National Library of Energy BETA

Sample records for monochromatic protein crystallography

  1. Johann Deisenhofer, Crystallography, and Proteins

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

    Johann Deisenhofer, Crystallography, and Proteins Resources with Additional Information Johann Deisenhofer Courtesy of UT Southwestern Medical Center "Johann Deisenhofer, Ph.D. is a Professor at UT Southwestern who shared the 1988 Nobel Prize in Chemistry for his research using X-ray crystallography to elucidate for the first time the three-dimensional structure of a large membrane-bound protein molecule. This structure helped explain the process of photosynthesis, by which sunlight is

  2. Protein crystallography prescreen kit

    DOE Patents [OSTI]

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

    2007-10-02

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

  3. Protein crystallography prescreen kit

    DOE Patents [OSTI]

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

    2005-07-12

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

  4. Lipidic phase membrane protein serial femtosecond crystallography

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

    Source: Nature Methods Year: 2012 Volume: 9 Pages: 263-265 ABSTRACT: X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method...

  5. 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

  6. 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.

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

    SciTech Connect (OSTI)

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

    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.

  8. 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.

  9. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOE Patents [OSTI]

    Craig, G.D.; Glass, R.; Rupp, B.

    1997-01-28

    A method is disclosed for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10{sup 6}V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved. 2 figs.

  10. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOE Patents [OSTI]

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

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

    Office of Scientific and Technical Information (OSTI)

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

  12. 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

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

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

    Damage by X-rays: A Case Study for Metallo-Protein Crystallography Junko Yano1,2, Jan Kern3, Klaus-Dieter Irrgang3, Matthew J. Latimer4, Uwe Bergmann4, Pieter Glatzel5, Yulia Pushkar1,2, Jacek Biesiadka6, Bernhard Loll6, Kenneth Sauer1,2, Johannes Messinger7, Athina Zouni3, Vittal K. Yachandra1 1Melvin Calvin Laboratory, Physical Biosciences Division, Lawrence Berkeley National Laboratory, and 2Department of Chemistry, University of California, Berkeley, CA, USA 3Max-Volmer-Laboratorium für

  14. 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

  15. Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation

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

    Das, Amit; Gerlits, Oksana O.; Parks, Jerry M.; Langan, Paul; Kovalevskyi, Andrey Y.; Heller, William T.

    2015-11-12

    The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg2+ binds first to the M1 site as a complex with ATP and is followed by Mg2+ binding to the M2 site. Furthermore, themore » target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. In conclusion, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.« less

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

    SciTech Connect (OSTI)

    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, which is highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome.

  17. 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/σI) 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, ΔF, 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.

  18. 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/σI) 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, ΔF,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

  19. Direct detection of x-rays for protein crystallography employing a thick, large area CCD

    DOE Patents [OSTI]

    Atac, Muzaffer; McKay, Timothy

    1999-01-01

    An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

  20. SMB, Macromolecular Crystallography

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

    Macromolecular Crystallography Home » Macromolecular Crystallography Macromolecular Crystallography The macromolecular crystallography (MC) program is a major experimental driver for structural biology research, serving the needs of a large number of academic and biotech groups working in this area, particularly in the Western U.S. Innovations in synchrotron-based crystallography have been catalyzed by challenges in this field, in particular the growing number of "non expert" user

  1. Johann Deisenhofer, Crystallography, and Proteins

    Office of Scientific and Technical Information (OSTI)

    Johann Deisenhofer Courtesy of UT Southwestern Medical Center "Johann Deisenhofer, Ph.D. is a Professor at UT Southwestern who shared the 1988 Nobel Prize in Chemistry for...

  2. 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.

  3. Diamondoid Monolayers as Monochromatic Electron Source

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

    Diamondoid Monolayers as Monochromatic Electron Source Diamondoid Monolayers as Monochromatic Electron Source Print Wednesday, 28 November 2007 00:00 Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential

  4. Diamondoid Monolayers as Monochromatic Electron Source

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

    Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have

  5. Diamondoid Monolayers as Monochromatic Electron Source

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

    Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have

  6. Diamondoid Monolayers as Monochromatic Electron Source

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

    Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have

  7. Diamondoid Monolayers as Monochromatic Electron Source

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

    Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have

  8. Diamondoid Monolayers as Monochromatic Electron Source

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

    Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have

  9. Diamondoid Monolayers as Monochromatic Electron Source

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

    Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have

  10. 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 ...

  11. Media invited to join students in crystallography experiment

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

    Media invited to join students in crystallography experiment Media invited to join students in crystallography experiment The student outreach effort is part of the events...

  12. 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, Sbastien; 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 4C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 resolution using 300 g 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.

  13. 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

  14. Gated monochromatic x-ray imager

    SciTech Connect (OSTI)

    Oertel, J.A.; Archuleta, T.; Clark, L.

    1995-09-01

    We have recently developed a gated monochromatic x-ray imaging diagnostic for the national Inertial-Confinement Fusion (ICF) program. This new imaging system will be one of the primary diagnostics to be utilized on University of Rochester`s Omega laser fusion facility. The new diagnostic is based upon a Kirkpatrick-Baez (KB) microscope dispersed by diffraction crystals, as first described by Marshall and Su. The dispersed images are gated by four individual proximity focused microchannel plates and recorded on film. Spectral coverage is tunable up to 8 keV, spectral resolution has been measured at 20 eV, temporal resolution is 80 ps, and spatial resolution is better than 10 {mu}m.

  15. Goniometer-based Femtosecond Macromolecular Crystallography | Stanford

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

    Synchrotron Radiation Lightsource Goniometer-based Femtosecond Macromolecular Crystallography Saturday, October 31, 2015 Scientists in the Structural Molecular Biology (SMB) program at the Stanford Synchrotron Radiation Lightsource (SSRL) in collaboration with scientists at Stanford University and at the Linac Coherent Light Source (LCLS) developed a goniometer-based system to study radiation-sensitive macromolecular complexes. The system operates in air and is complementary to the

  16. Instrumentation upgrades for the Macromolecular Crystallography beamlines

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

    of the Swiss Light Source | Stanford Synchrotron Radiation Lightsource Instrumentation upgrades for the Macromolecular Crystallography beamlines of the Swiss Light Source Monday, October 29, 2012 - 2:00am SSRL, Bldg. 137, Rm. 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 beamlines. The first of the instruments is in general user operation at beamline X10SA since April

  17. Media invited to join students in crystallography experiment

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

    Media invited to join students in crystallography experiment Media invited to join students in crystallography experiment The student outreach effort is part of the events commemorating 2014 as the International Year of Crystallography. May 16, 2014 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics and

  18. 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

  19. Holographic Methods in X-ray Crystallography

    Energy Science and Technology Software Center (OSTI)

    1995-07-28

    The holographic method makes use of partially modeled electron density and experimentally-measured structure factor amplitudes to recover electron density corresponding to the unmodeled part of a crystal structure. This paper describes a fast algorithm that makes it possible to apply the holographic method to sizable crystallographic problems. The algorithm uses positivity constraints on the electron density, and can incorporate a target electron density, making it similar to solvent flattening. Using both synthetic and experimental data,morewe assess the potential for applying the holographic method to macromolecular x-ray crystallography.less

  20. Computation of Diffractive Beam Propagation of Monochromatic Light

    Energy Science and Technology Software Center (OSTI)

    1999-02-20

    Computation of diffractive beam propagation of monochromatic light through a l-dimensional (slab) structure defined by a piecewise continuous complex index of refraction. Finite difference equations are fourth-order-accurate in the lateral grid size and include discontinuities of higher-order field derivatives at dielectric interfaces. Variable grid spacing is allowed, and all dielectric interfaces are assumed to coincide with grid points.

  1. Enabling X-ray free electron laser crystallography for challenging

    Office of Scientific and Technical Information (OSTI)

    biological systems from a limited number of crystals (Journal Article) | SciTech Connect Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals Citation Details In-Document Search Title: Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals Authors: Uervirojnangkoorn, Monarin ; Zeldin, Oliver B. ; Lyubimov, Artem Y. ; Hattne, Johan Search SciTech Connect for

  2. Genentech Uses ALS Crystallography for Therapeutic Antibody Research

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

    Genentech Uses ALS Crystallography for Therapeutic Antibody Research Genentech Uses ALS Crystallography for Therapeutic Antibody Research Print Wednesday, 29 January 2014 00:00 Therapeutic antibodies have revolutionized the treatment of human disease; however, antibody bivalency can limit their utility against some targets due to receptor crosslinking and activation. Genentech has developed a unique one-armed antibody, onartuzumab, which is now in late-stage clinical trials in multiple cancer

  3. Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic

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

    Materials by Ultra-High-Resolution Electron Microscopy and Related Methods | Department of Energy Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic Materials by Ultra-High-Resolution Electron Microscopy and Related Methods Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic Materials by Ultra-High-Resolution Electron Microscopy and Related Methods 2011 DOE Hydrogen and Fuel Cells Program, and Vehicle Technologies Program Annual Merit Review and Peer

  4. Towards time-resolved serial crystallography in a microfluidic device

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Towards time-resolved serial crystallography in a microfluidic device Citation Details In-Document Search Title: Towards time-resolved serial crystallography in a microfluidic device Authors: Pawate, Ashtamurthy S. ; Srajer, Vukica ; Schieferstein, Jeremy ; Guha, Sudipto ; Henning, Robert ; Kosheleva, Irina ; Schmidt, Marius ; Ren, Zhong ; Kenis, Paul J.A. ; Perry, Sarah L. [1] ; UC) [2] ; Renz) [2] ; UIUC) [2] + Show Author Affiliations (UW) ( Publication

  5. 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.

  6. JBlulce Data Acquisition Software for Macromolecular Crystallography

    Energy Science and Technology Software Center (OSTI)

    2010-06-01

    JBlulce (Java Beam Line Universal Integrated Configuration Environment is a data acquisition software for macromolecular crystallography conforming user interface of the SSRL Blulce that has become a de-factor standard in the field. Besides this interface conformity, JBlulce is a unique system in terms of architecture, speec, capability and osftware implementation. It features only two software layers, the JBlulce clients and the EPICS servers, as compared to three layers present in Blulc and most of similarmore » systems. This layers reduction provides a faster communication with hardware and an easier access to advanced hardware capabilities like on-the-fly scanning. Then JBlulc clients are designed to operate in parallel with the other beamline controls which streamlines the tasks performed by staff such as beamline preparation, maitenance, audting and user assistance. Another distinction is the deployment of multiple plugins that can be written in any programming languag thus involving more staff into the development. further on, JBlulce makes use of unified motion controls allowing for easy scanning and optimizing of any beamline component. Finally, the graphic interface is implemented in Java making full use of rich Java libraries and Jave IDE for debugging. to compare, Blulce user interface is implemented with aging Tcl/tk language providing very restricted capabilities. JBlulce makes full use of the industrial power and wide drivers selection of EPICS in controlling hardware; all hardware commuication is routed via multiple EPICS servers residing on local area network. JBlulce also includes several EPICS State Notation servers aimed at making hardware communication more robust. Besides using EPICS for controlling hardware, JBlulce extensively uses EPICS databases for efficien communications between multiple instances of JBlulce clients and JBlulce pplugins that can run in parallel on different computers. All of the above makes JBlulce one of the biggest and most sophisticated EPICS client projects to date. JBlulce configuraion is stored in my SQL database which provides flexibility in tuning the system. The database is also accessible by the plugins. From the users perspective JBlulce provides all standard features of data acquisition software for macromolecular crystallography plus such unique capabilities as:one click beamline energy change that may involve switching undulator harmonics, mirrors lanes and beam realignment, automated diffraction rtastering for finding small crystals and swwet spots on poorly diffracting crystals with automated scoring of raster cells by the number of reflections; data collection along a vector; automated on-the-fly fluorescent tastering, a faster and lower-irradiation compliment to the diffraction raster; fully automated fluorescence measurements for MAD that include signal optimization, fast on the fly energy scanning and automated adapting of scan range to chemical shifts; fly-scan mimibeam realighment; automated loop and crystal centering, controls for sample automounter, automated screening, data collectin audting, remoate access and a lot more.« less

  7. 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.

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

    Office of Scientific and Technical Information (OSTI)

    structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting...

  9. 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.

  10. 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.

  11. 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.

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

    SciTech Connect (OSTI)

    Tsai, Yingssu; McPhillips, Scott E.; Gonzlez, 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.

  13. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

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

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; Woldeyes, Rahel A.; Hopkins, Jesse B.; Thompson, Michael C.; Brewster, Aaron S.; Van Benschoten, Andrew H.; Baxter, Elizabeth L.; Uervirojnangkoorn, Monarin; et al

    2015-09-30

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences ofmore » these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.« less

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.}

  19. 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/cm~ 1 kW/cm, compared with the efficiency for the perfect anti-reflection treatment to the surface of a conventional solar cell.

  20. 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.

  1. Workshop: New Advances in Crystallography with Synchrotrons and X-FELs |

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

    Stanford Synchrotron Radiation Lightsource New Advances in Crystallography with Synchrotrons and X-FELs Tuesday, October 25, 2011 - 8:00am 2011 SSRL/LCLS Annual Users Conference This workshop, part of the 2011 SSRL/LCLS Annual Users Conference, will describe resources and results from synchrotron-based micro crystallography and X-FEL-based nanocrystallography, and explore the future of these tools in producing important scientific results

  2. Beam collimation with polycapillary x-ray optics for high contrast high resolution monochromatic imaging

    SciTech Connect (OSTI)

    Sugiro, Francisca R.; Li Danhong; MacDonald, C.A.

    2004-12-01

    Monochromatic imaging can provide better contrast and resolution than conventional broadband radiography. In broadband systems, low energy photons do not contribute to the image, but are merely absorbed, while high energy photons produce scattering that degrades the image. By tuning to the optimal energy, one can eliminate undesirable lower and higher energies. Monochromatization is achieved by diffraction from a single crystal. A crystal oriented to diffract at a particular energy, in this case the characteristic line energy, diffracts only those photons within a narrow range of angles. The resultant beam from a divergent source is nearly parallel, but not very intense. To increase the intensity, collimation was performed with polycapillary x-ray optics, which can collect radiation from a divergent source and redirect it into a quasi parallel beam. Contrast and resolution measurements were performed with diffracting crystals with both high and low angular acceptance. Testing was first done at 8 keV with an intense copper rotating anode x-ray source, then 17.5 keV measurements were made with a low power molybdenum source. At 8 keV, subject contrast was a factor of five higher than for the polychromatic case. At 17.5 keV, monochromatic contrast was two times greater than the conventional polychromatic contrast. The subject contrasts measured at both energies were in good agreement with theory. An additional factor of two increase in contrast, for a total gain of four, is expected at 17.5 keV from the removal of scatter. Scatter might be simply removed using an air gap, which does not degrade resolution with a parallel beam.

  3. 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, 240ns) [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.

  4. 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.

  5. 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

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

    SciTech Connect (OSTI)

    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 the 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.

  7. 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 student, Patricia Langan, changes the properties of a green fluorescent protein in order to create new fluorescent protein variants. Overview of Research and Highlights Scientists at Los Alamos apply a unique collection of tools and expertise to gain a comprehensive understanding of the structure and function of proteins

  8. 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.

  9. Structural analysis of flexible proteins in solution by SmallAngle...

    Office of Scientific and Technical Information (OSTI)

    Title: Structural analysis of flexible proteins in solution by SmallAngle X-ray Scattering combined with crystallography In the last few years, SAXS of biological materials has ...

  10. 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.

  11. 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 multitude of possibilities, such as enhancing cellulose degradation for biofuels or creating new therapeutics. Contact Us Tom Terwilliger Laboratory Fellow Email Andrew Bradbury Bioscience Group Leader Email Rebecca McDonald Bioscience Communications Email Los Alamos scientists are developing mosaic proteins that may one day

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

    SciTech Connect (OSTI)

    Schrder, 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 . Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  13. 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.

  14. The Application of Monochromatic Energies to Investigate Multiphase Porous Media Systems using Synchrotron X-ray Tomography

    SciTech Connect (OSTI)

    Ham, Kyungmin; Willson, Clinton S.

    2006-01-31

    X-ray computed tomography (CT) is becoming a useful tool for nondestructive imaging of many geoenvironmental and geotechnical systems. Conventional X-ray CT systems typically utilize a polychromatic X-ray beam. While providing a high throughput of photons, the use of polychromatic energy can make quantifying material concentrations, densities or composition very difficult or impossible without appropriate standards. Synchrotron X-rays have an extremely small angular divergence, thus permitting spatial resolution that is only limited by the optical components of the system. In addition, the ability to tune to a monochromatic X-ray energy allows better phase contrast by reducing beam hardening and allowing for elemental discrimination. In this work we will show how monochromatic energy can be used to provide high-quality images allowing for phase separation several different porous media systems thus improving our ability to quantify a range of processes and phenomena.

  15. Serial time-resolved crystallography of photosystem II using a femtosecond

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

    X-ray laser Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser Authors: Kupitz, Christopher; Basu, Shibom; Grotjohann, Ingo; Fromme, Raimund; Zatsepin, Nadia A.; Rendek, Kimberly N.; Hunter, Mark; Shoeman, Robert L.; White, Thomas A.; Wang, Dingjie; James, Daniel; Yang, Jay-How; Cobb, Danielle E.; Brenda, Reeder; Raymond, G. Sierra; Liu, Haiguang; Barty, Anton; Aquila, Andrew L.; Deponte, Daniel; Kirian, Richard A.; Bari, Sadia; Bergkamp, Jesse J.;

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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

    SciTech Connect (OSTI)

    Cohen, Aina E.; Soltis, S. Michael; Gonzlez, 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- 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.

  1. 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 β2-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

  2. 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

  3. Advanced Protein Characterization Facility | Argonne National Laboratory

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

    APCF Argonne's one-stop resource for genomic research, macromolecular crystallography, and synthetic biology More

  4. 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.

  5. 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 F.; Yegian, Derek T.; Earnest, Thomas N.; Jaklevich, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    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.

  6. 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.

  7. 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.

  8. 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.

  9. 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 μm 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

  10. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

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

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; Shehu, Amarda

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechainmore » conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.« less

  11. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    SciTech Connect (OSTI)

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; Shehu, Amarda

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  12. 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 strtlingite 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 strtlingite 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 strtlingite 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.

  13. 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.

  14. Macromolecular Crystallography - Beamline facilities

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

    the .forward file and save it. If you have more than one e-mail address or you want other people in your group to receive the notification, add one address per line. Use the...

  15. Monochromatic radio frequency accelerating cavity

    DOE Patents [OSTI]

    Giordano, Salvatore (Port Jefferson, NY)

    1985-01-01

    A radio frequency resonant cavity having a fundamental resonant frequency and characterized by being free of spurious modes. A plurality of spaced electrically conductive bars are arranged in a generally cylindrical array within the cavity to define a chamber between the bars and an outer solid cylindrically shaped wall of the cavity. A first and second plurality of mode perturbing rods are mounted in two groups at determined random locations to extend radially and axially into the cavity thereby to perturb spurious modes and cause their fields to extend through passageways between the bars and into the chamber. At least one body of lossy material is disposed within the chamber to damp all spurious modes that do extend into the chamber thereby enabling the cavity to operate free of undesired spurious modes.

  16. 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.

  17. 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 profilinactin 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 profilinactin 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. Robust, High-Throughput Analysis of Protein Structures

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

    three-dimensional shape. Although x-ray crystallography yields higher-resolution images, SAXS makes up for what it lacks in precision by providing fast, accurate...

  3. Beamline 5.0.1

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

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v)

  4. Beamline 5.0.1

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

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v)

  5. Beamline 5.0.1

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

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v)

  6. Beamline 5.0.1

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

    Beamline 5.0.1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0

  7. Beamline 5.0.1

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

    Beamline 5.0.1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0

  8. Beamline 5.0.1

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

    Beamline 5.0.1 Beamline 5.0.1 Print Tuesday, 20 October 2009 08:32 Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving

  9. Beamline 5.0.1

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

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v)

  10. Beamline 5.0.1

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

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v)

  11. Beamline 5.0.2

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

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  12. Beamline 5.0.2

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

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  13. Beamline 5.0.2

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

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  14. Beamline 5.0.2

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

    0.2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  15. Beamline 5.0.2

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

    Beamline 5.0.2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator

  16. Beamline 5.0.2

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

    Beamline 5.0.2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator

  17. Beamline 5.0.2

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

    0.2 Beamline 5.0.2 Print Tuesday, 20 October 2009 08:35 Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad

  18. Beamline 5.0.2

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

    Beamline 5.0.2 Beamline 5.0.2 Print Tuesday, 20 October 2009 08:35 Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with

  19. Beamline 5.0.2

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

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  20. Beamline 5.0.2

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

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  1. Beamline 5.0.3

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

    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole

  2. Beamline 5.0.3

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

    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole

  3. Beamline 5.0.3

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

    Beamline 5.0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm

  4. Beamline 5.0.3

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

    Beamline 5.0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm

  5. Beamline 5.0.3

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

    Beamline 5.0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm

  6. Beamline 5.0.3

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

    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole

  7. Beamline 5.0.3

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

    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole

  8. Beamline 5.0.1

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

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v)

  9. Beamline 5.0.1

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

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v)

  10. Beamline 5.0.2

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

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  11. Beamline 5.0.2

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

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving

  12. Beamline 5.0.3

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

    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole

  13. Beamline 5.0.3

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

    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole

  14. Proteinligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI)

    SciTech Connect (OSTI)

    Grftehauge, Morten K. Hajizadeh, Nelly R.; Swann, Marcus J.; Pohl, Ehmke

    2015-01-01

    The biophysical characterization of proteinligand 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 proteinligand 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.

  15. Neutron crystallography aids drug design

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

    Los Alamos and currently at Oak Ridge National Laboratory, and Robert McKenna, David Silverman and Mayank Aggarwal of the University of Florida. The U.S. Department of Energy...

  16. Powder Diffraction Crystallography Instructional Materials

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

    to Least-squares Fitting: A mostly descriptive approach A non-rigorous introduction to linear algebra, linear and non-linear least squares and related concepts. Software...

  17. Diamondoid Monolayers as Monochromatic Electron Source

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

    atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have been made to synthesize the larger diamondoid molecules,...

  18. Diamondoid Monolayers as Monochromatic Electron Source

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

    Willey, J.R.I. Lee, and T. van Buuren (Lawrence Livermore National Laboratory); J.E. Dahl and R.M.K. Carlson (MolecularDiamond Technologies, Chevron Technology Ventures); P.R....

  19. Diamondoid Monolayers as Monochromatic Electron Source

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

    cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of...

  20. Diamondoid Monolayers as Monochromatic Electron Source

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

    nanotubes will serve as the electron emitters for FED technology, but there's a new kid on the block-diamondoids In this study, Yang et al. have provided the first...

  1. Diamondoid Monolayers as Monochromatic Electron Source

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

    beyond flat-panel displays, for example in the microwave telecommunications and microelectronics industries. Scientific applications also stand to benefit greatly, such as...

  2. Diamondoid Monolayers as Monochromatic Electron Source

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

    BES. Publication about this research: W.L. Yang, J.D. Fabbri, T.M. Willey, J.R.I. Lee, J.E. Dahl, R.M.K. Carlson, P.R. Schreiner, A.A. Fokin, B.A. Tkachenko, N.A. Fokina, W....

  3. 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.

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

    SciTech Connect (OSTI)

    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; 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 Frster 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

  5. 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

  6. Structure and proteinprotein 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 ~450560 kDa forms at higher protein concentrations. The 2.57 resolution crystal structure reveals an overall fold and ???? dimeric architecture similar to those of other MDH structures. In addition, biolayer interferometry studies demonstrate specific proteinprotein 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.

  7. 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

  8. Shotgun protein sequencing.

    SciTech Connect (OSTI)

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

    2009-06-01

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

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

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

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

  10. 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.

  11. Destabilized bioluminescent proteins

    DOE Patents [OSTI]

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

    2007-07-31

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

  12. Resources for Macromolecular Crystallography | Advanced Photon...

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

    Time GUP Login Proposal Calendar Publications Database CAT Websites: BioCARS GMCA-CAT IMCA-CAT LRL-CAT LS-CAT NE-CAT SBC-CAT SER-CAT Reports and Presentations: Stuctural Bio...

  13. Goniometer-based Femtosecond Macromolecular Crystallography ...

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

    E. G. Kovaleva, A. C. Kruse, H. T. Lemke, G. Lin, A. Y. Lyubimov, A. Manglik, I. I. Mathews, S. E. McPhillips, S. Nelson, J. W. Peters, N. K. Sauter, C. A. Smith, J. Song, H. P....

  14. Microcrystallization techniques for serial femtosecond crystallography...

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

    X-ray diffraction data are collected from a fully hydrated stream of nano- or microcrystals of biomolecules in their mother liquor using high-energy, X-ray free-electron lasers. ...

  15. Introduction to Bayesian methods in macromolecular crystallography...

    Office of Scientific and Technical Information (OSTI)

    Research Org: Los Alamos National Laboratory (LANL) Sponsoring Org: DOE Country of Publication: United States Language: English Subject: 97 Word Cloud More Like This Full Text File ...

  16. Instrumentation upgrades for the Macromolecular Crystallography...

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

    Robotics Inspired Goniometer). On-axis micro-spectrophotometer MS3 for microscopic sample imaging with one micron image resolution. The multi-mode optical spectroscopy module is...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

    SciTech Connect (OSTI)

    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 redox 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.

  3. 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.

  4. Experimental Station 7-1 | Stanford Synchrotron Radiation Lightsource

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

    1 Beamline 7-1 is a wiggler side-station beamline dedicated for monochromatic, high-throughput, high-resolution macromolecular crystallography. It is SAD and MAD capable and can be run in a full remote access mode. It is equipped with an ADSC Q315R CCD detector. For aditional information about the experimental capabilities, see http://smb.slac.stanford.edu/index.shtml. Status Open Supported Techniques Macromolecular Crystallography Multi wavelength anomalous diffraction (MAD) Single wavelength

  5. Pressure cryocooling protein crystals

    DOE Patents [OSTI]

    Kim, Chae Un; Gruner, Sol M.

    2011-10-04

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

  6. 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.

  7. 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 natures most valued proteinaceous robots.

  8. 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

  9. What Triggers Asthma - Newcomer

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

    PROTEIN CRYSTALLOGRAPHY (PX): determine molecular structures with x-ray diffraction a protein crystal is a uniform array of individual proteins Prepare crystals of the...

  10. LANSCE | Lujan Center | Instruments | PCS

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

    Protein Crystallography Station | PCS Structural Enzymology The Protein Crystallography Station (PCS) at LANSCE is a high performance beam line that is funded by DOE-OBER. It forms the core of a capability for joint neutron and X-ray macromolecular structure and function determination. The PCS is the first protein crystallography beam line to be built at a spallation neutron source in North America and is one of the world's premier neutron crystallography instruments. The beam-line exploits the

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

    Office of Scientific and Technical Information (OSTI)

    Targeting diverse protein-protein interaction interfaces with -peptides derived from the Z-domain scaffold Citation Details In-Document Search Title: Targeting diverse ...

  12. ProteinShop: A Tool for Interactive Protein

    Office of Scientific and Technical Information (OSTI)

    ... and discuss future research. 2. Methodology ProteinShop can be used in two phases of the prediction process: the protein structure creation phase and the optimization phase. ...

  13. Protein Dynamics and Biocatalysis

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

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

  14. Algae Protein Fermentation

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

    Protein Fermentation March 24, 2015 Ryan W Davis, PhD Sandia National Laboratory This presentation does not contain any proprietary, confidential, or otherwise restricted information Algal Feedstocks DOE Bioenergy Technologies Office (BETO) 2015 Project Peer Review Goal Statement * Optimize bioconversion 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 pools to achieve BETO's

  15. 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...

  16. 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

  17. 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.

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

    DOE Patents [OSTI]

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

    2001-07-03

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

  19. 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.

  20. 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.

  1. 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.

  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. Bayesian Estimator of Protein-Protein Association Probabilities

    Energy Science and Technology Software Center (OSTI)

    2008-05-28

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

  4. 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.

  5. 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.

  6. Stabilized polyacrylic saccharide protein conjugates

    DOE Patents [OSTI]

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

    1996-01-01

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

  7. 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.

  8. Protein Flips Lipids Across Membranes

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

    Protein Flips Lipids Across Membranes Protein Flips Lipids 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 (ABC) transporter family have been implicated in both antibiotic and cancer-drug resistance. The mechanisms used by these proteins to expel toxins from cells therefore represent key targets for the development of drugs designed to combat the growing problem of

  9. Protein subcellular localization assays using split fluorescent proteins

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2009-09-08

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

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

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

    Translocator Protein Structure and Function Monday, November 30, 2015 Translocator protein (TSPO) is an ancient conserved protein whose functions in bacteria and higher eukaryotes...

  11. Microsoft Word - Translocator_protein bh

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

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

  12. Signature Product Code for Predicting Protein-Protein Interactions

    Energy Science and Technology Software Center (OSTI)

    2004-09-25

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

  13. Targeting diverse protein-protein interaction interfaces with

    Office of Scientific and Technical Information (OSTI)

    α/β-peptides derived from the Z-domain scaffold (Journal Article) | SciTech Connect Targeting diverse protein-protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold Citation Details In-Document Search Title: Targeting diverse protein-protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of

  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. 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 family have been implicated in both antibiotic and cancer-drug resistance. The mechanisms used by these proteins to expel toxins from cells therefore represent key targets for the development of drugs designed to combat the growing problem of multidrug resistance. Toward this end, researchers from The Scripps Research

  16. 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.

  17. High throughput protein production screening

    DOE Patents [OSTI]

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

    2009-09-08

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

  18. Structural Genomics of Protein Phosphatases

    SciTech Connect (OSTI)

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

    2007-01-01

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  2. Expression of multiple proteins in transgenic plants

    DOE Patents [OSTI]

    Vierstra, Richard D.; Walker, Joseph M.

    2002-01-01

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

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

    DOE Patents [OSTI]

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

    2003-05-13

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

  4. Adhesives from modified soy protein

    DOE Patents [OSTI]

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

    2008-08-26

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

  5. Structural studies of conformational changes of proteins upon phosphorylation: Structures of activated CheY, CheY-N16-FliM complex, and AAA {sup +} ATPase domain of NtrC1 in both inactive and active states

    SciTech Connect (OSTI)

    Lee, Seok-Yong

    2003-04-10

    Protein phosphorylation is a general mechanism for signal transduction as well as regulation of cellular function. Unlike phosphorylation in eukaryotic systems that uses Ser/Thr for the sites of modification, two-component signal transduction systems, which are prevalent in bacteria, archea, and lower eukaryotes, use an aspartate as the site of phosphorylation. Two-component systems comprise a histidine kinase and a receiver domain. The conformational change of the receiver domain upon phosphorylation leads to signal transfer to the downstream target, a process that had not been understood well at the molecular level. The transient nature of the phospho-Asp bond had made structural studies difficult. The discovery of an excellent analogue for acylphosphate, BeF{sub 3}{sup -}, enabled structural study of activated receiver domains. The structure of activated Chemotaxis protein Y (CheY) was determined both by NMR spectroscopy and X-ray crystallography. These structures revealed the molecular basis of the conformational change that is coupled to phosphorylation. Phosphorylation of the conserved Asp residue in the active site allows hydrogen bonding of the T87 O{gamma} to phospho-aspartate, which in turn leads to the rotation of Y106 into the ''in'' position (termed Y-T coupling). The structure of activated CheY complexed with the 16 N-terminal residues of FliM (N16-FliM), its target, was also determined by X-ray crystallography and confirmed the proposed mechanism of activation (Y-T coupling). First, N16-FliM binds to the region on CheY that undergoes a significant conformational change. Second, the ''in'' position of Y106 presents a better binding surface for FliM because the sidechain of Y106 in the inactive form of CheY (''out'' position) sterically interferes with binding of N16-FliM. In addition to confirmation of Y-T coupling, the structure of the activated CheY-N16-FliM complex suggested that the N16-FliM might be sandwiched between CheY and the remainder of FliM to change the direction of flagellar rotation.

  6. 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 ...

  7. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    biological sciences (4) crystallography (4) crystals (4) proteins (3) atoms (2) biophysics (2) crystal structure (2) escherichia coli (2) lipids (2) liquid crystals (2) ...

  8. 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...

  9. 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...

  10. Intriguing DNA Editor Has a Structural Trigger

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

    representing large and small versions, from Streptococcus pyogenes (SpyCas) and Actinomyces naeslundii (AnaCas9) respectively. Using protein crystallography Beamlines 8.2.2...

  11. 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.

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

    Membrane Protein Crystallization in Lipidic Mesophases. Hosting Lipid Effects on the ... Citation Details In-Document Search Title: Membrane Protein Crystallization in Lipidic ...

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

    Office of Scientific and Technical Information (OSTI)

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

  15. Protein Instability and Lou Gehrig's Disease

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

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

  16. 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:...

  17. 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...

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

    DOE Patents [OSTI]

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

    2002-10-15

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

  19. 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,...

  20. Genentech Uses ALS Crystallography for Therapeutic Antibody Research

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

    antibody bivalency can limit their utility against some targets due to receptor crosslinking and activation. Genentech has developed a unique one-armed antibody, onartuzumab,...

  1. 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

  2. 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...

  3. 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.

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

    Office of Scientific and Technical Information (OSTI)

    ; Nelson, Silke ; Peters, John W. ; Sauter, Nicholas K. ; Smith, Clyde A. ; Song, Jinhu ; Stevenson, Hilary P. ; Tsai, Yingssu ; Uervirojnangkoorn, Monarin ; Vinetsky, Vladimir ;...

  5. Time-resolved serial crystallography captures high-resolution...

    Office of Scientific and Technical Information (OSTI)

    ; Srajer, Vukica ; Henning, Robert ; Schwander, Peter ; Fromme, Raimund ; Ourmazd, Abbas ; Moffat, Keith ; Van Thor, Jasper J. ; Spence, John C.H. ; Fromme, Petra ; Chapman,...

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

    Office of Scientific and Technical Information (OSTI)

    L. ; Brehmer, Winnie ; Brewster, Aaron S. ; Brunger, Axel T. ; Calero, Guillermo ; Chang, Joseph F. ; Chollet, Matthieu ; Ehrensberger, Paul ; Eriksson, Thomas L. ; Feng,...

  7. Towards time-resolved serial crystallography in a microfluidic...

    Office of Scientific and Technical Information (OSTI)

    Henning, Robert ; Kosheleva, Irina ; Schmidt, Marius ; Ren, Zhong ; Kenis, Paul J.A. ; Perry, Sarah L. 1 ; UC) 2 ; Renz) 2 ; UIUC) 2 + Show Author Affiliations (UW) ( ...

  8. 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.

  9. 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.

  10. 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.

  11. Recombinant fluorescent protein microsphere calibration standard

    DOE Patents [OSTI]

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

    2001-01-01

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

  12. 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.

  13. Links

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

    Useful Links BIOSYNC: Structural Biology Synchrotron Users Organization X-ray Anomalous Scattering Going MAD at CHESS Protein Data Bank Protein Data Bank Search International Union of Crystallography American Crystallographic Association Crystallography 101 Teaching Crystallography Periodic Table Periodic Table and X-ray Properties X-ray data booklet Merohedral crystal twinning server Software Links CCP4 MOSFLM HKL Research, Inc. homepage Solve/Resolve The O-files - Useful reference to the O

  14. Protein Dynamics Hit the Big Screen

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

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

  15. Protein Structure Suggests Role as Molecular Adapter

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

    Protein Structure Suggests Role as Molecular Adapter Protein Structure Suggests Role as Molecular Adapter Print Wednesday, 24 June 2009 00:00 To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the replisome. An essential step in replisome assembly is the loading of ring-shaped helicases (motor proteins) onto the separated strands of DNA. Dedicated ATP-fueled proteins regulate the loading; however, the mechanism by which these proteins

  16. 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.

  17. 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.

  18. 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.

  19. Method for voltage-gated protein fractionation

    DOE Patents [OSTI]

    Hatch, Anson; Singh, Anup K.

    2012-04-24

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

  20. Proteins

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

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

  1. Proteins

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

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

  2. 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.

  3. A Designed Protein Maps Brain Activity

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

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

  4. A Designed Protein Maps Brain Activity

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

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

  5. Translocator Protein Structure and Function | Stanford Synchrotron

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

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

  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 a powerful ally: computers. Researchers have now figured out a way to use computational protein design to generate small, stable proteins that accurately mimic key viral structures; these can then be used in vaccines to induce potent neutralizing antibodies. The results were validated in part using protein structures

  7. Protein Instability and Lou Gehrig's Disease

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

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  8. Protein Instability and Lou Gehrig's Disease

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

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  9. Protein Instability and Lou Gehrig's Disease

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

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  10. Protein Instability and Lou Gehrig's Disease

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

    Protein Instability and Lou Gehrig's Disease Protein Instability and Lou Gehrig's Disease Print Wednesday, 25 March 2015 00:00 A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called

  11. Protein Structure Suggests Role as Molecular Adapter

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

    Protein Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the replisome. An essential step in replisome assembly is the loading of ring-shaped helicases (motor proteins) onto the separated strands of DNA. Dedicated ATP-fueled proteins regulate the loading; however, the mechanism by which these proteins recruit and deposit helicases has remained unclear. To better understand this

  12. Protein Structure Suggests Role as Molecular Adapter

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

    Protein Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the replisome. An essential step in replisome assembly is the loading of ring-shaped helicases (motor proteins) onto the separated strands of DNA. Dedicated ATP-fueled proteins regulate the loading; however, the mechanism by which these proteins recruit and deposit helicases has remained unclear. To better understand this

  13. Protein Structure Suggests Role as Molecular Adapter

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

    Protein Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the replisome. An essential step in replisome assembly is the loading of ring-shaped helicases (motor proteins) onto the separated strands of DNA. Dedicated ATP-fueled proteins regulate the loading; however, the mechanism by which these proteins recruit and deposit helicases has remained unclear. To better understand this

  14. Microsoft Word - Translocator_protein bh

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

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

  15. 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 a powerful ally: computers. Researchers have now figured out a way to use computational protein design to generate small, stable proteins that accurately mimic key viral structures; these can then be used in vaccines to induce potent neutralizing antibodies. The results were validated in part using protein structures

  16. 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 a powerful ally: computers. Researchers have now figured out a way to use computational protein design to generate small, stable proteins that accurately mimic key viral structures; these can then be used in vaccines to induce potent neutralizing antibodies. The results were validated in part using protein structures

  17. 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 a powerful ally: computers. Researchers have now figured out a way to use computational protein design to generate small, stable proteins that accurately mimic key viral structures; these can then be used in vaccines to induce potent neutralizing antibodies. The results were validated in part using protein structures

  18. 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 Validating Computer-Designed Proteins for Vaccines Print Thursday, 21 August 2014 12:05 In the struggle to keep up with microbes whose rapid mutations outpace our ability to produce vaccines, the human race has a powerful ally: computers. Researchers have now figured out a way to use computational protein design to generate small, stable proteins that accurately mimic key viral structures; these can then be used in vaccines to induce potent

  19. Protein Instability and Lou Gehrig's Disease

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

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  20. Protein Structure Suggests Role as Molecular Adapter

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

    Protein Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the replisome. An essential step in replisome assembly is the loading of ring-shaped helicases (motor proteins) onto the separated strands of DNA. Dedicated ATP-fueled proteins regulate the loading; however, the mechanism by which these proteins recruit and deposit helicases has remained unclear. To better understand this

  1. A Designed Protein Maps Brain Activity

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

    A Designed Protein Maps Brain Activity A Designed Protein Maps Brain Activity Print Wednesday, 28 October 2015 00:00 A team of scientists from the Howard Hughes Medical Institute's Janelia Research Campus designed and validated via x-ray crystallographic studies a fluorescent protein (CaMPARI) that allows the permanent marking of active brain cells. The protein was then used to study live changes via fluorescence in the active nerve cells in brains of fruit flies, zebrafish, and mice. The Neural

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

    Office of Scientific and Technical Information (OSTI)

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

  3. 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.

  4. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K.

    1997-01-01

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

  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. Radioactive Lysine in Protein Metabolism Studies

    DOE R&D Accomplishments [OSTI]

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

    1950-01-09

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

  7. 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.

  8. 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.

  9. Manipulating and Visualizing Proteins (Technical Report) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    origami, is what determines how the protein functions and translates genetic information. ... PROTEIN STRUCTURE PREDICTION PROTEIN MANIPULATION Word Cloud More Like This Full Text ...

  10. Activity-Based Protein Profiling of Microbes

    SciTech Connect (OSTI)

    Sadler, Natalie C.; Wright, Aaron T.

    2015-02-01

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

  11. 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.

  12. A Designed Protein Maps Brain Activity

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

    A Designed Protein Maps Brain Activity Print A team of scientists from the Howard Hughes Medical Institute's Janelia Research Campus designed and validated via x-ray crystallographic studies a fluorescent protein (CaMPARI) that allows the permanent marking of active brain cells. The protein was then used to study live changes via fluorescence in the active nerve cells in brains of fruit flies, zebrafish, and mice. The Neural Basis of Behavior Signals in our brains are propagated with voltage and

  13. A Designed Protein Maps Brain Activity

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

    A Designed Protein Maps Brain Activity Print A team of scientists from the Howard Hughes Medical Institute's Janelia Research Campus designed and validated via x-ray crystallographic studies a fluorescent protein (CaMPARI) that allows the permanent marking of active brain cells. The protein was then used to study live changes via fluorescence in the active nerve cells in brains of fruit flies, zebrafish, and mice. The Neural Basis of Behavior Signals in our brains are propagated with voltage and

  14. A Designed Protein Maps Brain Activity

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

    A Designed Protein Maps Brain Activity Print A team of scientists from the Howard Hughes Medical Institute's Janelia Research Campus designed and validated via x-ray crystallographic studies a fluorescent protein (CaMPARI) that allows the permanent marking of active brain cells. The protein was then used to study live changes via fluorescence in the active nerve cells in brains of fruit flies, zebrafish, and mice. The Neural Basis of Behavior Signals in our brains are propagated with voltage and

  15. Protein Instability and Lou Gehrig's Disease

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

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

  16. A Designed Protein Maps Brain Activity

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

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

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

    Office of Scientific and Technical Information (OSTI)

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

  18. 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.

  19. Protein Structure Suggests Role as Molecular Adapter

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

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

  20. Antimicrobial protein protects grapevines from pathogen

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

    produce a hybrid antimicrobial protein to block infection Your evening glass of wine will still be available-despite the potential attack of a bacterium that causes...

  1. Protein Instability and Lou Gehrig's Disease

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

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

  2. 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)

  3. Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor

    Office of Scientific and Technical Information (OSTI)

    Crystallogenesis (Journal Article) | SciTech Connect Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor Crystallogenesis Citation Details In-Document Search Title: Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor Crystallogenesis Authors: Thorsen, Thor Seneca ; Matt, Rachel ; Weis, William I. ; Kobilka, Brian K. [1] + Show Author Affiliations (Stanford-MED) Publication Date: 2014-11-01 OSTI Identifier: 1182298 Resource Type: Journal Article

  4. 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.

  5. 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.

  6. 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.

  7. Monochromatic x-ray imaging experiments on the Sandia National Laboratories Z facility (invited)

    SciTech Connect (OSTI)

    Sinars, D.B.; Bennett, G.R.; Wenger, D.F.; Cuneo, M.E.; Hanson, D.L.; Porter, J.L.; Adams, R.G.; Rambo, P.K.; Rovang, D.C.; Smith, I.C.

    2004-10-01

    The Z facility is a 20 MA, 100 ns rise time, pulsed power driver for z-pinch plasma radiation sources. The Z facility can make >200 TW, 1-2 MJ, near-blackbody radiation sources through the compression of cylindrical wire arrays. These sources are being used as drivers to study inertial-confinement fusion capsule implosions, complex radiation-hydrodynamic jet experiments, and wire-array z-pinch physics tests. To backlight plasmas in this environment we have built diagnostics based on spherically bent crystals that provide high spatial resolution (9-10 {mu}m), a narrow spectral bandpass (<0.5 eV), and a large field of view (4 mmx20 mm). These diagnostics use the 2 TW, multi-kJ Z-Beamlet laser to produce x-ray emission sources at 1.865 or 6.151 keV for backlighting.

  8. 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.

  9. Protein Scaffolding for Small Molecule Catalysts

    SciTech Connect (OSTI)

    Baker, David

    2014-09-14

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

  10. Biomimetic materials for protein storage and transport

    DOE Patents [OSTI]

    Firestone, Millicent A.; Laible, Philip D.

    2012-05-01

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

  11. 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.

  12. A Designed Protein Maps Brain Activity

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

    are connected and how the engineered mutations in each allow the combined proteins to function together as one unit. Crystal structure of calcium-free CaMPARI. Three orthogonal...

  13. 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...

  14. Femtosecond X-ray protein nanocrystallography

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

    Femtosecond X-ray protein nanocrystallography Authors: Chapman, H.N., Fromme, P., Barty, A., White, T.A., Kirian, R.A., Aquila, A., Hunter, M.S., Schulz, J., DePonte, D.P.,...

  15. 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...

  16. Crystal Structure of a Protein Kinase A Complex

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

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

  17. Exo-endo cellulase fusion protein

    DOE Patents [OSTI]

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

    2012-01-17

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

  18. Positive modulator of bone morphogenic protein-2

    DOE Patents [OSTI]

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

    2009-01-27

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

  19. Collaboration drives achievement in protein structure research

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

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

  20. 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, Berkeley Lab's National Center for Electron Microscopy (NCEM), and Lawrence Livermore National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material

  1. Collaboration drives achievement in protein structure research

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

    Protein structure research Collaboration drives achievement in protein structure research By tracking down how bacterial defense systems work, the scientists can potentially fight infectious diseases and genetic disorders. September 15, 2014 Thomas Terwilliger Thomas Terwilliger Contact Nancy Ambrosiano Communications Office (505) 667-0471 Email "It is tremendously exciting working with researchers around the world, helping them apply the software and algorithms that we have developed to

  2. A Tool for Interactive Protein Manipulation

    Energy Science and Technology Software Center (OSTI)

    2005-03-28

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

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

    Office of Scientific and Technical Information (OSTI)

    Patent: Artificial oxygen transport protein Citation Details In-Document Search Title: Artificial oxygen transport protein You are accessing a document from the Department of...

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

    Office of Scientific and Technical Information (OSTI)

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

  5. Rhodobacter System for the Expression of Membrane Proteins |...

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

    Rhodobacter System for the Expression of Membrane Proteins Technology available for licensing: A unique system for membrane protein expression makes it possible to obtain...

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

    Office of Scientific and Technical Information (OSTI)

    Studies of Protein Folding KineticsFinal Report Cover Page Citation Details In-Document Search Title: Development of a Fast Microfluidic Mixer for Studies of Protein Folding ...

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

    Office of Scientific and Technical Information (OSTI)

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

  8. Integrated Analysis of Protein Complexes and Regulatory Networks...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Integrated Analysis of Protein Complexes and Regulatory Networks ... Citation Details In-Document Search Title: Integrated Analysis of Protein Complexes and ...

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

    ThesisDissertation: Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method Citation Details In-Document Search Title: Protein Structure ...

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  14. Pharmacologic Profile of the Adnectin BMS-962476, a Small Protein...

    Office of Scientific and Technical Information (OSTI)

    Pharmacologic Profile of the Adnectin BMS-962476, a Small Protein Biologic Alternative to ... Title: Pharmacologic Profile of the Adnectin BMS-962476, a Small Protein Biologic ...

  15. Photoswitchable Red Fluorescent Protein with a Large Stokes Shift...

    Office of Scientific and Technical Information (OSTI)

    Photoswitchable Red Fluorescent Protein with a Large Stokes Shift Citation Details In-Document Search Title: Photoswitchable Red Fluorescent Protein with a Large Stokes Shift ...

  16. Structural bases of dimerization of yeast telomere protein Cdc13...

    Office of Scientific and Technical Information (OSTI)

    Search Results Journal Article: Structural bases of dimerization of yeast telomere protein ... Title: Structural bases of dimerization of yeast telomere protein Cdc13 and its ...

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

    Office of Scientific and Technical Information (OSTI)

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

  18. A challenging interpretation of a hexagonally layered protein...

    Office of Scientific and Technical Information (OSTI)

    A challenging interpretation of a hexagonally layered protein structure Citation Details In-Document Search Title: A challenging interpretation of a hexagonally layered protein ...

  19. Structure of a designed tetrahedral protein assembly variant...

    Office of Scientific and Technical Information (OSTI)

    protein assembly variant engineered to have improved soluble expression Citation Details In-Document Search Title: Structure of a designed tetrahedral protein assembly ...

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

    Open Energy Info (EERE)

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

  1. 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 ...

  2. 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...

  3. 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...

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

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

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

  5. 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...

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

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

    Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting homologous protein...

  7. 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...

  8. 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...

  9. 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 ...

  10. Robust, High-Throughput Analysis of Protein Structures

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

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

  11. Synthesizing Membrane Proteins Using In Vitro Methodology | Argonne...

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

    Proteins Using In Vitro Methodology Technology available for licensing: in vitro, cell-free expression system that caters to the production of protein types that are challenging...

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect 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 Complexes Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of

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

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01

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

  15. Amber Plug-In for Protein Shop

    Energy Science and Technology Software Center (OSTI)

    2004-05-10

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

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

    DOE 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

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

    DOE Patents [OSTI]

    Mayfield, Stephen P

    2015-01-13

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

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

    DOE Patents [OSTI]

    Mayfield, Stephen P.

    2010-03-16

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

  19. Some thermodynamical aspects of protein hydration water

    SciTech Connect (OSTI)

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

    2015-06-07

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

  20. Compositions and methods for improved protein production

    DOE Patents [OSTI]

    Bodie, Elizabeth A.; Kim, Steve

    2012-07-10

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

  1. 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.

  2. 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.

  3. Structural determination of intact proteins using mass spectrometry

    DOE Patents [OSTI]

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

    2008-05-06

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

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

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting 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 regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

  5. 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 kinase Blc-Abl, while not targeting 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 regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

  6. 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 kinase Blc-Abl, while not targeting 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 regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

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

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Applications of molecular replacement to G protein-coupled receptors Citation Details In-Document Search Title: Applications of molecular replacement 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 in detail. G protein-coupled receptors (GPCRs) are a large class of integral membrane proteins involved in regulating virtually every

  8. 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 kinase Blc-Abl, while not targeting 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 regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

  9. 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 Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print Tuesday, 23 June 2015 13:00 The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting 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 regulating cell

  10. 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.

  11. Transcriptional enhancer from milk protein genes

    DOE Patents [OSTI]

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

    1999-01-01

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

  12. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11

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

  13. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15

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

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

    SciTech Connect (OSTI)

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

    2007-01-01

    Zinc finger transcription factors represent the largest single class of metalloproteins in the human genome. Binding of Zn(II) to their canonical Cys4, Cys3His1, or Cys2His2 sites results in metal-induced protein folding events required to achieve their proper structure for biological activity. The thermodynamic contribution of Zn(II) in each of these coordination spheres toward protein folding is poorly understood because of the coupled nature of the metal-ligand and protein-protein interactions. Using an unstructured peptide scaffold, GGG, we have employed fluorimetry, potentiometry, and calorimetry to determine the thermodynamics of Zn(II) binding to the Cys4, Cys3His1, and Cys2His2 ligand sets with minimal interference from protein folding effects. The data show that Zn(II) complexation is entropy driven and modulated by proton release. The formation constants for Zn(II)-GGG with a Cys4, Cys3His1, or Cys2His2 site are 5.6 x 1016, 1.5 x 1015, or 2.5 x 1013 M-1, respectively. Thus, the Zn(II)-Cys4, Zn(II)-Cys3His1, and Zn(II)-Cys2His2 interactions can provide up to 22.8, 20.7, and 18.3 kcal/mol, respectively, in driving force for protein stabilization, folding, and/or assembly at pH values above the ligand pKa values. While the contributions from the three coordination motifs differ by 4.5 kcal/mol in Zn(II) affinity at pH 9.0, they are equivalent at physiological pH, ?G = -16.8 kcal/mol or a Ka = 2.0 x 1012 M-1. Calorimetric data show that this is due to proton-based enthalpy-entropy compensation between the favorable entropic term from proton release and the unfavorable enthalpic term due to thiol deprotonation. Since protein folding effects have been minimized in the GGG scaffold, these peptides possess nearly the tightest Zn(II) affinities possible for their coordination motifs. The Zn(II) affinities in each coordination motif are compared between the GGG scaffold and natural zinc finger proteins to determine the free energy required to fold the latter. Several proteins have identical Zn(II) affinities to GGG. That is, little, if any, of their Zn(II) binding energy is required to fold the protein, whereas some have affinities weakened by up to 5.7 kcal/mol; i.e., the Zn(II) binding energy is being used to fold the protein.

  16. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    SciTech Connect (OSTI)

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

    2014-03-15

    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.

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

    SciTech Connect (OSTI)

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

    2015-12-24

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

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

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

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

    2015-12-24

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

  19. Michael Levitt and Computational Biology

    Office of Scientific and Technical Information (OSTI)

    At that time, X-ray crystallography was used to ascertain the location of atoms like hydrogen, carbon and oxygen in larger molecules like proteins or DNA. Researchers then used the ...

  20. MEDIA ADVISORY

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

    advanced-placement chemistry class will get to put their wits and crystal-growing skills to the test Monday in the Protein Crystallography Station at the Los Alamos Research...

  1. 2011 User Meeting Workshops

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

    54-130 (Pers. Hall) Industrial Protein Crystallography Corie Ralston (LBNL) and Gyorgy Snell (Takeda, Inc.) 6-1105 (Wed.) New Computational Approaches for X-Ray Science Alex...

  2. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

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

    2010-05-25

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

  3. Methods and devices for protein assays

    DOE Patents [OSTI]

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

    2009-11-03

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

  4. 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 National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material and metals, particularly how organics affect mobility, and its potential for

  5. 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 National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material and metals, particularly how organics affect mobility, and its potential for

  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 Print Researchers from the ALS, Berkeley Lab's National Center for Electron Microscopy (NCEM), and Lawrence Livermore National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material and metals, particularly how organics affect mobility, and its potential for

  7. 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 National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material and metals, particularly how organics affect mobility, and its potential for

  8. Extracellular Proteins Promote Zinc Sulfide Aggregation

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

    Extracellular Proteins Promote Zinc Sulfide Aggregation Print Researchers from the ALS, Berkeley Lab's National Center for Electron Microscopy (NCEM), and Lawrence Livermore National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material and metals, particularly how organics affect mobility, and its potential for

  9. 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 National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material and metals, particularly how organics affect mobility, and its potential for

  10. Allostery through protein-induced DNA bubbles

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

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

    2015-03-12

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

  11. Nucleic acids encoding human trithorax protein

    DOE Patents [OSTI]

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

    2001-01-01

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  14. How the Membrane Protein AmtB Transports Ammonia

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

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

  15. Crystal Structure of a Protein Kinase A Complex

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

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

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

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

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

  17. Patent: Fast computational methods for predicting protein structure from

    Office of Scientific and Technical Information (OSTI)

    primary amino acid sequence | DOEpatents Fast computational methods for predicting protein structure from primary amino acid sequence Citation Details Title: Fast computational methods for predicting protein structure from primary amino acid sequence

  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 Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print Tuesday, 23 June 2015 13:00 The cancer drug...

  19. Multidomain Carbohydrate-binding Proteins Involved in Bacteroides...

    Office of Scientific and Technical Information (OSTI)

    Title: Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism Authors: Cameron, Elizabeth A. ; Maynard, Mallory A. ; Smith, ...

  20. 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 Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Wednesday, 28 April 2010 00:00 Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded

  1. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Wednesday, 28 October 2009 00:00 Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has

  2. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding New Crystal Structures Lift Fog around Protein Folding Print Wednesday, 25 July 2012 00:00 Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a

  3. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

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

  4. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

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

  5. Computational Design of Self-Assembling Protein Nanomaterials with Atomic

    Office of Scientific and Technical Information (OSTI)

    Level Accuracy (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy Citation Details In-Document Search Title: Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together

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

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

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

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

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

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

  8. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

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

    2012-02-14

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

  9. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

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

    2011-03-22

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

  10. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

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

    2011-12-06

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

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

    DOE Patents [OSTI]

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

    1996-01-01

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

  12. Methods for production of proteins in host cells

    DOE Patents [OSTI]

    Donnelly, Mark; Joachimiak, Andrzej

    2004-01-13

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

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

    DOE Patents [OSTI]

    Camarero, Julio A. (Livermore, CA); DeYoreo, James J. (Clayton, CA); Kwon, Youngeun (Livermore, CA)

    2011-07-05

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

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

    DOE Patents [OSTI]

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

    2010-04-20

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

  15. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

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

    2008-10-07

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

  16. Site specific incorporation of keto amino acids into proteins

    DOE Patents [OSTI]

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

    2009-04-28

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

  17. Experimental Station 11-1 | Stanford Synchrotron Radiation Lightsource

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

    1 Beamline 11-1 is a PRT station, available to general users 33%; it is a wiggler side-station beamline dedicated for monochromatic, high-throughput and high-resolution macromolecular crystallography. It is SAD and MAD capable and can be run in a full remote access mode. It is equipped with an Dectris PILATUS 6M detector and a remote access controlled UV-Vis microspectrophotometer. For aditional information about the experimental capabilities, see http://smb.slac.stanford.edu/index.shtml. Status

  18. Experimental Station 12-2 | Stanford Synchrotron Radiation Lightsource

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

    2-2 Beamline 12-2 is a PRT station, realized through third party funding from the Gordon and Betty Moore Foundation via the California Institute of Technology and available to general users 60%; it is an undulator beamline with fully adjustable focus from 100 to 15 microns. Micron-sized beams can be achieved by the use of microcollimators. It is optimized for microdiffraction, monochromatic, high-throughput and high-resolution macromolecular crystallography. It is SAD and MAD capable and can be

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

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

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

    2015-05-08

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

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

    SciTech Connect (OSTI)

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

    2015-05-08

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

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

    SciTech Connect (OSTI)

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

    2010-10-22

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

  2. Protein-Based Nanomedicine Platforms for Drug Delivery

    SciTech Connect (OSTI)

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

    2009-08-03

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

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

    SciTech Connect (OSTI)

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

    2005-06-17

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

  4. Multicomponent Protein Cage Architectures for Photocatalysis

    SciTech Connect (OSTI)

    Douglas, Trevor

    2014-11-21

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

  5. TIGRFAMS: The TIGRFAMs database of protein families

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

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

  6. Gene encoding herbicide safener binding protein

    DOE Patents [OSTI]

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

    1999-01-01

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

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

    DOE Patents [OSTI]

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

    2013-06-18

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

  8. Graph representation of protein free energy landscape

    SciTech Connect (OSTI)

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

    2013-11-14

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

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

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

    Yao, Jianzhuang; Guo, Hong; Yang, Xiaohan

    2015-01-01

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

  10. DAPS: Database of Aligned Protein Structures

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

    Mallick, Parag; Rice, Danny; Eisenberg, David

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

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

    SciTech Connect (OSTI)

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

    2012-06-29

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

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

    SciTech Connect (OSTI)

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

    2011-05-01

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

  13. Engineering and Characterization of a Superfolder Green Fluorescent Protein

    SciTech Connect (OSTI)

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

    2006-01-01

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

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

    SciTech Connect (OSTI)

    Jae-Hyung Lee

    2007-12-01

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

  15. Structures for Three Membrane Transport Proteins Yield Functional Insights

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

    Structures for Three Membrane Transport Proteins Yield Functional Insights Print Cells depend on contact with their outside environment in order to thrive. Two examples illustrate why: In one, information needed to guide cellular processes is constantly transmitted across cell membranes by specialized proteins, and in the other, maintaining the right gradient of ions across the membrane is a process critical to the life and death of a cell. Membrane transport proteins-functioning either as

  16. Structures for Three Membrane Transport Proteins Yield Functional Insights

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

    Structures for Three Membrane Transport Proteins Yield Functional Insights Print Cells depend on contact with their outside environment in order to thrive. Two examples illustrate why: In one, information needed to guide cellular processes is constantly transmitted across cell membranes by specialized proteins, and in the other, maintaining the right gradient of ions across the membrane is a process critical to the life and death of a cell. Membrane transport proteins-functioning either as

  17. Structures for Three Membrane Transport Proteins Yield Functional Insights

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

    Structures for Three Membrane Transport Proteins Yield Functional Insights Print Cells depend on contact with their outside environment in order to thrive. Two examples illustrate why: In one, information needed to guide cellular processes is constantly transmitted across cell membranes by specialized proteins, and in the other, maintaining the right gradient of ions across the membrane is a process critical to the life and death of a cell. Membrane transport proteins-functioning either as

  18. Structures for Three Membrane Transport Proteins Yield Functional Insights

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

    Structures for Three Membrane Transport Proteins Yield Functional Insights Structures for Three Membrane Transport Proteins Yield Functional Insights Print Wednesday, 27 January 2010 00:00 Cells depend on contact with their outside environment in order to thrive. Two examples illustrate why: In one, information needed to guide cellular processes is constantly transmitted across cell membranes by specialized proteins, and in the other, maintaining the right gradient of ions across the membrane is

  19. Structures for Three Membrane Transport Proteins Yield Functional Insights

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

    Structures for Three Membrane Transport Proteins Yield Functional Insights Print Cells depend on contact with their outside environment in order to thrive. Two examples illustrate why: In one, information needed to guide cellular processes is constantly transmitted across cell membranes by specialized proteins, and in the other, maintaining the right gradient of ions across the membrane is a process critical to the life and death of a cell. Membrane transport proteins-functioning either as

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

    DOE Patents [OSTI]

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

    1996-09-03

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

  1. 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 often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling genomic-scale protein-structure characterization. Coupling brilliant x rays from one of the

  2. 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 often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling genomic-scale protein-structure characterization. Coupling brilliant x rays from one of the

  3. 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 often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling genomic-scale protein-structure characterization. Coupling brilliant x rays from one of the

  4. 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 fast and efficient way to determine the structure of proteins, shortening a process that often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling

  5. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  6. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  7. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  8. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  9. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  10. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  11. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  12. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  13. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  14. 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 biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  15. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  16. 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 biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

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

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

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

  18. Non-destructively shattered mesoporous silica for protein drug delivery

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Non-destructively shattered mesoporous silica for protein drug delivery Citation Details In-Document Search Title: Non-destructively shattered mesoporous silica for protein drug delivery Mesoporous silicas have been extensively used for entrapping small chemical molecules and biomacromolecules. We hypothesize that the loading density of biomacromlecules such as proteins in mesoporous silicas could be limited due to mesopore disorderness and depth because

  19. Microsecond Microfluidic Mixing for Investigation of Protein Folding

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  1. Diverse and divergent protein post-translational modifications in two

    Office of Scientific and Technical Information (OSTI)

    growth stages of a natural microbial community (Journal Article) | SciTech Connect Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community Citation Details In-Document Search Title: Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community Detailed characterization of posttranslational modifications (PTMs) of proteins in microbial communities remains a significant

  2. Experimental phasing for structure determination using membrane-protein

    Office of Scientific and Technical Information (OSTI)

    crystals grown by the lipid cubic phase method (Journal Article) | SciTech Connect Experimental phasing for structure determination using membrane-protein crystals grown by the lipid cubic phase method Citation Details In-Document Search Title: Experimental phasing for structure determination using membrane-protein crystals grown by the lipid cubic phase method Very little information is available in the literature concerning the experimental heavy-atom phasing of membrane-protein structures

  3. A challenging interpretation of a hexagonally layered protein structure

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect A challenging interpretation of a hexagonally layered protein structure Citation Details In-Document Search Title: A challenging interpretation of a hexagonally layered protein structure The authors describe the structure determination of a hexagonally layered protein structure that suffered from a complicated combination of translational non-crystallographic symmetry and hemihedral twinning. This case serves as a reminder that broken crystallographic

  4. 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 biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  5. 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 often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling genomic-scale protein-structure characterization. Coupling brilliant x rays from one of the

  6. 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 often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling genomic-scale protein-structure characterization. Coupling brilliant x rays from one of the

  7. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  8. 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 biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand

  9. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

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

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

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

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

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

    Constricting the Nuclear Pore From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore Print Wednesday, 28 August 2013 00:00 Nuclear pore complexes (NPCs) act as the central gatekeepers for selective transport between the cytoplasm and the nucleus. They allow the exchange of selected proteins and ribonucleoproteins, while preventing the transport of material not

  12. Lab partners with local company to market protein technology

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

    Protein technology Lab partners with local company to market protein technology Theranostech Inc. honed its skills in protein purification by developing an efficient test for Human Immunodeficiency Virus (HIV). July 14, 2008 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics and new materials. Los Alamos

  13. Crystal Structure of a Protein Kinase A Complex

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

    Crystal Structure of a Protein Kinase A Complex Crystal Structure of a Protein Kinase A Complex Print Wednesday, 26 October 2005 00:00 Protein kinase A (PKA) is an enzyme that regulates processes as diverse as growth, memory, and metabolism. In its unactivated state, PKA exists as a tetrameric complex of two catalytic subunits and a regulatory subunit dimer, but when the intracellular signaling molecule cyclic adenosine monophosphate (cAMP) binds to the regulatory subunit, it facilitates

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

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

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

  15. DOE Science Showcase - Understanding Protein Membranes | OSTI, US Dept of

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

    Energy, Office of Scientific and Technical Information Understanding Protein Membranes Protein membrane simulation and predictability made possible by vast computing resources hold the promise for improved processes in drug discovery. DOE 2010 INCITE Award Program Protein Research Documents from DOE Databases Information Bridge Energy Citations Database DOE R&D Accomplishments Database DOE R&D Project Summaries DOE Data Explorer Drug Research Documents from DOE Databases Information

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

    Office of Scientific and Technical Information (OSTI)

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

  17. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING

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

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

  18. Proteins' Amazing Origami Powers: Insight for Potential Disease Treatments

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

    | Department of Energy Proteins' Amazing Origami Powers: Insight for Potential Disease Treatments Proteins' Amazing Origami Powers: Insight for Potential Disease Treatments October 4, 2011 - 12:46pm Addthis This is a visualization of drug molecules ("parade day-like balloons") in a simulated attack of the ribbon-like protein fibrils that are believed to be the cause of Alzheimer’s disease. <a

  19. MEDIA ADVISORY

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

    invited to join students in crystallography experiment May 16, 2014 MEDIA ADVISORY Los Alamos High School chemistry students to get hands-on x-ray experience LOS ALAMOS, N.M., May 16, 2014-Some 20 students from Los Alamos High School's advanced-placement chemistry class will get to put their wits and crystal-growing skills to the test Monday in the Protein Crystallography Station at the Los Alamos Research Park. The students will learn about the history and theory of X-ray crystallography in the

  20. MTBreg: The Database of Conditionally Regulated Proteins in Mycobacterium Tuberculosis

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

    Kaufman, Markus; Pal, Debnath; Eisenberg, David

    Proteins up- and down- regulated in Mycobacterium tuberculosis grown under conditions mimicking infection are included in this database. It also includes information on proteins that are regulated by selected transcription factors or other regulatory proteins. The literature data provided here is complimentary to the databases provided by Michael Strong that include recent TB computational functional linkages and the Prolinks Database by Peter Bowers. The experimental condition, the experimental dataset and a literature reference will be displayed, including links to the computationally linked proteins in the Prolinks Database and the entry in the Mycobacterium tuberculosis Structural Genomics Database.[Copied from information at http://www.doe-mbi.ucla.edu/Services/MTBreg/

  1. New Crystal Structures Lift Fog around Protein Folding

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

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

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

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

    "de novo" is not a new field, but until recently designer proteins were rarely also functional. In this study, new design approaches were defined and then used successfully...

  3. Computational Design of Self-Assembling Protein Nanomaterials...

    Office of Scientific and Technical Information (OSTI)

    Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy Citation Details In-Document Search Title: Computational Design of Self-Assembling ...

  4. Phenylpropanoid related regulatory protein-regulatory region associations

    DOE Patents [OSTI]

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

    2012-01-03

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

  5. New Crystal Structures Lift Fog around Protein Folding

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

    incorrect or "misfolding" of proteins has been linked to many diseases, including Alzheimer's, Parkinson's, and some forms of cancer. So far, however, a complete...

  6. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  8. Crystal Structure of a Protein Kinase A Complex

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

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

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

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

    Storage and Transport Technology available for licensing: Unique, first-of-its-kind method for storing proteins in their native state for assay, application and delivery to...

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

    Office of Scientific and Technical Information (OSTI)

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

  11. Mapping protein collapse with single molecule fluorescence and...

    Office of Scientific and Technical Information (OSTI)

    single molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy Citation Details In-Document Search Title: Mapping protein collapse with single...

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

    Office of Scientific and Technical Information (OSTI)

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

  13. Recoding of Bacterial Genome Produces Proteins with New Functions...

    Office of Science (SC) Website

    implications for engineering organisms to produce novel proteins that perform new functions needed in processes relevant to the DOE mission, including biofuel production. ...

  14. How the Membrane Protein AmtB Transports Ammonia

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

    How the Membrane Protein AmtB Transports Ammonia How the Membrane Protein AmtB Transports Ammonia Print Wednesday, 25 May 2005 00:00 Membrane proteins provide molecular-sized entry and exit portals for the various substances that pass into and out of cells. While life scientists have solved the structures of protein channels for ions, uncharged solutes, and even water, up to now they have only been able to guess at the precise mechanisms by which gases (such as NH3, CO2, O2, NO, N2O, etc.) cross

  15. Transparent Gold as a Platform for Adsorbed ProteinSpectroelectrochem...

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

    Transparent Gold as a Platform for Adsorbed Protein Spectroelectrochemistry: Investigation of Cytochrome c and Azurin Authors: Ashur, I., Schulz, O., McIntosh, C. L., Pinkas, I.,...

  16. The structures of synaptic cell adhesion proteins neuroligin...

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

    In the brain, neurexins and neuroligins are cell adhesion proteins on the pre-synaptic and post-synaptic cell membranes, respectively. Their extracellular domains interact with ...

  17. In meso in situ serial X-ray crystallography of soluble and membrane...

    Office of Scientific and Technical Information (OSTI)

    Agency (IAEA) Country of Publication: Denmark Language: English Subject: 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY...

  18. The crystallography of fatigue crack initiation in Incoloy-908 and A-286 steel

    SciTech Connect (OSTI)

    Krenn, C.R. |

    1996-12-01

    Fatigue crack initiation in the austenitic Fe-Ni superalloys Incoloy-908 and A-286 is examined using local crystallographic orientation measurements. Results are consistent with sharp transgranular initiation and propagation occurring almost exclusively on {l_brace}111{r_brace} planes in Incoloy-908 but on a variety of low index planes in A-286. This difference is attributed to the influence of the semicoherent grain boundary {eta} phase in A-286. Initiation in each alloy occurred both intergranularly and transgranularly and was often associated with blocky surface oxide and carbide inclusions. Taylor factor and resolved shear stress and strain crack initiation hypotheses were tested, but despite an inconclusive suggestion of a minimum required {l_brace}111{r_brace} shear stress, none of the hypotheses were found to convincingly describe preferred initiation sites, even within the subsets of transgranular cracks apparently free from the influence of surface inclusions. Subsurface inclusions are thought to play a significant role in crack initiation. These materials have applications for use in structural conduit for high field superconducting magnets designed for fusion energy use.

  19. Kinks, loops, and protein folding, with protein A as an example

    SciTech Connect (OSTI)

    Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden)] [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Liwo, Adam, E-mail: adam@chem.univ.gda.pl [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland)] [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland); Maisuradze, Gia G., E-mail: gm56@cornell.edu; Scheraga, Harold A., E-mail: has5@cornell.edu [Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301 (United States); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours, France and Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2014-01-14

    The dynamics and energetics of formation of loops in the 46-residue N-terminal fragment of the B-domain of staphylococcal protein A has been studied. Numerical simulations have been performed using coarse-grained molecular dynamics with the united-residue (UNRES) force field. The results have been analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrdinger (DNLS) equation. In the case of proteins, the DNLS equation arises from a C{sup ?}-trace-based energy function. Three individual kink profiles were identified in the experimental three-?-helix structure of protein A, in the range of the Glu16-Asn29, Leu20-Asn29, and Gln33-Asn44 residues, respectively; these correspond to two loops in the native structure. UNRES simulations were started from the full right-handed ?-helix to obtain a clear picture of kink formation, which would otherwise be blurred by helix formation. All three kinks emerged during coarse-grained simulations. It was found that the formation of each is accompanied by a local free energy increase; this is expressed as the change of UNRES energy which has the physical sense of the potential of mean force of a polypeptide chain. The increase is about 7 kcal/mol. This value can thus be considered as the free energy barrier to kink formation in full ?-helical segments of polypeptide chains. During the simulations, the kinks emerge, disappear, propagate, and annihilate each other many times. It was found that the formation of a kink is initiated by an abrupt change in the orientation of a pair of consecutive side chains in the loop region. This resembles the formation of a Bloch wall along a spin chain, where the C{sup ?} backbone corresponds to the chain, and the amino acid side chains are interpreted as the spin variables. This observation suggests that nearest-neighbor side chainside chain interactions are responsible for initiation of loop formation. It was also found that the individual kinks are reflected as clear peaks in the principal modes of the analyzed trajectory of protein A, the shapes of which resemble the directional derivatives of the kinks along the chain. These observations suggest that the kinks of the DNLS equation determine the functionally important motions of proteins.

  20. Orpinomyces cellulase celf protein and coding sequences

    DOE Patents [OSTI]

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

    2000-09-05

    A cDNA (1,520 bp), designated celF, consisting of an open reading frame (ORF) encoding a polypeptide (CelF) of 432 amino acids was isolated from a cDNA library of the anaerobic rumen fungus Orpinomyces PC-2 constructed in Escherichia coli. Analysis of the deduced amino acid sequence showed that starting from the N-terminus, CelF consists of a signal peptide, a cellulose binding domain (CBD) followed by an extremely Asn-rich linker region which separate the CBD and the catalytic domains. The latter is located at the C-terminus. The catalytic domain of CelF is highly homologous to CelA and CelC of Orpinomyces PC-2, to CelA of Neocallimastix patriciarum and also to cellobiohydrolase IIs (CBHIIs) from aerobic fungi. However, Like CelA of Neocallimastix patriciarum, CelF does not have the noncatalytic repeated peptide domain (NCRPD) found in CelA and CelC from the same organism. The recombinant protein CelF hydrolyzes cellooligosaccharides in the pattern of CBHII, yielding only cellobiose as product with cellotetraose as the substrate. The genomic celF is interrupted by a 111 bp intron, located within the region coding for the CBD. The intron of the celF has features in common with genes from aerobic filamentous fungi.

  1. Construction of artificial pigment-protein antennae

    SciTech Connect (OSTI)

    Sibbald, J.

    1997-01-10

    Photosynthesis is a complex process which results in the conversion of solar radiation into chemical energy. This chemical energy is then used as the free energy source for all living organisms. In its basic form, photosynthesis can be described as the light-activated synthesis of carbohydrates from the simple molecules of water and carbon dioxide: 6H{sub 2}O + 6 CO{sub 2} light C{sub 6}H{sub 12}O{sub 6} + 6 O{sub 2} This basic mechanism actually requires numerous reaction steps. The two primary steps being: the capture of light by pigment molecules in light-harvesting antenna complexes and the transfer of this captured energy to the so-called photochemical reaction center. While the preferred pathway for energy absorbed by the chromophores in the antenna complexes is transfer to the reaction center, energy can be lost to competing processes such as internal conversion or radiative decay. Therefore, the energy transfer must be rapid, typically on the order of picoseconds, to successfully compete. The focus of the present work is on the construction of light-harvesting antenna complexes incorporating modular pigment-proteins.

  2. Electrorheological crystallization of proteins and other molecules

    DOE Patents [OSTI]

    Craig, George D. (Lafayette, CA); Rupp, Bernhard (Dublin, CA)

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  3. Electrorheological crystallization of proteins and other molecules

    DOE Patents [OSTI]

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  4. Facilitating protein solubility by use of peptide extensions

    DOE Patents [OSTI]

    Freimuth, Paul I; Zhang, Yian-Biao; Howitt, Jason

    2013-09-17

    Expression vectors for expression of a protein or polypeptide of interest as a fusion product composed of the protein or polypeptide of interest fused at one terminus to a solubility enhancing peptide extension are provided. Sequences encoding the peptide extensions are provided. The invention further comprises antibodies which bind specifically to one or more of the solubility enhancing peptide extensions.

  5. LucY: A versatile new fluorescent reporter protein

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

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

    2015-04-23

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

  6. Multidomain Carbohydrate-binding Proteins Involved in Bacteroides

    Office of Scientific and Technical Information (OSTI)

    thetaiotaomicron Starch Metabolism (Journal Article) | SciTech Connect Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism Citation Details In-Document Search Title: Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism Authors: Cameron, Elizabeth A. ; Maynard, Mallory A. ; Smith, Christopher J. ; Smith, Thomas J. ; Koropatkin, Nicole M. ; Martens, Eric C. [1] ; Danforth) [2] + Show Author

  7. Promoters and proteins from Clostridium thermocellum and uses thereof

    DOE Patents [OSTI]

    Wu, J. H. David; Newcomb, Michael

    2012-11-13

    The present invention relates to an inducible and a high expression nucleic acid promoter isolated from Clostridium thermocellum. These promoters are useful for directing expression of a protein or polypeptide encoded by a nucleic acid molecule operably associated with the nucleic acid promoters. The present invention also relates to nucleic acid constructs including the C. thermocellum promoters, and expression vectors and hosts containing such nucleic acid constructs. The present invention also relates to protein isolated from Clostridium thermocellum, including a repressor protein. The present invention also provides methods of using the isolated promoters and proteins from Clostridium thermocellum, including methods for directing inducible in vitro and in vivo expression of a protein or polypeptide in a host, and methods of producing ethanol from a cellulosic biomass.

  8. Method For Determining And Modifying Protein/Peptide Solubilty

    DOE Patents [OSTI]

    Waldo, Geoffrey S.

    2005-03-15

    A solubility reporter for measuring a protein's solubility in vivo or in vitro is described. The reporter, which can be used in a single living cell, gives a specific signal suitable for determining whether the cell bears a soluble version of the protein of interest. A pool of random mutants of an arbitrary protein, generated using error-prone in vitro recombination, may also be screened for more soluble versions using the reporter, and these versions may be recombined to yield variants having further-enhanced solubility. The method of the present invention includes "irrational" (random mutagenesis) methods, which do not require a priori knowledge of the three-dimensional structure of the protein of interest. Multiple sequences of mutation/genetic recombination and selection for improved solubility are demonstrated to yield versions of the protein which display enhanced solubility.

  9. Determining the role of hydration forces in protein folding

    SciTech Connect (OSTI)

    Sorenson, J.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry] [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Hura, G. [Univ. of California, Berkeley, CA (United States)] [Univ. of California, Berkeley, CA (United States); [Lawrence Berkeley National Lab., CA (United States). Life Sciences Div.; Soper, A.K. [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility] [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility; Pertsemlidis, A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry] [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Head-Gordon, T. [Lawrence Berkeley National Lab., CA (United States)] [Lawrence Berkeley National Lab., CA (United States)

    1999-07-01

    One of the primary issues in protein folding is determining what forces drive folding and eventually stabilize the native state. A delicate balance exists between electrostatic forces such as hydrogen bonding and salt bridges, and the hydrophobic effect, which are present for both intramolecular protein interactions and intermolecular contributions with the surrounding aqueous environment. This article describes a combined experimental, theoretical, and computational effort to show how the complexity of aqueous hydration can influence the structure, folding and aggregation, and stability of model protein systems. The unification of the theoretical and experimental work is the development or discovery of effective amino acid interactions that implicitly include the effects of aqueous solvent. The authors show that consideration of the full range of complexity of aqueous hydration forces such as many-body effects, long-ranged character of aqueous solvation, and the assumptions made about the degree of protein hydrophobicity can directly impact the observed structure, folding, and stability of model protein systems.

  10. Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

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

    Yu, Peiqiang

    2006-01-01

    Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in biological tissues at ultraspatial resolutions.« less

  11. Bioscience

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

    Bioscience Bioscience Print Bioscience research at the ALS can be divided into two areas: general biology (microscopy/spectroscopy) and structural biology (crystallography/diffraction). These fields provide complementary approaches to the study of living organisms from the molecular to the cellular levels. Crystallography is used to determine the atomic-resolution, three-dimensional structures of proteins and nucleic acids-the building blocks of life-as well as complexes of these molecules, the

  12. Stable isotope, site-specific mass tagging for protein identification

    DOE Patents [OSTI]

    Chen, Xian

    2006-10-24

    Proteolytic peptide mass mapping as measured by mass spectrometry provides an important method for the identification of proteins, which are usually identified by matching the measured and calculated m/z values of the proteolytic peptides. A unique identification is, however, heavily dependent upon the mass accuracy and sequence coverage of the fragment ions generated by peptide ionization. The present invention describes a method for increasing the specificity, accuracy and efficiency of the assignments of particular proteolytic peptides and consequent protein identification, by the incorporation of selected amino acid residue(s) enriched with stable isotope(s) into the protein sequence without the need for ultrahigh instrumental accuracy. Selected amino acid(s) are labeled with .sup.13C/.sup.15N/.sup.2H and incorporated into proteins in a sequence-specific manner during cell culturing. Each of these labeled amino acids carries a defined mass change encoded in its monoisotopic distribution pattern. Through their characteristic patterns, the peptides with mass tag(s) can then be readily distinguished from other peptides in mass spectra. The present method of identifying unique proteins can also be extended to protein complexes and will significantly increase data search specificity, efficiency and accuracy for protein identifications.

  13. Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

    SciTech Connect (OSTI)

    Mereghetti, Paolo; Gabdoulline, Razif; Wade, Rebecca C.

    2010-12-01

    The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments.

  14. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  15. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

    SciTech Connect (OSTI)

    Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Datta, Susmita; Payne, Samuel H.; Kang, Jiyun; Bramer, Lisa M.; Nicora, Carrie D.; Shukla, Anil K.; Metz, Thomas O.; Rodland, Karin D.; Smith, Richard D.; Tardiff, Mark F.; McDermott, Jason E.; Pounds, Joel G.; Waters, Katrina M.

    2014-12-01

    As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

  16. Protein receptor-independent plasma membrane remodeling by HAMLET: A tumoricidal protein-lipid complex

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

    Nadeem, Aftab; Sanborn, Jeremy; Gettel, Douglas L.; James, Ho C. S.; Rydström, Anna; Ngassam, Viviane N.; Klausen, Thomas Kjaer; Pedersen, Stine Falsig; Lam, Matti; Parikh, Atul N.; et al

    2015-11-12

    A central tenet of signal transduction in eukaryotic cells is that extra-cellular ligands activate specific cell surface receptors, which orchestrate downstream responses. This ‘’protein-centric” view is increasingly challenged by evidence for the involvement of specialized membrane domains in signal transduction. Here, we propose that membrane perturbation may serve as an alternative mechanism to activate a conserved cell-death program in cancer cells. This view emerges from the extraordinary manner in which HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) kills a wide range of tumor cells in vitro and demonstrates therapeutic efficacy and selectivity in cancer models and clinical studies. Wemore » identify a ‘’receptor independent” transformation of vesicular motifs in model membranes, which is paralleled by gross remodeling of tumor cell membranes. Furthermore, we find that HAMLET accumulates within these de novo membrane conformations and define membrane blebs as cellular compartments for direct interactions of HAMLET with essential target proteins such as the Ras family of GTPases. In conclusion, we demonstrate lower sensitivity of healthy cell membranes to HAMLET challenge. These features suggest that HAMLET-induced curvature-dependent membrane conformations serve as surrogate receptors for initiating signal transduction cascades, ultimately leading to cell death.« less

  17. The role of hydrogen bonds in protein folding and protein association

    SciTech Connect (OSTI)

    Ben-Naim, A. (National Inst. of Health, Bethesda, MD (USA))

    1991-02-07

    The contribution of a pair of functional groups that can form either intermolecular or intramolecular hydrogen bonds to the total standard free energy of the process of protein folding or protein association is examined. It is found that this contribution can be quite large, either positive or negative, depending on the particular process and on the solvent density. This is in contrast to the common belief that the hydrogen-bond energies tend to be compensated in these processes. For the binding process, in which the two functional groups are completely removed from the aqueous environment, the contribution of such a pair of functional groups to {Delta}G can be as high as +6.4 kcal/mol. This is the main reason why hydrophobic rather than hydrophilic surfaces tend to attach to each other. In contrast, when the two functional groups are only partially removed from the aqueous environment, as in the case of the formation of {alpha}-helix, their contribution to {Delta}G can be negative and of the order of about 1 kcal/mol.

  18. Hydration water dynamics and instigation of protein structuralrelaxation

    SciTech Connect (OSTI)

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

    2003-09-01

    Until a critical hydration level is reached, proteins do not function. This critical level of hydration is analogous to a similar lack of protein function observed for temperatures below a dynamical temperature range of 180-220K that also is connected to the dynamics of protein surface water. Restoration of some enzymatic activity is observed in partially hydrated protein powders, sometimes corresponding to less than a single hydration layer on the protein surface, which indicates that the dynamical and structural properties of the surface water is intimately connected to protein stability and function. Many elegant studies using both experiment and simulation have contributed important information about protein hydration structure and timescales. The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use experimental quasi-elastic neutron scattering (QENS) and molecular dynamics simulation to investigate hydration water dynamics near a greatly simplified protein system. We consider the hydration water dynamics near the completely deuterated N-acetyl-leucine-methylamide (NALMA) solute, a hydrophobic amino acid side chain attached to a polar blocked polypeptide backbone, as a function of concentration between 0.5M-2.0M under ambient conditions. We note that roughly 50-60% of a folded protein's surface is equally distributed between hydrophobic and hydrophilic domains, domains whose lengths are on the order of a few water diameters, that justify our study of hydration dynamics of this simple model protein system. The QENS experiment was performed at the NIST Center for Neutron Research, using the disk chopper time of flight spectrometer (DCS). In order to separate the translational and rotational components in the spectra, two sets of experiments were carried out using different incident neutron wavelengths of 7.5{angstrom} and 5.5{angstrom} to give two different time resolutions. All the spectra have been measure at room temperature. The spectra were corrected for the sample holder contribution and normalized using the vanadium standard. The resulting data were analyzed with DAVE programs (http://www.ncnr.nist.gov/dave/). The AMBER force field and SPCE water model were used for modeling the NALMA solute and water, respectively. For the analysis of the water dynamics in the NALMA aqueous solutions, we performed simulations of a dispersed solute configuration consistent with our previous structural analysis, where we had primarily focused on the structural organization of these peptide solutions and their connection to protein folding. Further details of the QENS experiment and molecular dynamics simulations are reported elsewhere.

  19. Water dynamics clue to key residues in protein folding

    SciTech Connect (OSTI)

    Gao, Meng [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Zhu, Huaiqiu, E-mail: hqzhu@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Yao, Xin-Qiu [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China) [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Department of Biophysics, Kyoto University, Sakyo Kyoto 606-8502 (Japan); She, Zhen-Su, E-mail: she@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)

    2010-01-29

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  20. How the Membrane Protein AmtB Transports Ammonia

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

    How the Membrane Protein AmtB Transports Ammonia Print Membrane proteins provide molecular-sized entry and exit portals for the various substances that pass into and out of cells. While life scientists have solved the structures of protein channels for ions, uncharged solutes, and even water, up to now they have only been able to guess at the precise mechanisms by which gases (such as NH3, CO2, O2, NO, N2O, etc.) cross biological membranes. But, with the first high-resolution structure of a