Sample records for monochromatic protein crystallography

  1. MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY

    E-Print Network [OSTI]

    Quake, Stephen R.

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

  2. Serial Femtosecond Crystallography of G Protein-Coupled Receptors

    SciTech Connect (OSTI)

    Liu, Liu

    2013-10-23T23:59:59.000Z

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

  3. Serial Femtosecond Crystallography of G Protein-Coupled Receptors

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

    Liu, Liu

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

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

    SciTech Connect (OSTI)

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

    2014-01-01T23:59:59.000Z

    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.

  5. Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

    SciTech Connect (OSTI)

    Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.; Sasajima, K.; Matsugaki, N.; Suzuki, M.; Kosuge, T.; Wakatsuki, S. [Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba (Japan)

    2004-05-12T23:59:59.000Z

    An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view, create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.

  6. Development of Control Applications for High-Throughput Protein Crystallography Experiments

    SciTech Connect (OSTI)

    Gaponov, Yurii A.; Matsugaki, Naohiro; Honda, Nobuo; Sasajima, Kumiko; Igarashi, Noriyuki; Hiraki, Masahiko; Yamada, Yusuke; Wakatsuki, Soichi [Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki (Japan)

    2007-01-19T23:59:59.000Z

    An integrated client-server control system (PCCS) with a unified relational database (PCDB) has been developed for high-throughput protein crystallography experiments on synchrotron beamlines. The major steps in protein crystallographic experiments (purification, crystallization, crystal harvesting, data collection, and data processing) are integrated into the software. All information necessary for performing protein crystallography experiments is stored in the PCDB database (except raw X-ray diffraction data, which is stored in the Network File Server). To allow all members of a protein crystallography group to participate in experiments, the system was developed as a multi-user system with secure network access based on TCP/IP secure UNIX sockets. Secure remote access to the system is possible from any operating system with X-terminal and SSH/X11 (Secure Shell with graphical user interface) support. Currently, the system covers the high-throughput X-ray data collection stages and is being commissioned at BL5A and NW12A (PF, PF-AR, KEK, Tsukuba, Japan)

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

    SciTech Connect (OSTI)

    Terwilliger, T.C.; Berendzen, J.

    1998-02-25T23:59:59.000Z

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

  8. 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

    2015-01-01T23:59:59.000Z

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

  9. Proteins

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

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

  10. Ultrahigh resolution protein crystallography: Concanavalin A to 0.94 A and beyond

    SciTech Connect (OSTI)

    Deacon, A.M.; Gleichmann, T.; Harrop, S.J.; Helliwell, J.R. [Department of Chemistry, University of Manchester, Manchester M13 9PL (England)] [Department of Chemistry, University of Manchester, Manchester M13 9PL (England); Kalb Gilboa, A.J.; Yariv, J. [The Weizmann Institute (Israel)] [The Weizmann Institute (Israel)

    1996-09-01T23:59:59.000Z

    Many years ago the idea of collecting voluminous quantities of weak reflection intensities from a protein crystal, at high resolution, was a particular challenge [J.R. Helliwell (1979) Daresbury Study Weekend DL/SCI R13, pp. 1{endash}6]. The combination of insertion devices with very high x-ray fluxes at short x-ray wavelengths, sensitive CCD detectors, and freezing of crystals have provided the means to certainly match those best hopes. So much so that the data can best be described as ultrahigh resolution, at least as evidenced in our studies of the 25000 molecular weight plant protein concanavalin A. (The intrinsic property of this protein is to bind sugar molecules; it is implicated in cell-to-cell recognition processes and is widely used as a laboratory diagnostic tool.) At CHESS we have used a 0.9 A wavelength beam on station A1, fed by a 24 pole multipole wiggler. Both an imaging plate system and the Princeton 1k CCD detector [M. Tate {ital et} {ital al}., J. Appl. Cryst. {bold 28}, 196 (1995)] have been used on this experimental setup to collect diffraction data sets from frozen concanavalin A crystals (saccharide-free crystal form). The rapid readout of the CCD was most convenient compared with the image plate and its associated scanning and erasing. Moreover the data processing results towards the edges of the detectors, 0.98 A, show that the CCD is much better than the image plate at recording these weaker data (Rmerge(I) 13{percent} versus 44{percent}, respectively). The poor performance of the image plate with weak signals has of course been documented by the Daresbury detector group [R. Lewis, J. Synchrotron Radiation {bold 1}, 43 (1994)]. However, the aperture of the CCD used was limiting here. Very recently, in another run at CHESS with the CCD on A1, we have been able to record diffraction data to 0.94 A by further offsetting the detector. We again found that the reflections are still strong at the edge. (Abstract Truncated)

  11. Proteins

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

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

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

    E-Print Network [OSTI]

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

    2006-01-01T23:59:59.000Z

    and V.N. Uversky, 2005. Flexible nets - The roles ofand T. Ellenberger, 2006. A flexible interface between DNAStructural analysis of flexible proteins in solution by

  13. electronic reprint Crystallography

    E-Print Network [OSTI]

    Kemner, Ken

    of Crystallography Author(s) of this paper may load this reprint on their own web site or institutional repository-stream, starting with the temperature profile, is presented. Using silicon single crystals and flexible mounting loops, an approximate force/vibration profile of the cold-stream is obtained. Results indicate

  14. Communication between the Micro VAX II and Motorola System-1000 for the protein crystallography data acquisition system

    SciTech Connect (OSTI)

    Wang, Hong; Kelley, M.A.

    1989-02-07T23:59:59.000Z

    The HFBR H3A project is designed to study internal structure of biological protein. The data acquisition system will make possible the collection of images in a real-time environment. A Motorola System-1000 with 68020/68881 processor and coprocessor is a real-time microcomputer that controls the data acquisition from two dimensional detectors, a spectrometer controlled by five motors etc. A Micro VAX II is the experimental computer, requesting control functions and defining parameters to the Motorola, and performing final data analysis. In this project, the commands and data are transferred from a Micro VAX II to a Motorola System-1000, the data and return parameters are transferred from the Motorola System-1000 to the Micro VAX II. It is necessary that the same device transfer to/from the Motorola be shared on the Micro VAX II side. Real-time data transfer and real-time control are needed for this data acquisition. The communication between the Motorola System-1000 and the Micro VAX II is performed by the VMIVME-DR11W card of the VME Microsystems International Corporation and the MV-DR11-W card of the MDB Systems Inc. 4 figs.

  15. Johann Deisenhofer, Crystallography, and Proteins

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville PowerCherries 82981-1cnHigh SchoolIn12electron beam chargesJenniferJohann Deisenhofer,

  16. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

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

  17. Modulation of kinase-inhibitor interactions by auxiliary protein binding: Crystallography studies on Aurora A interactions with VX-680 and with TPX2

    SciTech Connect (OSTI)

    Zhao, Baoguang; Smallwood, Angela; Yang, Jingsong; Koretke, Kristin; Nurse, Kelvin; Calamari, Amy; Kirkpatrick, Robert B.; Lai, Zhihong (GSKPA)

    2008-10-24T23:59:59.000Z

    VX-680, also known as MK-0457, is an ATP-competitive small molecule inhibitor of the Aurora kinases that has entered phase II clinical trials for the treatment of cancer. We have solved the cocrystal structure of AurA/TPX2/VX-680 at 2.3 {angstrom} resolution. In the crystal structure, VX-680 binds to the active conformation of AurA. The glycine-rich loop in AurA adopts a unique bent conformation, forming a {pi}-{pi} interaction with the phenyl group of VX-680. In contrast, in the published AurA/VX-680 structure, VX-680 binds to AurA in the inactive conformation, interacting with a hydrophobic pocket only present in the inactive conformation. These data suggest that TPX2, a protein cofactor, can alter the binding mode of VX-680 with AurA. More generally, the presence of physiologically relevant cofactor proteins can alter the kinetics, binding interactions, and inhibition of enzymes, and studies with these multiprotein complexes may be beneficial to the discovery and optimization of enzyme inhibitors as therapeutic agents.

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

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

    Review | Response BioSync: BioSync Home Synchrotron PDB Deposits APS Deposits by Year Resources for Macromolecular Crystallography Interactive Map beta | View Energy Ranges for all...

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

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

    Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic Materials by Ultra-High-Resolution Electron Microscopy and Related Methods DOE 2011 Vehicle Technologies...

  20. 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...

  1. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

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

  2. Lipidic phase membrane protein serial femtosecond crystallography

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated Codes |Is Your HomeLatestCenter (LMI-EFRC) -Choices toLeeLinearb A

  3. A heat-driven monochromatic light source

    SciTech Connect (OSTI)

    Stefani, F.; Lawless, J.L.

    1989-04-01T23:59:59.000Z

    This work investigates theoretically the efficiency with which heat may be converted into resonance radiation in a cesium thermionic diode. An analytical model of a thermionic converter is employed which combines the coupled effects of line radiation transport, excited-state kinetics, and plasma diffusion. Operating regimes are established for various degrees of optical density in the plasma. The results indicate that monochromatic radiation can be produced with efficiencies on the order of 30 percent provided there is an adequate voltage drop across the plasma. In this study, a drop of one volt was used since it can be maintained without any electrical power input to the device. It is found that high efficiencies come by virtue of the higher interelectrode distances which the solutions will accommodate, and that radiation can be generated efficiently, even with optically dense gases.

  4. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

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

  5. SciTech Connect: White and Monochromatic X-ray Microbeam Investigation...

    Office of Scientific and Technical Information (OSTI)

    White and Monochromatic X-ray Microbeam Investigations of Materials Microstructure and Tri-Axial Stress Citation Details In-Document Search Title: White and Monochromatic X-ray...

  6. Distribution of excited species in plasmas by monochromatic imaging

    SciTech Connect (OSTI)

    Hareland, W.A.; Buss, R.J. [Sandia National Labs., Albuquerque, NM (United States)] [Sandia National Labs., Albuquerque, NM (United States)

    1996-02-01T23:59:59.000Z

    Optical emissions from glow discharges have been measured for more than a century and have yielded much of the data on atomic and molecular spectroscopy. In recent years, measuring the intensity of specific emission lines from processing plasmas has become a routine method for process monitoring and control. Here, spatial maps of individual argon atomic emissions are measured in the GEC (gaseous electronic conference) reference reactor by monochromatic imaging. The plasma discharge is viewed through a grating monochromator, and the images are recorded with an intensified charge-coupled device (CCD) array detector. Each atomic emission has a unique spatial profile that is related to the spatial energy distribution in the plasma.

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

    E-Print Network [OSTI]

    Jackson, Jennifer M.

    2000-01-01T23:59:59.000Z

    Hyperfine Interactions 125 (2000) 3­28 3 Monochromatization of synchrotron radiation for nuclear for a variety of nuclear resonances in this energy range. 1. Introduction Synchrotron radiation sources have, IL 60439, USA An introduction to monochromatization of synchrotron radiation in the energy range of 5

  8. Dose, exposure time, and resolution in Serial X-ray Crystallography

    SciTech Connect (OSTI)

    Starodub, D; Rez, P; Hembree, G; Howells, M; Shapiro, D; Chapman, H N; Fromme, P; Schmidt, K; Weierstall, U; Doak, R B; Spence, J C

    2007-03-22T23:59:59.000Z

    Using detailed simulation and analytical models, the exposure time is estimated for serial crystallography, where hydrated laser-aligned proteins are sprayed across a continuous synchrotron beam. The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available fluxes of molecules and X-rays. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of a density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 7 {angstrom} should be possible with short (below 100 s) exposures.

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

    E-Print Network [OSTI]

    Phillips, George N. Jr.

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

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

    E-Print Network [OSTI]

    Ramakrishnan, Venki

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

  11. 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)

    2000-03-14T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Nguyen, Thanhhai; Lu, Xun; Lee, Chang Jun; Jeon, Insu, E-mail: i-jeon@chonnam.ac.kr [School of Mechanical Engineering, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757 (Korea, Republic of); Jung, Jin-Ho [Pro-optics Co., Ltd., 475 Ami-ri, Bubal-eup, Icheon 467-866 (Korea, Republic of); Jin, Gye-Hwan [Department of Radiology, Nambu University, 76 Chumdan Jungang 1-ro, Gwangsan-gu, Gwangju 506-706 (Korea, Republic of); Kim, Sung Youb [School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Eonyang-eup, Ulju-gun, Ulsan 689-798 (Korea, Republic of)

    2014-09-15T23:59:59.000Z

    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.

  13. Dispersion-free monochromatization method for selecting a single-order harmonic beam

    E-Print Network [OSTI]

    Takahashi, Eiji J; Ichimaru, Satoshi; Midorikawa, Katsumi

    2015-01-01T23:59:59.000Z

    We propose a method to monochromatize multiple orders of high harmonics by using a proper designed multilayer mirror. Multilayer mirrors designed by our concept realize the perfect extraction of a single-order harmonic from multiple-order harmonic beam, and exhibit broadband tenability and high reflectivity in the soft-x-ray region. Furthermore, the proposed monochromatization method can preserve the femtosecond to attosecond pulse duration for the reflected beam. This device is very useful for ultrafast soft x-ray experiments that require high-order harmonic beams, such as femtosecond/attosecond, time-resolved, pump-probe spectroscopy.

  14. Extending The Methodology Of X-ray Crystallography To Allow X-ray

    E-Print Network [OSTI]

    Miao, Jianwei "John"

    , the radiation damage. While the radiation damage problem can be mitigated somewhat by using cryogenic techniques resolution without serious radiation damage to the specimens. Although X-ray crystallography becomesExtending The Methodology Of X-ray Crystallography To Allow X-ray Microscopy Without X-ray Optics

  15. Solution-processed infrared photovoltaic devices with >10% monochromatic internal quantum efficiency

    E-Print Network [OSTI]

    photovolta- ics are limited to about 3%. This arises partly from the lim- ited efficiency with which carriers applications emit predominantly in the 1­3 m range; these require efficient infrared photovoltaicsSolution-processed infrared photovoltaic devices with >10% monochromatic internal quantum

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

    E-Print Network [OSTI]

    Martin, Langdon James

    2008-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Takeda, Yasuhiko, E-mail: takeda@mosk.tytlabs.co.jp; Iizuka, Hideo; Mizuno, Shintaro; Hasegawa, Kazuo; Ichikawa, Tadashi; Ito, Hiroshi; Kajino, Tsutomu [Toyota Central Research and Development Laboratories, Inc., 41-1, Yokomichi, Nagakute, Aichi 480-1192 (Japan); Ichiki, Akihisa; Motohiro, Tomoyoshi [Green Mobility Collaborative Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan)

    2014-09-28T23:59:59.000Z

    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{sup 2?}??1?kW/cm{sup 2}, compared with the efficiency for the perfect anti-reflection treatment to the surface of a conventional solar cell.

  18. Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling.

    SciTech Connect (OSTI)

    Fang, Bin; Fu, Guoxing; Agniswamy, Johnson; Harrison, Robert W.; Weber, Irene T.; (GSU)

    2009-03-31T23:59:59.000Z

    Caspase-3 recognition of various P4 residues in its numerous protein substrates was investigated by crystallography, kinetics, and calculations on model complexes. Asp is the most frequent P4 residue in peptide substrates, although a wide variety of P4 residues are found in the cellular proteins cleaved by caspase-3. The binding of peptidic inhibitors with hydrophobic P4 residues, or no P4 residue, is illustrated by crystal structures of caspase-3 complexes with Ac-IEPD-Cho, Ac-WEHD-Cho, Ac-YVAD-Cho, and Boc-D(OMe)-Fmk at resolutions of 1.9-2.6 {angstrom}. The P4 residues formed favorable hydrophobic interactions in two separate hydrophobic regions of the binding site. The side chains of P4 Ile and Tyr form hydrophobic interactions with caspase-3 residues Trp206 and Trp214 within a non-polar pocket of the S4 subsite, while P4 Trp interacts with Phe250 and Phe252 that can also form the S5 subsite. These interactions of hydrophobic P4 residues are distinct from those for polar P4 Asp, which indicates the adaptability of caspase-3 for binding diverse P4 residues. The predicted trends in peptide binding from molecular models had high correlation with experimental values for peptide inhibitors. Analysis of structural models for the binding of 20 different amino acids at P4 in the aldehyde peptide Ac-XEVD-Cho suggested that the majority of hydrophilic P4 residues interact with Phe250, while hydrophobic residues interact with Trp206, Phe250, and Trp214. Overall, the S4 pocket of caspase-3 exhibits flexible adaptation for different residues and the new structures and models, especially for hydrophobic P4 residues, will be helpful for the design of caspase-3 based drugs.

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

    SciTech Connect (OSTI)

    Hall, G. N., E-mail: gareth.hall@imperial.ac.uk; 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. [The Blackett Laboratory, Imperial College, London SW7 2BW (United Kingdom)

    2014-11-15T23:59:59.000Z

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

  20. A monochromatic x-ray imaging system for characterizing low-density foams

    SciTech Connect (OSTI)

    Lanier, Nicholas E. [Los Alamos National Laboratory; Taccetti, Jose M. [Los Alamos National Laboratory; Hamilton, Christopher E. [Los Alamos National Laboratory

    2012-05-04T23:59:59.000Z

    In High Energy Density (HED) laser experiments, targets often require small, low-density, foam components. However, their limited size can preclude single component characterization, forcing one to rely solely on less accurate bulk measurements. We have developed a monochromatic imaging a system to characterize both the density and uniformity of single component low-mass foams. This x-ray assembly is capable of determining line-averaged density variations near the 1% level, and provides statistically identical results to those obtained at the Brookhaven's NSLS. This system has the added benefit of providing two-dimensional density data, allowing an assessment of density uniformity.

  1. Monochromatic imaging of scattered laser light from in situ generated particles in plasmas

    SciTech Connect (OSTI)

    Hareland, W.A.; Buss, R.J.; Brown, D.A. [Sandia National Labs., Albuquerque, NM (United States)] [Sandia National Labs., Albuquerque, NM (United States); Collins, S.M. [Univ. of Arizona, Tucson, AZ (United States)] [Univ. of Arizona, Tucson, AZ (United States)

    1996-02-01T23:59:59.000Z

    In recent years, there has been a great deal of interest in the behavior of particles in plasmas because of the negative economic impact of contamination during processing of silicon for microelectronics manufacture. Here, spatially resolved images of particle distributions are measured in steady-state plasmas in a GEC (gaseous electronics conference) plasma reactor. Images are obtained by monochromatic imaging of scattered laser light using a microchannel plate (MCP) image intensifier and a high-speed video camera. The observed distributions of particulates generated by adding small quantities of CHF{sub 3} to an argon plasma are extremely complex and diverse. The patterns observed are temporally varying, and rarely as simple as domes and rings observed in other reactors. The forces acting on the particles are sufficiently complex that reproducing specific spatial patterns by controlling processing parameters if often impossible.

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

    SciTech Connect (OSTI)

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

    2011-07-15T23:59:59.000Z

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

  3. Virtual monochromatic imaging in dual-source and dual-energy CT for visualization of acute ischemic stroke

    E-Print Network [OSTI]

    Hara, Hidetake; Matsuzawa, Hiroki; Inoue, Toshiyuki; Abe, Shinji; Satoh, Hitoshi; Nakajima, Yasuo

    2015-01-01T23:59:59.000Z

    We have recently developed a phantom that simulates acute ischemic stroke. We attempted to visualize acute-stage cerebral infarction by applying virtual monochromatic images to this phantom using dual-energy CT (DECT). Virtual monochromatic images were created using DECT from 40 to 100 keV at every 10 keV and from 60 to 80 keV at every 1 keV, under three energy conditions of tube voltages with thin (Sn) filters. Calculation of the CNR values allowed us to evaluate the visualization of acute-stage cerebral infarction. The CNR value of a virtual monochromatic image was the highest at 68 keV under 80 kV / Sn 140 kV, at 72 keV under 100 kV / Sn 140 kV, and at 67 keV under 140 kV / 80 kV. The CNR values of virtual monochromatic images between 65 and 75 keV were significantly higher than those obtained for all other created energy images. Therefore, optimal conditions for visualizing acute ischemic stroke were achievable.

  4. Broadband and Monochromatic X-ray Irradiation of Platinum: Monte Carlo Simulations for Dose Enhancement Factors and Resonant Theranostics

    E-Print Network [OSTI]

    Nahar, Sultana Nurun

    Enhancement Factors and Resonant Theranostics S. Lim1 , M.Montenegro2 , A.K. Pradhan1, 3 , S.N. Nahar3 , E with platinum as an agent for killing cancerous cells via increased linear-energy-transfer (LET) and dose enhancement. We also describe a simple de- vice for broadband-to-monochromatic (B2M) conversion. Materials

  5. PublishedbyManeyPublishing(c)IOMCommunicationsLtd Crystallography of Widmanstatten austenite in

    E-Print Network [OSTI]

    Cambridge, University of

    in duplex stainless steel weld metal J. W. Abtibol Menezes1 , H. Abreu1,2 , S. Kundu3 , H. K. D. H of austenite. Keywords: Duplex stainless steels, Welding, Crystallography, Texture Introduction The combination of good mechanical properties and corrosion resistance of duplex stainless steel is attributed

  6. WHAT DOES DATABASE FEDERATION MEAN TO CRYSTALLOGRAPHY? Philip E. Bourne123

    E-Print Network [OSTI]

    Bourne, Philip E.

    WHAT DOES DATABASE FEDERATION MEAN TO CRYSTALLOGRAPHY? Philip E. Bourne123 , Ilya N. Shindyalov1 More than ever crystallographers are faced with using a variety of databases, each with its own content, organization and query interface. Database federation offers the promise of a unified view of these disparate

  7. INTRODUCTION TO FOURIER-SPACE CRYSTALLOGRAPHY Lecture notes for the International School on Quasicrystals

    E-Print Network [OSTI]

    Lifshitz, Ron

    INTRODUCTION TO FOURIER-SPACE CRYSTALLOGRAPHY Lecture notes for the International School- sential attribute of crystallinity from position space to Fourier space.1 Within the family of crystals is to describe the corresponding shift to Fourier space in the crystallographic classification scheme, proposed

  8. Proteins

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtectingSciTech Connect ProteinShop:

  9. LISA data analysis: The monochromatic binary detection and initial guess problems

    E-Print Network [OSTI]

    Ronald W. Hellings

    2002-06-07T23:59:59.000Z

    We consider the detection and initial guess problems for the LISA gravitational wave detector. The detection problem is the problem of how to determine if there is a signal present in instrumental data and how to identify it. Because of the Doppler and plane-precession spreading of the spectral power of the LISA signal, the usual power spectrum approach to detection will have difficulty identifying sources. A better method must be found. The initial guess problem involves how to generate {\\it a priori} values for the parameters of a parameter-estimation problem that are close enough to the final values for a linear least-squares estimator to converge to the correct result. A useful approach to simultaneously solving the detection and initial guess problems for LISA is to divide the sky into many pixels and to demodulate the Doppler spreading for each set of pixel coordinates. The demodulated power spectra may then be searched for spectral features. We demonstrate that the procedure works well as a first step in the search for gravitational waves from monochromatic binaries.

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

    SciTech Connect (OSTI)

    Gao, Xinliang; Lu, Quanming; Shan, Lican; Wang, Shui [CAS Key Laboratory of Geospace Environment, Department of Geophysics and Planetary Science, University of Science and Technology of China, Hefei 230026 (China)] [CAS Key Laboratory of Geospace Environment, Department of Geophysics and Planetary Science, University of Science and Technology of China, Hefei 230026 (China); Li, Xing [Institute of Mathematics and Physics, Aberystwyth University, Aberystwyth SY23 3BZ (United Kingdom)] [Institute of Mathematics and Physics, Aberystwyth University, Aberystwyth SY23 3BZ (United Kingdom)

    2013-07-15T23:59:59.000Z

    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.

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration wouldDECOMPOSITION OFSupplemental TechnologySummary of DSO 216Daily780

  12. Electron crystallography as an informative method for studying the structure of nanoparticles

    SciTech Connect (OSTI)

    Avilov, A. S., E-mail: avilovanatoly@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Gubin, S. P. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)] [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Zaporozhets, M. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)] [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2013-11-15T23:59:59.000Z

    The overwhelming majority of modern nanotechnologies deal with nanoparticles owing to the great variety of their unusual properties, which make them irreplaceable in various fields of science and technology. Since the physical properties of nanoparticles depend on their composition, structure, and shape, the problem of monitoring these parameters both after and during formation of nanoparticles is very important. Methods of electron crystallography are most informative and appropriate for studying and monitoring nanoparticle parameters. In this review, we briefly report the main modern methods based on the use of electron diffraction and electron microscopy, along with examples of their applications for nanoparticles, to solve a number of urgent structural problems of nanomaterials science.

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

    E-Print Network [OSTI]

    Herschlag, Dan

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

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

    E-Print Network [OSTI]

    Agard, David

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

  15. LEED crystallography studies of the structure of clean and adsorbate-covered Ir, Pt and Rh crystal surfaces

    SciTech Connect (OSTI)

    Koestner, R.J.

    1982-08-01T23:59:59.000Z

    There have only been a few Low Energy Electron Diffraction (LEED) intensity analyses carried out to determine the structure of molecules adsorbed on metal surfaces; most surface crystallography studies concentrated on the structure of clean unreconstructed or atomic adsorbate-covered transition metal faces. The few molecular adsorption systems already investigated by dynamical LEED are CO on Ni(100), Cu(100) and Pd(100) as well as C/sub 2/H/sub 2/ and C/sub 2/H/sub 4/ adsorbed on Pt(111). The emphasis of this thesis research has been to extend the applicability of LEED crystallography to the more complicated unit cells found in molecular overlayers on transition metals or in there constructed surfaces of clean transition metals.

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

    E-Print Network [OSTI]

    Bru, Jean-Bernard; Westrich, Matthias

    2012-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2012-01-27T23:59:59.000Z

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

  18. 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

    2010-04-08T23:59:59.000Z

    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.

  19. Recoilless Resonant Absorption of Monochromatic Neutrino Beam for Measuring Delta m^2_{31} and theta_{13}

    E-Print Network [OSTI]

    Hisakazu Minakata; Shoichi Uchinami

    2006-08-05T23:59:59.000Z

    We discuss, in the context of precision measurement of Delta m^2_{31} and theta_{13}, physics capabilities enabled by the recoilless resonant absorption of monochromatic antineutrino beam enhanced by the M\\"ossbauer effect recently proposed by Raghavan. Under the assumption of small relative systematic error of a few tenth of percent level between measurement at different detector locations, we give analytical and numerical estimates of the sensitivities to Delta m^2_{31} and sin^2 2theta_{13}. The accuracies of determination of them are enormous; The fractional uncertainty in Delta m^2_{31} achievable by 10 point measurement is 0.6% (2.4%) for sin^2 2theta_{13} = 0.05, and the uncertainty of sin^2 2theta_{13} is 0.002 (0.008) both at 1 sigma CL with the optimistic (pessimistic) assumption of systematic error of 0.2% (1%). The former opens a new possibility of determining the neutrino mass hierarchy by comparing the measured value of Delta m^2_{31} with the one by accelerator experiments, while the latter will help resolving the theta_{23} octant degeneracy.

  20. 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.

    2015-02-01T23:59:59.000Z

    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 Ĺ resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

  1. Computational Assignment of Chemical Shifts for Protein Residues

    E-Print Network [OSTI]

    Bratholm, Lars A

    2013-01-01T23:59:59.000Z

    Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel properties. X-ray crystallography is the most common approach even with its low success rate, but lately NMR based approaches have gained popularity. The general approach involves a set of distance restraints used to guide a structure prediction, but simple NMR triple-resonance experiments often provide enough structural information to predict the structure of small proteins. Previous protein folding simulations that have utilised experimental data have weighted the experimental data and physical force field terms more or less arbitrarily, and the method is thus not generally applicable to new proteins. Furthermore a complete and near error-free assignment of chemical shifts obtained by the NMR experiments is needed, due to the static, or deterministic, assignment. In this ...

  2. Multistable monochromatic laser solitons

    SciTech Connect (OSTI)

    Genevet, P.; Columbo, L.; Barland, S.; Giudici, M.; Gil, L.; Tredicce, J. R. [Universite de Nice Sophia Antipolis, Institut Non-Lineaire de Nice, UMR 6618, F-06560 Valbonne (France)

    2010-05-15T23:59:59.000Z

    We study the spectral properties of stationary laser solitons (LSs) generated in two broad-area vertical cavity surface emitting lasers coupled to each other in face-to-face configuration [P. Genevet et al., Phys. Rev. Lett. 101, 123905 (2008)]. We demonstrate experimentally that LS emission occurs on a single longitudinal mode frequency of the compound cavity. Multistability is reported among differently 'colored' LSs. We also develop a theoretical model beyond the single longitudinal mode approximation whose numerical simulation results are in good agreement with the experimental observations.

  3. The e/{pi} and {pi}{sup 0}/{pi} ratios measured, and monochromatic {gamma} and {pi}{sup 0} beams explored in the D0 test calorimeter

    SciTech Connect (OSTI)

    Tartaglia, M.A.; D0 Collaboration

    1992-10-01T23:59:59.000Z

    The e/{pi} response ratio of the DO end calorimeter has been measured by comparing data from 10 to 150 GeV/c electron and pion beams. The ``intrinsic`` e/{pi} of the fine-hadronic module has also been studied with the pions alone, by selecting {pi}{sup 0}-like showers contained within individual layers of the calorimeter. The measurements are compared to GEANT Monte Carlo simulations. A technique to generate monochromatic test beams of photons and neutral pions was successfully investigated. Preliminary results from central calorimeter modules exposed to these beams are discussed, and are compared to calculated expectations.

  4. Femtosecond X-ray protein nanocrystallography

    SciTech Connect (OSTI)

    Chapman, Henry N.; Fromme, Petra; Barty, Anton; White, Thomas A.; Kirian, Richard A.; Aquila, Andrew; Hunter, Mark S.; Schulz, Joachim; DePonte, Daniel P.; Weierstall, Uwe; Doak, R. Bruce; Maia, Filipe R. N. C.; Martin, Andrew V.; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L.; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sebastien; Bogan, Michael J.; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Sasa; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Homke, Andre; Reich, Christian; Pietschner, Daniel; Struder, Lothar; Hauser, Gunter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kuhnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D.; Hau-Riege, Stefan P.; Frank, Matthias; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Williams, Garth J.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jonsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schroter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E.; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M.; Barends, Thomas R. M.; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Bjorn; Spence, John C. H.

    2011-01-01T23:59:59.000Z

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200?nm to 2??m in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  5. Fluorescence-type Monochromatic X-ray Beam-position Monitor with High-spatial Resolution for the NSLS-II Beamlines

    SciTech Connect (OSTI)

    Yoon, Phil S. [Experimental Facility Division, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973 (United States); Siddons, D. Peter [Experimental Systems, NSLS, Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2010-06-23T23:59:59.000Z

    We developed a fluorescence-type monochromatic X-ray beam-position monitor (X-BPM) with high-spatial resolution for end-station experiments at the initial project beamlines of the NSLS-II. We designed a ring array of multi-segmented Si PIN-junction photodiodes to use as a position sensor. Further, we integrated a low-noise charge-preamplification HERMES4 ASIC chip into an electronic readout system for photon-counting application. A series of precision measurements to characterize electronically the Si-photodiode sensor and the ASIC chip demonstrated that the inherent noise from the detector system is sufficiently low to meet our stringent requirements. Using a Gaussian beam, we parametrically modeled the optimum working distance to ensure the detector's best performance. Based upon the results from the parametric modeling, prototypes of the next versions of the X-BPM are being developed. In this paper, we describe the methodology for developing the new compact monochromatic X-ray BPM, including its instrumentation, detector modeling, and future plan.

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

    DOE Patents [OSTI]

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

    2007-09-25T23:59:59.000Z

    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.

  7. 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.

    2005-07-19T23:59:59.000Z

    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.

  8. 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

    2009-06-08T23:59:59.000Z

    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.

  9. 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)

    2013-08-01T23:59:59.000Z

    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.

  10. 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 [European Synchrotron Radiation Facility, F-38043 Grenoble (France); Terrien, Maxime [Université Grenoble Alpes, IBS, F-38044 Grenoble (France); CNRS, IBS, F-38044 Grenoble (France); CEA, IBS, F-38044 Grenoble (France); Dobias, Fabien [European Synchrotron Radiation Facility, F-38043 Grenoble (France); Juers, Douglas H. [Whitman College, Walla Walla, WA 99362 (United States); Flot, David; Mueller-Dieckmann, Christoph; Leonard, Gordon A.; Sanctis, Daniele de [European Synchrotron Radiation Facility, F-38043 Grenoble (France); Royant, Antoine, E-mail: antoine.royant@ibs.fr [European Synchrotron Radiation Facility, F-38043 Grenoble (France); Université Grenoble Alpes, IBS, F-38044 Grenoble (France); CNRS, IBS, F-38044 Grenoble (France); CEA, IBS, F-38044 Grenoble (France)

    2015-01-01T23:59:59.000Z

    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.

  11. Verification of TG-61 dose for synchrotron-produced monochromatic x-ray beams using fluence-normalized MCNP5 calculations

    SciTech Connect (OSTI)

    Brown, Thomas A. D.; Hogstrom, Kenneth R.; Alvarez, Diane; Matthews, Kenneth L. II; Ham, Kyungmin [Mary Bird Perkins Cancer Center, 4950 Essen Lane, Baton Rouge, Louisiana 70809 and Department of Physics and Astronomy, Louisiana State University and A and M College, 202 Nicholson Hall, Baton Rouge, Louisiana 70803 (United States); Department of Physics and Astronomy, Louisiana State University and A and M College, 202 Nicholson Hall, Baton Rouge, Louisiana 70803 (United States); Center for Advanced Microstructures and Devices, Louisiana State University and A and M College, 6980 Jefferson Highway, Baton Rouge, Louisiana 70806 (United States)

    2012-12-15T23:59:59.000Z

    Purpose: Ion chamber dosimetry is being used to calibrate dose for cell irradiations designed to investigate photoactivated Auger electron therapy at the Louisiana State University Center for Advanced Microstructures and Devices (CAMD) synchrotron facility. This study performed a dosimetry intercomparison for synchrotron-produced monochromatic x-ray beams at 25 and 35 keV. Ion chamber depth-dose measurements in a polymethylmethacrylate (PMMA) phantom were compared with the product of MCNP5 Monte Carlo calculations of dose per fluence and measured incident fluence. Methods: Monochromatic beams of 25 and 35 keV were generated on the tomography beamline at CAMD. A cylindrical, air-equivalent ion chamber was used to measure the ionization created in a 10 Multiplication-Sign 10 Multiplication-Sign 10-cm{sup 3} PMMA phantom for depths from 0.6 to 7.7 cm. The American Association of Physicists in Medicine TG-61 protocol was applied to convert measured ionization into dose. Photon fluence was determined using a NaI detector to make scattering measurements of the beam from a thin polyethylene target at angles 30 Degree-Sign -60 Degree-Sign . Differential Compton and Rayleigh scattering cross sections obtained from xraylib, an ANSI C library for x-ray-matter interactions, were applied to derive the incident fluence. MCNP5 simulations of the irradiation geometry provided the dose deposition per photon fluence as a function of depth in the phantom. Results: At 25 keV the fluence-normalized MCNP5 dose overestimated the ion-chamber measured dose by an average of 7.2 {+-} 3.0%-2.1 {+-} 3.0% for PMMA depths from 0.6 to 7.7 cm, respectively. At 35 keV the fluence-normalized MCNP5 dose underestimated the ion-chamber measured dose by an average of 1.0 {+-} 3.4%-2.5 {+-} 3.4%, respectively. Conclusions: These results showed that TG-61 ion chamber dosimetry, used to calibrate dose output for cell irradiations, agreed with fluence-normalized MCNP5 calculations to within approximately 7% and 3% at 25 and 35 keV, respectively.

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

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

  13. 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

    2015-07-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Lorenzo Iorio

    2014-09-12T23:59:59.000Z

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

  15. Rotational order–disorder structure of fluorescent protein FP480

    SciTech Connect (OSTI)

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

    2009-09-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Wallace, B.

    2009-01-01T23:59:59.000Z

    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.

  17. electronic reprint Crystallography

    E-Print Network [OSTI]

    Meagher, Mary

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

  18. electronic reprint Crystallography

    E-Print Network [OSTI]

    Jacobsen, Steven D.

    of commonly used pressure media, including nitrogen, argon, 2-propanol, a 4:1 methanol­ethanol mixture curves of quartz is detected at $9.8 GPa in a 4:1 mixture of methanol and ethanol and at $4.2 GPa in 2 transition in 4:1 methanol­ethanol and 16:3:1 methanol­ ethanol­water, which were observed to support shear

  19. electronic reprint Crystallography

    E-Print Network [OSTI]

    Ismagilov, Rustem F.

    , Cory J. Gerdts, Ruslan Sanishvili, Ward W. Smith, L. Spencer Roach, Rustem F. Ismagilov, Peter Kuhn Sanishvili,c Ward W. Smith,c L. Spencer Roach,b Rustem F. Ismagilov,b Peter Kuhna and Raymond C. Stevensd

  20. electronic reprint Crystallography

    E-Print Network [OSTI]

    Borgstahl, Gloria

    . Fine-'-sliced topographic data (0.002 ) stills were collected with a digital topography system Tracking reflections through cryogenic cooling with topography Jeffrey J. Lovelace, Cameron R. Murphy et al. Ż Cryogenic cooling with topography #12;research papers J. Appl. Cryst. (2006). 39, 425

  1. electronic reprint Crystallography

    E-Print Network [OSTI]

    Schmidt, Marius

    -probe type. A reaction is initiated in a crystal usually by an intense, ultra-short laser flash (the pump

  2. SMB, Macromolecular Crystallography

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiation Protection245C Unlimited ReleaseWelcome to the LCLSTransportationMacromolecular

  3. Macromolecular Crystallography - Beamline facilities

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated Codes |IsLove Your Home and It'll Love YouTokamak |MPCTraining5Search Home

  4. Protein-Protein Interactions in Crystals of the Human Receptor-Type Protein Tyrosine Phosphatase ICA512 Ectodomain

    SciTech Connect (OSTI)

    Primo M. E.; Jakoncic J.; Noguera M.E.; Risso V.A.; Sosa L.; Sica M.P.; Solimena M.; Poskus E. and Ermacora M.

    2011-09-15T23:59:59.000Z

    ICA512 (or IA-2) is a transmembrane protein-tyrosine phosphatase located in secretory granules of neuroendocrine cells. Initially, it was identified as one of the main antigens of autoimmune diabetes. Later, it was found that during insulin secretion, the cytoplasmic domain of ICA512 is cleaved and relocated to the nucleus, where it stimulates the transcription of the insulin gene. The role of the other parts of the receptor in insulin secretion is yet to be unveiled. The structures of the intracellular pseudocatalytic and mature extracellular domains are known, but the transmembrane domain and several intracellular and extracellular parts of the receptor are poorly characterized. Moreover the overall structure of the receptor remains to be established. We started to address this issue studying by X-ray crystallography the structure of the mature ectodomain of ICA512 (ME ICA512) and variants thereof. The variants and crystallization conditions were chosen with the purpose of exploring putative association interfaces, metal binding sites and all other structural details that might help, in subsequent works, to build a model of the entire receptor. Several structural features were clarified and three main different association modes of ME ICA512 were identified. The results provide essential pieces of information for the design of new experiments aimed to assess the structure in vivo.

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

    SciTech Connect (OSTI)

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

    2015-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2014-01-01T23:59:59.000Z

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

  7. Computational tools for experimental determination and theoretical prediction of protein structure

    SciTech Connect (OSTI)

    O`Donoghue, S.; Rost, B.

    1995-12-31T23:59:59.000Z

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

  8. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

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

  9. Powder Diffraction Crystallography Instructional Materials

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

    a set of exercises, and a Flash movie made of the demo for the first exercise. Learning to Use CMPR CMPR is a multipurpose program that can be used for displaying...

  10. Neutron crystallography aids drug design

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated CodesTransparency VisitSilverNephelineNeural probe design

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

    SciTech Connect (OSTI)

    Barends, Thomas, R.M.

    2013-11-25T23:59:59.000Z

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

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

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

    Barends, Thomas, R.M.

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

  13. From: Methods in Molecular Biology, vol. 363: Macromolecular Crystallography Protocols: Volume 1: Preparation and Crystallization of Macromolecules Edited by: S. Doubli Humana Press Inc., Totowa, NJ

    E-Print Network [OSTI]

    (MBP) has emerged as an attractive vehicle for the production of recombinant proteins (1,2). However protocol should be readily amenable to automation for high-throughput applications. 2. Materials 2

  14. The E3 Ubiquitin Ligase- and Protein Phosphatase 2A (PP2A)-binding Domains of the Alpha4 Protein Are Both Required for Alpha4 to Inhibit PP2A Degradation

    SciTech Connect (OSTI)

    LeNoue-Newton, Michele; Watkins, Guy R.; Zou, Ping; Germane, Katherine L.; McCorvey, Lisa R.; Wadzinski, Brian E.; Spiller, Benjamin W. (Vanderbilt)

    2012-04-30T23:59:59.000Z

    Protein phosphatase 2A (PP2A) is regulated through a variety of mechanisms, including post-translational modifications and association with regulatory proteins. Alpha4 is one such regulatory protein that binds the PP2A catalytic subunit (PP2Ac) and protects it from polyubiquitination and degradation. Alpha4 is a multidomain protein with a C-terminal domain that binds Mid1, a putative E3 ubiquitin ligase, and an N-terminal domain containing the PP2Ac-binding site. In this work, we present the structure of the N-terminal domain of mammalian Alpha4 determined by x-ray crystallography and use double electron-electron resonance spectroscopy to show that it is a flexible tetratricopeptide repeat-like protein. Structurally, Alpha4 differs from its yeast homolog, Tap42, in two important ways: (1) the position of the helix containing the PP2Ac-binding residues is in a more open conformation, showing flexibility in this region; and (2) Alpha4 contains a ubiquitin-interacting motif. The effects of wild-type and mutant Alpha4 on PP2Ac ubiquitination and stability were examined in mammalian cells by performing tandem ubiquitin-binding entity precipitations and cycloheximide chase experiments. Our results reveal that both the C-terminal Mid1-binding domain and the PP2Ac-binding determinants are required for Alpha4-mediated protection of PP2Ac from polyubiquitination and degradation.

  15. High efficiency quasi-monochromatic infrared emitter

    SciTech Connect (OSTI)

    Brucoli, Giovanni; Besbes, Mondher; Benisty, Henri, E-mail: henri.benisty@institutoptique.fr; Greffet, Jean-Jacques [Laboratoire Charles Fabry, UMR 8501, Institut d’Optique, CNRS, Université Paris-Sud 11, 2, Avenue Augustin Fresnel, 91127 Palaiseau Cedex (France); Bouchon, Patrick; Haďdar, Riad [Office National d’Études et de Recherches Aérospatiales, Chemin de la Huničre, 91761 Palaiseau (France)

    2014-02-24T23:59:59.000Z

    Incandescent radiation sources are widely used as mid-infrared emitters owing to the lack of alternative for compact and low cost sources. A drawback of miniature hot systems such as membranes is their low efficiency, e.g., for battery powered systems. For targeted narrow-band applications such as gas spectroscopy, the efficiency is even lower. In this paper, we introduce design rules valid for very generic membranes demonstrating that their energy efficiency for use as incandescent infrared sources can be increased by two orders of magnitude.

  16. Diamondoid Monolayers as Monochromatic Electron Source

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

    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...

  17. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract Management FermiDavid TurnerExperimental Capabilities NIF

  18. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract Management FermiDavid TurnerExperimental Capabilities NIFDiamondoid

  19. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign: Potential ApplicationYu, James CowinPhysicsDiamondoid

  20. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign: Potential ApplicationYu, James

  1. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign: Potential ApplicationYu, JamesDiamondoid Monolayers as

  2. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign: Potential ApplicationYu, JamesDiamondoid Monolayers

  3. Diamondoid Monolayers as Monochromatic Electron Source

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign: Potential ApplicationYu, JamesDiamondoid MonolayersDiamondoid

  4. Shotgun protein sequencing.

    SciTech Connect (OSTI)

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

    2009-06-01T23:59:59.000Z

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

  5. Protein-protein complexation in bioluminescence

    E-Print Network [OSTI]

    Zhijie, Liu

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

  6. 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...

  7. Culex quinquefasciatus Storage Proteins

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

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

  8. Engineering novel fluorescent proteins

    E-Print Network [OSTI]

    Shaner, Nathan Christopher

    2006-01-01T23:59:59.000Z

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

  9. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

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

  10. Probing the MgATP-Bound Conformation of the Nitrogenase Fe Protein By Solution Small-Angle X-Ray Scattering

    SciTech Connect (OSTI)

    Sarma, R.; Mulder, D.W.; Brecht, E.; Szilagyi, R.K.; Seefeldt, L.C.; Tsuruta, H.; Peters, J.W.; /Montana State U. /SLAC, SSRL /Utah State U.

    2009-04-30T23:59:59.000Z

    The MgATP-bound conformation of the Fe protein of nitrogenase from Azotobacter vinelandii has been examined in solution by small-angle X-ray scattering (SAXS) and compared to existing crystallographically characterized Fe protein conformations. The results of the analysis of the crystal structure of an Fe protein variant with a Switch II single-amino acid deletion recently suggested that the MgATP-bound state of the Fe protein may exist in a conformation that involves a large-scale reorientation of the dimer subunits, resulting in an overall elongated structure relative to the more compact structure of the MgADP-bound state. It was hypothesized that the Fe protein variant may be a conformational mimic of the MgATP-bound state of the native Fe protein largely on the basis of the observation that the spectroscopic properties of the [4Fe-4S] cluster of the variant mimicked in part the spectroscopic signatures of the native nitrogenase Fe protein in the MgATP-bound state. In this work, SAXS studies reveal that the large-scale conformational differences between the native Fe protein and the variant observed by X-ray crystallography are also observed in solution. In addition, comparison of the SAXS curves of the Fe protein nucleotide-bound states to the nucleotide-free states indicates that the conformation of the MgATP-bound state in solution does not resemble the structure of the variant as initially proposed, but rather, at the resolution of this experiment, it resembles the structure of the nucleotide-free state. These results provide insights into the Fe protein conformations that define the role of MgATP in nitrogenase catalysis.

  11. 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.

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

    DOE Patents [OSTI]

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

    2010-02-23T23:59:59.000Z

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

  13. Protein Structure Analysis Iosif Vaisman

    E-Print Network [OSTI]

    Vaisman, Iosif

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

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

    SciTech Connect (OSTI)

    Cuttitta, Christina M. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314 (United States); Ericson, Daniel L. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260 (United States); Scalia, Alexander [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Binghamton University, 4400 Vestal Parkway East, Binghamton, NY 11973-5000 (United States); Roessler, Christian G. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Teplitsky, Ella [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Stony Brook University, Stony Brook, NY 11794-5215 (United States); Joshi, Karan [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); PEC University of Technology, Chandigarh (India); Campos, Olven [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33414 (United States); Agarwal, Rakhi; Allaire, Marc [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Orville, Allen M. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Sweet, Robert M.; Soares, Alexei S., E-mail: soares@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)

    2015-01-01T23:59:59.000Z

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

  15. LANSCE | Lujan Center | Instruments

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

    HIPPO, NPDF, SMARTS Engineering Diffraction: SMARTS Reflectometer: ASTERIX Small Angle Neutron Scattering: LQD Protein Crystallography: PCS Single Crystal Diffractometer:...

  16. Destabilized bioluminescent proteins

    DOE Patents [OSTI]

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

    2007-07-31T23:59:59.000Z

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

  17. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    NONE

    1995-12-31T23:59:59.000Z

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

  19. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Fernández Suárez, Marta

    2008-01-01T23:59:59.000Z

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

  1. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12T23:59:59.000Z

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

  2. Pressure cryocooling protein crystals

    DOE Patents [OSTI]

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

    2011-10-04T23:59:59.000Z

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

  3. Self assembling proteins

    DOE Patents [OSTI]

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

    2004-06-29T23:59:59.000Z

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

  4. . DNA, RNA, Protein

    E-Print Network [OSTI]

    Yoo, SukIn

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

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

    E-Print Network [OSTI]

    Haspel, Nurit

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

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

    E-Print Network [OSTI]

    Fusco, Diana

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

  7. Peptidomimetics to mimic protein-protein interactions

    E-Print Network [OSTI]

    Xia, Zebin

    2005-08-29T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Podgornaia, Anna Igorevna

    2014-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2012-06-27T23:59:59.000Z

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

  10. Interfacial rheology of globular proteins

    E-Print Network [OSTI]

    Jaishankar, Aditya

    2011-01-01T23:59:59.000Z

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

  11. Protein folding and cosmology

    E-Print Network [OSTI]

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

    1997-06-04T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    2001-07-03T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Neumaier, Arnold

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

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

    E-Print Network [OSTI]

    Neumaier, Arnold

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

  15. The unfolded-protein-response

    E-Print Network [OSTI]

    Walter, Peter

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

  16. INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION

    E-Print Network [OSTI]

    Halligan, Daniel

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

  17. Computer Simulations of Protein Folding

    E-Print Network [OSTI]

    Sorin, Eric J.

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

  18. Expression of Recombinant Proteins in Microalgae

    E-Print Network [OSTI]

    Mayfield, Stephen P.; Franklin, Scott E.

    2003-01-01T23:59:59.000Z

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

  19. Protein sequence databases Rolf Apweiler1,

    E-Print Network [OSTI]

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

  20. COMPUTATIONAL METHODOLOGY IN CRYSTALLOGRAPHY: EVALUATION AND EXTENSION

    E-Print Network [OSTI]

    Templeton Ed, D.

    2011-01-01T23:59:59.000Z

    Chandra, R. (1978). "Conjugate Gradient Methods for Partial1918). "On the Conjugate Gradient Method for Solving Linearto the constraints) then a conjugate gradient method is not

  1. COMPUTATIONAL METHODOLOGY IN CRYSTALLOGRAPHY: EVALUATION AND EXTENSION

    E-Print Network [OSTI]

    Templeton Ed, D.

    2011-01-01T23:59:59.000Z

    provide line drawing graphics. The control circuitry for thegraphics, voice input, voice output, the ability to controlcontrol, data reduction), Fourier and in-/erse Fourier transforma.tion, direct methods, phase extension and refinement, model ~Jilding (computer graphics,

  2. Advancing Methods for Biomolecular 1 Crystallography 2

    E-Print Network [OSTI]

    Richardson, David

    on microfilms 67 or in any other physical way, and transmission or information storage and retrieval, 68 Dordrecht, The Netherlands. 58 59 www.springer.com 60 Printed on acid-free paper 61 62 All Rights Reserved 63 © Springer Science+Business Media Dordrecht 2013 64 This work is subject to copyright. All rights

  3. Microcrystallization techniques for serial femtosecond crystallography

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItemResearch > The EnergyCenterDioxide Capture in the Presence of Waterusing

  4. Instrumentation upgrades for the Macromolecular Crystallography beamlines

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC) EnvironmentalGyroSolé(tm)HydrogenRFPTri-PartyForTheAppendix for Schedule 8Dof the

  5. Introduction to Bayesian methods in macromolecular crystallography |

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOn AprilAElectronicCurves | SciTech Connect Journal Article:SciTechSciTech Connect

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

    E-Print Network [OSTI]

    Raines, Ronald T.

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

  7. Expression of a soluble form of iodotyrosine deiodinase for active site characterization by engineering the native membrane protein from Mus musculus

    SciTech Connect (OSTI)

    Buss, Jennifer M.; McTamney, Patrick M.; Rokita, Steven E. (Maryland)

    2012-06-27T23:59:59.000Z

    Reductive deiodination is critical for thyroid function and represents an unusual exception to the more common oxidative and hydrolytic mechanisms of dehalogenation in mammals. Studies on the reductive processes have been limited by a lack of convenient methods for heterologous expression of the appropriate proteins in large scale. The enzyme responsible for iodide salvage in the thyroid, iodotyrosine deodinase, is now readily generated after engineering its gene from Mus musculus. High expression of a truncated derivative lacking the membrane domain at its N-terminal was observed in Sf9 cells, whereas expression in Pichia pastoris remained low despite codon optimization. Ultimately, the desired expression in Escherichia coli was achieved after replacing the two conserved Cys residues of the deiodinase with Ala and fusing the resulting protein to thioredoxin. This final construct provided abundant enzyme for crystallography and mutagenesis. Utility of the E. coli system was demonstrated by examining a set of active site residues critical for binding to the zwitterionic portion of substrate.

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

    E-Print Network [OSTI]

    Bigelow, Stephen

    Topological Aspects of DNA Function and Protein Folding 523 Knotting pathways in proteins Joanna I Key words: artificial knot, chaperone, free energy landscape, knotted protein, protein folding

  9. Cellulose binding domain proteins

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

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

  10. Cellulose binding domain proteins

    DOE Patents [OSTI]

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

    1998-11-17T23:59:59.000Z

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

  11. Annotation Transfer Between Genomes: ProteinProtein Interologs and

    E-Print Network [OSTI]

    Gerstein, Mark

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

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

    E-Print Network [OSTI]

    Hosur, Raghavendra

    2012-01-01T23:59:59.000Z

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

  13. Potential of Mean Force for ProteinProtein Interaction Studies

    E-Print Network [OSTI]

    Luhua, Lai

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

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

    E-Print Network [OSTI]

    Kolesov, Grigory

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

  15. Dipolar response of hydrated proteins

    E-Print Network [OSTI]

    Dmitry V. Matyushov

    2011-08-12T23:59:59.000Z

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

  16. 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,...

  17. Carbon Nanotube Templated Asembly of Protein. | EMSL

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

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

  18. Convergent evolution of protein structure

    E-Print Network [OSTI]

    Fischer, Daniel

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

  19. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

    Thirumalai, Devarajan

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

  20. Petaflop Computing for Protein Folding

    E-Print Network [OSTI]

    Izaguirre, JesĂşs A.

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

  1. Fluorescent Protein Applications in Microscopy

    E-Print Network [OSTI]

    Straight, Aaron

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

  2. Protein subcellular localization assays using split fluorescent proteins

    DOE Patents [OSTI]

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

    2009-09-08T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2012-04-24T23:59:59.000Z

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

  4. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2010-01-01T23:59:59.000Z

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

  6. Mathematical methods for protein science

    SciTech Connect (OSTI)

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

    1997-12-31T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2003-04-10T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2006-01-01T23:59:59.000Z

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

  9. High throughput protein production screening

    DOE Patents [OSTI]

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

    2009-09-08T23:59:59.000Z

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

  10. Protein Flips Lipids Across Membranes

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

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

  11. Protein detection system

    DOE Patents [OSTI]

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

    2009-05-05T23:59:59.000Z

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

  12. Expression of multiple proteins in transgenic plants

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

  13. Introduction to Grid computing Protein folding

    E-Print Network [OSTI]

    Boyar, Joan

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

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

    E-Print Network [OSTI]

    Zhu, L; Kaback, HR; Dalbey, RE

    2013-01-01T23:59:59.000Z

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

  15. LCLS-scheduling-run_V_Ver9c.xlsx

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

    Wide Angle X-ray Scattering and Nano- Crystallography Diffraction Studies of Ultrafast Membrane Protein DynamicsMerged with L433 L401 CXI ABBEY, BRIAN...

  16. LANSCE | Lujan Center | Software | popLA

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

    Asterix Powder Diffractometers HIPD HIPPO NPDF Engineering Diffraction SMARTS Small Angle Scattering LQD Protein Crystallography PCS Neutron Imaging Capability Neutron Radiography...

  17. PowerPoint Presentation

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

    The Bioscience Division has built a Protein Crystallography Station (PCS) at the Lujan Neutron Scattering Center for the international structural biology community to...

  18. Published: February 18, 2011 r 2011 American Chemical Society 2470 dx.doi.org/10.1021/jp1122294 |J. Phys. Chem. B 2011, 115, 24702476

    E-Print Network [OSTI]

    States Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute of a fatal neurodegenerative disease, classical late-infantile neuronal ceroid lipofuscinosis.3

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

    E-Print Network [OSTI]

    Amos, Joseph Edward

    2013-02-22T23:59:59.000Z

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

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

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

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

  1. Optimized Null Model for Protein Structure Networks

    E-Print Network [OSTI]

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

    2009-01-01T23:59:59.000Z

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

  2. A motion planning approach to protein folding

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

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

  3. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01T23:59:59.000Z

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

  4. A motion planning approach to protein folding 

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

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

  5. GWIDD: Genome-wide protein docking database

    E-Print Network [OSTI]

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

    2009-11-09T23:59:59.000Z

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

  6. EVA: evaluation of protein structure prediction servers

    E-Print Network [OSTI]

    Sali, Andrej

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

  7. MODELING PROTEIN INTERACTIONS THROUGH STRUCTURE ALIGNMENT

    E-Print Network [OSTI]

    Sinha, Rohita

    2011-08-31T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Barakat, Nora Hisham

    2007-01-01T23:59:59.000Z

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

  9. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01T23:59:59.000Z

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

  10. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

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

    2010-07-18T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Bayro, Marvin J

    2010-01-01T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    2003-05-13T23:59:59.000Z

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

  13. Discrete restraint-based protein modeling and the C -trace problem

    E-Print Network [OSTI]

    de Bakker, Paul

    , Cambridge CB2 1GA, England (RECEIVED March 13, 2003; FINAL REVISION May 23, 2003; ACCEPTED May 27, 2003 experimental observations from X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy experi@cryst.bioc.cam.ac.uk; fax: 44-(0)-1223-766082. 1 Present address: Biological Engineering Division, Massachusetts Insti- tute

  14. Crystallographic study of red fluorescent protein eqFP578 and its far-red variant

    E-Print Network [OSTI]

    cause lesser damage to cells. The most favorable ``optical window'' for the visualization in living, Frederick, Maryland 21702 4 Synchrotron Radiation Research Section, Macromolecular Crystallography of FPs in cell biology, biotech- nology, and biomedical studies enabled optical imag- ing of gene

  15. Adhesives from modified soy protein

    DOE Patents [OSTI]

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

    2008-08-26T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01T23:59:59.000Z

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

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

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

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

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

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

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

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

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

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

  20. Computational prediction and analysis of protein structure

    E-Print Network [OSTI]

    Meruelo, Alejandro Daniel

    2012-01-01T23:59:59.000Z

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

  1. Protein Folding Sculpting Evolutionary Change

    E-Print Network [OSTI]

    Lindquist, Susan

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

  2. Fast events in protein folding

    SciTech Connect (OSTI)

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

    1996-04-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Chen, Ting

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

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

    E-Print Network [OSTI]

    Stevenson, Calum

    2012-11-30T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    2002-10-15T23:59:59.000Z

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

  6. Recombinant fluorescent protein microsphere calibration standard

    DOE Patents [OSTI]

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

    2001-01-01T23:59:59.000Z

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

  7. 272 Dispatch Protein folding: Chaperones get Hip

    E-Print Network [OSTI]

    Craig, Elizabeth A

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

  8. Thermodynamics of Protein Folding Erik Sandelin

    E-Print Network [OSTI]

    Sandelin, Erik

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

  9. How Hydrogen Bond Redundancy Affects Protein Flexibility

    E-Print Network [OSTI]

    Naomi Fox; Filip Jagodzinski; Jeanne Hardy; Ileana Streinu

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

  10. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01T23:59:59.000Z

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

  11. SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION

    SciTech Connect (OSTI)

    JOHN C WALKER

    2011-11-01T23:59:59.000Z

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

  12. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Bigelow, Stephen

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

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

    E-Print Network [OSTI]

    Yang, Sichun

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

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

    E-Print Network [OSTI]

    Weston, Ken

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

  16. Protein folding in the ER.

    SciTech Connect (OSTI)

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

    1999-10-01T23:59:59.000Z

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

  17. Method for protein structure alignment

    DOE Patents [OSTI]

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

    2005-02-22T23:59:59.000Z

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

  18. Protein Flips Lipids Across Membranes

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips LipidsProtein

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

    E-Print Network [OSTI]

    Ihee, Hyotcherl

    , Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic solvent heating. Although the heating mostly affects q region above 1.5 Ĺ­1 the heating signal should, in the case of PYP, the solvent heating signal is much smaller than the contribution from the protein

  20. Method for voltage-gated protein fractionation

    DOE Patents [OSTI]

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

    2012-04-24T23:59:59.000Z

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

  1. Protein phase feeding of poultry

    E-Print Network [OSTI]

    Vest, Larry Rufus

    1966-01-01T23:59:59.000Z

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

  2. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

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

    1998-02-17T23:59:59.000Z

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

  3. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Baker, David

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

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

    E-Print Network [OSTI]

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

    2013-01-01T23:59:59.000Z

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

  6. Contributions to the analysis of proteins

    E-Print Network [OSTI]

    Sharifi Sedeh, Reza

    2011-01-01T23:59:59.000Z

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

  7. Protein Thioester Synthesis Enabled by Sortase

    E-Print Network [OSTI]

    Ling, Jingjing

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

  8. Protein Identification Using Top-Down. | EMSL

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

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

  9. Evolutionary Approaches to Protein Engineering B. STEIPETEIPE

    E-Print Network [OSTI]

    Steipe, Boris

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

  10. Exact rotamer optimization for computational protein design

    E-Print Network [OSTI]

    Hong, Eun-Jong, 1975-

    2008-01-01T23:59:59.000Z

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

  11. Topology to geometry in protein folding: -Lactoglobulin

    E-Print Network [OSTI]

    Berry, R. Stephen

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

  12. Biophysical characterization of protein folding and misfolding. 

    E-Print Network [OSTI]

    Schmittschmitt, Jason Peter

    2004-09-30T23:59:59.000Z

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

  13. Global Optimization and Protein Structure Prediction

    E-Print Network [OSTI]

    Neumaier, Arnold

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

  14. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01T23:59:59.000Z

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

  15. The unfolded protein response during prostate cancer development

    E-Print Network [OSTI]

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

    2009-01-01T23:59:59.000Z

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

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

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

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

  17. Computational Modeling of Protein Interactions at Multiple Lengthscales

    E-Print Network [OSTI]

    Yap, Eng Hui

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Anderson, William David

    2007-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    McMahon, Heather Eileen

    2007-01-01T23:59:59.000Z

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

  20. Iterative Information Model Development Protein sequence

    E-Print Network [OSTI]

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

  1. Intracellular Signaling by the Unfolded Protein

    E-Print Network [OSTI]

    Mullins, Dyche

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

  2. Approximate Inference and Protein-Folding

    E-Print Network [OSTI]

    Weiss, Yair

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

  3. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K. (Berkeley, CA)

    1997-01-01T23:59:59.000Z

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

  4. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, G.K.

    1997-04-29T23:59:59.000Z

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

  5. GREEN FLUORESCENT PROTEIN The green revolution

    E-Print Network [OSTI]

    Stearns, Tim

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

  6. On the Complexity of Protein Folding

    E-Print Network [OSTI]

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

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

  7. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Hura, Greg

    2013-05-29T23:59:59.000Z

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

  8. Protein Structures Revealed at Record Pace

    ScienceCinema (OSTI)

    Greg Hura

    2010-01-08T23:59:59.000Z

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

  9. Protein Structures Revealed at Record Pace

    SciTech Connect (OSTI)

    Hura, Greg

    2009-01-01T23:59:59.000Z

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

  10. REGULATION OF TELOMERASE BY TELOMERIC PROTEINS

    E-Print Network [OSTI]

    de Lange, Titia

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

  11. Amphiphiles for protein solubilization and stabilization

    DOE Patents [OSTI]

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

    2012-09-11T23:59:59.000Z

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

  12. Disulfide-Linked Protein Folding Pathways

    E-Print Network [OSTI]

    Bardwell, James

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

  13. EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS

    E-Print Network [OSTI]

    Guibas, Leonidas J.

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

  14. UNCORRECTED 3 Protein folding: Then and now

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

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

  15. STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS

    E-Print Network [OSTI]

    Dinner, Aaron

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

  16. Protein folding: not just another optimization

    E-Print Network [OSTI]

    Karplus, Kevin

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

  17. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Snow, Christopher

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

  18. Protein Patterning with Programmable Surface Chemistry Chips

    E-Print Network [OSTI]

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

  19. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

    Langmead, Christopher James

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

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

    E-Print Network [OSTI]

    Dinner, Aaron

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

  4. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Studying submicrosecond protein folding

    E-Print Network [OSTI]

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

  5. Extracellular secretion of recombinant proteins

    DOE Patents [OSTI]

    Linger, Jeffrey G.; Darzins, Aldis

    2014-07-22T23:59:59.000Z

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

  6. Proteins

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)IntegratedSpeedingTechnical News,Program90803

  7. Computational and experimental investigations of forces in protein folding

    E-Print Network [OSTI]

    Schell, David Andrew

    2005-02-17T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Domany, Eytan

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

  9. Protein Sequence, Structure, Stability and Functionality

    E-Print Network [OSTI]

    J. C. Phillips

    2008-02-25T23:59:59.000Z

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

  10. Soliton concepts and the protein structure

    E-Print Network [OSTI]

    Andrei Krokhotin; Antti J. Niemi; Xubiao Peng

    2011-09-18T23:59:59.000Z

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

  11. Protein Identification Using Top-Down

    SciTech Connect (OSTI)

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

    2012-06-01T23:59:59.000Z

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

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

    DOE Patents [OSTI]

    Laible, Philip D; Hanson, Deborah K

    2013-06-04T23:59:59.000Z

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

  13. Protein Flips Lipids Across Membranes

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips Lipids Across

  14. Protein Flips Lipids Across Membranes

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips Lipids

  15. Protein Flips Lipids Across Membranes

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein Flips

  16. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

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

    2006-07-27T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Moon, Soon Young

    2012-05-04T23:59:59.000Z

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

  18. Automated Streak Seeding With Micromachined Silicon Tools Atanas Georgiev,a*

    E-Print Network [OSTI]

    Allen, Peter K.

    -throughput (HTP) protein crystallography, there are still several bottlenecks, which hold up the large-scale X for data collection and structure solution by modern HTP software. In Phase 1 of the Protein Structure

  19. Streak Seeding Automation Using Silicon Tools CUCS-015-06

    E-Print Network [OSTI]

    Georgiev, Atanas

    diseases. Despite the recent impressive achievements in the high-throughput (HTP) protein crystallography solution by the modern HTP software. In pilot studies of Phase 1 of the Protein Structure Initiative (PSI

  20. Studies involving low protein broiler diets

    E-Print Network [OSTI]

    Parkin, David Palmer

    1971-01-01T23:59:59.000Z

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

  1. 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)

  2. Class II virus membrane fusion proteins

    SciTech Connect (OSTI)

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

    2006-01-05T23:59:59.000Z

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

  3. Amyloid Deposits: Protection Against Toxic Protein Species?

    E-Print Network [OSTI]

    Lindquist, Susan

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

  4. 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...

  5. Top-to-Bottom Protein Characterization | EMSL

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

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

  6. Knots and Swelling in Protein Folding

    E-Print Network [OSTI]

    Martin Lundgren; Antti J. Niemi

    2009-06-26T23:59:59.000Z

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

  7. 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...

  8. SciTech Connect: Goniometer-based femtosecond crystallography...

    Office of Scientific and Technical Information (OSTI)

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

  9. Chemistry 6181 MWF 11:05 Course title: "Chemical Crystallography"

    E-Print Network [OSTI]

    Sherrill, David

    : Classroom: MoSE G021 Texts: Course not based on a single text. The following books will be useful resources. Neutrons: Radioactive sources, reactors, spallation, moderation c. Polarization 3) Introduction to waves, charge generation in semiconductors, and nuclear reactions. 5) Scattering from clusters and particles ­ a

  10. CrystalPlan: an Experiment Planning Tool for Crystallography

    SciTech Connect (OSTI)

    Zikovsky, Janik L [ORNL; Peterson, Peter F [ORNL; Wang, Xiaoping [ORNL; Frost, Matthew J [ORNL; Hoffmann, Christina [ORNL

    2011-01-01T23:59:59.000Z

    Beam time at large user program based x-ray and neutron scattering facilities is in high demand and always at a premium. CrystalPlan, a highly efficient experiment planning software has been developed to maximize the use of available beamtime per sample per experiment. This program can calculate and optimize the data coverage of a crystal in reciprocal space in a single-crystal diffraction time-of- flight experiment. CrystalPlan can help a user build an experiment plan that will acquire the most data possible, with sufficient coverage but limited redundancy, therefore increasing scientific productivity. A user friendly GUI including a 3D viewer, an automated coverage optimizer, and an option to reorient the crystal for the measurement of selected hkls on specific detector positions are among its useful features. A sample use case of the program with the TOPAZ beamline at SNS will be presented.

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

    SciTech Connect (OSTI)

    Terwilliger, Thomas C. (Santa Fe, NM)

    2006-08-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-10-01T23:59:59.000Z

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

  13. Crystallography of TWIP Steel Graduate Institute of Ferrous Technology

    E-Print Network [OSTI]

    Cambridge, University of

    Metallurgy at Pohang University of Science and Technology. The research described herein was conducted under the supervision of Professor H. K. D. H. Bhadeshia, Adjunct Professor of Computational Metallurgy in the Graduate Metallurgy, University of Cambridge, between May 2006 and June 2007. This work is to the best of my knowledge

  14. Media invited to join students in crystallography experiment

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated Codes |IsLove Your Home andDispositionMechanical R&D Contact:1March

  15. Genentech Uses ALS Crystallography for Therapeutic Antibody Research

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC) Environmental AssessmentsGeoffrey Campbelllong version) The U.S.short176674Genentech

  16. Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn'tOrigin of Contamination in Many Devils Wash,EnergyNanophosphate technologyDepartment

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

    E-Print Network [OSTI]

    Pace, Norman

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

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

    E-Print Network [OSTI]

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

    2011-07-29T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Fu, Hailong

    2010-07-14T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    B Wallace; R Janes

    2011-12-31T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

  2. Multiscale Approach to Protein Engineering in Bioluminescence

    E-Print Network [OSTI]

    Maryland at College Park, University of

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

  3. MP 33200 EZQ Protein Quantitation Kit

    E-Print Network [OSTI]

    Lebendiker, Mario

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

  4. RESEARCH ARTICLES Protein Domain Movements: Detection

    E-Print Network [OSTI]

    Wriggers, Willy

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

  5. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

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

    1990-08-23T23:59:59.000Z

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

  6. Mining Protein Contact Maps Jingjing Hu

    E-Print Network [OSTI]

    Bystroff, Chris

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

  7. Production of Therapeutic Proteins in Plants

    E-Print Network [OSTI]

    Bradford, Kent

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

  8. Can Contact Potentials Reliably Predict Stability of Proteins?

    E-Print Network [OSTI]

    Khatun, Jainab

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

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

    E-Print Network [OSTI]

    Baliga, Bantval Prabhakara

    1956-01-01T23:59:59.000Z

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

  10. Protein Folding Challenge and Theoretical Computer Science Somenath Biswas

    E-Print Network [OSTI]

    Biswas, Somenath

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

  11. A newly discovered protein export machine in malaria parasites

    E-Print Network [OSTI]

    Arnold, Jonathan

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

  12. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2003-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Wensel, Theodore G.

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

  15. 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...

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

    E-Print Network [OSTI]

    Landman, Allison Simone

    2009-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2011-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Baker, David

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

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

    E-Print Network [OSTI]

    Baer, Christina Elizabeth

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2011-01-01T23:59:59.000Z

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

  1. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01T23:59:59.000Z

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

  2. Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding

    E-Print Network [OSTI]

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

  3. THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES

    E-Print Network [OSTI]

    Sosnick, Tobin R.

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

  4. Preparation of white sunflower protein isolates

    E-Print Network [OSTI]

    Wen, Hwei-Mei

    1982-01-01T23:59:59.000Z

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

  5. Introducing Protein Folding Using Simple Models

    E-Print Network [OSTI]

    D. Thirumalai; D. K. Klimov

    2001-01-04T23:59:59.000Z

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

  6. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01T23:59:59.000Z

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

  7. Protein Instability and Lou Gehrig's Disease

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein FlipsProteinProtein

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

    E-Print Network [OSTI]

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

    2012-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Boyer, Edmond

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  7. 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...

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

    E-Print Network [OSTI]

    Berry, R. Stephen

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

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

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

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

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

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

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

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

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

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

  12. CLP-based protein fragment assembly

    E-Print Network [OSTI]

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

    2010-01-01T23:59:59.000Z

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

  13. 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...

  14. Prion protein in health and disease

    E-Print Network [OSTI]

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

    2008-01-01T23:59:59.000Z

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

  15. Structural and Energetic Heterogeneity in Protein Folding

    E-Print Network [OSTI]

    Steven S. Plotkin; Jose N. Onuchic

    2000-09-27T23:59:59.000Z

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

  16. STATISTICAL CHARACTERIZATION OF PROTEIN ENSEMBLES Diego Rother

    E-Print Network [OSTI]

    Minnesota, University of

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

  17. Exploring the mechanisms of fibrillar protein aggregation 

    E-Print Network [OSTI]

    Ryan, Morris

    2013-11-28T23:59:59.000Z

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

  18. IDENTIFYING CANDIDATE PROTEIN FOR REMOVAL OF ENVIRONMENTALLY

    E-Print Network [OSTI]

    Uppsala Universitet

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

  19. Energetics of protein charge transfer and photosynthesis

    E-Print Network [OSTI]

    Matyushov, Dmitry

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

  20. Purification of recombinant proteins with magnetic nanoclusters

    E-Print Network [OSTI]

    Ditsch, Andre (Andre Paul)

    2005-01-01T23:59:59.000Z

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

  1. Telomere-associated proteins in Arabidopsis thaliana

    E-Print Network [OSTI]

    Surovtseva, Yulia V.

    2009-05-15T23:59:59.000Z

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

  2. Photovoltaic devices using photosynthetic protein complexes

    E-Print Network [OSTI]

    Das, Rupa, 1980-

    2004-01-01T23:59:59.000Z

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

  3. Ensemble modeling of [beta]-sheet proteins

    E-Print Network [OSTI]

    O'Donnell, Charles William

    2011-01-01T23:59:59.000Z

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

  4. Genetic analysis of protein N-Glycosylation 

    E-Print Network [OSTI]

    Huffman, Jennifer Elizabeth

    2014-11-28T23:59:59.000Z

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

  5. Orpinomyces xylanase proteins and coding sequences

    DOE Patents [OSTI]

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

    1998-10-20T23:59:59.000Z

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

  6. Biomimetic materials for protein storage and transport

    DOE Patents [OSTI]

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

    2012-05-01T23:59:59.000Z

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

  7. Characterisation of endogenous KRAB zinc finger proteins 

    E-Print Network [OSTI]

    Crawford, Catherine

    2009-01-01T23:59:59.000Z

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

  8. Exo-endo cellulase fusion protein

    DOE Patents [OSTI]

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

    2012-01-17T23:59:59.000Z

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

  9. Positive modulator of bone morphogenic protein-2

    DOE Patents [OSTI]

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

    2009-01-27T23:59:59.000Z

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

  10. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2013-12-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Izaguirre, JesĂşs A.

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

  14. Folding simulations of small proteins Seung-Yeon Kima

    E-Print Network [OSTI]

    Lee, Jooyoung

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

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

    E-Print Network [OSTI]

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

  16. Membrane Proteins DOI: 10.1002/anie.201107343

    E-Print Network [OSTI]

    Wallace, Mark

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

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

    E-Print Network [OSTI]

    Langmead, Christopher James

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

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

    E-Print Network [OSTI]

    Santiago, Juan G.

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

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

    E-Print Network [OSTI]

    Liang, Faming

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

  20. Cellular mechanisms of membrane protein folding William R Skach

    E-Print Network [OSTI]

    Cai, Long

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

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

    E-Print Network [OSTI]

    Smith, J. MacGregor

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

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

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

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

    DOE Patents [OSTI]

    Mayfield, Stephen P. (Cardiff, CA)

    2010-03-16T23:59:59.000Z

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

  4. Structural determination of intact proteins using mass spectrometry

    DOE Patents [OSTI]

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

    2008-05-06T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Powers, Robert

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

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

    E-Print Network [OSTI]

    Song, Xueyu

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

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

    E-Print Network [OSTI]

    Chen, Xin

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving taxonomy-based protein fold recognition methods can be broadly classified into two categories, that is, template-based1­6 and taxonomy- based.7­13 In recent years, the taxonomy-based method has attracted great attention due to its encouraging performance

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

    E-Print Network [OSTI]

    Schwarz, Ulrich

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

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

    E-Print Network [OSTI]

    Vajda, Sandor

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

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

    E-Print Network [OSTI]

    Lathrop, Richard H.

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

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

    E-Print Network [OSTI]

    Ramakrishnan, Venki

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

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

    E-Print Network [OSTI]

    Baker, David

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

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

    E-Print Network [OSTI]

    Jayaram, Bhyravabotla

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

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

    E-Print Network [OSTI]

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

  15. A comparative study of HPr proteins from extremophilic organisms

    E-Print Network [OSTI]

    Syed Ali, Abbas Razvi

    2006-04-12T23:59:59.000Z

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

  16. Prion protein induced signaling cascades in monocytes

    SciTech Connect (OSTI)

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

    2006-02-03T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2007-07-06T23:59:59.000Z

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

  18. Differential stoichiometry among core ribosomal proteins

    E-Print Network [OSTI]

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

    2015-04-15T23:59:59.000Z

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

  19. Compositions and methods for improved protein production

    DOE Patents [OSTI]

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

    2012-07-10T23:59:59.000Z

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

  20. Bayesian Nonparametric Methods for Protein Structure Prediction

    E-Print Network [OSTI]

    Lennox, Kristin Patricia

    2011-10-21T23:59:59.000Z

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

  1. Proteotronics: Electronic devices based on proteins

    E-Print Network [OSTI]

    E. Alfinito; L. Reggiani; J. Pousset

    2014-05-15T23:59:59.000Z

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

  2. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17T23:59:59.000Z

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

  3. Protein synthesis driven by dynamical stochastic transcription

    E-Print Network [OSTI]

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

    2014-12-23T23:59:59.000Z

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

  4. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    The present invention provides a novel telomere associated protein (Trf1-interacting nuclear protein 2 "Tin2") that hinders the binding of Trf1 to its specific telomere repeat sequence and mediates the formation of a Tin2-Trf1-telomeric DNA complex that limits telomerase access to the telomere. Also included are the corresponding nucleic acids that encode the Tin2 of the present invention, as well as mutants of Tin2. Methods of making, purifying and using Tin2 of the present invention are described. In addition, drug screening assays to identify drugs that mimic and/or complement the effect of Tin2 are presented.

  5. Protein Dynamics Hit the Big Screen

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting your personalSedimentProteinProtein

  6. Protein Instability and Lou Gehrig's Disease

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein FlipsProtein Instability

  7. Protein Instability and Lou Gehrig's Disease

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein FlipsProtein

  8. Protein Structure Suggests Role as Molecular Adapter

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProteinThreading Method |Protein

  9. Protein Structure Suggests Role as Molecular Adapter

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProteinThreading MethodProtein

  10. Protein shake-up | ornl.gov

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProteinThreadingProtein shake-up

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

    E-Print Network [OSTI]

    Zeng, Bin

    2009-05-15T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Slavoff, Sarah Ann

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Alibes, Andreu

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

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

    E-Print Network [OSTI]

    Shang, Yue

    2007-09-17T23:59:59.000Z

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

  15. Energy use by biological protein transport pathways

    E-Print Network [OSTI]

    Economou, Tassos

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

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

    E-Print Network [OSTI]

    Powers, Robert

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

  17. Protein Data Bank Project at Rutgers University

    SciTech Connect (OSTI)

    Berman, Helen

    2002-07-18T23:59:59.000Z

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

  18. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

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

    1998-01-13T23:59:59.000Z

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

  19. Protein Models Comparator Scalable Bioinformatics Computing on

    E-Print Network [OSTI]

    Krasnogor, Natalio

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

  20. COMMUNICATION Protein Chemistry at Membrane Interfaces

    E-Print Network [OSTI]

    White, Stephen

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

  1. January, 2003 1 The Protein Space

    E-Print Network [OSTI]

    Linial, Michal

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

  2. Towards a Molecular Understanding of Protein Solubility

    E-Print Network [OSTI]

    Kramer, Ryan 1984-

    2011-05-31T23:59:59.000Z

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

  3. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11T23:59:59.000Z

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

  4. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

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

  5. Elucidating Amyloid -Protein Folding and Assembly: A

    E-Print Network [OSTI]

    Stanley, H. Eugene

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

  6. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13T23:59:59.000Z

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

  7. Histone H1 proteins in Chlamydomonas reinhardtii

    E-Print Network [OSTI]

    Salinger, Andrew Paul

    1994-01-01T23:59:59.000Z

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

  8. Neurofilament Proteins in Avian Auditory Hair Cells

    E-Print Network [OSTI]

    Rubel, Edwin

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

  9. Metal-directed protein self-assembly

    E-Print Network [OSTI]

    Salgado. Eric N.

    2010-01-01T23:59:59.000Z

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

  10. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    SciTech Connect (OSTI)

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

    2014-03-15T23:59:59.000Z

    This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction.

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

    SciTech Connect (OSTI)

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

    2009-03-01T23:59:59.000Z

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

  12. Corn Storage Protein - A Molecular Genetic Model

    SciTech Connect (OSTI)

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

    2013-05-31T23:59:59.000Z

    Corn is the highest yielding crop on earth and probably the most valuable agricultural product of the United States. Because it converts sun energy through photosynthesis into starch and proteins, we addressed energy savings by focusing on protein quality. People and animals require essential amino acids derived from the digestion of proteins. If proteins are relatively low in certain essential amino acids, the crop becomes nutritionally defective and has to be supplemented. Such deficiency affects meat and fish production and countries where corn is a staple. Because corn seed proteins have relatively low levels of lysine and methionine, a diet has to be supplemented with soybeans for the missing lysine and with chemically synthesized methionine. We therefore have studied genes expressed during maize seed development and their chromosomal organization. A critical technical requirement for the understanding of the molecular structure of genes and their positional information was DNA sequencing. Because of the length of sequences, DNA sequencing methods themselves were insufficient for this type of analysis. We therefore developed the so-called “DNA shotgun sequencing” strategy, where overlapping DNA fragments were sequenced in parallel and used to reconstruct large DNA molecules via overlaps. Our publications became the most frequently cited ones during the decade of 1981-1990 and former Associate Director of Science for the Office of Basic Energy Sciences Patricia M. Dehmer presented our work as one of the great successes of this program. A major component of the sequencing strategy was the development of bacterial strains and vectors, which were also used to develop the first biotechnology crops. These crops possessed new traits thanks to the expression of foreign genes in plants. To enable such expression, chimeric genes had to be constructed using our materials and methods by the industry. Because we made our materials and methods freely available to academia and industry, progress in plant research and new crop development could accelerate and benefit the public.

  13. The Effects of Wave Energy Converters on a Monochromatic Wave Climate

    E-Print Network [OSTI]

    Fox-Kemper, Baylor

    at a rate of 1.25 percent annually. The Calfornia Global Warming Act of 2006 states that twenty percent The interest in renewable energies is currently increasing due to the reported rise in global temperature of California's electricity must come from renewable energy sources by 2010. However, due to the increases

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

    E-Print Network [OSTI]

    Umstadter, Donald

    facility at the University of Nebraska- Lincoln (UNL) is a 100-TW, 30-fs pulsed Ti:sapphire laser system submitted on November 13, 2009. S. D. Clarke is with the Department of Nuclear Engineering and Radiological@umich.edu). S. A. Pozzi is with the Department of Nuclear Engineering and Radiological Sciences

  15. Application of a Laser-Wakefield Driven Monochromatic Photon Source to

    E-Print Network [OSTI]

    Umstadter, Donald

    of approximately 170. I. INTRODUCTION HE Diocles laser facility at The University of Nebraska- Lincoln (UNL is with the Department of Nuclear Engineering and Radiological Sciences of the University of Michigan, Ann Arbor, MI and Radiological Sciences of the University of Michigan, Ann Arbor, MI 48109 USA (tel: 734-615-7830, e

  16. X-ray imaging with monochromatic and small focal spot size sources

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

    of x-ray energy and intensity (under investigation) Measurements at the Elettra (Trieste) synchrotron Edge Response Function at ATF * Spot size * He Pipe added * 10 7 10 8...

  17. Coherent interaction of a monochromatic gravitational wave with both elastic bodies and electromagnetic circuits

    E-Print Network [OSTI]

    Enrico Montanari; Pierluigi Fortini

    1998-08-26T23:59:59.000Z

    The interaction of a gravitational wave with a system made of an RLC circuit forming one end of a mechanical harmonic oscillator is investigated. We show that, in some configurations, the coherent interaction of the wave with both the mechanical oscillator and the RLC circuit gives rise to a mechanical quality factor increase of the electromagnetic signal. When this system is used as an amplifier of gravitational periodic signals in the frequency range 50-1000 Hz, at ultracryogenic temperatures and for sufficiently long integration times (up to 4 months), a sensitivity of 10^(-24)-10^(-27) on the amplitude of the metric could be achieved when thermal noise, shot noise and amplifier back--action are considered.

  18. Sheet flow dynamics under monochromatic nonbreaking waves C. Marjolein Dohmen-Janssen

    E-Print Network [OSTI]

    Kirby, James T.

    % of the velocity outside the wave boundary layer. The observations are compared to previous experimental work model for oscillatory flow with enhanced boundary roughness and a two-phase collisional grain flow model measurements of sediment concentrations and grain velocities inside the sheet flow layer under prototype

  19. On Axion's Effect on Propagation of Monochromatic Electromagnetic Wave Through Strong Magnetic Field

    E-Print Network [OSTI]

    Mikhail Khankhasayev; Carol Scarlett

    2012-02-07T23:59:59.000Z

    A possibility of detecting the effect of photon-axion mixing in a cavity experiment is discussed. There are two photon-axion modes that acquire different indices of refraction and split in an inhomogeneous magnetic field. For a magnetic field inhomogeneous in the direction transverse to the light propagation an analytical solution is obtained both for the index of refraction and the beams' trajectories. In a cavity experiment, the beam splitting creates a bifurcation effect, which results in a decrease of the light intensity in the central region. Modulation of magnetic field can separate this effect from background by providing a narrow frequency range for any observed signal. When one integrates this effect over time and accounts for bandwidth, the overall drop in FWHM intensity is of order 10-2%. This is a very measurable effect.

  20. Partitioning 2-edge-colored Ore-type graphs by monochromatic cycles

    E-Print Network [OSTI]

    Sarkozy, Gabor

    . A more elementary proof, still for large enough n, was obtained by Allen [1]. Finally, Bessy and Thomass, the above mentioned Bessy-Thomass´e result [5] would hold for graphs with minimum degree larger than 3n/4

  1. Reflection and transmission of a monochromatic gravity wave at oblique incidence to a step

    E-Print Network [OSTI]

    Wanstrath, John Joseph

    1971-01-01T23:59:59.000Z

    and Transmission Amplitude Coefficients 4. Error Function, E and E2. 5. Verification Checks. 6. 1 Eigenvalues For The Situation Where The Water Depth 71 73 75 77 10 Ft. aud T = 15 Sec. Sl 6. 2 Eigenvalues For The Situation Where The Water Depth 5 Ft.... and T = 15 Sec 32 6. 3 Eigenvalues For The Situation There The Water Depth 2 Ft. and T = 15 Sec 6. 4 Figenvalues For The Situation [lhcre The Water 10 Ft. and T = 10 Sec S4 6, 5 Eigenvalues For The Situation Whaere The Water Den ch 2 Ft. and T = 10 Sec...

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

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

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

    E-Print Network [OSTI]

    Olsen, Rachel Lee

    2012-12-31T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Tovchigrechko, Andrey; Vakser, Ilya A.

    2006-07-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Mukherjee, Srayanta

    2011-12-31T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2007-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Ruvinsky, Anatoly M.; Vakser, Ilya A.

    2008-09-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Vekich, John Alan

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Baker, David

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

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

    E-Print Network [OSTI]

    Singh, Jaswinder Pal

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

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

    E-Print Network [OSTI]

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

    2007-10-04T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Dixit, Anshuman; Verkhivker, Gennady M.

    2011-10-06T23:59:59.000Z

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

  13. A Complete Microfluidic Screening Platform for Rational Protein Crystallization

    E-Print Network [OSTI]

    Hansen, Carl L.

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

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

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

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

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

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

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

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

    E-Print Network [OSTI]

    Powers, Robert

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

  17. Optimizing a global alignment of protein interaction networks

    E-Print Network [OSTI]

    Ma, C.-Y.

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

  18. Computational approaches for identifying inhibitors of protein interactions 

    E-Print Network [OSTI]

    Mehio, Wissam

    2011-06-27T23:59:59.000Z

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

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

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

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

  20. A genetic bistable switch utilizing nonlinear protein degradation

    E-Print Network [OSTI]

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

    2012-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Schubert, Christian Reinhold

    2009-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Slutsky, Michael

    2005-01-01T23:59:59.000Z

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

  3. Function of the anterior gradient protein family in cancer 

    E-Print Network [OSTI]

    Fourtouna, Argyro

    2009-01-01T23:59:59.000Z

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

  4. Synthesis of Proteins with Homogenous Chemical and Posttranslational Modifications

    E-Print Network [OSTI]

    Wu, Bo

    2014-06-19T23:59:59.000Z

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

  5. Lipid-dependent regulation of the unfolded protein response

    E-Print Network [OSTI]

    Volmer, Romain; Ron, David

    2014-12-25T23:59:59.000Z

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

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

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

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

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

    E-Print Network [OSTI]

    Wei, Yun

    2010-07-14T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Nerukh, Dmitry

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

  9. Protein Folding Simulation in CCP Luca Bortolussi1

    E-Print Network [OSTI]

    Bortolussi, Luca

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

  10. Rational design of additives for inhibition of protein aggregation

    E-Print Network [OSTI]

    Shukla, Diwakar

    2011-01-01T23:59:59.000Z

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

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

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

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

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

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

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

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

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

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

  14. A comparative study of HPr proteins from extremophilic organisms 

    E-Print Network [OSTI]

    Syed Ali, Abbas Razvi

    2006-04-12T23:59:59.000Z

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

  15. How the Membrane Protein AmtB Transports Ammonia

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

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

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

    E-Print Network [OSTI]

    Thomas, Carla S. (Carla Stephanie)

    2014-01-01T23:59:59.000Z

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

  17. Rotary Firing in Ring-Shaped Protein Explains Unidirectionality

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

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

  18. Fragile X mental retardation protein and synaptic plasticity

    E-Print Network [OSTI]

    Sidorov, Michael Samuel

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    E-Print Network [OSTI]

    Neal, Sonya Elina

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Pantazatos, Dennis Peter

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2014-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Polinkovsky, Mark E.; Polinkovsky, Mark E.

    2012-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Sagle, Laura B.

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Radisky, Derek C.

    2009-01-01T23:59:59.000Z

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

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

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

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

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

    E-Print Network [OSTI]

    Cho, Samuel Sung-Il

    2007-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

    Glembotski, Christopher

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

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

    E-Print Network [OSTI]

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

    2011-01-01T23:59:59.000Z

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

  16. Utilization of oilseed proteins in precooked breakfast sausage

    E-Print Network [OSTI]

    Harward, Eugene Rees

    1979-01-01T23:59:59.000Z

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

  17. C. -Aliments protiques ; acides amins. Proteins supplements ; amino-acids.

    E-Print Network [OSTI]

    Boyer, Edmond

    . SUMMARY ESTIMATION OF THE PROTEIN VALUE OF SULPHITE AND AI,KAN! YEASTS IN PIG FEEDING The supplementation

  18. Hydrophobicity of protein surfaces: Separating geometry from chemistry

    E-Print Network [OSTI]

    scenarios for events such as protein folding and directed self-assembly are summarized well in ref. 8, in the context of protein folding. The basic feature distinguishing these scenarios is the relationship between; the processes are sequential. Illustrative examples summarized from available protein folding studies (8

  19. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS SHORT COMMUNICATION

    E-Print Network [OSTI]

    Weston, Ken

    crowding agents on protein folding Huan-Xiang Zhou* Department of Physics and Institute of Molecular Most of our knowledge on protein folding has been gained through studies in dilute solutions. To understand protein folding under physiological conditions, in a growing number of studies, some aspects

  20. 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)

    2011-07-05T23:59:59.000Z

    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.