OSTI)

    Takeda, Yasuhiko Iizuka, Hideo; Mizuno, Shintaro; Hasegawa, Kazuo; Ichikawa, Tadashi; Ito, Hiroshi; Kajino, Tsutomu; Ichiki, Akihisa; Motohiro, Tomoyoshi

    2014-09-28

    We have theoretically demonstrated a new light-trapping mechanism to reduce emission from a photovoltaic (PV) cell used for a monochromatic light source, which improves limiting conversion efficiency determined by the detailed balance. A multilayered bandpass filter formed on the surface of a PV cell has been found to prevent the light generated inside by radiative recombination from escaping the cell, resulting in a remarkable decrease of the effective solid angle for the emission. We have clarified a guide to design a suitable configuration of the bandpass filter and achieved significant reduction of the emission. The resultant gain in monochromatic conversion efficiency in the radiative limit due to the optimally designed 18-layerd bandpass filters is as high as 6% under normally incident 1064 nm illumination of 10 mW/cm²~ 1 kW/cm², compared with the efficiency for the perfect anti-reflection treatment to the surface of a conventional solar cell.

  14. Monochromatic wavelength dispersive x-ray fluorescence providing sensitive and selective detection of uranium

    SciTech Connect (OSTI)

    Havrilla, George J [Los Alamos National Laboratory; Collins, Michael L [Los Alamos National Laboratory; Montoya, Velma M [Los Alamos National Laboratory; Chen, Zewu [XOS; Wei, Fuzhong [XOS

    2010-01-01

    Monochromatic wavelength dispersive X-ray fluorescence (MWDXRF) is a sensitive and selective method for elemental compositional analyses. The basis for this instrumental advance is the doubly curved crystal (DCC) optic. Previous work has demonstrated the feasibility of sensitive trace element detection for yttrium as a surrogate for curium in aqueous solutions. Additional measurements have demonstrated similar sensitivity in several different matrix environments which attests to the selectivity of the DCC optic as well as the capabilities of the MWDXRF concept. The objective of this effort is to develop an improved Pu characterization method for nuclear fuel reprocessing plants. The MWDXRF prototype instrument is the second step in a multi-year effort to achieve an improved Pu assay. This work will describe a prototype MWDXRF instrument designed for uranium detection and characterization. The prototype consists of an X-ray tube with a rhodium anode and a DCC excitation optic incorporated into the source. The DCC optic passes the RhK{alpha} line at 20.214 keV for monochromatic excitation of the sample. The source is capable of 50 W power at 50 kV and 1.0 mA operation. The x-ray emission from the sample is collected by a DCC optic set at the UL{alpha} line of 13.613 keV. The collection optic transmits the UL{alpha} x-rays to the silicon drift detector. The x-ray source, sample, collection optic and detector are all mounted on motion controlled stages for the critical alignment of these components. The sensitivity and selectivity of the instrument is obtained through the monochromatic excitation and the monochromatic detection. The prototype instrument performance has a demonstrated for sensitivity for uranium detection of around 2 ppm at the current state of development. Further improvement in sensitivity is expected with more detailed alignment.

  15. Engineering Encodable Lanthanide-Binding Tags (LBTs) into Loop Regions of Proteins

    E-Print Network [OSTI]

    Barthelmes, Katja

    Lanthanide-binding tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography, and luminescence studies. We have inserted LBTs into three different ...

  16. Dark Matter Decay to a Photon and a Neutrino: the Double Monochromatic Smoking Gun Scenario

    E-Print Network [OSTI]

    Chaïmae El Aisati; Michael Gustafsson; Thomas Hambye; Tiziana Scarna

    2015-10-16

    In the energy range from few TeV to 25 TeV, upper bounds on the dark matter decay rate into high energy monochromatic neutrinos have recently become comparable to those on monochromatic gamma-ray lines. This implies clear possibilities of a future double "smoking-gun" evidence for the dark matter particle, from the observation of both a gamma and a neutrino line at the same energy. In particular, we show that a scenario where both lines are induced from the same dark matter particle decay leads to correlations that can already be tested. We study this "double monochromatic" scenario by considering the complete list of lowest dimensional effective operators that could induce such a decay. Furthermore, we argue that, on top of lines from decays into two-body final states, three-body final states can also be highly relevant. In addition to producing a distinct hard photon spectrum, three-body final states also produce a line-like feature in the neutrino spectrum that can be searched for by neutrino telescopes.

  17. Dark Matter Decay to a Photon and a Neutrino: the Double Monochromatic Smoking Gun Scenario

    E-Print Network [OSTI]

    Aisati, Chaïmae El; Hambye, Thomas; Scarna, Tiziana

    2015-01-01

    In the energy range from few TeV to 25 TeV, upper bounds on the dark matter decay rate into high energy monochromatic neutrinos have recently become comparable to those on monochromatic gamma-ray lines. This implies clear possibilities of a future double "smoking-gun" evidence for the dark matter particle, from the observation of both a gamma and a neutrino line at the same energy. In particular, we show that a scenario where both lines are induced from the same dark matter particle decay leads to correlations that can already be tested. We study this "double monochromatic" scenario by considering the complete list of lowest dimensional effective operators that could induce such a decay. Furthermore, we argue that, on top of lines from decays into two-body final states, three-body final states can also be highly relevant. In addition to producing a distinct hard photon spectrum, three-body final states also produce a line-like feature in the neutrino spectrum that can be searched for by neutrino telescopes.

  18. Proteins

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

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

  19. John Pendry: His Contributions to the Development of LEED Surface Crystallography

    E-Print Network [OSTI]

    Rous, P.J.

    2008-01-01

    of Surface Structure by LEED (IBM Research Symposia Series)Surface Crystallography by LEED. M.A. Van Hove and S.Y.Surface Science 300(1-3), LEED Analysis of Acetylene and

  20. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

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

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; Hattne, Johan; Brewster, Aaron S.; Sauter, Nicholas K.; Brunger, Axel T.; Weis, William I.

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore »resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

  1. Monochromatic radiography of high energy density physics experiments on the MAGPIE generator

    SciTech Connect (OSTI)

    Hall, G. N. Burdiak, G. C.; Suttle, L.; Stuart, N. H.; Swadling, G. F.; Lebedev, S. V.; Smith, R. A.; Patankar, S.; Suzuki-Vidal, F.; Grouchy, P. de; Harvey-Thompson, A. J.; Bennett, M.; Bland, S. N.; Pickworth, L.; Skidmore, J.

    2014-11-15

    A monochromatic X-ray backlighter based on Bragg reflection from a spherically bent quartz crystal has been developed for the MAGPIE pulsed power generator at Imperial College (1.4 MA, 240 ns) [I. H. Mitchell et al., Rev. Sci. Instrum. 67, 1533 (2005)]. This instrument has been used to diagnose high energy density physics experiments with 1.865 keV radiation (Silicon He-?) from a laser plasma source driven by a ?7 J, 1 ns pulse from the Cerberus laser. The design of the diagnostic, its characterisation and performance, and initial results in which the instrument was used to radiograph a shock physics experiment on MAGPIE are discussed.

  2. Monochromatic x-ray sampling streak imager for fast-ignitor plasma observation

    SciTech Connect (OSTI)

    Tanabe, Minoru; Fujiwara, Takashi; Fujioka, Shinsuke; Nishimura, Hiroaki; Shiraga, Hiroyuki; Azechi, Hiroshi; Mima, Kunioki

    2008-10-15

    Ultrafast two-dimensional (2D) x-ray imaging is required to investigate the dynamics of fast-heated core plasma in inertial confinement fusion research. A novel x-ray imager, consisting of two toroidally bent Bragg crystals and an ultrafast 2D x-ray imaging camera, has been demonstrated. Sequential and 2D monochromatic x-ray images of laser-imploded core plasma were obtained with a temporal resolution of 20 ps, a spatial resolution of 31 {mu}m, and a spectral resolution of over 200, simultaneously.

  3. Proteins

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

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

  4. APPENDIX 6 --X-Ray Crystallography Reports Relevant to Chapter 3 861 X-Ray Crystallography Reports Relevant to Chapter 3

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Compound 262 (NBB04) Contents Table A6.1. Crystal data. Table A6.2. Atomic coordinates. Table A6.3. Full coordinates and isotropic displacement parameters. Table A6.6. Hydrogen bond distances and angles. Figure A6-Ray Crystallography Reports Relevant to Chapter 3 865 Table A6.2. Atomic coordinates (x 104 ) and equivalent isotropic

  5. Detection limits for actinides in a monochromatic, wavelength-dispersive x-ray fluorescence instrument

    SciTech Connect (OSTI)

    Collins, Michael L [Los Alamos National Laboratory; Havrilla, George J [Los Alamos National Laboratory

    2009-01-01

    Recent developments in x-ray optics have made it possible to examine the L x-rays of actinides using doubly-curved crystals in a bench-top device. A doubly-curved crystal (DCC) acts as a focusing monochromatic filter for polychromatic x-rays. A Monochromatic, Wavelength-Dispersive X-Ray Fluorescence (MWDXRF) instrument that uses DCCs to measure Cm and Pu in reprocessing plant liquors was proposed in 2007 by the authors at Los Alamos National Laboratory. A prototype design of this MWDXRF instrument was developed in collaboration with X-ray Optical Systems Inc. (XOS), of East Greenbush, New York. In the MWDXRF instrument, x-rays from a Rhodium-anode x-ray tube are passed through a primary DCC to produce a monochromatic beam of 20.2-keV photons. This beam is focused on a specimen that may contain actinides. The 20.2-keV interrogating beam is just above the L3 edge of Californium; each actinide (with Z = 90 to 98) present in the specimen emits characteristic L x-rays as the result of L3-shell vacancies. In the LANL-XOS prototype MWDXRf, these x-rays enter a secondary DCC optic that preferentially passes 14.961-keV photons, corresponding to the L-alpha-1 x-ray peak of Curium. In the present stage of experimentation, Curium-bearing specimens have not been analyzed with the prototype MWDXRF instrument. Surrogate materials for Curium include Rubidium, which has a K-beta-l x-ray at 14.961 keV, and Yttrium, which has a K-alpha-1 x-ray at 14.958 keV. In this paper, the lower limit of detection for Curium in the LANL-XOS prototype MWDXRF instrument is estimated. The basis for this estimate is described, including a description of computational models and benchmarking techniques used. Detection limits for other actinides are considered, as well as future safeguards applications for MWDXRF instrumentation.

  6. Two-bent-crystal schemes for monochromatic x-ray imaging

    SciTech Connect (OSTI)

    Foerster, E.; Chang, W.Z.; Dirksmoeller, M.

    1995-12-31

    For monochromatic imaging applications the advantages of combining two bent crystals in one system are demonstrated in comparison to a single crystal. The investigation shows that considerable improvements in resolution and spectral selectivity can be achieved by successive reflections from two bent crystals. The x-ray imaging device can be designed to a compact optical device mounted with the detector to a single port of the experimental chamber. This type of arrangement is of particular interest to large laser facilities such as those at LLNL, ILE and CEA where a high X-ray photon flux is available but the space available for diagnostics is restricted. A design for an experimental setup planned for imaging of indirect driven fusion experiments at Lawrence Livermore National Laboratory will be discussed here as an example. In general, improvements of spatial resolution by a factor of about 4 and spectral selectivity by a factor of about 10 can be achieved.

  7. The Effect of the LISA Response Function on Observations of Monochromatic Sources

    E-Print Network [OSTI]

    A. Vecchio; E. D. L. Wickham

    2004-06-25

    The Laser Interferometer Space Antenna (LISA) is expected to provide the largest observational sample of binary systems of faint sub-solar mass compact objects, in particular white-dwarfs, whose radiation is monochromatic over most of the LISA observational window. Current astrophysical estimates suggest that the instrument will be able to resolve about 10000 such systems, with a large fraction of them at frequencies above 3 mHz, where the wavelength of gravitational waves becomes comparable to or shorter than the LISA arm-length. This affects the structure of the so-called LISA transfer function which cannot be treated as constant in this frequency range: it introduces characteristic phase and amplitude modulations that depend on the source location in the sky and the emission frequency. Here we investigate the effect of the LISA transfer function on detection and parameter estimation for monochromatic sources. For signal detection we show that filters constructed by approximating the transfer function as a constant (long wavelength approximation) introduce a negligible loss of signal-to-noise ratio -- the fitting factor always exceeds 0.97 -- for f below 10mHz, therefore in a frequency range where one would actually expect the approximation to fail. For parameter estimation, we conclude that in the range 3mHz to 30mHz the errors associated with parameter measurements differ from about 5% up to a factor of 10 (depending on the actual source parameters and emission frequency) with respect to those computed using the long wavelength approximation.

  8. Dynamics of laser-produced Sn-based plasmas for a monochromatic 13.5 nm extreme ultraviolet source

    E-Print Network [OSTI]

    Najmabadi, Farrokh

    EUV spectrum. It was shown that for CO2 laser most of the laser energy deposition is localized around to monochromatic 13.5 nm EUV emission can be expected. It was found that 0.5% Sn- doped foam targets show an almost

  9. APPENDIX 3 --X-Ray Crystallography Reports Relevant to Chapter 2 686 X-Ray Crystallography Reports Relevant to Chapter 2

    E-Print Network [OSTI]

    Stoltz, Brian M.

    ) Contents Table A3.1. Crystal data Table A3.2. Atomic coordinates Table A3.3. Full bond distances and angles Table A3.4. Anisotropic displacement parameters Table A3.5. Hydrogen bond distances and angles #12.ccdc.cam.ac.uk/data_request/cif. #12;APPENDIX 3 -- X-Ray Crystallography Reports Relevant to Chapter 2 689 Table A3.1. Crystal data

  10. Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals

    SciTech Connect (OSTI)

    Gipson, Bryant R.; Stahlberg, Henning [Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University Basel, WRO-1058 Mattenstrasse 26, CH-4058 Basel (Switzerland); Masiel, Daniel J.; Browning, Nigel D. [Department of Chemical Engineering and Materials Sciences, University of California at Davis, Davis, California 95616 (United States); Spence, John [Department of Physics, Arizona State University, Tempe, Arizona 85287 (United States); Mitsuoka, Kaoru [Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064 (Japan)

    2011-07-15

    Electron crystallography of 2D protein crystals provides a powerful tool for the determination of membrane protein structure. In this method, data is acquired in the Fourier domain as randomly sampled, uncoupled, amplitudes and phases. Due to physical constraints on specimen tilting, those Fourier data show a vast un-sampled ''missing cone'' of information, producing resolution loss in the direction perpendicular to the membrane plane. Based on the flexible language of projection onto sets, we provide a full solution for these problems with a projective constraint optimization algorithm that, for sufficiently oversampled data, produces complete recovery of unmeasured data in the missing cone. We apply this method to an experimental data set of Bacteriorhodopsin and show that, in addition to producing superior results compared to traditional reconstruction methods, full, reproducible, recovery of the missing cone from noisy data is possible. Finally, we present an automatic implementation of the refinement routine as open source, freely distributed, software that will be included in our 2dx software package.

  11. Materials Science/Crystallography 30m SANS Measurements on Intercalated and Delaminated Phenolic

    E-Print Network [OSTI]

    Materials Science/Crystallography 30m SANS Measurements on Intercalated and Delaminated Phenolic Resin/Clay Dispersions and Nanocomposites Yoonessi, M.725 , Toghiani, H.725 , Pittman, C.725 A SANS on AOT Reverse Micelle Dynamics in Liquid, Compressed and Supercritical Alkanes Measured by SANS Kitchens

  12. First-principles codes for computational crystallography in the Quantum-ESPRESSO package

    E-Print Network [OSTI]

    Giannozzi, Paolo

    crystallography Abstract. The Quantum-ESPRESSO package is a multi- purpose and multi-platform software for ab-purpose and multi-platform package, called Quantum-ESPRESSO (standing for Quan- tum-opEn-Source Package for Research and others (Baroni, de Gironcoli, Dal Corso, Giannozzi, 2001); CP (Car-Parrinello), developed by A

  13. Appears in the Working Notes of the ICML Workshop on Machine Learning in Bioinformatics, August 2003 Using Pictorial Structures to Identify Proteins

    E-Print Network [OSTI]

    Shavlik, Jude W.

    2003 Using Pictorial Structures to Identify Proteins in X-ray Crystallographic Electron Density Maps in determining a protein's structure via x-ray crystallography is interpretation of the electron density map of a protein. However, due to the intractably large space of conformations the protein can adopt, building

  14. Deformable elastic network refinement for low-resolution macromolecular crystallography

    SciTech Connect (OSTI)

    Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T.

    2014-09-01

    An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage. Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  15. Parametric instability of a monochromatic Alfven wave: Perpendicular decay in low beta plasma

    SciTech Connect (OSTI)

    Gao, Xinliang; Lu, Quanming; Shan, Lican; Wang, Shui; Li, Xing

    2013-07-15

    Two-dimensional hybrid simulations are performed to investigate the parametric decay of a monochromatic Alfven wave in low beta plasma. Both the linearly and left-hand polarized pump Alfven waves are considered in the paper. For the linearly polarized pump Alfven wave, either a parallel or obliquely propagating wave can lead to the decay along the perpendicular direction. Initially, the parametric decay takes place along the propagating direction of the pump wave, and then the decay occurs in the perpendicular direction. With the increase of the amplitude and the propagating angle of the pump wave (the angle between the propagating direction of the pump wave and the ambient magnetic field), the spectral range of the excited waves becomes broad in the perpendicular direction. But the effects of the plasma beta on the spectral range of the excited waves in perpendicular direction are negligible. However, for the left-hand polarized pump Alfven wave, when the pump wave propagates along the ambient magnetic field, the parametric decay occurs nearly along the ambient magnetic field, and there is no obvious decay in the perpendicular direction. Significant decay in the perpendicular direction can only be found when the pump wave propagates obliquely.

  16. Damage by X-rays: A Case Study for Metallo-Protein Crystallography

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost2 DOE HQSiteo n n(Technical Report) |Damage by

  17. Generation of virtual monochromatic CBCT from dual kV/MV beam projections

    SciTech Connect (OSTI)

    Li, Hao [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 and Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)] [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 and Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States); Liu, Bo [Image Processing Center, Beihang University, Beijing 100191 (China)] [Image Processing Center, Beihang University, Beijing 100191 (China); Yin, Fang-Fang, E-mail: fangfang.yin@duke.edu [Medical Physics Graduate Program,Duke University, Durham, North Carolina 27710 and Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)] [Medical Physics Graduate Program,Duke University, Durham, North Carolina 27710 and Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)

    2013-12-15

    Purpose: To develop a novel on-board imaging technique which allows generation of virtual monochromatic (VM) cone-beam CT (CBCT) with a selected energy from combined kilovoltage (kV)/megavoltage (MV) beam projections. Methods: With the current orthogonal kV/MV imaging hardware equipped in modern linear accelerators, both MV projections (from gantry angle of 0°–100°) and kV projections (90°–200°) were acquired as gantry rotated a total of 110°. A selected range of overlap projections between 90° to 100° were then decomposed into two material projections using experimentally determined parameters from orthogonally stacked aluminum and acrylic step-wedges. Given attenuation coefficients of aluminum and acrylic at a predetermined energy, one set of VM projections could be synthesized from two corresponding sets of decomposed projections. Two linear functions were generated using projection information at overlap angles to convert kV and MV projections at nonoverlap angles to approximate VM projections for CBCT reconstruction. The contrast-to-noise ratios (CNRs) were calculated for different inserts in VM CBCTs of a CatPhan phantom with various selected energies and compared with those in kV and MV CBCTs. The effect of overlap projection number on CNR was evaluated. Additionally, the effect of beam orientation was studied by scanning the CatPhan sandwiched with two 5 cm solid-water phantoms on both lateral sides and an electronic density phantom with two metal bolt inserts. Results: Proper selection of VM energy [30 and 40 keV for low-density polyethylene (LDPE), polymethylpentene, 2 MeV for Delrin] provided comparable or even better CNR results as compared with kV or MV CBCT. An increased number of overlap kV and MV projection demonstrated only marginal improvements of CNR for different inserts (with the exception of LDPE) and therefore one projection overlap was found to be sufficient for the CatPhan study. It was also evident that the optimal CBCT image quality was achieved when MV beams penetrated through the heavy attenuation direction of the object. Conclusions: A novel technique was developed to generate VM CBCTs from kV/MV projections. This technique has the potential to improve CNR at selected VM energies and to suppress artifacts at appropriate beam orientations.

  18. Description and procedures for synchrotron radiation, small molecule, single crystal crystallography of plutonium complexes at ALS beamline 11.3.1

    E-Print Network [OSTI]

    Gorden, A.E.V.; Raymond, K.N.; Shuh, D.K.

    2008-01-01

    Crystallography of Plutonium Complexes at ALS Beamlineof the Structural Parameters of Plutonium Complexes by Smallpreparation and growth of the plutonium complexes (crystals)

  19. Ligand migration pathway and protein dynamics in myoglobin: A time-resolved crystallographic

    E-Print Network [OSTI]

    Schmidt, Marius

    Ligand migration pathway and protein dynamics in myoglobin: A time-resolved crystallographic study-resolved x-ray crystallography at room temperature, structural relaxations and ligand migration were examined completely relaxed into its domed deoxy structure, and there is no photodissociated CO visible at the primary

  20. Hydrogen bond dynamics in the active site of photoactive yellow protein

    E-Print Network [OSTI]

    Herschlag, Dan

    Hydrogen bond dynamics in the active site of photoactive yellow protein Paul A. Sigala, Mark A for review February 5, 2009) Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural

  1. Soft Matter Perspective on Protein Crystal Assembly

    E-Print Network [OSTI]

    Diana Fusco; Patrick Charbonneau

    2015-07-10

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

  2. Monochromatic x-ray radiography for areal-density measurement of inertial fusion energy fuel in fast ignition experiment

    SciTech Connect (OSTI)

    Fujioka, Shinsuke; Fujiwara, Takashi; Tanabe, Minoru; Nishimura, Hiroaki; Nagatomo, Hideo; Ohira, Shinji; Shiraga, Hiroyuki; Azechi, Hiroshi; Inubushi, Yuichi

    2010-10-15

    Ultrafast, two-dimensional x-ray imaging is an important diagnostics for the inertial fusion energy research, especially in investigating implosion dynamics at the final stage of the fuel compression. Although x-ray radiography was applied to observing the implosion dynamics, intense x-rays emitted from the high temperature and dense fuel core itself are often superimposed on the radiograph. This problem can be solved by coupling the x-ray radiography with monochromatic x-ray imaging technique. In the experiment, 2.8 or 5.2 keV backlight x-rays emitted from laser-irradiated polyvinyl chloride or vanadium foils were selectively imaged by spherically bent quartz crystals with discriminating the out-of-band emission from the fuel core. This x-ray radiography system achieved 24 {mu}m and 100 ps of spatial and temporal resolutions, respectively.

  3. Subangstrom Crystallography Reveals that Short Ionic Hydrogen Bonds, and Not a His-Asp Low-Barrier Hydrogen

    E-Print Network [OSTI]

    Agard, David

    Subangstrom Crystallography Reveals that Short Ionic Hydrogen Bonds, and Not a His-Asp Low-Barrier Hydrogen Bond, Stabilize the Transition State in Serine Protease Catalysis Cynthia N. Fuhrmann, Matthew D that destabilizes the His57-Ser195 hydrogen bond, preventing the back-reaction. In both structures the His57-Asp102

  4. [18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful,

    E-Print Network [OSTI]

    Richardson, David

    [18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful, and effective, and it has transformed our understanding of biology at the mo.2 Much of the sensitivity and the power of those tools derives from their independence of the target

  5. There exist graphs with super-exponential Ramsey multiplicity The Ramsey multiplicity M(G; n) of a graph G is the minimum number of monochromatic

    E-Print Network [OSTI]

    Fox, Jacob

    There exist graphs with super-exponential Ramsey multiplicity constant Jacob Fox Abstract The Ramsey multiplicity M(G; n) of a graph G is the minimum number of monochromatic copies of G over all 2, it is natural to define the Ramsey multiplicity constant C(G) to be limn M(G;n)a v!(n v) , which is the limit

  6. Crystallography Without Crystals: Determining the Structure of Individual Biological Molecules and Nanoparticles

    ScienceCinema (OSTI)

    Ourmazd, Abbas [University of Wisconsin, Milwaukee, Wisconsin, USA

    2010-01-08

    Ever shattered a valuable vase into 10 to the 6th power pieces and tried to reassemble it under a light providing a mean photon count of 10 minus 2 per detector pixel with shot noise? If you can do that, you can do single-molecule crystallography. This talk will outline how this can be done in principle. In more technical terms, the talk will describe how the combination of scattering physics and Bayesian algorithms can be used to reconstruct the 3-D diffracted intensity distribution from a collection of individual 2-D diffiraction patterns down to a mean photon count of 10 minus 2 per pixel, the signal level anticipated from the Linac Coherent Light Source, and hence determine the structure of individual macromolecules and nanoparticles.

  7. Characterization of the Quasi-Stationary State of an Impurity Driven by Monochromatic Light I - The Effective Theory

    E-Print Network [OSTI]

    Bru, Jean-Bernard; Westrich, Matthias

    2012-01-01

    We consider an impurity ($N$--level atom) driven by monochromatic light in a host environment which is a fermionic thermal reservoir. The external light source is a time--periodic perturbation of the atomic Hamiltonian stimulating transitions between two atomic energy levels $E_{1}$ and $E_{N}$ and thus acts as an optical pump. The purpose of the present work is the analysis of the effective atomic dynamics resulting from the full microscopic time--evolution of the compound system. We prove, in particular, that the atomic dynamics of population relaxes for large times to a quasi-stationary state, that is, a stationary state up to small oscillations driven by the external light source. This state turns out to be uniquely determined by a balance condition. The latter is related to \\textquotedblleft generalized Einstein relations\\textquotedblright relations of spontaneous/stimulated emission/absorption rates, which are conceptually similar to the phenomenological relations derived by Einstein in 1916. As an appl...

  8. Characterization of the Quasi-Stationary State of an Impurity Driven by Monochromatic Light I - The Effective Theory

    E-Print Network [OSTI]

    Jean-Bernard Bru; Walter de Siqueira Pedra; Matthias Westrich

    2012-01-27

    We consider an impurity ($N$--level atom) driven by monochromatic light in a host environment which is a fermionic thermal reservoir. The external light source is a time--periodic perturbation of the atomic Hamiltonian stimulating transitions between two atomic energy levels $E_{1}$ and $E_{N}$ and thus acts as an optical pump. The purpose of the present work is the analysis of the effective atomic dynamics resulting from the full microscopic time--evolution of the compound system. We prove, in particular, that the atomic dynamics of population relaxes for large times to a quasi-stationary state, that is, a stationary state up to small oscillations driven by the external light source. This state turns out to be uniquely determined by a balance condition. The latter is related to \\textquotedblleft generalized Einstein relations\\textquotedblright relations of spontaneous/stimulated emission/absorption rates, which are conceptually similar to the phenomenological relations derived by Einstein in 1916. As an application we show from quantum mechanical first principles how an inversion of population of energy levels of an impurity in a crystal can appear. Our results are based on the spectral analysis of the generator of the evolution semigroup related to a non--autonomous Cauchy problem effectively describing the atomic dynamics.

  9. Mapping the Ionization State of Laser-Irradiated Ar Gas Jets With Multi-Wavelength Monochromatic X-Ray Imaging

    SciTech Connect (OSTI)

    Kugland, N L; Doppner, T; Kemp, A; Schaeffer, D; Glenzer, S H; Niemann, C

    2010-04-08

    Two-dimensional monochromatic images of fast-electron stimulated Ar K{alpha} and He-{alpha} x-ray self-emission have recorded a time-integrated map of the extent of Ar{sup {approx}6+} and Ar{sup 16+} ions, respectively, within a high density (10{sup 20} cm{sup -3} atomic density) Ar plasma. This plasma was produced by irradiating a 2 mm wide clustering Ar gas jet with an ultra-high intensity (10{sup 19} W/cm{sup 2}, 200 fs) Ti:Sapphire laser operating at 800 nm. Spherically bent quartz crystals in the 200 (for K{alpha}) and 201 (for He-{alpha}) planes were used as near-normal incidence reflective x-ray optics. We see that a large (830 {micro}m long) region of plasma emits K{alpha} primarily along the laser axis, while the He-{alpha} emission is confined to smaller hot spot (230 {micro}m long) region that likely corresponds to the focal volume of the f/8 laser beam. X-ray spectra from a Bragg spectrometer operating in the von Hamos geometry, which images in one dimension, indicate that the centroids of the K{alpha} and He-{alpha} emission regions are separated by approximately 330 {micro}m along the laser axis.

  10. Mapping the ionization state of laser-irradiated Ar gas jets with multiwavelength monochromatic x-ray imaging

    SciTech Connect (OSTI)

    Kugland, N. L.; Niemann, C.; Doeppner, T.; Kemp, A.; Glenzer, S. H.; Schaeffer, D.

    2010-10-15

    Two-dimensional monochromatic images of fast-electron stimulated Ar K{alpha} and He-{alpha} x-ray self-emission have recorded a time-integrated map of the extent of Ar{sup {approx_equal}6+} and Ar{sup 16+} ions, respectively, within a high density (10{sup 20} cm{sup -3} atomic density) Ar plasma. This plasma was produced by irradiating a 2 mm wide clustering Ar gas jet with an ultrahigh intensity (10{sup 19} W/cm{sup 2}, 50 TW) Ti:sapphire laser operating at 800 nm. Spherically bent quartz crystals in the 200 (for K{alpha}) and 201 (for He-{alpha}) planes were used as near-normal incidence reflective x-ray optics. We see that a large (830 {mu}m long) region of plasma emits K{alpha} primarily along the laser axis, while the He-{alpha} emission is confined to smaller hot spot (230 {mu}m long) region that likely corresponds to the focal volume of the f/8 laser beam. X-ray spectra from a Bragg spectrometer operating in the von Hamos geometry indicate that the centroids of the K{alpha} and He-{alpha} emission regions are separated by approximately 330 {mu}m along the laser axis.

  11. Solving coiled-coil protein structures

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

    Dauter, Zbigniew

    2015-02-26

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

  12. The macromolecular crystallography station at beamline BM16 at the ESRF

    SciTech Connect (OSTI)

    Juanhuix, Jordi; Labrador, Ana; Beltran, David; Herranz, Juan F.; Carpentier, Philippe; Bordas, Joan [CELLS, Campus UAB, 08193 Bellaterra, Barcelona (Spain)

    2005-08-15

    A beamline previously used for powder diffraction (BM16) at the European Synchrotron Radiation Facility has been redesigned and rebuilt to carry out both mcromolecular crystallography (MX) and noncrystalline diffraction/scattering (NCD/S) experiments. The MX station has become available for routine user experiments since September 2003 and the NCD/S station is currently being commissioned. The optics are designed so that both the focal spot and flux are good in the 6-17 keV energy range (2.1-0.73 A), while the performance is optimal at the selenium K-edge (12.658 keV,0.98 A). The MX facility is fully equipped to carry out multiwavelength anomalous dispersion experiments, in particular at the Se K-edge. Moreover, experiments using lower energies such as those of the Mn and Fe K-edges are also possible. Here we describe the optical configuration and the setup for MX experiments, as well as a typical example of the experiments carried out so far.

  13. Goniometer-based femtosecond crystallography with X-ray free electron lasers

    SciTech Connect (OSTI)

    Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; Calero, Guillermo; Chang, Joseph F.; Chollet, Matthieu; Ehrensberger, Paul; Eriksson, Thomas L.; Feng, Yiping; Hattne, Johan; Hedman, Britt; Hollenbeck, Michael; Holton, James M.; Keable, Stephen; Kobilka, Brian K.; Kovaleva, Elena G.; Kruse, Andrew C.; Lemke, Henrik T.; Lin, Guowu; Lyubimov, Artem Y.; Manglik, Aashish; Mathews, Irimpan I.; McPhillips, Scott E.; Nelson, Silke; Peters, John W.; Sauter, Nicholas K.; Smith, Clyde A.; Song, Jinhu; Stevenson, Hilary P.; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Vinetsky, Vladimir; Wakatsuki, Soichi; Weis, William I.; Zadvornyy, Oleg A.; Zeldin, Oliver B.; Zhu, Diling; Hodgson, Keith O.

    2014-10-31

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of ?2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.

  14. Goniometer-based femtosecond crystallography with X-ray free electron lasers

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

    Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; et al

    2014-10-31

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were usedmore »to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of ?2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.« less

  15. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

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

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-23

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patternsmore »with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

  16. Structural analysis of flexible proteins in solution by Small Angle X-ray Scattering combined with crystallography

    E-Print Network [OSTI]

    Tsutakawa, Susan E.; Hura, Greg L.; Frankel, Ken A.; Cooper, Priscilla K.; Tainer, John A.

    2006-01-01

    suite of programs, including CREDO, based on their ab initioas input to the program CREDO, which built density on theadditional density built by CREDO. The regulatory domain was

  17. Perspective of monochromatic gamma-ray line detection with the High Energy cosmic-Radiation Detection (HERD) facility onboard China's Space Station

    E-Print Network [OSTI]

    Huang, Xiaoyuan; Tsai, Yue-Lin Sming; Xu, Ming; Yuan, Qiang; Chang, Jin; Dong, Yong-Wei; Hu, Bing-Liang; Lü, Jun-Guang; Wang, Le; Wu, Bo-Bing; Zhang, Shuang-Nan

    2015-01-01

    HERD is the High Energy cosmic-Radiation Detection instrument proposed to operate onboard China's space station in the 2020s. It is designed to detect energetic cosmic ray nuclei, leptons and photons with a high energy resolution ($\\sim1\\%$ for electrons and photons and $20\\%$ for nuclei) and a large geometry factor ($>3\\, m^2sr$ for electrons and diffuse photons and $>2\\, m^2sr$ for nuclei). In this work we discuss the capability of HERD to detect monochromatic $\\gamma$-ray lines, based on simulations of the detector performance. It is shown that HERD will be one of the most sensitive instruments for monochromatic $\\gamma$-ray searches at energies between $\\sim10$ to a few hundred GeV. Above hundreds of GeV, Cherenkov telescopes will be more sensitive due to their large effective area. As a specific example, we show that a good portion of the parameter space of a supersymmetric dark matter model can be probed with HERD.

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

    SciTech Connect (OSTI)

    Fenglei Li

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition, evaporation rate can be controlled or adjusted in this method during the crystallization process to favor either nucleation or growing processes for optimizing crystallization process. The protein crystals gotten by this method were experimentally proven to possess high x-ray diffraction qualities. Finally, we crystallized human lactate dehydrogenase 1 (H4) complexed with NADH and determined its structure by x-ray crystallography. The structure of LDH/NADH displays a significantly different structural feature, compared with LDH/NADH/inhibitor ternary complex structure, that subunits in LDH/NADH complex show open conformation or two conformations on the active site while the subunits in LDH/NADH/inhibitor are all in close conformation. Multiple LDH/NADH crystals were obtained and used for x-ray diffraction experiments. Difference in subunit conformation was observed among the structures independently solved from multiple individual LDH/NADH crystals. Structural differences observed among crystals suggest the existence of multiple conformers in solution.

  19. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOE Patents [OSTI]

    Nordmeyer, Robert A.; Snell, Gyorgy P.; Cornell, Earl W.; Kolbe, William; Yegian, Derek; Earnest, Thomas N.; Jaklevic, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    2005-07-19

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  20. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOE Patents [OSTI]

    Nordmeyer, Robert A. (San Leandro, CA); Snell, Gyorgy P. (Richmond, CA); Cornell, Earl W. (Antioch, CA); Kolbe, William F. (Moraga, CA); Yegian, Derek T. (Oakland, CA); Earnest, Thomas N. (Berkeley, CA); Jaklevich, Joseph M. (Lafayette, CA); Cork, Carl W. (Walnut Creek, CA); Santarsiero, Bernard D. (Chicago, IL); Stevens, Raymond C. (La Jolla, CA)

    2007-09-25

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  1. Crystallization Process of Protein Rv0731c from Mycobacterium Tuberculosis for a Successful Atomic Resolution Crystal Structure at 1.2 Angstrom

    SciTech Connect (OSTI)

    Zhu, Liang Cong

    2009-06-08

    Proteins are bio-macromolecules consisting of basic 20 amino acids and have distinct three-dimensional folds. They are essential parts of organisms and participate in every process within cells. Proteins are crucial for human life, and each protein within the body has a specific function, such as antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins and transport proteins. Determining three-dimensional structure of a protein can help researchers discover the remarkable protein folding, binding site, conformation and etc, in order to understand well of protein interaction and aid for possible drug design. The research on protein structure by X-ray protein crystallography carried by Li-Wei Hung's research group in the Physical Bioscience Division at Lawrence Berkeley National Laboratory (LBNL) is focusing on protein crystallography. The research in this lab is in the process of from crystallizing the proteins to determining the three dimensional crystal structures of proteins. Most protein targets are selected from Mycobacterium Tuberculosis. TB (Tuberculosis) is a possible fatal infectious disease. By studying TB target protein can help discover antituberculer drugs, and find treatment for TB. The high-throughput mode of crystallization, crystal harvesting, crystal screening and data collection are applied to the research pipeline (Figure 1). The X-ray diffraction data by protein crystals can be processed and analyzed to result in a three dimensional representation of electron density, producing a detailed model of protein structure. Rv0731c is a conserved hypothetical protein with unknown function from Mycobacterium Tuberculosis. This paper is going to report the crystallization process and brief structure information of Rv0731c.

  2. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    SciTech Connect (OSTI)

    Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de [MPI for Medical Research, Heidelberg (Germany); Brosi, Richard W. W. [Freie Universitat Berlin, Berlin (Germany); Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten [MPI for Medical Research, Heidelberg (Germany); Seidel, Ralf [MPI for Molecular Physiology, Dortmund (Germany); Shoeman, Robert L.; Zimmermann, Sabine [MPI for Medical Research, Heidelberg (Germany); Bittl, Robert [Freie Universitat Berlin, Berlin (Germany); Schlichting, Ilme; Reinstein, Jochen [MPI for Medical Research, Heidelberg (Germany)

    2013-08-01

    The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

  3. Processing incommensurately modulated protein diffraction data with Eval15

    SciTech Connect (OSTI)

    Porta, Jason [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Lovelace, Jeffrey J. [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Schreurs, Antoine M. M.; Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Borgstahl, Gloria E. O., E-mail: gborgstahl@unmc.edu [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Nebraska Medical Center, Omaha, NE 68198-7696 (United States)

    2011-07-01

    Data processing of an incommensurately modulated profilin–actin crystal is described. Recent challenges in biological X-ray crystallography include the processing of modulated diffraction data. A modulated crystal has lost its three-dimensional translational symmetry but retains long-range order that can be restored by refining a periodic modulation function. The presence of a crystal modulation is indicated by an X-ray diffraction pattern with periodic main reflections flanked by off-lattice satellite reflections. While the periodic main reflections can easily be indexed using three reciprocal-lattice vectors a*, b*, c*, the satellite reflections have a non-integral relationship to the main lattice and require a q vector for indexing. While methods for the processing of diffraction intensities from modulated small-molecule crystals are well developed, they have not been applied in protein crystallography. A recipe is presented here for processing incommensurately modulated data from a macromolecular crystal using the Eval program suite. The diffraction data are from an incommensurately modulated crystal of profilin–actin with single-order satellites parallel to b*. The steps taken in this report can be used as a guide for protein crystallographers when encountering crystal modulations. To our knowledge, this is the first report of the processing of data from an incommensurately modulated macromolecular crystal.

  4. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF

    SciTech Connect (OSTI)

    Stetten, David von; Giraud, Thierry; Carpentier, Philippe; Sever, Franc; Terrien, Maxime; Dobias, Fabien; Juers, Douglas H.; Flot, David; Mueller-Dieckmann, Christoph; Leonard, Gordon A.; Sanctis, Daniele de; Royant, Antoine

    2015-01-01

    The current version of the Cryobench in crystallo optical spectroscopy facility of the ESRF is presented. The diverse experiments that can be performed at the Cryobench are also reviewed. The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for ‘spectroscopy’). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.

  5. BCL::MP-Fold: membrane protein structure prediction guided by EPR restraints

    E-Print Network [OSTI]

    Fischer, Axel Walter; Woetzel, Nils; Karakas, Mert; Weiner, Brian; Meiler, Jens

    2015-01-01

    For many membrane proteins the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold (BioChemical Library membrane protein fold) algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The RMSD100 value of the most accurate model is better than 8{\\AA} for twenty-seven, better than 6{\\AA} for twenty-two and better than 4{\\AA} for fifte...

  6. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

    SciTech Connect (OSTI)

    Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; Goldman, Peter J.; Deerinck, Thomas J.; Yao, Jennifer Z.; Richardson, Douglas; Phipps, William S.; Ye, Anne Z.; Ellisman, Mark H.; Drennan, Catherine L.; Baker, David; Ting, Alice Y.

    2014-10-13

    In this study, chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.

  7. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

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

    Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; Goldman, Peter J.; Deerinck, Thomas J.; Yao, Jennifer Z.; Richardson, Douglas; Phipps, William S.; Ye, Anne Z.; Ellisman, Mark H.; et al

    2014-10-13

    In this study, chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of themore »intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.« less

  8. Orbital effects of a monochromatic plane gravitational wave with ultra-low frequency incident on a gravitationally bound two-body system

    E-Print Network [OSTI]

    Lorenzo Iorio

    2014-09-12

    We analytically compute the long-term orbital variations of a test particle orbiting a central body acted upon by an incident monochromatic plane gravitational wave. We assume that the characteristic size of the perturbed two-body system is much smaller than the wavelength of the wave. Moreover, we also suppose that the wave's frequency is much smaller than the particle's orbital one. We make neither a priori assumptions about the direction of the wavevector nor on the orbital geometry of the planet. We find that, while the semi-major axis is left unaffected, the eccentricity, the inclination, the longitude of the ascending node, the longitude of pericenter and the mean anomaly undergo non-vanishing long-term changes. They are not secular trends because of the slow modulation introduced by the tidal matrix coefficients and by the orbital elements themselves. They could be useful to indepenedently constrain the ultra-low frequency waves which may have been indirectly detected in the BICEP2 experiment. Our calculation holds, in general, for any gravitationally bound two-body system whose characteristic frequency is much larger than the frequency of the external wave. It is also valid for a generic perturbation of tidal type with constant coefficients over timescales of the order of the orbital period of the perturbed particle.

  9. Characterization of morphology and hydration products of high-volume fly ash paste by monochromatic scanning x-ray micro-diffraction (?-SXRD)

    SciTech Connect (OSTI)

    Bae, Sungchul; Meral, Cagla; Oh, Jae-eun; Moon, Juhyuk; Kunz, Martin; Monteiro, Paulo J.M.

    2014-05-01

    The present study focuses on identification and micro-structural characterization of the hydration products formed in high-volume fly ash (HVFA)/portland cement (PC) systems using monochromatic scanning x-ray micro-diffraction (?-SXRD) and SEM-EDS. Pastes with up to 80% fly ash replacement were studied. Phase maps for HVFA samples using ?-SXRD patterns prove that ?-SXRD is an effective method to identify and visualize the distribution of phases in the matrix. ?-SXRD and SEM-EDS analysis shows that the C-S-H formed in HVFA system containing 50% or more of fly ash has a similar structure as C-S-H(I) with comparatively lower Ca/Si ratio than the one produced in PC system. Moreover, coexistence of C-S-H(I) and strätlingite is observed in the system containing 80% of fly ash, confirming that the amount of alumina and silicate phases provided by the fly ash is a major factor for the formation of C-S-H(I) and strätlingite in HVFA system. - Highlights: • High-volume fly ash (HVFA) paste was studied by scanning x-ray micro-diffraction. • Coexistence of C-S-H(I) and strätlingite in the HVFA system is clearly shown. • The distribution of minor phases in the HVFA system is shown. • Differences between inner and outer products of fly ash are observed by SEM-EDS.

  10. Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures

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

    Ibrahim, Mohamed; Chatterjee, Ruchira; Hellmich, Julia; Tran, Rosalie; Bommer, Martin; Yachandra, Vittal K.; Yano, Junko; Kern, Jan; Zouni, Athina

    2015-07-01

    In photosynthesis, photosystem II (PSII) is the multi-subunit membrane protein complex that catalyzes photo-oxidation of water into dioxygen through the oxygen evolving complex (OEC). To understand the water oxidation reaction, it is important to get structural information about the transient and intermediate states of the OEC in the dimeric PSII core complex (dPSIIcc). In recent times, femtosecond X-ray pulses from the free electron laser (XFEL) are being used to obtain X-ray diffraction (XRD) data of dPSIIcc microcrystals at room temperature that are free of radiation damage. In our experiments at the XFEL, we used an electrospun liquid microjet setup thatmore »requires microcrystals less than 40 ?m in size. In this study, we explored various microseeding techniques to get a high yield of monodisperse uniform-sized microcrystals. Monodisperse microcrystals of dPSIIcc of uniform size were a key to improve the stability of the jet and the quality of XRD data obtained at the XFEL. This was evident by an improvement of the quality of the datasets obtained, from 6.5 Å, using crystals grown without the micro seeding approach, to 4.5 Å using crystals generated with the new method.« less

  11. Rotational order–disorder structure of fluorescent protein FP480

    SciTech Connect (OSTI)

    Pletnev, Sergei, E-mail: svp@ncifcrf.gov [SAIC-Frederick Inc., Basic Research Program, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Morozova, Kateryna S.; Verkhusha, Vladislav V. [Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461 (United States); Dauter, Zbigniew, E-mail: svp@ncifcrf.gov [Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States); SAIC-Frederick Inc., Basic Research Program, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States)

    2009-09-01

    An analysis of the rotational order–disorder structure of fluorescent protein FP480 is presented. In the last decade, advances in instrumentation and software development have made crystallography a powerful tool in structural biology. Using this method, structural information can now be acquired from pathological crystals that would have been abandoned in earlier times. In this paper, the order–disorder (OD) structure of fluorescent protein FP480 is discussed. The structure is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, namely rotated 90° with respect to each other around the crystal c axis, with tetramer axes coincident with crystallographic twofold axes. The random distribution of alternatively oriented tetramers in the crystal creates a rotational OD structure with statistically averaged I422 symmetry, although the presence of very weak and diffuse additional reflections suggests that the randomness is only approximate.

  12. Protein Characterisation by Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy

    SciTech Connect (OSTI)

    Wallace, B.

    2009-01-01

    Circular dichroism (CD) spectroscopy is a well-established technique for the study of proteins. Synchrotron radiation circular dichroism (SRCD) spectroscopy extends the utility of conventional CD spectroscopy (i.e. using laboratory-based instruments) because the high light flux from a synchrotron enables collection of data to lower wavelengths, detection of spectra with higher signal-to-noise levels and measurements in the presence of strongly absorbing non-chiral components such as salts, buffers, lipids and detergents. This review describes developments in instrumentation, methodologies and bioinformatics that have enabled new applications of the SRCD technique for the study of proteins. It includes examples of the use of SRCD spectroscopy for providing static and dynamic structural information on molecules, including determinations of secondary structures of intact proteins and domains, assessment of protein stability, detection of conformational changes associated with ligand and drug binding, monitoring of environmental effects, examination of the processes of protein folding and membrane insertion, comparisons of mutant and modified proteins, identification of intermolecular interactions and complex formation, determination of the dispositions of proteins in membranes, identification of natively disordered proteins and their binding partners and examination of the carbohydrate components of glycoproteins. It also discusses how SRCD can be used in conjunction with macromolecular crystallography and other biophysical techniques to provide a more complete picture of protein structures and functions, including how proteins interact with other macromolecules and ligands. This review also includes a discussion of potential new applications in structural and functional genomics using SRCD spectroscopy and future instrumentation and bioinformatics developments that will enable such studies. Finally, the appendix describes a number of computational/bioinformatics resources for secondary structure analyses that take advantage of the improved data quality available from SRCD. In summary, this review discusses how SRCD can be used for a wide range of structural and functional studies of proteins.

  13. electronic reprint Crystallography

    E-Print Network [OSTI]

    Read, Randy J.

    for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK, b Lawrence Berkeley was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from, to the crystallographic community. 1. Introduction Improved crystallographic methods rely on both improved automation

  14. electronic reprint Crystallography

    E-Print Network [OSTI]

    Meagher, Mary

    remarkable progress in X-ray and neutron scattering instrumentation (see e.g. Pedersen, 2002, for a review-based system for small-angle scattering data analysis Petr V. Konarev, Vladimir V. Volkov, Anna V. Sokolova-based system for small- angle scattering data analysis Petr V. Konarev,a,b Vladimir V. Volkov,a,b Anna V

  15. electronic reprint Crystallography

    E-Print Network [OSTI]

    Gruner, Sol M.

    , PEG 400 and glycerol necessary for complete vitrification under pressure cryocooling were determined et al., 2006; Manjasetty et al., 2008). These developments substantially reduce the costs

  16. electronic reprint Crystallography

    E-Print Network [OSTI]

    topics in condensed matter research, materials science and the life sci- ences make use University and Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy

  17. electronic reprint Crystallography

    E-Print Network [OSTI]

    Winter, Rudolf

    SAXS studies of the morphological changes of an alumina­zirconia­silicate ceramic during its formation et al. ¯ Alumina­zirconia­silicate ceramic #12;research papers J. Appl. Cryst. (2006). 39, 589 ­ all rights reserved In situ SAXS studies of the morphological changes of an alumina­zirconia

  18. electronic reprint Crystallography

    E-Print Network [OSTI]

    Gruner, Sol M.

    include SAXS characterization of hydrogen storage materials, solid oxide fuel cells, chalcogenide glasses etc. In most SAXS applications the samples are enclosed in a sample cell with X-ray windows, DC 20015, USA, and d Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA

  19. Macromolecular Crystallography - Beamline facilities

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJesse BergkampCentermillion toMSDS on the internet The OfficeSearch Home Site

  20. Protein Assay Technical Handbook

    E-Print Network [OSTI]

    Lebendiker, Mario

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

  1. Automating crystallographic structure solution and refinement of protein–ligand complexes

    SciTech Connect (OSTI)

    Echols, Nathaniel, E-mail: nechols@lbl.gov; Moriarty, Nigel W., E-mail: nechols@lbl.gov; Klei, Herbert E.; Afonine, Pavel V. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235 (United States); Bunkóczi, Gábor [University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY (United Kingdom); Headd, Jeffrey J. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235 (United States); McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J. [University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY (United Kingdom); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States); Adams, Paul D., E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235 (United States); University of California at Berkeley, Berkeley, CA 94720-1762 (United States)

    2014-01-01

    A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies. High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.

  2. Protein–ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI)

    SciTech Connect (OSTI)

    Grøftehauge, Morten K., E-mail: m.k.groftehauge@durham.ac.uk; Hajizadeh, Nelly R. [Durham University, South Road, Durham DH1 3LE (United Kingdom); Swann, Marcus J. [Biolin Scientific, 62 Wellington Road South, Stockport, Cheshire SK1 3SU (United Kingdom); Pohl, Ehmke, E-mail: m.k.groftehauge@durham.ac.uk [Durham University, South Road, Durham DH1 3LE (United Kingdom)

    2015-01-01

    The biophysical characterization of protein–ligand interactions in solution using techniques such as thermal shift assay, or on surfaces using, for example, dual polarization interferometry, plays an increasingly important role in complementing crystal structure determinations. Over the last decades, a wide range of biophysical techniques investigating protein–ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.

  3. Introduzione alle Proteine e al Protein Folding

    E-Print Network [OSTI]

    Giannozzi, Paolo

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

  4. Structure and Dynamics of NBD1 from CFTR Characterized Using Crystallography and Hydrogen/Deuterium Exchange Mass Spectrometry

    SciTech Connect (OSTI)

    Lewis, H.A.; Wang, C.; Zhao, X.; Hamuro, Y.; Conners, K.; Kearins, M.C.; Lu, F.; Sauder, J.M.; Molnar, K.S.; Coales, S.J.; Maloney, P.C.; Guggino, W.B.; Wetmore, D.R.; Weber, P.C.; Hunt, J.F. (SGX); (ExSAR); (Cystic); (JHU-MED); (Columbia)

    2012-04-30

    The {Delta}F508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and {Delta}F508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because {Delta}F508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and {Delta}F508 constructs, and the {Delta}F508 structure contained additional mutations that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide {sup 1}H/{sup 2}H exchange rates in matched F508 and {Delta}F508 constructs reveal that {Delta}F508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the {Delta}F508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-{Delta}F508 structures but completely solvent exposed in all {Delta}F508 structures. These results reinforce the importance of the perturbation {Delta}F508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased exposure of the 509-511 loop and increased dynamics in its vicinity could promote aggregation in vitro and aberrant intermolecular interactions that impede trafficking in vivo.

  5. Engineering novel fluorescent proteins

    E-Print Network [OSTI]

    Shaner, Nathan Christopher

    2006-01-01

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

  6. Evidence for posttranslational protein flavinylation in the syphilis spirochete Treponema pallidum: Structural and biochemical insights from the catalytic core of a periplasmic flavin-trafficking protein

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

    Deka, Ranjit K.; Brautigam, Chad A.; Liu, Wei Z.; Tomchick, Diana R.; Norgard, Michael V.

    2015-05-05

    The syphilis spirochete Treponema pallidum is an important human pathogen but a highly enigmatic bacterium that cannot be cultivated in vitro. T. pallidum lacks many biosynthetic pathways and therefore has evolved the capability to exploit host-derived metabolites via its periplasmic lipoprotein repertoire. We recently reported a flavin-trafficking protein in T. pallidum (Ftp_Tp; TP0796) as the first bacterial metal-dependent flavin adenine dinucleotide (FAD) pyrophosphatase that hydrolyzes FAD into AMP and flavin mononucleotide (FMN) in the spirochete’s periplasm. However, orthologs of Ftp_Tp from other bacteria appear to lack this hydrolytic activity; rather, they bind and flavinylate subunits of a cytoplasmic membrane redoxmore »system (Nqr/Rnf). To further explore this dichotomy, biochemical analyses, protein crystallography, and structure-based mutagenesis were used to show that a single amino acid change (N55Y) in Ftp_Tp converts it from an Mg²?-dependent FAD pyrophosphatase to an FAD-binding protein. We also demonstrated that Ftp_Tp has a second enzymatic activity (Mg²?-FMN transferase); it flavinylates protein(s) covalently with FMN on a threonine side chain of an appropriate sequence motif using FAD as the substrate. Moreover, mutation of a metal-binding residue (D284A) eliminates Ftp_Tp’s dual activities, thereby underscoring the role of Mg²? in the enzyme-catalyzed reactions. The posttranslational flavinylation activity that can target a periplasmic lipoprotein (TP0171) has not previously been described. The observed activities reveal the catalytic flexibility of a treponemal protein to perform multiple functions. Together, these findings imply mechanisms by which a dynamic pool of flavin cofactor is maintained and how flavoproteins are generated by Ftp_Tp locally in the T. pallidum periplasm.« less

  7. Powder Diffraction Crystallography Instructional Materials

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgram Guidelines This document outlinesPotential partnerships andSoftware

  8. Neutron crystallography aids drug design

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJessework usesofPublications TheScience4.21Reviews

  9. Structure and protein–protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath)

    SciTech Connect (OSTI)

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2014-10-07

    In the initial steps of their metabolic pathway, methanotrophic bacteria oxidize methane to methanol with methane monooxygenases (MMOs) and methanol to formaldehyde with methanol dehydrogenases (MDHs). Several lines of evidence suggest that the membrane-bound or particulate MMO (pMMO) and MDH interact to form a metabolic supercomplex. To further investigate the possible existence of such a supercomplex, native MDH from Methylococcus capsulatus (Bath) has been purified and characterized by size exclusion chromatography with multi-angle light scattering and X-ray crystallography. M. capsulatus (Bath) MDH is primarily a dimer in solution, although an oligomeric species with a molecular mass of ~450–560 kDa forms at higher protein concentrations. The 2.57 Å resolution crystal structure reveals an overall fold and ???? dimeric architecture similar to those of other MDH structures. In addition, biolayer interferometry studies demonstrate specific protein–protein interactions between MDH and M. capsulatus (Bath) pMMO as well as between MDH and the truncated recombinant periplasmic domains of M. capsulatus (Bath) pMMO (spmoB). These interactions exhibit KD values of 833 ± 409 nM and 9.0 ± 7.7 ?M, respectively. The biochemical data combined with analysis of the crystal lattice interactions observed in the MDH structure suggest a model in which MDH and pMMO associate not as a discrete, stoichiometric complex but as a larger assembly scaffolded by the intracytoplasmic membranes.

  10. Two-Stage Robotic Crystal Mounting of Protein Crystals for X-Ray Data Collection

    E-Print Network [OSTI]

    Georgiev, Atanas

    Beamline Mounting Freezing Fig. 1. A simplified crystallography pipeline. The top row shows a basic outline it into a cryoprotecting liquid, cryogenically fre

  11. De novo protein crystal structure determination from X-ray free-electron laser data

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

    Barends, Thomas, R.M.

    Serial femtosecond crystallography (SFX) data of microcrystals of a lysozyme gadolinium derivative. The data was used to demonstrate de-novo phasing by single anomalous dispersion.

  12. De novo protein crystal structure determination from X-ray free-electron laser data

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

    Barends, Thomas, R.M.

    2013-11-25

    Serial femtosecond crystallography (SFX) data of microcrystals of a lysozyme gadolinium derivative. The data was used to demonstrate de-novo phasing by single anomalous dispersion.

  13. Culex quinquefasciatus Storage Proteins

    E-Print Network [OSTI]

    2013-01-01

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

  14. Diamondoid Monolayers as Monochromatic Electron Source

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

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

  15. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent BondingMeeting |DesignCommunitiesYuDiamondoid Monolayers as

  16. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent BondingMeeting |DesignCommunitiesYuDiamondoid Monolayers

  17. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent BondingMeeting |DesignCommunitiesYuDiamondoid MonolayersDiamondoid

  18. Diamondoid Monolayers as Monochromatic Electron Source

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

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

  19. Diamondoid Monolayers as Monochromatic Electron Source

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

    A.A. Fokin (Justus-Liebig University, Germany, and Kiev Polytechnic Institute, Ukraine); and Z. Hussain (ALS). Research funding: U.S. Department of Energy, Office of Basic...

  20. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet HanfordDOEDanielDeSmallDevelopment ofBrowse by

  1. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet HanfordDOEDanielDeSmallDevelopment ofBrowse byDiamondoid

  2. Calculation of Proteins' Total Side-Chain Torsional Entropy and Its Influence on ProteinLigand Interactions

    E-Print Network [OSTI]

    Geissler, Phillip

    are extremely dense, with packing fractions comparable to those of organic crystals.1 This observation motivated maps from crystallography expe- riments.11 The data accumulating from such studies paint a consistent

  3. 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

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

    DOE Patents [OSTI]

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

    2010-02-23

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

  5. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17

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

  6. Biological Macromolecular Structures Data from the RCSB Protein Data Bank (RCSB PDB)

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

    The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium that works to improve understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. The RCSB PDB is one of three sites serving as deposition, data processing, and distribution sites of the Protein Data Bank Archive. Each site provides its own view of the primary data, thus providing a variety of tools and resources for the global community. RCSB is also the official keeper for the PDB archive, with sole access authority to the PDB archive directory structure and contents. The RCSB PDB Information Portal for Biological Macromolecular Structures offers online tools for search and retrieval, for visualizing structures, for depositing, validating, or downloading data, news and highlights, a discussion forum, and links to other areas of related research. The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB. Results can be viewed as 3-D images or models.

  7. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

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

    2011-03-22

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

  8. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

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

    2011-11-29

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

  9. Highly thermostable fluorescent proteins

    DOE Patents [OSTI]

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

    2012-05-01

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

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

    SciTech Connect (OSTI)

    NONE

    1995-12-31

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

  11. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01

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

  12. Structure-Based Design of Robust Glucose Biosensors using a Thermotoga maritima Periplasmic Glucose-Binding Protein

    SciTech Connect (OSTI)

    Tian,Y.; Cunco, M.; Changela, A.; Hocker, B.; Beese, L.; Hellinga, H.

    2007-01-01

    We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Angstroms resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 {+-} 1 C and 144 {+-} 2 C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1-30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature.

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

    E-Print Network [OSTI]

    Fernández Suárez, Marta

    2008-01-01

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

  14. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

    SciTech Connect (OSTI)

    Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander; Roessler, Christian G.; Teplitsky, Ella; Joshi, Karan; Campos, Olven; Agarwal, Rakhi; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

    2015-01-01

    An acoustic high-throughput screening method is described for harvesting protein crystals and combining the protein crystals with chemicals such as a fragment library. Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s{sup ?1}) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.

  15. Interactions of a potent cyclic peptide inhibitor with the light chain of botulinum neurotoxin A: insights from x-ray crystallography

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

    Kumaran, D.; Adler, M.; Levit, M.; Krebs, M.; Sweeney, R.; Swaminathan, S.

    2015-10-17

    The seven antigenically distinct serotypes (A to G) of botulinum neurotoxin (BoNT) are responsible for the deadly disease botulism. BoNT serotype A (BoNT/A) exerts its lethal action by cleaving the SNARE protein SNAP-25, leading to inhibition of neurotransmitter release, flaccid paralysis and autonomic dysfunction. BoNTs are dichain proteins: the heavy chain is responsible for neurospecific binding, internalization and translocation, and the light chain is responsible for substrate cleavage. Because of their extreme toxicity and prior history of weaponization, the BoNTs are considered to be potential bioterrorism agents. No post-symptomatic therapeutic interventions are available for BoNT intoxication other than critical care;more »therefore it is imperative to develop specific antidotes against this neurotoxin. To this end, a cyclic peptide inhibitor (CPI-1) was synthesized and found to inhibit BoNT/A light chain (Balc) with high affinity. When tested in a cell-free Förster resonance excitation transfer (FRET) assay, CPI-1 was found to have a Ki of 13.9 nM using full-length Balc448 and 42.1 nM using a truncated crystallizable form of light chain (Balc424). Co-crystallization of CPI-1 with Balc424 revealed that in the Balc-CPI-1 complex, the inhibitor adopts a helical conformation, occupies a high percentage of the active site cavity and interacts in an amphipathic manner with critical active site residues. The data suggest that CPI-1 prevents SNAP-25 from accessing the Balc active site by blocking both the substrate binding path at the surface and the Zn2+ binding region involved in catalysis. This is in contrast to linear peptide inhibitors described to date which block only the latter« less

  16. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12

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

  17. Algae Protein Fermentation

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

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

  18. Self assembling proteins

    DOE Patents [OSTI]

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

    2004-06-29

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

  19. 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

  20. A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes

    SciTech Connect (OSTI)

    Caffrey, Martin, E-mail: martin.caffrey@tcd.ie [Trinity College Dublin, Dublin (Ireland)

    2015-01-01

    A comprehensive and up-to-date review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes is reported. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained using in meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that the in meso method also works with soluble proteins should not be overlooked. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature’s most valued proteinaceous robots.

  1. Recombinant Protein Purification Handbook

    E-Print Network [OSTI]

    Lebendiker, Mario

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

  2. Interfacial rheology of globular proteins

    E-Print Network [OSTI]

    Jaishankar, Aditya

    2011-01-01

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

  3. Protein arginine deiminase 2 binds calcium in an ordered fashion: Implications for inhibitor design

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

    Slade, Daniel J.; Fang, Pengfei; Dreyton, Christina J.; Zhang, Ying; Fuhrmann, Jakob; Rempel, Don; Bax, Benjamin D.; Coonrod, Scott A.; Lewis, Huw D.; Guo, Min; et al

    2015-01-26

    Protein arginine deiminases (PADs) are calcium-dependent histone-modifying enzymes whose activity is dysregulated in inflammatory diseases and cancer. PAD2 functions as an Estrogen Receptor (ER) coactivator in breast cancer cells via the citrullination of histone tail arginine residues at ER binding sites. Although an attractive therapeutic target, the mechanisms that regulate PAD2 activity are largely unknown, especially the detailed role of how calcium facilitates enzyme activation. To gain insights into these regulatory processes, we determined the first structures of PAD2 (27 in total), and through calcium-titrations by X-ray crystallography, determined the order of binding and affinity for the six calcium ionsmore »that bind and activate this enzyme. These structures also identified several PAD2 regulatory elements, including a calcium switch that controls proper positioning of the catalytic cysteine residue, and a novel active site shielding mechanism. Additional biochemical and mass-spectrometry-based hydrogen/deuterium exchange studies support these structural findings. The identification of multiple intermediate calcium-bound structures along the PAD2 activation pathway provides critical insights that will aid the development of allosteric inhibitors targeting the PADs.« less

  4. Protein Flips Lipids Across Membranes

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

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

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

    E-Print Network [OSTI]

    Wong, Limsoon

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

  6. Protein folding and cosmology

    E-Print Network [OSTI]

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

    1997-06-04

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

  7. Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

    E-Print Network [OSTI]

    Fusco, Diana

    X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going ...

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

    E-Print Network [OSTI]

    Neumaier, Arnold

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

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

    E-Print Network [OSTI]

    Neumaier, Arnold

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

  10. Winter 2011 Evaluating Protein-Protein Docking Web Servers

    E-Print Network [OSTI]

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

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

    DOE Patents [OSTI]

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

    2001-07-03

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

  12. Differences in folate?protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate

    SciTech Connect (OSTI)

    Luka, Zigmund; Pakhomova, Svetlana; Loukachevitch, Lioudmila V.; Newcomer, Marcia E.; Wagner, Conrad (Vanderbilt); (LSU)

    2012-06-27

    Glycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism. In mammalian liver it reduces S-adenosylmethionine levels by using it to methylate glycine, producing N-methylglycine (sarcosine) and S-adenosylhomocysteine. GNMT is inhibited by binding two molecules of 5-methyltetrahydrofolate (mono- or polyglutamate forms) per tetramer of the active enzyme. Inhibition is sensitive to the status of the N-terminal valine of GNMT and to polyglutamation of the folate inhibitor. It is inhibited by pentaglutamate form more efficiently compared to monoglutamate form. The native rat liver GNMT contains an acetylated N-terminal valine and is inhibited much more efficiently compared to the recombinant protein expressed in E. coli where the N-terminus is not acetylated. In this work we used a protein crystallography approach to evaluate the structural basis for these differences. We show that in the folate-GNMT complexes with the native enzyme, two folate molecules establish three and four hydrogen bonds with the protein. In the folate-recombinant GNMT complex only one hydrogen bond is established. This difference results in more effective inhibition by folate of the native liver GNMT activity compared to the recombinant enzyme.

  13. 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

  14. 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

  15. A force field for virtual atom molecular mechanics of proteins

    E-Print Network [OSTI]

    Hendrickson, Wayne A.

    , Columbia University, New York, NY 10032 Contributed by Wayne A. Hendrickson, July 13, 2009 (sent for review for which crystallography can specify atomic details of alternative end states, but the course distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features

  16. Applying Near-Optimal Alignments to Protein Structure Prediction

    E-Print Network [OSTI]

    -ray crystallography and nuclear magnetic resonance (NMR), but this can be difficult as well as costly. Using homology BLAST search. IMPALA is a software package designed by NCBI that can search a target sequence against criteria and therefore may be more accurate (Gracy a

  17. Expression of Recombinant Proteins in Microalgae

    E-Print Network [OSTI]

    Mayfield, Stephen P.; Franklin, Scott E.

    2003-01-01

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

  18. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

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

    Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander; Roessler, Christian G.; Teplitsky, Ella; Joshi, Karan; Campos, Olven; Agarwal, Rakhi; Allaire, Marc; Orville, Allen M.; et al

    2014-06-01

    Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s-1) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from themore »inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.« less

  19. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

    SciTech Connect (OSTI)

    Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander; Roessler, Christian G.; Teplitsky, Ella; Joshi, Karan; Campos, Olven; Agarwal, Rakhi; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

    2014-06-01

    Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s-1) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.

  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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen Protein Dynamics

  1. Cellulose binding domain proteins

    DOE Patents [OSTI]

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

    1998-01-01

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

  2. Cellulose binding domain proteins

    DOE Patents [OSTI]

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

    1998-11-17

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

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

    E-Print Network [OSTI]

    Kolesov, Grigory

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

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

    E-Print Network [OSTI]

    Amos, Joseph Edward

    2013-02-22

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

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

    E-Print Network [OSTI]

    Hosur, Raghavendra

    2012-01-01

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

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

    DOE Patents [OSTI]

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

    2004-10-12

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

  7. Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

    SciTech Connect (OSTI)

    Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila; Cuttitta, Christina M.; Polizzo, Gina M.; Ericson, Daniel L.; Roessler, Christian G.; Campos, Olven; Ma, Millie Y.; Agarwal, Rakhi; Jackimowicz, Rick; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

    2014-05-01

    A method is presented for screening fragment libraries using acoustic droplet ejection to co-crystallize proteins and chemicals directly on micromeshes with as little as 2.5 nl of each component. This method was used to identify previously unreported fragments that bind to lysozyme, thermolysin, and trypsin. Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.

  8. Stabilization of Proteins against Aggregation

    E-Print Network [OSTI]

    Baynes, Brian M.

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

  9. Stabilized polyacrylic saccharide protein conjugates

    DOE Patents [OSTI]

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

    1996-02-20

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

  10. IFITM Proteins Restrict Viral Membrane Hemifusion

    E-Print Network [OSTI]

    2013-01-01

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

  11. Hydrogen Bond Shaping of Membrane Protein Structure

    E-Print Network [OSTI]

    Cao, Zheng

    2013-01-01

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

  12. Goniometer-based Femtosecond Macromolecular Crystallography ...

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

    on XPP until the MFX station is fully operational in 2016. References: 1. A. E. Cohen, et al., Proc. Natl. Acad. Sci. USA 111, 17122 (2014). 2. Q. Zhou, et al., Nature 525,...

  13. Instrumentation upgrades for the Macromolecular Crystallography...

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

    322 Martin Fuchs, MX Group, Swiss Light Source; Paul Scherrer Institute (Villigen, Switzerland) A new unified diffractometer - the D3 - has been developed for the three MX...

  14. PHASE RETRIEVAL METHODS FOR SURFACE CRYSTALLOGRAPHY

    E-Print Network [OSTI]

    Saldin, Dilano

    of current through a transistor in an integrated circuit, to the function of the catalyst in a car the method will be described in detail. The second is the case of low energy electron diffraction (LEED-time post-doc Valentin Shneerson. New topics and ideas often mystify each of us in the same way. I've had

  15. Goniometer-based Femtosecond Macromolecular Crystallography | Stanford

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory ofDid you not findGeoscience/EnvironmentGlobal Security GlobalGlossary A

  16. Microcrystallization techniques for serial femtosecond crystallography

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory ofDid you notHeatMaRIEdioxide capture | Center forDioxideFirst Neutrino

  17. Instrumentation upgrades for the Macromolecular Crystallography beamlines

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation CurrentHenryInhibiting Individual NotchInspiringAppendix for Schedule 8Dof the

  18. Resources for Macromolecular Crystallography | Advanced Photon Source

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

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

  19. 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

  20. 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

  1. 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

  2. Crystal and solution structures of an odorant-binding protein from the southern house mosquito complexed with an oviposition pheromone

    SciTech Connect (OSTI)

    Mao, Yang; Xu, Xianzhong; Xu, Wei; Ishida, Yuko; Leal, Walter S.; Ames, James B.; Clardy, Jon

    2010-11-15

    Culex mosquitoes introduce the pathogens responsible for filariasis, West Nile virus, St. Louis encephalitis, and other diseases into humans. Currently, traps baited with oviposition semiochemicals play an important role in detection efforts and could provide an environmentally friendly approach to controlling their populations. The odorant binding proteins (OBPs) in the female's antenna play a crucial, if yet imperfectly understood, role in sensing oviposition cues. Here, we report the X-ray crystallography and NMR 3D structures of OBP1 for Culex quinquefasciatus (CquiOBP1) bound to an oviposition pheromone (5R,6S)-6-acetoxy-5-hexadecanolide (MOP). In both studies, CquiOBP1 had the same overall six-helix structure seen in other insect OBPs, but a detailed analysis revealed an important previously undescribed feature. There are two models for OBP-mediated signal transduction: (i) direct release of the pheromone from an internal binding pocket in a pH-dependent fashion and (ii) detection of a pheromone-induced conformational change in the OBP {center_dot} pheromone complex. Although CquiOBP1 binds MOP in a pH-dependent fashion, it lacks the C terminus required for the pH-dependent release model. This study shows that CquiOBP binds MOP in an unprecedented fashion using both a small central cavity for the lactone head group and a long hydrophobic channel for its tail.

  3. Protein subcellular localization assays using split fluorescent proteins

    DOE Patents [OSTI]

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

    2009-09-08

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

  4. Solution Structure of an Amyloid-Forming Protein During Photoinitiated Hexamer-Dodecamer Transitions Revealed Through Small-Angle Neutron Scattering

    SciTech Connect (OSTI)

    Hamill,A.; Wang, S.; Lee, Jr., C.

    2007-01-01

    Shape-reconstruction analysis applied to small angle neutron scattering (SANS) data is used to determine the in vitro conformations of {alpha}-chymotrypsin oligomers that form as a result of partial unfolding with a photoresponsive surfactant. In the presence of the photoactive surfactant under visible light, the native oligomers (dimers or compact hexamers) rearrange into expanded corkscrew-like hexamers. Converting the surfactant to the photopassive form with UV light illumination causes the hexamers to laterally aggregate and intertwine into dodecamers with elongated, twisted conformations containing cross-sectional dimensions similar to amyloid protofilaments. Secondary-structure measurements with FT-IR indicate that this photoinduced hexamer-to-dodecamer association occurs through intermolecular {beta} sheets stabilized with hydrogen bonds, similar to amyloid formation. Traditional structural characterization techniques such as X-ray crystallography and NMR are not easily amenable to the study of these non-native protein conformations; however, SANS is ideally suited to the study of these associated intermediates, providing direct observation of the mechanism of oligomeric formation in an amyloid-forming protein. Combined with photoinitiated hexamer-to-dodecamer associations in the presence of the photoresponsive surfactant, this study could provide unique insight into the amyloidosis disease pathway, as well as novel disease treatment strategies.

  5. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

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

  6. Mathematical methods for protein science

    SciTech Connect (OSTI)

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

    1997-12-31

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

  7. Fragment-based structure-guided drug discovery: strategy, process, and lessons from human protein kinases

    SciTech Connect (OSTI)

    Burley, Stephen K.; Hirst, Gavin; Sprengeler, Paul; Reich, Siegfried

    2012-04-24

    The experimental roots of fragment-based drug discovery can be found in the work of Petsko, Ringe, and coworkers, who were the first to report flooding of protein crystals with small organic solutes (e.g., compounds such as benzene with ten or fewer nonhydrogen atoms) to identify bound functional groups that might ultimately be transformed into targeted ligands. The concept of linking fragments together to increase binding affinity was described as early as 1992 by Verlinde et al. Computational screening of fragments, using tools such as DOCK or MCSS, was also described in the early 1990s. Pharmaceutical industry application of fragment screening began at Abbott Laboratories, where Fesik and coworkers pioneered 'SAR by NMR' (structure/activity relationship by nuclear magnetic resonance). In this spectroscopic approach, bound fragments are detected by NMR screening and subsequently linked together to increase affinity, as envisaged by Verlinde and coworkers. Application of x-ray crystallography to detect and identify fragment hits was also pursued at Abbott. Fragment-based drug discovery has now been under way for more than a decade. Although Fesik and coworkers popularized the notion of linking fragments (as in their highly successful BCL-2 program), tactical emphasis appears to have largely shifted from fragment condensation to fragment engineering (or growing the fragment) to increase binding affinity and selectivity. Various biotechnology companies, including SGX Pharmaceuticals, Astex, and Plexxikon, have recently demonstrated that fragment-based approaches can indeed produce development candidates suitable for Phase I studies of safety and tolerability in patients (www.clinicaltrials.gov).

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

    SciTech Connect (OSTI)

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

    2006-01-01

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

  9. Protein Flips Lipids Across Membranes

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

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

  10. High throughput protein production screening

    DOE Patents [OSTI]

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

    2009-09-08

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

  11. Protein Flips Lipids Across Membranes

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

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

  12. Noise in protein expression scales with natural protein abundance

    E-Print Network [OSTI]

    Paulsson, Johan

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

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

    E-Print Network [OSTI]

    Pazos, Florencio

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

  14. Protein detection system

    DOE Patents [OSTI]

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

    2009-05-05

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

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

    Office of Scientific and Technical Information (OSTI)

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

  16. Water at interface with proteins

    E-Print Network [OSTI]

    Giancarlo Franzese; Valentino Bianco; Svilen Iskrov

    2010-12-07

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

  17. Expression of multiple proteins in transgenic plants

    DOE Patents [OSTI]

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

    2002-01-01

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

  18. 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

  19. Fusion Protein Products Screen Purify Detect Cleave

    E-Print Network [OSTI]

    Lebendiker, Mario

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

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

    E-Print Network [OSTI]

    Quinlan, Robert Jason

    2005-02-17

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

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

    E-Print Network [OSTI]

    Phillips, Aaron Hale

    2010-01-01

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

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

    E-Print Network [OSTI]

    Zhu, L; Kaback, HR; Dalbey, RE

    2013-01-01

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  5. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

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

    2010-07-18

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

  6. A survey of integral ?-helical membrane proteins

    E-Print Network [OSTI]

    2009-01-01

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

  7. Protein Interactions in Regulation and Assembly 

    E-Print Network [OSTI]

    Hsiao, Hao-Ching

    2015-03-17

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

  8. A survey of integral ?-helical membrane proteins

    E-Print Network [OSTI]

    2009-01-01

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

  9. A motion planning approach to protein folding 

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30

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

  10. Optimized Null Model for Protein Structure Networks

    E-Print Network [OSTI]

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

    2009-01-01

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

  11. A Novel Topology for Representing Protein Folds

    E-Print Network [OSTI]

    Segal, Mark R

    2009-01-01

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

  12. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01

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

  13. Towards a Molecular Understanding of Protein Solubility 

    E-Print Network [OSTI]

    Kramer, Ryan 1984-

    2011-05-31

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

  14. 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

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

    E-Print Network [OSTI]

    Bayro, Marvin J

    2010-01-01

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

  16. Optimal contact map alignment of protein–protein interfaces

    E-Print Network [OSTI]

    Pulim, Vinay

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

  17. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

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

  18. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

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

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

    E-Print Network [OSTI]

    Barakat, Nora Hisham

    2007-01-01

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

  20. Effective potentials for Folding Proteins

    E-Print Network [OSTI]

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

    2006-01-28

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

  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)

    2008-08-26

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

  2. Protein Flips Lipids Across Membranes

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

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

  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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big Screen ProteinProtein

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

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01

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

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

    Office of Scientific and Technical Information (OSTI)

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

  6. Extracellular Proteins Promote Zinc Sulfide Aggregation

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

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

  7. Protein shake-up | ornl.gov

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

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

  8. Validating Computer-Designed Proteins for Vaccines

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

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

  9. SciTech Connect: "protein folding"

    Office of Scientific and Technical Information (OSTI)

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

  10. ARTIFICIAL NEURAL NETWORKS IN PROTEIN

    E-Print Network [OSTI]

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

  11. Topological Solitons and Folded Proteins

    E-Print Network [OSTI]

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

    2010-03-23

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

  12. Order, disorder, and protein aggregation

    E-Print Network [OSTI]

    Gurry, Thomas

    2015-01-01

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

  13. 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, ...

  14. Fast events in protein folding

    SciTech Connect (OSTI)

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

    1996-04-01

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

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

    E-Print Network [OSTI]

    Chen, Ting

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

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

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

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

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

    E-Print Network [OSTI]

    Gwynne, Peter John

    2015-06-29

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

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

    E-Print Network [OSTI]

    Stevenson, Calum

    2012-11-30

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

  19. 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

  20. Proteins Wriggle Michael Cahill,* Sean Cahill,

    E-Print Network [OSTI]

    Cahill, Kevin

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

  1. EVA: evaluation of protein structure prediction servers

    E-Print Network [OSTI]

    Sali, Andrej

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

  2. Protein-Folding Dynamics: Overview of Molecular

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

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

  3. Protein Misfolding, Genetics, and Disease Anika Nagpal

    E-Print Network [OSTI]

    Brutlag, Doug

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

  4. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01

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

  5. Protein design for pathway engineering

    SciTech Connect (OSTI)

    Eriksen, DT; Lian, JZ; Zhao, HM

    2014-02-01

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

  6. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01

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

  7. Shining a spotlight on intact proteins

    SciTech Connect (OSTI)

    Pasa-Tolic, Ljiljana; Masselon, Christophe

    2014-05-01

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

  8. Exploiting Elements of Transcriptional Machinery to Enhance Protein Stability

    E-Print Network [OSTI]

    Love, John J.

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

  9. SSRLUO 2012 Executive Committee Members | Stanford Synchrotron...

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

    at SSRL since 1986, and has managed the administration of protein crystallography experiments since 2000. Lisa earned her Bachelor of Science degree from San Jose State...

  10. SSRLUO 2011 Executive Committee Members | Stanford Synchrotron...

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

    at SSRL since 1986, and has managed the administration of protein crystallography experiments since 2000. Lisa earned her Bachelor of Science degree from San Jose State...

  11. Structure of the Kinase Domain of CaMKII and Modeling the Holoenzyme

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

    A group from the University of California, Berkeley, the Yale University School of Medicine, and Berkeley Lab has combined protein crystallography and small-angle x-ray...

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

    E-Print Network [OSTI]

    Stockwell, Brent R.

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

  13. 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

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

    E-Print Network [OSTI]

    Bruck, Jehoshua (Shuki)

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

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

    E-Print Network [OSTI]

    Yang, Sichun

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

  16. Protein folding in the ER.

    SciTech Connect (OSTI)

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

    1999-10-01

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

  17. Method for protein structure alignment

    DOE Patents [OSTI]

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

    2005-02-22

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

  18. Protein Flips Lipids Across Membranes

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

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

  19. Method for voltage-gated protein fractionation

    DOE Patents [OSTI]

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

    2012-04-24

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

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

    E-Print Network [OSTI]

    Chen, Tsan-Chou Scott

    2012-01-01

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

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

    E-Print Network [OSTI]

    Fu, Hailong

    2010-07-14

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

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

    E-Print Network [OSTI]

    Ko, Eunhwa

    2012-07-16

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

  3. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

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

    1998-02-17

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

  4. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

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

    1998-01-01

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

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

    E-Print Network [OSTI]

    Scott, John D.

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

  6. Contributions to the analysis of proteins

    E-Print Network [OSTI]

    Sharifi Sedeh, Reza

    2011-01-01

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

  7. Lanthanide-tagged proteins – An illuminating partnership

    E-Print Network [OSTI]

    Imperiali, Barbara

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

  8. The Logic Linking Protein Acetylation and Metabolism

    E-Print Network [OSTI]

    Guarente, Leonard Pershing

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

  9. 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

  10. Protein Instability and Lou Gehrig's Disease

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

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

  11. Metal-directed protein self-assembly

    E-Print Network [OSTI]

    Salgado. Eric N.

    2010-01-01

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

  12. Protein-Folding Landscapes in Multi-Chain Systems

    E-Print Network [OSTI]

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

    2005-01-01

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

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

    E-Print Network [OSTI]

    Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

    2004-01-01

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

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

    E-Print Network [OSTI]

    Palczewski, Krzysztof

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

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

    E-Print Network [OSTI]

    2006-01-01

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

  16. Computational Modeling of Protein Interactions at Multiple Lengthscales

    E-Print Network [OSTI]

    Yap, Eng Hui

    2010-01-01

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

  17. The unfolded protein response during prostate cancer development

    E-Print Network [OSTI]

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

    2009-01-01

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

  18. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

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

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

    E-Print Network [OSTI]

    Anderson, William David

    2007-01-01

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

  20. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

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

  1. Bayesian Nonparametric Methods for Protein Structure Prediction 

    E-Print Network [OSTI]

    Lennox, Kristin Patricia

    2011-10-21

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

  2. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K. (Berkeley, CA)

    1997-01-01

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

  3. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Devadas, Srinivas

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

  4. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Will, Sebastian

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

  5. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, G.K.

    1997-04-29

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

  6. 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

  7. 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

  8. 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

  9. On Hydrophobicity and Conformational Specificity in Proteins

    E-Print Network [OSTI]

    Sandelin, Erik

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

  10. Amphiphiles for protein solubilization and stabilization

    DOE Patents [OSTI]

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

    2014-11-04

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

  11. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

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

  12. 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

  13. 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

  14. 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

  15. Protein Structures Revealed at Record Pace

    SciTech Connect (OSTI)

    Hura, Greg

    2009-01-01

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

  16. 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

  17. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Hura, Greg

    2013-05-29

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

  18. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Greg Hura

    2010-01-08

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

  19. Amphiphiles for protein solubilization and stabilization

    DOE Patents [OSTI]

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

    2012-09-11

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

  20. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21

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

  1. Extracellular secretion of recombinant proteins

    DOE Patents [OSTI]

    Linger, Jeffrey G.; Darzins, Aldis

    2014-07-22

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

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

    E-Print Network [OSTI]

    Bigelow, Stephen

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

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

    E-Print Network [OSTI]

    Powers, Robert

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

  4. 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

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

    E-Print Network [OSTI]

    Moreira, Bruno Contreras

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

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

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

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

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

    E-Print Network [OSTI]

    Chen, Xin

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

  8. 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

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

    E-Print Network [OSTI]

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

  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

    2012-01-01

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

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

    E-Print Network [OSTI]

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

    2012-01-01

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

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

    E-Print Network [OSTI]

    Portillo, Ostilio Rolando

    2009-05-15

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

  13. 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

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

    DOE Patents [OSTI]

    Laible, Philip D; Hanson, Deborah K

    2013-06-04

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

  15. Crystal Structure of Crataeva tapia Bark Protein (CrataBL) and Its Effect in Human Prostate Cancer Cell Lines

    E-Print Network [OSTI]

    Federal de Sa~o Paulo, Sa~o Paulo, Sa~o Paulo, Brazil, 2 Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America, 3 Centro de Engenharias e Cie^ncias Exatas, Universidade Estadual do Oeste do Parana´, Toledo, Parana´, Brazil, 4

  16. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

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

    2006-07-27

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

  17. Quantifying protein diffusion and capture on filaments

    E-Print Network [OSTI]

    Emanuel Reithmann; Louis Reese; Erwin Frey

    2015-03-03

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

  18. Quantifying protein diffusion and capture on filaments

    E-Print Network [OSTI]

    Reithmann, Emanuel; Frey, Erwin

    2015-01-01

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

  19. Protein Dynamics Hit the Big Screen

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

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

  20. A rational route to probing membrane proteins

    E-Print Network [OSTI]

    Keating, Amy E.

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

  1. Extracellular Proteins Promote Zinc Sulfide Aggregation

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

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

  2. Hydrogen Bond Shaping of Membrane Protein Structure

    E-Print Network [OSTI]

    Cao, Zheng

    2013-01-01

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

  3. Knots and Swelling in Protein Folding

    E-Print Network [OSTI]

    Martin Lundgren; Antti J. Niemi

    2009-06-26

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

  4. Year 2 Report: Protein Function Prediction Platform

    SciTech Connect (OSTI)

    Zhou, C E

    2012-04-27

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

  5. 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)

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

    E-Print Network [OSTI]

    Kim, Do-Nyun

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

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

    E-Print Network [OSTI]

    Mukherjee, Srayanta

    2011-12-31

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

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

    E-Print Network [OSTI]

    Zare, Richard N.

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

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

    E-Print Network [OSTI]

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

  10. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Protein structure mining using

    E-Print Network [OSTI]

    Srinivasan, N.

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

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

    SciTech Connect (OSTI)

    B Wallace; R Janes

    2011-12-31

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

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

    E-Print Network [OSTI]

    Lässig, Michael

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

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

    SciTech Connect (OSTI)

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

    2011-12-31

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

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

    SciTech Connect (OSTI)

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

    2011-05-15

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

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

    E-Print Network [OSTI]

    Forbes, Douglass

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

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

    E-Print Network [OSTI]

    Powers, Robert

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

  17. Experimental Observation of Bonding Electrons in Proteins*

    E-Print Network [OSTI]

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

  18. Protein Interactions in Regulation and Assembly 

    E-Print Network [OSTI]

    Hsiao, Hao-Ching

    2015-03-17

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

  19. Chemistry & Biology Conversion of Red Fluorescent Protein

    E-Print Network [OSTI]

    Verkhusha, Vladislav V.

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

  20. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

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

    1990-08-23

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

  1. Biophysical characterization of protein folding and misfolding. 

    E-Print Network [OSTI]

    Schmittschmitt, Jason Peter

    2004-09-30

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

  2. Thermodynamics of Protein Folding Erik Sandelin

    E-Print Network [OSTI]

    Sandelin, Erik

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

  3. PIC : Protein Interaction Calculator HELP AND GUIDELINES

    E-Print Network [OSTI]

    Srinivasan, N.

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

  4. Solvent dramatically affects protein structure refinement

    E-Print Network [OSTI]

    Summa, Christopher M.

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

  5. Mismatch String Kernels for SVM Protein Classification

    E-Print Network [OSTI]

    Noble, William Stafford

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

  6. Rotary protein motors George Oster1

    E-Print Network [OSTI]

    Oster, George

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

  7. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01

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

  8. 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

  9. 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

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

    SciTech Connect (OSTI)

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

    2003-01-01

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    E-Print Network [OSTI]

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

    2010-01-01

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

  13. Development of anomalous diffusion among crowding proteins

    E-Print Network [OSTI]

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

    2010-03-19

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

  14. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

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

  15. 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

  16. Intrinsically Disordered Proteins May Select Partners by Fold 

    E-Print Network [OSTI]

    Gonzalez, Kim 1988-

    2010-12-08

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

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

    E-Print Network [OSTI]

    Spears, Tatsinda Verity

    2010-01-01

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

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

    E-Print Network [OSTI]

    Bigelow, Stephen

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

  19. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

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

  20. Functional Delivery of Proteins Using Engineered Degradable Polymeric Nanocapsules

    E-Print Network [OSTI]

    Biswas, Anuradha

    2013-01-01

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

  1. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

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

  2. 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

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

    E-Print Network [OSTI]

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

    2011-01-01

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

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

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

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

  5. Mutations that suppress the thermosensitivity of green fluorescent protein

    E-Print Network [OSTI]

    Haseloff, Jim

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

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

    E-Print Network [OSTI]

    Langmead, Christopher James

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

  7. 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

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

    E-Print Network [OSTI]

    Landman, Allison Simone

    2009-01-01

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

  9. Workshop: New Advances in Crystallography with Synchrotrons and...

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

    with Synchrotrons and X-FELs Tuesday, October 25, 2011 - 8:00am 2011 SSRLLCLS Annual Users Conference This workshop, part of the 2011 SSRLLCLS Annual Users...

  10. Serial snapshot crystallography for materials science with SwissFEL

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

    Dejoie, Catherine; Smeets, Stef; Baerlocher, Christian; Tamura, Nobumichi; Pattison, Philip; Abela, Rafael; McCusker, Lynne B.

    2015-04-21

    New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of datamore »can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10–50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.« less

  11. 37A Focus on Crystallography Crystals and mathematics

    E-Print Network [OSTI]

    Greuel, Gert-Martin

    , or as polished gems. Less known is that the largest part (about 98%) of the solid ground is crystalline. This means that crystals are a stable state of the condensed matter. The term "crystal" is derived from

  12. Goniometer-based femtosecond crystallography with X-ray free...

    Office of Scientific and Technical Information (OSTI)

    I. ; McPhillips, Scott E. ; Nelson, Silke ; Peters, John W. ; Sauter, Nicholas K. ; Smith, Clyde A. ; Song, Jinhu ; Stevenson, Hilary P. ; Tsai, Yingssu ; Uervirojnangkoorn,...

  13. Eighth Shull Fellow to Focus on Biochemistry and Crystallography...

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

    program began in 2006. Named for the 1994 Nobel Prize winner in Physics who did his early neutron scattering research at Oak Ridge from 1946 to 1955, the Shull fellowship program...

  14. Time-Resolved Biochemical Crystallography: A Mechanistic Perspective Keith Moffat*

    E-Print Network [OSTI]

    Moffat, Keith

    of Biochemistry & Molecular Biology, The Institute for Biophysical Dynamics and The Center for Advanced Radiation enforces a phase change in the crystal that alters the cell dimensions, the space group, or both with different reaction intermediate and * To whom correspondence should be addressed. Phone: (773) 702- 2116

  15. Operation of the Australian Store.Synchrotron for macromolecular crystallography

    SciTech Connect (OSTI)

    Meyer, Grischa R. [Monash University, Clayton, Victoria 3800 (Australia); Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T. [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia); McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M. [Monash University, Clayton, Victoria 3800 (Australia); Bond, Charles S. [The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia (Australia); Buckle, Ashley M. [Monash University, Clayton, Victoria 3800 (Australia); Androulakis, Steve, E-mail: steve.androulakis@monash.edu [Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800 (Australia)

    2014-10-01

    The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (?1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

  16. Crystallography The new Anatrace Neopentyl Glycol (NG) class detergents

    E-Print Network [OSTI]

    Lebendiker, Mario

    -1008. Lauryl Maltose Neopentyl Glycol NG310 1 gm 5 gm 25 gm Octyl Glucose Neopentyl Glycol NG311 1 gm 5 gm 25 gm Decyl Maltose Neopentyl Glycol NG322 1 gm 5 gm 25 gm #12;Affymetrix, Inc. Anatrace® Products 434 W

  17. Method for removing atomic-model bias in macromolecular crystallography

    DOE Patents [OSTI]

    Terwilliger, Thomas C. (Santa Fe, NM)

    2006-08-01

    Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

  18. Goniometer-based femtosecond crystallography with X-ray free...

    Office of Scientific and Technical Information (OSTI)

    Sciences (SC-22) Country of Publication: United States Language: English Subject: solar (fuels), biofuels (including algae and biomass), bio-inspired, hydrogen and fuel cells...

  19. Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURING OFFICESpecialAPPENDIX FOriginMaterials by Ultra-High-Resolution Electron

  20. Time-resolved serial crystallography captures high-resolution intermediates

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory of rare Kaon and Pion decaysArticle) |errors(Technicalof photoactive yellow

  1. Genentech Uses ALS Crystallography for Therapeutic Antibody Research

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HABFESOpportunities Nuclearlong version)shortGate Hours &Gearing

  2. Introduction to Bayesian methods in macromolecular crystallography (Journal

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverseIMPACT EVALUATIONIntroducing the Richard P. Feynman Center toArticle) |

  3. Media invited to join students in crystallography experiment

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJesse BergkampCentermillion Measurement of Muon

  4. Functionality and Protein-Water Interactions

    E-Print Network [OSTI]

    J. C. Phillips

    2008-03-02

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

  5. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01

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

  6. Protein Structure Suggests Role as Molecular Adapter

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

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

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

    E-Print Network [OSTI]

    Gibney, Brian R.

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

  8. 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...

  9. Robust, High-Throughput Analysis of Protein Structures

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

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

  10. Robust, High-Throughput Analysis of Protein Structures

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

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  13. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

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

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

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

    Office of Scientific and Technical Information (OSTI)

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

  15. 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

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

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

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

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

    E-Print Network [OSTI]

    Rothman, Stephen

    2010-01-01

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

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

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

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

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

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

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

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

    E-Print Network [OSTI]

    Guan, Xiao

    2006-01-01

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

  1. Biomimetic materials for protein storage and transport

    DOE Patents [OSTI]

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

    2012-05-01

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

  2. Simultaneous alignment and folding of protein sequences

    E-Print Network [OSTI]

    Waldispuhl, Jerome

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

  3. Exploring the mechanisms of fibrillar protein aggregation 

    E-Print Network [OSTI]

    Ryan, Morris

    2013-11-28

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

  4. IDENTIFYING CANDIDATE PROTEIN FOR REMOVAL OF ENVIRONMENTALLY

    E-Print Network [OSTI]

    Uppsala Universitet

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

  5. Characterisation of endogenous KRAB zinc finger proteins 

    E-Print Network [OSTI]

    Crawford, Catherine

    2009-01-01

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

  6. 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...

  7. Validating Computer-Designed Proteins for Vaccines

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

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

  8. Mapping the Protein Universe | Argonne National Laboratory

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

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

  9. Histone H1 proteins in Chlamydomonas reinhardtii 

    E-Print Network [OSTI]

    Salinger, Andrew Paul

    1994-01-01

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

  10. Purification of recombinant proteins with magnetic nanoclusters

    E-Print Network [OSTI]

    Ditsch, Andre (Andre Paul)

    2005-01-01

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

  11. Selenomethionine Biotransformation and Incorporation into Proteins

    E-Print Network [OSTI]

    Hopkins, William A.

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

  12. Protein Scaffolding for Small Molecule Catalysts

    SciTech Connect (OSTI)

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

    2014-09-14

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

  13. Photovoltaic devices using photosynthetic protein complexes

    E-Print Network [OSTI]

    Das, Rupa, 1980-

    2004-01-01

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

  14. Orpinomyces xylanase proteins and coding sequences

    DOE Patents [OSTI]

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

    1998-10-20

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

  15. Positive modulator of bone morphogenic protein-2

    DOE Patents [OSTI]

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

    2009-01-27

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

  16. Complement Evasion by S. aureus Surface Proteins 

    E-Print Network [OSTI]

    Kang, Mingsong

    2014-08-28

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

  17. Exo-endo cellulase fusion protein

    DOE Patents [OSTI]

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

    2012-01-17

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

  18. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26

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

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

    E-Print Network [OSTI]

    Jain, Ajay N.

    2009-01-01

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

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

    SciTech Connect (OSTI)

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

    2013-12-01

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

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

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01

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

  2. 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

  3. 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

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

    E-Print Network [OSTI]

    Weng, Zhiping

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

  5. DNA topology confers sequence specificity to nonspecific architectural proteins

    E-Print Network [OSTI]

    Swigon, David

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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

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

    DOE Patents [OSTI]

    Mayfield, Stephen P. (Cardiff, CA)

    2010-03-16

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

  12. Directional interactions and cooperativity between mechanosensitive membrane proteins

    E-Print Network [OSTI]

    Christoph A. Haselwandter; Rob Phillips

    2013-05-24

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

  13. Structural determination of intact proteins using mass spectrometry

    DOE Patents [OSTI]

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

    2008-05-06

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

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

    E-Print Network [OSTI]

    Schwarz, Ulrich

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

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

    E-Print Network [OSTI]

    Cunningham, Brian

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

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

    E-Print Network [OSTI]

    Baker, David

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

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

    E-Print Network [OSTI]

    Morante, Silvia

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

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

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

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

    2014-12-18

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

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

    E-Print Network [OSTI]

    Bong, Dennis

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

  20. Universality of Vibrational Spectra of Globular Proteins

    E-Print Network [OSTI]

    Na, Hyuntae; ben-Avraham, Daniel

    2015-01-01

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

    Barton, Geoffrey J.

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

  3. 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

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

    E-Print Network [OSTI]

    Benedek, George B.

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

  5. Cotranslational folding of deeply knotted proteins

    E-Print Network [OSTI]

    Chwastyk, Mateusz

    2015-01-01

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

  6. Protein search for multiple targets on DNA

    E-Print Network [OSTI]

    Martin Lange; Maria Kochugaeva; Anatoly B. Kolomeisky

    2015-08-03

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

  7. Compositions and methods for improved protein production

    DOE Patents [OSTI]

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

    2012-07-10

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

  8. Compositions and methods for improved protein production

    SciTech Connect (OSTI)

    Bodie, Elizabeth A.; Kim, Steve Sungjin

    2014-06-03

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

  9. Facilitated diffusion of proteins on chromatin

    E-Print Network [OSTI]

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

    2011-01-26

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

  10. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17

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

  11. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

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

    2002-01-01

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

  12. Protein Dynamics Hit the Big Screen

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

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

  13. Protein Instability and Lou Gehrig's Disease

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

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

  14. Protein Instability and Lou Gehrig's Disease

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

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

  15. Protein Structure Suggests Role as Molecular Adapter

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

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

  16. Protein Structure Suggests Role as Molecular Adapter

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

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

  17. Protein Instability and Lou Gehrig's Disease

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

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

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

    E-Print Network [OSTI]

    Slavoff, Sarah Ann

    2010-01-01

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

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

    SciTech Connect (OSTI)

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

    2009-05-15

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

  20. Predicting Protein Secondary and Supersecondary Structure

    E-Print Network [OSTI]

    Singh, Mona

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

  1. Protein Structure Modeling With MODELLER Narayanan Eswar$

    E-Print Network [OSTI]

    Sali, Andrej

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

  2. Energy use by biological protein transport pathways

    E-Print Network [OSTI]

    Economou, Tassos

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

  3. Assembly mechanism of recombinant spider silk proteins

    E-Print Network [OSTI]

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

  4. Chemistry & Biology Red Fluorescent Protein with Reversibly

    E-Print Network [OSTI]

    Verkhusha, Vladislav V.

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

  5. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13

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

  6. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

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

    1998-01-13

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

  7. Metal-directed protein self-assembly

    E-Print Network [OSTI]

    Salgado. Eric N.

    2010-01-01

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

  8. January, 2003 1 The Protein Space

    E-Print Network [OSTI]

    Linial, Michal

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

  9. Frequent Subsequence-Based Protein Localization

    E-Print Network [OSTI]

    Zaiane, Osmar R.

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

  10. Flavors of Protein Disorder Slobodan Vucetic,1

    E-Print Network [OSTI]

    Vucetic, Slobodan

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

  11. Using qualitative uncertainty in protein topology prediction

    E-Print Network [OSTI]

    Parsons, Simon

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

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

    E-Print Network [OSTI]

    Toumi, Melinda L.

    2010-05-31

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

  13. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    SciTech Connect (OSTI)

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

    2014-03-15

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

  14. Corn Storage Protein - A Molecular Genetic Model

    SciTech Connect (OSTI)

    Messing, Joachim

    2013-05-31

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

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

    E-Print Network [OSTI]

    Lee, Jooyoung

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

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

    E-Print Network [OSTI]

    Levy, Michaella J

    2014-06-05

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

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

    E-Print Network [OSTI]

    Shang, Yue

    2007-09-17

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

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

    E-Print Network [OSTI]

    Fischer, Tiffany Brink

    2007-04-25

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

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

    E-Print Network [OSTI]

    Ryan, Jeremy Adam

    2005-01-01

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

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

    E-Print Network [OSTI]

    Tovchigrechko, Andrey; Vakser, Ilya A.

    2006-07-01

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