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Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
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1

Protein structures by spallation neutron crystallography  

Science Journals Connector (OSTI)

The capabilities of the Protein Crystallography Station at Los Alamos Neutron Science Center for determining protein structures by spallation neutron crystallography are illustrated, and the methodological and technological advances that are emerging from the Macromolecular Neutron Crystallography consortium are described.

Langan, P.

2008-04-18T23:59:59.000Z

2

Protein crystallography with spallation neutrons  

SciTech Connect (OSTI)

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

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

2003-01-01T23:59:59.000Z

3

Neutron protein crystallography: beyond the folding structure of biological macromolecules  

Science Journals Connector (OSTI)

Several results from neutron protein crystallography relating H-atom positions and hydration patterns in proteins and oligonucleotides are reviewed.

Niimura, N.

2007-12-21T23:59:59.000Z

4

MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY  

E-Print Network [OSTI]

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

Quake, Stephen R.

5

How many water molecules can be detected by protein crystallography?  

Science Journals Connector (OSTI)

The number of water molecules which are expected to be experimentally located by protein crystallography is determined by analysis of known protein crystal structures.

Carugo, O.

1999-02-01T23:59:59.000Z

6

Lipidic phase membrane protein serial femtosecond crystallography  

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

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

7

Neutron protein crystallography at ultra-low (<15 K) temperatures  

Science Journals Connector (OSTI)

Techniques used to cryocool large protein crystals (1-6 mm3) successfully are described. High-resolution cryo-neutron crystallography data were collected at 15 K for three test systems.

Myles, D.A.A.

2012-06-20T23:59:59.000Z

8

Protein crystallography with spallation neutrons: collecting and processing wavelength-resolved Laue protein data  

Science Journals Connector (OSTI)

Methods for collecting and processing wavelength-resolved Laue data at the protein crystallography station at Los Alamos Neutron Science Center have been developed.

Langan, P.

2004-03-17T23:59:59.000Z

9

Protein crystallography with spallation neutrons: the user facility at Los Alamos Neutron Science Center  

Science Journals Connector (OSTI)

The protein crystallography user facility at the neutron spallation source run by Los Alamos Neutron Science Center is described.

Langan, P.

2004-01-17T23:59:59.000Z

10

Serial Femtosecond Crystallography of G Protein-Coupled Receptors  

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

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

Liu, Liu

11

Cryogenic Neutron Protein Crystallography: routine methods and potential benefits  

SciTech Connect (OSTI)

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.

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

2014-01-01T23:59:59.000Z

12

Water–protein interactions from high–resolution protein crystallography  

Science Journals Connector (OSTI)

...protein crystals showing solvent channels indicated by...hetero-tetrameric enzyme (blue and green, -subunits; yellow...et al. 2002b). The green, yellow and purple spheres...water molecules, and the green line indicates the possible...polar protein atoms. solvent density high low (a...

2004-01-01T23:59:59.000Z

13

Water–protein interactions from high–resolution protein crystallography  

Science Journals Connector (OSTI)

...the destruction of the three- dimensional structures of proteins. R. McKendry (London Centre for Nanotechnology & Department of Medicine, University College London, London, UK). Your very nice work, showing the rearrangement of hexameric...

2004-01-01T23:59:59.000Z

14

X-ray instrumentation for protein crystallography with SR (abstract)  

SciTech Connect (OSTI)

The station is intended for x-ray analysis of single crystals, primarily that of proteins with the beam of synchrotron radiation from the superconducting wiggler of a special storage ring {ital E}=2.0 GeV, {ital I}=0.3 A in the town of Zelenograd (TNK).{sup 1} The dimensions of the radiation source are 2.35{sup 2} {sigma}{sub {ital x}}{center dot}{sigma}{sub {ital z}}=1.5{times}0.05 mm{sup 2}, the brightness for {lambda}=1.5 A is 10{sup 15} photon/(s mm{sup 2} mrad.{sup 2} 0.1% ({Delta}{lambda}/{lambda})). The station comprises the device forming the monochromatized primary beam ({lambda}=0.5--2.2 A, {Delta}{lambda}/{lambda}{sup {minus}3}{similar to}10{sup {minus}4}) that consists of an asymmetric focusing monochromator with triangular-shaped Si or Ge crystal curved as a round cylinder,{sup 2} a segmented mirror of total external reflection placed behind the monochromator on a rotating bench consisting of 8 flat glass 200{times}50{times}25 mm{sup 2} segments that form a surface imitating an elliptical cylinder, three pairs of horizontal and vertical slits, monitor--ionization chamber, four-circle diffractometer with scintillation counter and horizontal main axis placed on the adjustable carriage that can turn about the monochromator axis; position-sensitive proportional chamber with spherical drift space, 512{times}512 elements of space resolution and time resolution of 10{sup 6} photons per second that can be vertically shifted and bent around the holder horizontal axis. The monochromator goniometer as well as the crystal bend and the mirror segments are driven by the multiple-turn potientiometers by the computer and CAMAC interface.

Popov, A.N.; Kheiker, D.M.; Harutunyan, E.G. (Institute of Crystallography of the USSR Academy of Sciences, Leninsky Prospect 59, Moscow, 117333 (USSR))

1992-01-01T23:59:59.000Z

15

Bibliometric analysis for science policy: An evaluation of the United Kingdom's research performance in ocean currents and protein crystallography  

Science Journals Connector (OSTI)

This paper presents the results of a study of Britain's scientific performance in the fields of ocean currents and protein crystallography carried out for the...

D. Crouch; J. Irvine; B. R. Martin

1986-05-01T23:59:59.000Z

16

Automation of the EMBL Hamburg protein crystallography beamline BW7B  

Science Journals Connector (OSTI)

The automation of the EMBL Hamburg wiggler beamline BW7B for protein crystallography is described. The beamline features an automated end-station, a robotic sample changer, semi-automated sample centering based on UV fluorescence and new control software including intuitive graphical user interfaces.

Pohl, E.

2004-08-17T23:59:59.000Z

17

Time-of-flight neutron diffraction study of bovine [gamma]-chymotrypsin at the Protein Crystallography Station  

SciTech Connect (OSTI)

The overarching goal of this research project is to determine, for a subset of proteins, exact hydrogen positions using neutron diffraction, thereby improving H-atom placement in proteins so that they may be better used in various computational methods that are critically dependent upon said placement. In order to be considered applicable for neutron diffraction studies, the protein of choice must be amenable to ultrahigh-resolution X-ray crystallography, be able to form large crystals (1 mm{sup 3} or greater) and have a modestly sized unit cell (no dimension longer than 100 {angstrom}). As such, {gamma}-chymotrypsin is a perfect candidate for neutron diffraction. To understand and probe the role of specific active-site residues and hydrogen-bonding patterns in {gamma}-chymotrypsin, neutron diffraction studies were initiated at the Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center (LANSCE). A large single crystal was subjected to H/D exchange prior to data collection. Time-of-flight neutron diffraction data were collected to 2.0 {angstrom} resolution at the PCS with 85% completeness. Here, the first time-of-flight neutron data collection from {gamma}-chymotrypsin is reported.

Lazar, Louis M.; Fisher, S. Zoe; Moulin, Aaron G.; Kovalevsky, Andrey; Novak, Walter R.P.; Langan, Paul; Petsko, Gregory A.; Ringe, Dagmar (Brandeis); (LANL)

2012-02-06T23:59:59.000Z

19

Hydrogen bonds of DsrD protein revealed by neutron crystallography  

Science Journals Connector (OSTI)

Hydrogen bonds of DNA-binding protein DsrD have been determined by neutron diffraction. In terms of proton donors and acceptors, DsrD protein shows striking differences from other proteins.

Chatake, T.

2008-04-18T23:59:59.000Z

20

Crystallography of Quasiperiodic Crystals  

Science Journals Connector (OSTI)

A unified description is given of modulated crystals and quasicrystals based on higher-dimensional crystallography.

Yamamoto, A.

1996-07-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Neutron crystallography aids drug design  

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

Neutron crystallography aids drug design Neutron crystallography aids drug design Researchers have used neutron crystallography for the first time to determine the structure of a...

22

Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases  

Science Journals Connector (OSTI)

Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? ... In brief, a grid box of 70 Ĺ × 70 Ĺ × 70 Ĺ was centered on the active site (the residue cluster displaying chemical shift perturbation upon inhibitor addition) with a grid spacing of 0.375 Ĺ. Crossover-, mutation-, and elitism weights were set to 0.80, 0.02, and 1.0, respectively. ... Support from the EU-NMR Integrated Infrastructure Initiative, contract no. ...

Johan Isaksson; Susanne Nyström; Dean Derbyshire; Hans Wallberg; Tatiana Agback; Helena Kovacs; Ivano Bertini; Andrea Giachetti; Claudio Luchinat

2009-02-24T23:59:59.000Z

23

Neutron macromolecular crystallography with LADI-III  

Science Journals Connector (OSTI)

The LADI-III instrument for measuring neutron macromolecular crystallography diffraction data is described. The data collection of type-III perdeuterated antifreeze protein is given as an example.

Blakeley, M.P.

2010-10-20T23:59:59.000Z

24

The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm  

Science Journals Connector (OSTI)

An expectation maximization algorithm is implemented to resolve the indexing ambiguity which arises when merging data from many crystals in protein crystallography, especially in cases where partial reflections are recorded in serial femtosecond crystallography (SFX) at XFELs.

Liu, H.

2014-09-23T23:59:59.000Z

25

Diamondoid Monolayers as Monochromatic Electron Source  

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

Diamondoid Monolayers as Monochromatic Electron Source Diamondoid Monolayers as Monochromatic Electron Source Print Wednesday, 28 November 2007 00:00 Diamondoids are...

26

Prospects for mathematical crystallography  

Science Journals Connector (OSTI)

Considered as an emerging field, how mathematical crystallography grows during the 21st century may depend on how it addresses demand and attracts recruits within the chemical, physical and mathematical communities.

McColm, G.

2014-02-12T23:59:59.000Z

27

High-pressure crystallography  

Science Journals Connector (OSTI)

The history and development of high-pressure crystallography are briefly described and examples of structural transformations in compressed compounds are given. The review is focused on the diamond-anvil cell, celebrating its 50th anniversary this year, the principles of its operation and the impact it has had on high-pressure X-ray diffraction.

Katrusiak, A.

2007-12-21T23:59:59.000Z

28

Dose, exposure time and resolution in serial X-ray crystallography  

Science Journals Connector (OSTI)

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.

Starodub, D.

2007-12-18T23:59:59.000Z

29

Crystallography of metal-organic frameworks  

Science Journals Connector (OSTI)

Recent advances in the crystallography of metal-organic frameworks (MOFs) are reviewed, including crystal growth, structural elucidation, in-situ and non-ambient crystallography.

G?ndara, F.

2014-10-28T23:59:59.000Z

30

Diamondoid Monolayers as Monochromatic Electron Source  

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

Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member...

31

Automation in X-Ray Crystallography  

Science Journals Connector (OSTI)

Automation in X-Ray Crystallography ... But in the past few years, automation procedures have been applied to intrinsically superior experimental methods. ...

S.C. ABRAHAMS

1963-06-03T23:59:59.000Z

32

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...

33

Diamondoid Monolayers as Monochromatic Electron Source  

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

Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have been made to synthesize the larger diamondoid molecules, but to no avail. This situation was finally changed in 2003 when significant quantities of higher diamondoids were found in petroleum by researchers in MolecularDiamond Technologies. Now, scientists from Berkeley Lab, Stanford University, Lawrence Livermore National Laboratory, and Germany have used photoelectron spectroscopy at the ALS to reveal an intriguing feature: monochromatized electron emission from a self-assembled monolayer of diamondoids. This discovery has immediately attracted the attention of people who are searching for materials for next-generation electron emitters.

34

Diamondoid Monolayers as Monochromatic Electron Source  

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

Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoid Monolayers as Monochromatic Electron Source Print Diamondoids are nanometer-sized molecules that feature diamond-crystal cage structures. Adamantane, the smallest member in the family, consists of one cage structure, diamantane two, triamantane three, tetramantane four, and so on. On all of these, the dangling bonds on the outer surfaces are terminated by hydrogen atoms. Because of their potential to possess novel properties of both diamond and nanomaterial, intensive efforts have been made to synthesize the larger diamondoid molecules, but to no avail. This situation was finally changed in 2003 when significant quantities of higher diamondoids were found in petroleum by researchers in MolecularDiamond Technologies. Now, scientists from Berkeley Lab, Stanford University, Lawrence Livermore National Laboratory, and Germany have used photoelectron spectroscopy at the ALS to reveal an intriguing feature: monochromatized electron emission from a self-assembled monolayer of diamondoids. This discovery has immediately attracted the attention of people who are searching for materials for next-generation electron emitters.

35

Phasing Out the Phase Problem in Interfacial Crystallography  

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

BESSRC/XOR BESSRC/XOR Phasing Out the Phase Problem in Interfacial Crystallography Photo of Paul Fenter (left) and Zhan Zhang at the mineral-fluid interface spectrometer at 12-ID-D (BESSRC/XOR). Paul Fenter (left) and Zhan Zhang at the mineral-fluid interface spectrometer at 12-ID-D (BESSRC/XOR). Since the advent of dedicated synchrotron radiation facilities, the applications of x-ray diffraction and scattering for structure determination have expanded to include a broad range of materials, from proteins and interfaces to nanoparticles. However, the well-known "phase problem" of crystallography limits these applications. The phase problem arises because the complete description of a structure requires a complex structure factor having both a magnitude and a phase. The measured x-ray

36

Instrumentation upgrades for the Macromolecular Crystallography beamlines  

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

Instrumentation upgrades for the Macromolecular Crystallography beamlines Instrumentation upgrades for the Macromolecular Crystallography beamlines of the Swiss Light Source Monday, October 29, 2012 - 2:00am SSRL, Bldg. 137, Rm. 322 Martin Fuchs, MX Group, Swiss Light Source; Paul Scherrer Institute (Villigen, Switzerland) A new unified diffractometer - the D3 - has been developed for the three MX beamlines. The first of the instruments is in general user operation at beamline X10SA since April 2012. The varied demands from both challenging academic research projects as well as high throughput industrial applications on today's macromolecular crystallography beamlines drive developments to both endstations and beamline optics. Recent instrumentation upgrades to the macromolecular crystallography (MX) beamlines of the Swiss Light Source therefore aimed to

37

Proteins  

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

Bioscience: Bioenergy, Biosecurity, and Health » Bioscience: Bioenergy, Biosecurity, and Health » Proteins Protein Engineering, Structure, and Function Los Alamos scientists seek a comprehensive understanding of the structure and function of proteins which can lead to a multitude of possibilities, such as enhancing cellulose degradation for biofuels or creating new therapeutics. Get Expertise Cliff Unkefer Director, Protein Crystallography Station Email Tom Terwilliger Laboratory Fellow Email Andrew Bradbury Bioscience Group Leader Email Rebecca McDonald Bioscience Communications Email Los Alamos scientists are developing mosaic proteins that may one day become the first viable vaccine that can protect humans from HIV, the virus that causes AIDS. Scientists manipulate and mimic proteins for use in creating solutions for

38

A heat-driven monochromatic light source  

SciTech Connect (OSTI)

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.

Stefani, F.; Lawless, J.L.

1989-04-01T23:59:59.000Z

39

Introduction to Crystallography | Advanced Photon Source  

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

Jump to Lectures: Jump to Lectures: Introduction Crystals Symmetry and Point Groups Plane and Space Groups Diffraction Reciprocal Space Reciprocal Space 2 Structure Factors Fourier Transforms Data Collection Structure Solutions Refinement and Interpretation Rietveld Synchrotrons and Neutrons Introduction to Crystallography This web page contains 15 lectures and handout notes given by Dr. Cora Lind for her Chem 4980/6850/8850: X-ray Crystallography course at the University of Toledo (Ohio). The preparation of these lectures was in part supported by National Science Foundation CAREER award DMR-0545517. Thanks to Prof. Lind and the University of Toledo Department of Chemistry for permission to post these videos and notes. All lecture notes are in PDF format. Lecture 1: Introduction Slides: Introduction [condensed version] This lecture introduces

40

Macromolecular crystallography beamline X25 at the NSLS  

Science Journals Connector (OSTI)

A description of the upgraded beamline X25 at the NSLS, operated by the PXRR and the Photon Sciences Directorate serving the Macromolecular Crystallography community, is presented.

H?roux, A.

2014-04-08T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

International Union of Crystallography Twenty-First General Assembly and International Congress of Crystallography, Osaka, Japan, 23-31 August 2008  

Science Journals Connector (OSTI)

A report of the Twenty-First General Assembly and International Congress of Crystallography is given.

IUCr

2009-08-14T23:59:59.000Z

42

Phase recovery for x-ray crystallography  

Science Journals Connector (OSTI)

For many years people have believed that in conventional x-ray crystallography one can only record the diffraction intensities but not the phases. In order to obtain the atomic arrangements, one usually has to guess a structure and then fit the intensity data by refining its parameters. Here, we show that the phases are in fact hidden in the intensity data, and can be directly recovered from the peak profiles. This method is demonstrated by the normal two-beam x-ray diffraction of a noncentrosymmetric crystal, and nontrivial phases are recovered from the intensity data alone.

G. Xu, G. E. Zhou, and X. Y. Zhang

1999-04-01T23:59:59.000Z

43

Fast microtomography using bright monochromatic x-rays  

SciTech Connect (OSTI)

A fast microtomography system for high-resolution high-speed imaging has been developed using bright monochromatic x-rays at the BL29XU beamline of SPring-8. The shortest scan time for microtomography we attained was 0.25 s in 1.25 {mu}m effective pixel size by combining the bright monochromatic x-rays, a fast rotating sample stage, and a high performance x-ray imaging detector. The feasibility of the tomography system was successfully demonstrated by visualization of rising bubbles in a viscous liquid, an interesting issue in multiphase flow physics. This system also provides a high spatial (a measurable feature size of 300 nm) or a very high temporal (9.8 {mu}s) resolution in radiographs.

Jung, J. W.; Lee, J. S.; Park, S. J.; Chang, S.; Pyo, J. [X-ray Imaging Center, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784 (Korea, Republic of); Department of Materials Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784 (Korea, Republic of); Kwon, N.; Kim, J. [X-ray Imaging Center, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784 (Korea, Republic of); School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784 (Korea, Republic of); Kohmura, Y.; Nishino, Y.; Yamamoto, M.; Ishikawa, T. [RIKEN/SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan); Je, J. H. [X-ray Imaging Center, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784 (Korea, Republic of); Department of Materials Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784 (Korea, Republic of); School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784 (Korea, Republic of); RIKEN/SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan)

2012-09-15T23:59:59.000Z

44

Resources for Macromolecular Crystallography | Advanced Photon Source  

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

APS Links: APS Links: User Registration Apply for Beam Time GUP Login | Calendar Publications Database CAT Websites: BioCARS GM/CA-CAT IMCA-CAT LRL-CAT LS-CAT NE-CAT SBC-CAT SER-CAT Reports and Presentations: Stuctural Bio Cross-Cut: Review | Response BioSync: BioSync Home Synchrotron PDB Deposits APS Deposits by Year Resources for Macromolecular Crystallography The next GUP deadline is: October 28, 2011 Interactive Map beta | View Energy Ranges for all MAD/SAD Beamlines 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 26 30 31 32 33 34 29 Filter by: Disciplines Techniques Chemistry Environmental Science GeoScience Life Science Materials Science Physics Polymer Science Highlight: Operator Access Mode X-ray Operations and Research (XOR) Collaborative Access Team (CAT) How to use this map | Reset Sector [ HIDE ]

45

Proposal Review Panels (Areas Other Than Crystallography)  

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

Proposal Review Panels Proposal Review Panels High Pressure Instrumentation Imaging/ Microbeam Macromolecular Crystallography Scattering Applied Materials Stanislav Sinogeikin, Chair Tim Graber, Chair Patrick LaRiviere, Chair John Rose, Chair Robert Suter, Chair Ercan Alp Maria Baldini Bin Chen Przemyslaw Dera Lars Ehm Ravi Kumar Barbara Lavina Sang-Heon (Dan) Shim Heather Watson Keith Brister Wenjun Liu Darren Dale Matthew Ginder-Vogel Xiaojing Huang (guest) Tony Lanzirotti Lisa Miller Mark Pfeifer Martina Ralle Xianghui Xiao Hanfei Yan Arnon Lavie Anne Mulichak Armand Beaudoin Dillon Fong Dileep Singh Mike Toney Bob Von Dreele Scattering Condensed Matter Scattering Chem/Biol/Environ Small Angle Scattering (SAXS) Spectroscopy Structural Science Roy Clarke, Chair Lynda Soderholm, Chair Peter Jemian, Chair Mali Balasubramanian, Chair

46

Mao of HP-CAT Awarded Aminoff Prize in Crystallography  

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

Mao of HP-CAT Awarded Aminoff Prize in Crystallography Mao of HP-CAT Awarded Aminoff Prize in Crystallography The Royal Swedish Academy of Sciences has awarded David H. Mao of the Geophysical Laboratory the Gregori Aminoff Prize in Crystallography 2005 "for pioneering research of materials at ultrahigh pressures and temperatures." Dr. Mao is the Director of the High Pressure Collaborative Access Team, which manages the beamlines at Advanced Photon Source (APS) sector 16. Named after Gregori Aminoff, the pioneering Swedish crystallographer, the prize is given annually to recognized scientists, or to a group of no more than three persons of international distinction, who have made a major contribution to crystallography. David H. Mao showing a panoramic high-pressure diamond-anvil cell to Murray Gibson

47

Serial crystallography on in vivo grown microcrystals using synchrotron radiation  

Science Journals Connector (OSTI)

The structure solution of T. brucei cathepsin B from 80 in vivo grown crystals with an average volume of 9 ?m3 obtained by serial synchrotron crystallography at a microfocus beamline is reported.

Gati, C.

2014-02-10T23:59:59.000Z

48

Monte Carlo Characterization of a Pulsed Laser-Wakefield Driven Monochromatic  

E-Print Network [OSTI]

Monte Carlo Characterization of a Pulsed Laser-Wakefield Driven Monochromatic X-Ray Source S. D determination of the incident X-ray energy by using unfolding techniques. I. INTRODUCTION HE Diocles laser light from the same laser system, producing monochromatic X-rays with energy and spectral width

Umstadter, Donald

49

Cryogenic neutron protein crystallography: routine methods and potential benefits  

Science Journals Connector (OSTI)

This article highlights routine methods and the benefits of collecting cryogenic macromolecular neutron diffraction data.

Coates, L.

2014-06-14T23:59:59.000Z

50

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

E-Print Network [OSTI]

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

Ramakrishnan, Venki

51

Neutron Macromolecular Crystallography (NMC) can provide accurate hydrogen atom  

E-Print Network [OSTI]

Neutron Macromolecular Crystallography (NMC) can provide accurate hydrogen atom positions crystals at a moderate 2 Ă? resolution. The advent of the Spallation Neutron Source (SNS neutron diffractometer (MaNDi) has been constructed at the SNS and is now operational. July 15-16, 2014

Pennycook, Steve

52

Twenty-Second General Assembly and International Congress of Crystallography, Madrid, Spain, 22-30 August 2011  

Science Journals Connector (OSTI)

A report of the Twenty-Second General Assembly and International Congress of Crystallography is given.

IUCr

2012-07-26T23:59:59.000Z

53

Phase coherence in multiple scattering : weak and intense monochromatic light wave propagating in a cold strontium  

E-Print Network [OSTI]

in a cold strontium cloud David Wilkowski, Yannick Bidel, Thierry Chaneli`ere, Robin Kaiser, Bruce Klappauf coherence of a monochromatic laser light propagating in an optically thick sample of laser-cooled strontium

54

Improved color coordinates of green monochromatic pc-LED capped with a band-pass filter  

Science Journals Connector (OSTI)

This study introduces a “greener” green monochromatic phosphor-converted light-emitting diode (pc-LED) using a band-pass filter (BPF) combined with a long-pass dichroic...

Oh, Ji Hye; Yang, Su Ji; Sung, Yeon-Goog; Do, Young Rag

2013-01-01T23:59:59.000Z

55

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

DOE Patents [OSTI]

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.

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

56

E-Print Network 3.0 - acid x-ray crystallography Sample Search...  

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

crystallography would you recommend?" Unfortunately... this list when choosing their top ten books to read on the subject of X-ray ... Source: Meagher, Mary - Department of...

57

Maximum Entropy and Bayesian Statistics in Crystallography: a Review of Practical Applications  

Science Journals Connector (OSTI)

The applications of the maximum entropy and Bayesian methods to problems in X-ray, neutron and electron crystallography are reviewed.

Gilmore, C.J.

1996-07-01T23:59:59.000Z

58

Nano Letters 8, 4477-4482 (2008) NANO-CRYSTALLOGRAPHY OF INDIVIDUAL CARBON NANOTUBES  

E-Print Network [OSTI]

Nano Letters 8, 4477- 4482 (2008) 1 NANO-CRYSTALLOGRAPHY OF INDIVIDUAL CARBON NANOTUBES N. Bozovi 1 meV energy resolution and 1 nm spatial resolution.1 The later should enable nano-crystallography ­ XRD study of individual nano-particles. The commissioning of NSLS II will take some time -- the plan

Homes, Christopher C.

59

JBluIce-EPICS control system for macromolecular crystallography.  

SciTech Connect (OSTI)

The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J. L.; Fischetti, R. F. (Biosciences Division); (Univ. of Michigan)

2011-01-01T23:59:59.000Z

60

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

E-Print Network [OSTI]

the critical density, a narrower EUV x-ray spectrum and a higher conversion efficiency from laserDynamics of laser-produced Sn-based plasmas for a monochromatic 13.5 nm extreme ultraviolet source-0417 ABSTRACT Dynamics of laser-produced Sn-based plasmas were investigated for a monochromatic EUV lithography

Najmabadi, Farrokh

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

Novel X-Ray Imaging Opportunities for the RPI Linear Accelerator's Tunable, Quasi-monochromatic X-ray Source  

E-Print Network [OSTI]

Novel X-Ray Imaging Opportunities for the RPI Linear Accelerator's Tunable, Quasi-monochromatic X-ray of an intense, tunable, polarized, and quasi-monochromatic X-ray source has been ongoing at Rensselaer Polytechnic Institute since 2001 [1, 2, 3, 4, 5, 6]. This X-ray source, known as Parametric X-rays (PXR

Danon, Yaron

62

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

E-Print Network [OSTI]

, solution-cast photovoltaics are of urgent interest to realize low-cost solar cells. Polymer, polymerSolution-processed infrared photovoltaic devices with >10% monochromatic internal quantum-fullerene, and polymer-nanocrystal photovoltaics absorb light only to wavelengths as long as 750 nm, with the exception

63

Efforts to enhance coverage of crystallography in United States secondary education  

Science Journals Connector (OSTI)

This article describes activities whose objective is to enhance secondary education in the United States by raising crystallography awareness through workshops, summer schools, student/teacher research internships and remote-enabling technologies.

Kantardjieff, K.A.

2010-09-11T23:59:59.000Z

64

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

SciTech Connect (OSTI)

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

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

2010-01-01T23:59:59.000Z

65

Three-dimensional reconstruction of the -AlCrFe phase by electron crystallography  

Science Journals Connector (OSTI)

The three-dimensional structure of the huge quasicrystal approxi­mant -AlFeCr was solved by electron crystallography, using high-resolution transmission-electron-microscopy (HREM) images and selected-area electron diffraction patterns from 13 different zone axes. This is the first example of an inorganic structure with over 100 unique atoms being solved to atomic resolution by electron crystallography.

Zou, X.D.

2003-10-28T23:59:59.000Z

66

A Beam line for Macromolecular Crystallography in ALBA  

SciTech Connect (OSTI)

ALBA is a third generation 3 GeV storage ring being built near Barcelona and foreseen to be operational in 2010. Out of the seven beamlines already funded in ALBA, one will be dedicated to macromolecular crystallography (MX). The beamline, dubbed XALOC, shall cope with a broad range of crystal structures and sizes. To this aim, a flexible optical design involving variable focusing optics has been incorporated into the beamline optics. The photon source will be a 2 m long, in-vacuum undulator with a period of 21.3 mm. The optics will consist in a Si(111), double-crystal monochromator cryogenically cooled, and a pair of mirrors placed in a Kirkpatrick-Baez configuration. The beamline will deliver a high flux beam in the 5-15 keV energy range, with an energy resolution of {delta}E/E {approx}2 x 10-4. In addition to the main beamline, it is being considered the possibility to use a diamond laue monochromator to provide photons at a fixed wavelength to an ancillary branch. This report shows the present status of the beamline design.

Juanhuix, Jordi; Ferrer, Salvador [CELLS -ALBA Synchrotron, Ed. Ciencies, Campus UAB, 08193 Bellaterra, Barcelona (Spain)

2007-01-19T23:59:59.000Z

67

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

E-Print Network [OSTI]

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 ...

Martin, Langdon James

2008-01-01T23:59:59.000Z

68

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

SciTech Connect (OSTI)

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

Tanabe, Minoru; Fujiwara, Takashi; Fujioka, Shinsuke; Nishimura, Hiroaki; Shiraga, Hiroyuki; Azechi, Hiroshi; Mima, Kunioki [Institute of Laser Engineering, Osaka University, 2-6 Yamada-Oka, Suita, Osaka 565-0871 (Japan)

2008-10-15T23:59:59.000Z

69

Crystal Structure of DNA Recombination Protein RuvA and a Model for Its Binding to the Holliday Junction  

Science Journals Connector (OSTI)

...We thank M. Legg (Zeneca Agrochemicals, Jealott's Hill, UK...Proteins chemistry metabolism Base Composition Crystallography, X-Ray DNA...We thank M. Legg (Zeneca Agrochemicals, Jea-lott's Hill, UK...

John B. Rafferty; Svetlana E. Sedelnikova; David Hargreaves; Peter J. Artymiuk; Patrick J. Baker; Gary J. Sharples; Akeel A. Mahdi; Robert G. Lloyd; David W. Rice

1996-10-18T23:59:59.000Z

70

Crystallography of Interfaces and Grain Size Distributions in Sr-Doped LaMnO3  

E-Print Network [OSTI]

Crystallography of Interfaces and Grain Size Distributions in Sr-Doped LaMnO3 Qinyuan Liu,§ Sudip systems are similar. I. Introduction HIGH-TEMPERATURE solid oxide fuel cells (SOFCs) offer highly efficient, clean, direct conversion of chemical to electrical energy.1 SOFC performance is dictated

Rohrer, Gregory S.

71

Role of Delamination and Crystallography on Anisotropy of Charpy toughness in API-X80 steel  

E-Print Network [OSTI]

Role of Delamination and Crystallography on Anisotropy of Charpy toughness in API-X80 steel M. S dependence of Charpy toughness has been investigated in API-X80 linepipe steel. The occurrence the origin of anisotropy in Charpy energy in API-X80 linepipe steel, as a function of test temperature

Cambridge, University of

72

Proteins  

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

Proteins Proteins Scientists manipulate and mimic proteins for use in creating solutions for medicine, sustainable energy, and more Read caption + Los Alamos National Laboratory graduate student, Patricia Langan, changes the properties of a green fluorescent protein in order to create new fluorescent protein variants. Overview of Research and Highlights Scientists at Los Alamos apply a unique collection of tools and expertise to gain a comprehensive understanding of the structure and function of proteins as well as to manipulate and mimic proteins for use in research. This knowledge can lead to a multitude of possibilities, such as enhancing cellulose degradation for biofuels based on understanding the enzymes that naturally degrade it (cellulases) or creating new therapeutics for tuberculosis patients.

73

Macromolecular Crystallography conventional and high-throughput methods  

SciTech Connect (OSTI)

High-throughput data collection requires the seamless interoperation of various hardware components. User-supplied descriptions of protein crystals must also be directly linked with the diffraction data. Such linkages can be achieved efficiently with computer databases. A database that tracks production of the protein samples, crystallization, and diffraction from the resultant crystals serves as the glue that holds the entire gene-to-structure process together. This chapter begins by discussing data collection processes and hardware. It then illustrates how a well-constructed database ensures information flow through the steps of data acquisition. Such a database allows synchrotron beamline measurements to be directly and efficiently integrated into the process of protein crystallographic structure determination.

Wasserman, Stephen R.; Smith, David W.; D'Amico, Kevin L.; Koss, John W.; Morisco, Laura L.; Burley, Stephen K.

2007-09-27T23:59:59.000Z

74

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

SciTech Connect (OSTI)

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.

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

75

Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics  

Science Journals Connector (OSTI)

...From the initial planning stages of free-electron...transfer of vibrational energy to the surrounding...completely in the distribution of spikes from pulse...shape and energy distribution. The total flux...over a much wider energy range (approx...temperature, pressure, electric field, etc...

2014-01-01T23:59:59.000Z

76

Testing commercial protein crystallography sample mounting loops for movement in a cold-stream  

Science Journals Connector (OSTI)

Several commercial sample mounting loops are tested for rigidity using silicon single crystals. Final testing is performed using crystals of tetragonal lysozyme to look for motion under typical data collection conditions.

Alkire, R.W.

2013-03-14T23:59:59.000Z

77

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein  

Science Journals Connector (OSTI)

...mu}s, at a laser pulse energy of 15 {mu}J focused to a 150...TR-SFX DED map at 10 ns. Light green structure: I CT intermediate...the I CT intermediate (4) in green as a guide to the eye. Figure...upper limit on the useful laser energy, which for PYP crystals is...

Jason Tenboer; Shibom Basu; Nadia Zatsepin; Kanupriya Pande; Despina Milathianaki; Matthias Frank; Mark Hunter; Sébastien Boutet; Garth J. Williams; Jason E. Koglin; Dominik Oberthuer; Michael Heymann; Christopher Kupitz; Chelsie Conrad; Jesse Coe; Shatabdi Roy-Chowdhury; Uwe Weierstall; Daniel James; Dingjie Wang; Thomas Grant; Anton Barty; Oleksandr Yefanov; Jennifer Scales; Cornelius Gati; Carolin Seuring; Vukica Srajer; Robert Henning; Peter Schwander; Raimund Fromme; Abbas Ourmazd; Keith Moffat; Jasper J. Van Thor; John C. H. Spence; Petra Fromme; Henry N. Chapman; Marius Schmidt

2014-12-05T23:59:59.000Z

78

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

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

of California, Berkeley, CA, USA 3Max-Volmer-Laboratorium fr Biophysikalische Chemie, Technische Universitt, and 6 Institut fr Kristallographie, Freie Universitt,...

79

Crystallography Explained  

Science Journals Connector (OSTI)

...Australian surfing authority, Thor Svenson, once said that...hundreds ofwell-drawn diagrams. The final chapter synthe-sizes...example and an equally thor-ough discussion of...ed. A Guide to Manual Materials Handling. A. Mital, A. S...

William Bassett

1993-06-25T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Implementation of dual-energy technique for virtual monochromatic and linearly mixed CBCTs  

SciTech Connect (OSTI)

Purpose: To implement dual-energy imaging technique for virtual monochromatic (VM) and linearly mixed (LM) cone beam CTs (CBCTs) and to demonstrate their potential applications in metal artifact reduction and contrast enhancement in image-guided radiation therapy (IGRT). Methods: A bench-top CBCT system was used to acquire 80 kVp and 150 kVp projections, with an additional 0.8 mm tin filtration. To implement the VM technique, these projections were first decomposed into acrylic and aluminum basis material projections to synthesize VM projections, which were then used to reconstruct VM CBCTs. The effect of VM CBCT on the metal artifact reduction was evaluated with an in-house titanium-BB phantom. The optimal VM energy to maximize contrast-to-noise ratio (CNR) for iodine contrast and minimize beam hardening in VM CBCT was determined using a water phantom containing two iodine concentrations. The LM technique was implemented by linearly combining the low-energy (80 kVp) and high-energy (150 kVp) CBCTs. The dose partitioning between low-energy and high-energy CBCTs was varied (20%, 40%, 60%, and 80% for low-energy) while keeping total dose approximately equal to single-energy CBCTs, measured using an ion chamber. Noise levels and CNRs for four tissue types were investigated for dual-energy LM CBCTs in comparison with single-energy CBCTs at 80, 100, 125, and 150 kVp. Results: The VM technique showed substantial reduction of metal artifacts at 100 keV with a 40% reduction in the background standard deviation compared to a 125 kVp single-energy scan of equal dose. The VM energy to maximize CNR for both iodine concentrations and minimize beam hardening in the metal-free object was 50 keV and 60 keV, respectively. The difference of average noise levels measured in the phantom background was 1.2% between dual-energy LM CBCTs and equivalent-dose single-energy CBCTs. CNR values in the LM CBCTs of any dose partitioning are better than those of 150 kVp single-energy CBCTs. The average CNR for four tissue types with 80% dose fraction at low-energy showed 9.0% and 4.1% improvement relative to 100 kVp and 125 kVp single-energy CBCTs, respectively. CNRs for low-contrast objects improved as dose partitioning was more heavily weighted toward low-energy (80 kVp) for LM CBCTs. Conclusions: Dual-energy CBCT imaging techniques were implemented to synthesize VM CBCT and LM CBCTs. VM CBCT was effective at achieving metal artifact reduction. Depending on the dose-partitioning scheme, LM CBCT demonstrated the potential to improve CNR for low contrast objects compared to single-energy CBCT acquired with equivalent dose.

Li Hao; Giles, William; Ren Lei; Bowsher, James; Yin Fangfang [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)

2012-10-15T23:59:59.000Z

82

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

E-Print Network [OSTI]

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

Agard, David

83

X-Ray Crystallography What do you need? A crystal. But not just any crystal a well ordered crystal  

E-Print Network [OSTI]

X-Ray Crystallography What do you need? A crystal. But not just any crystal­ a well ordered crystal that will diffract x-rays strongly. A crystal handedness. This reduces number to 6- 12. #12;#12;Generally X-ray beam

Cavanagh, John

84

May 15, 2003 9:58 WSPC/INSTRUCTION FILE JBCBr RAPTOR: OPTIMAL PROTEIN THREADING BY LINEAR PROGRAMMING  

E-Print Network [OSTI]

(3D) struc­ ture prediction via threading. Based on the contact map graph of the protein 3D structure technologies. A protein structure is typically solved using x­ray crystallography or nuclear magnetic resonance spectroscopy (NMR), which are costly and very time­consuming (ranging from months to years per structure

Xu, Jinbo

85

Consider tweaking horizontal dispersion at the IP in order to achieve monochromatic collisions, and remove energy bias  

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

4 4 SLAC-TN-04-003 February 19, 2004 Abstract This note documents a set of expressions used to explore the issue of whether or not it is reasonable to consider a conventional positron source for a Tesla formatted beam. The critical issu Monochromatization Option for NLC Collisions Andrei Seryi, Tor Raubenheimer Stanford Linear Accelerator Center Stanford University 2575 Sand Hill Road Menlo Park, CA Abstract: In this note, we consider an option for NLC operation where the Interaction Point beam parameters are adjusted in order to increase the energy resolution. This is achieved by squeezing the horizontal betatron function at the IP and simultaneously introducing a horizontal dispersion (with a different sign for electron and positron

86

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

SciTech Connect (OSTI)

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

Fujioka, Shinsuke; Fujiwara, Takashi; Tanabe, Minoru; Nishimura, Hiroaki; Nagatomo, Hideo; Ohira, Shinji; Shiraga, Hiroyuki; Azechi, Hiroshi [Institute of Laser Engineering, Osaka University, 2-6 Yamada-oka, Suita Osaka, 565-0871 (Japan); Inubushi, Yuichi [Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871 (Japan)

2010-10-15T23:59:59.000Z

87

Two dimensionally space-resolved electron temperature measurement of fusion plasma by x-ray monochromatic imaging method  

SciTech Connect (OSTI)

Electron temperature distributions of laser created fusion plasma were measured by using toroidally bent Bragg crystals. A tiny amount of argon was seeded in deuterium fuel gas and monochromatic images of Ar{sup +17} (1{ital s}{minus}3{ital p}) Ly{beta} and Ar{sup +16} (1{ital s}{sup 2}{minus}1{ital s}3{ital p}) He{beta} lines were taken to provide temperature distribution of the compressed core from their intensity ratios. A fusion core created by laser-generated x rays in a micro-cavity showed the temperature structure corresponding to the illumination asymmetry caused by the cavity irradiation geometry. The experimental distribution of the line-ratio of Ly{beta} to He{beta} was compared with the postprocessed outputs from one dimensional simulation, assuming perfect spherical implosion, to discuss degradation of pellet implosion. {copyright} {ital 1996 American Institute of Physics.}

Fujita, K.; Nishimura, H.; Uschmann, I.; Foerster, E.; Takabe, H.; Kato, Y.; Nakai, S. [Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka 565 (Japan)

1996-05-01T23:59:59.000Z

88

A relativistic beam of monochromatic muons produced in the upper atmo-sphere is incident vertically on the earth's surface at velocity v z c, where c  

E-Print Network [OSTI]

of the muons. Express your answer in terms of the energy E of a muon as measured by an observer at restPart A A relativistic beam of monochromatic muons produced in the upper atmo- sphere is incident of the muon number reaching the ground to the number at a height H above sea level. Assume that the beam moves

Ha, Taekjip

89

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

SciTech Connect (OSTI)

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.

Koestner, R.J.

1982-08-01T23:59:59.000Z

90

Hydrogen bond dynamics in the active site of photoactive yellow protein  

E-Print Network [OSTI]

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

Herschlag, Dan

91

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

SciTech Connect (OSTI)

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.

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

2010-04-08T23:59:59.000Z

92

Protein Puzzles and Scientific Solutions  

Office of Science (SC) Website

Articles » 2014 » Protein Articles » 2014 » Protein Puzzles and Scientific Solutions News Featured Articles 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 Science Headlines Presentations & Testimony News Archives Contact Information Office of Science U.S. Department of Energy 1000 Independence Ave., SW Washington, DC 20585 P: (202) 586-5430 01.06.14 Protein Puzzles and Scientific Solutions Researchers at SLAC National Accelerator Laboratory solve fiendishly complicated structures using X-ray savvy and serious computing power. Print Text Size: A A A Subscribe FeedbackShare Page Click to enlarge photo. Enlarge Photo The Coherent X-ray Imaging experimental station at SLAC's Linac Coherent Light Source. Photo courtesy of Brad Plummer/SLAC In crystallography experiments at the Coherent X-ray Imaging experimental

93

AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory  

SciTech Connect (OSTI)

Recent advances in high-throughput techniques for macromolecular crystallography have highlighted the importance of structure-based drug design (SBDD), and the demand for synchrotron use by pharmaceutical researchers has increased. Thus, in collaboration with Astellas Pharma Inc., we have constructed a new high-throughput macromolecular crystallography beamline, AR-NE3A, which is dedicated to SBDD. At AR-NE3A, a photon flux up to three times higher than those at existing high-throughput beams at the Photon Factory, AR-NW12A and BL-5A, can be realized at the same sample positions. Installed in the experimental hutch are a high-precision diffractometer, fast-readout, high-gain CCD detector, and sample exchange robot capable of handling more than two hundred cryo-cooled samples stored in a Dewar. To facilitate high-throughput data collection required for pharmaceutical research, fully automated data collection and processing systems have been developed. Thus, sample exchange, centering, data collection, and data processing are automatically carried out based on the user's pre-defined schedule. Although Astellas Pharma Inc. has a priority access to AR-NE3A, the remaining beam time is allocated to general academic and other industrial users.

Yamada, Yusuke; Hiraki, Masahiko; Sasajima, Kumiko; Matsugaki, Naohiro; Igarashi, Noriyuki; Kikuchi, Takashi; Mori, Takeharu; Toyoshima, Akio; Kishimoto, Shunji; Wakatsuki, Soichi [Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801 (Japan); Amano, Yasushi; Warizaya, Masaichi; Sakashita, Hitoshi [Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tukuba, Ibaraki, 300-8585 (Japan)

2010-06-23T23:59:59.000Z

94

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

DOE Patents [OSTI]

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.

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

95

1,3-Alternate calix[4]arene nitronyl nitroxide tetraradical and diradical: synthesis, X-ray crystallography, paramagnetic NMR spectroscopy, EPR spectroscopy, and magnetic studies  

SciTech Connect (OSTI)

Calix[4]arenes constrained to 1,3-alternate conformation and functionalized at the upper rim with four and two nitronyl nitroxides have been synthesized, and characterized by X-ray crystallography, magnetic resonance (EPR and {sup 1}H NMR) spectroscopy, and magnetic studies. Such calix[4]arene tetraradicals and diradicals provide scaffolds for through-bond and through-space intramolecular exchange couplings.

Rajca, Andrzej; Pink, Maren; Mukherjee, Sumit; Rajca, Suchada; Das, Kausik (UNL); (Indiana)

2008-04-02T23:59:59.000Z

96

X-ray Crystallographic Center (XCC) User Registration Form Peter Y. Zavalij X-ray Crystallographi Center 091 Chemistry Bldg. / College Park, MD 20742  

E-Print Network [OSTI]

X-ray Crystallographic Center (XCC) User Registration Form Peter Y. Zavalij X-ray Crystallographi. or advisor confirmation e-mail X-ray Diffractometer that will be used: User Level and Status Smart Apex2X'Pert Pro MRD (Reflectivity & low angles) Xeuss (Small/Wide Angle X-ray Scattering) Submitting user ­ only

Thirumalai, Devarajan

97

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

SciTech Connect (OSTI)

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.

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

98

NMR contributions to structural dynamics studies of intrinsically disordered proteins  

Science Journals Connector (OSTI)

Abstract Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions.

Robert Konrat

2014-01-01T23:59:59.000Z

99

ISPyB: an information management system for synchrotron macromolecular crystallography  

Science Journals Connector (OSTI)

......DATA AND TEXT MINING ISPyB: an information...Blundell, 2010 for a review). Increased...biologists to plan, direct and document...uniform and standard interface to ISPyB...data collection plan is also provided...Managing and mining protein crystallization...commercialized standard. J. Synchrotron......

Solange Delageničre; Patrice Brenchereau; Ludovic Launer; Alun W. Ashton; Ricardo Leal; Stéphanie Veyrier; José Gabadinho; Elspeth J. Gordon; Samuel D. Jones; Karl Erik Levik; Seán M. McSweeney; Stéphanie Monaco; Max Nanao; Darren Spruce; Olof Svensson; Martin A. Walsh; Gordon A. Leonard

2011-11-15T23:59:59.000Z

100

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

SciTech Connect (OSTI)

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.

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

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

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

SciTech Connect (OSTI)

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.

Zhu, Liang Cong

2009-06-08T23:59:59.000Z

102

Trapping Conformational Intermediate States in the Reaction Center Protein from Photosynthetic Bacteria  

E-Print Network [OSTI]

neutron scattering and X-ray crystallography measure- ments of bacteriorhodopsin (10) and myoglobin (4

Gunner, Marilyn

103

SMB, Macromolecular Crystallography  

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

give rise to increased user demand and scientific productivity. BL 7-1 Donec id elit non mi porta gravida at eget metus. Fusce dapibus, tellus ac cursus commodo, tortor mauris...

104

electronic reprint Crystallography  

E-Print Network [OSTI]

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

Meagher, Mary

105

electronic reprint Crystallography  

E-Print Network [OSTI]

-rod calculations of a lognormal crystal size distribution in the layer plane and an empirical function. The layer microstructure, responsible for the long-range lateral disorder, is modeled with spherically and cylindrically bent crystallites having volume-averaged radii of 20­40 A° . The b unit-cell parameter from

106

Anticancer steroid sulfatase inhibitors: synthesis of a potent fluorinated second-generation agent, in vitro and in vivo activities, molecular modeling, and protein crystallography  

Science Journals Connector (OSTI)

...spectrometer at 270, 67.9, and 376 MHz, respectively, and chemical...chromatography-mass spectrometry (atmospheric pressure chemical ionization...chromatography-mass spectrometry (atmospheric pressure), m/z 394.26...unsequestered ligand in the plasma over time. Hence, and given...

L.W. Lawrence Woo; Delphine S. Fischer; Christopher M. Sharland; Melanie Trusselle; Paul A. Foster; Surinder K. Chander; Anna Di Fiore; Claudiu T. Supuran; Giuseppina De Simone; Atul Purohit; Michael J. Reed; and Barry V.L. Potter

2008-08-01T23:59:59.000Z

107

Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction  

Science Journals Connector (OSTI)

An emulsion-based serial crystallographic technology has been developed, in which single crystals are grown in nanolitre-sized droplets inside an X-ray semi-transparent microfluidic chip exploiting a negative feedback mechanism. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored in the chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals to solve the structure of glucose isomerase to 2.1 ?.

Heymann, M.

2014-08-25T23:59:59.000Z

108

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Protein Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Wednesday, 28 April 2010 00:00 Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

109

Protein Characterisation by Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy  

SciTech Connect (OSTI)

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.

Wallace, B.

2009-01-01T23:59:59.000Z

110

Preliminary Crystallography Confirms that the Archaeal DNA-binding and Tryptophan-sensing Regulator TrpY is a Dimer  

SciTech Connect (OSTI)

TrpY regulates the transcription of the metabolically expensive tryptophan-biosynthetic operon in the thermophilic archaeon Methanothermobacter thermautotrophicus. TrpY was crystallized using the hanging-drop method with ammonium sulfate as the precipitant. The crystals belonged to the tetragonal space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 87, c = 147 {angstrom}, and diffracted to 2.9 {angstrom} resolution. The possible packing of molecules within the cell based on the values of the Matthews coefficient (V{sub M}) and analysis of the self-rotation function are consistent with the asymmetric unit being a dimer. Determining the structure of TrpY in detail will provide insight into the mechanisms of DNA binding, tryptophan sensing and transcription regulation at high temperature by this novel archaeal protein.

J Cafasso; B Manjasetty; E Karr; K Sandman; M Chance; J Reeve

2011-12-31T23:59:59.000Z

111

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Wednesday, 28 April 2010 00:00 Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

112

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

113

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

114

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

115

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

116

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

117

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Print Hexameric motor proteins represent a complex class of molecular machines that variously push and pull on biological molecules using adenosine triphosphate (ATP) as chemical fuel. A specialized class of ring-shaped motor proteins, hexameric helicases, can unwind DNA strands and perform large-scale manipulations of single-stranded nucleic acids in processes such as DNA replication, DNA repair, and gene expression. To understand how certain hexameric helicases walk with directional polarity along single-stranded nucleic acids, Berkeley researchers used x-ray crystallography at the ALS to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through its interior. Interestingly, the rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain.

118

Pressure-tuning spectroscopy of charge-transfer salts. X-ray crystallography and comparative studies in solution and in the solid state  

SciTech Connect (OSTI)

The highly colored pyridinium (P{sup +}) and cobaltocenium (C{sup +}) iodides are charge-transfer salts by virtue of the new electronic absorption bands that follow Mulliken theory. X-ray crystallography establishes the relevant interionic separation and steric orientation of the cation/anion pairs P{sup +}I{sup {minus}} and C{sup +}I{sup {minus}} constrained for optimum charge-transfer interaction in the crystal lattice. Spectral comparisons of the charge-transfer (CT) transitions by absorption (solution) and by diffuse reflectance (solid-state) measurements reveals the commonality of contact ion pairs (CIP) in aprotic nonpolar solvents (dichloromethane) with those extant in crystalline charge-transfer salts. As such, the compression of the charge-transfer salts P{sup +}I{sup {minus}} in the solid state by the application of pressures up to 140 kbar leads to unusual red shifts of the CT bands indicative of the dominance of destabilizing charge-transfer interactions.

Bockman, T.M.; Kochi, J.K. (Univ. of Houston, TX (USA)); Chang, H.R.; Drickamer, H.G. (Univ. of Illinois, Urbana (USA))

1990-11-01T23:59:59.000Z

119

Conformational Exchange in a Membrane Transport Protein Is Altered in Protein Crystals  

SciTech Connect (OSTI)

Successful macromolecular crystallography requires solution conditions that may alter the conformational sampling of a macromolecule. Here, site-directed spin labeling is used to examine a conformational equilibrium within BtuB, the Escherichia coli outer membrane transporter for vitamin B{sub 12}. Electron paramagnetic resonance (EPR) spectra from a spin label placed within the N-terminal energy coupling motif (Ton box) of BtuB indicate that this segment is in equilibrium between folded and unfolded forms. In bilayers, substrate binding shifts this equilibrium toward the unfolded form; however, EPR spectra from this same spin-labeled mutant indicate that this unfolding transition is blocked in protein crystals. Moreover, crystal structures of this spin-labeled mutant are consistent with the EPR result. When the free energy difference between substates is estimated from the EPR spectra, the crystal environment is found to alter this energy by 3 kcal/mol when compared to the bilayer state. Approximately half of this energy change is due to solutes or osmolytes in the crystallization buffer, and the remainder is contributed by the crystal lattice. These data provide a quantitative measure of how a conformational equilibrium in BtuB is modified in the crystal environment, and suggest that more-compact, less-hydrated substates will be favored in protein crystals.

D Freed; P Horanyi; M Wiener; D Cafiso

2011-12-31T23:59:59.000Z

120

Conformational Exchange in a Membrane Transport Protein Is Altered in Protein Crystals  

SciTech Connect (OSTI)

Successful macromolecular crystallography requires solution conditions that may alter the conformational sampling of a macromolecule. Here, site-directed spin labeling is used to examine a conformational equilibrium within BtuB, the Escherichia coli outer membrane transporter for vitamin B{sub 12}. Electron paramagnetic resonance (EPR) spectra from a spin label placed within the N-terminal energy coupling motif (Ton box) of BtuB indicate that this segment is in equilibrium between folded and unfolded forms. In bilayers, substrate binding shifts this equilibrium toward the unfolded form; however, EPR spectra from this same spin-labeled mutant indicate that this unfolding transition is blocked in protein crystals. Moreover, crystal structures of this spin-labeled mutant are consistent with the EPR result. When the free energy difference between substates is estimated from the EPR spectra, the crystal environment is found to alter this energy by 3 kcal/mol when compared to the bilayer state. Approximately half of this energy change is due to solutes or osmolytes in the crystallization buffer, and the remainder is contributed by the crystal lattice. These data provide a quantitative measure of how a conformational equilibrium in BtuB is modified in the crystal environment, and suggest that more-compact, less-hydrated substates will be favored in protein crystals.

Freed, Daniel M.; Horanyi, Peter S.; Wiener, Michael C.; Cafiso, David S. (UV)

2010-09-27T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis  

SciTech Connect (OSTI)

We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the HIV-1 protease in which the flexibility of the 'flap' structures (residues 37-61 in each monomer of the homodimeric protein molecule) was systematically varied. These analogue enzymes were further studied by X-ray crystallography, NMR relaxation, and pulse-EPR methods, in conjunction with molecular dynamics simulations. We show that conformational isomerization in the flaps is correlated with structural reorganization of residues in the active site, and that it is preorganization of the active site that is a rate-limiting factor in catalysis.

Torbeev, Vladimir Yu.; Raghuraman, H.; Hamelberg, Donald; Tonelli, Marco; Westler, William M.; Perozo, Eduardo; Kent, Stephen B.H. (GSU); (UW); (UC)

2013-09-17T23:59:59.000Z

122

EMSL - proteins  

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

proteins en Structures and Stabilities of (MgO)n Nanoclusters. http:www.emsl.pnl.govemslwebpublicationsstructures-and-stabilities-mgon-nanoclusters

123

Serial crystallography using synchrotron radiation  

Science Journals Connector (OSTI)

A brief history is given of how X-ray diffraction data from crystals have been recorded. Today there are new possibilities, spawned by the availability of free electron lasers that produce powerful femtosecond long X-ray pulses.

Rossmann, M.G.

2014-02-28T23:59:59.000Z

124

Dynamical Observations of Membrane Proteins: The Case of Bacteriorhodopsin  

SciTech Connect (OSTI)

A new x-ray methodology, Diffracted X-ray Tracking (DXT), has been proven to be a valuable tool in observing intramolecular conformational changes of individual single molecules in real time and space. In order to achieve DXT, the fabrication of dispersive nanocrystals is one of the most important technologies, because DXT system monitors the diffracted x-ray (Laue) spots from nanocrystals labeled with single bio-molecules. In this study, we fabricated one-dimensional gold nanocrystals with an average diameter size of 16 nm using vacuum evaporation. Furthermore, using these nanocrystals, we succeeded in observing normal Brownian motions and momentary structural changes of a single-membrane protein (Bacteriorhodopsin: BR) in a membrane due to the expression of its function. The average movement of the momentarily structural changes in the 35th residue of BR was 76 {+-} 48 pm, and this agrees with estimated movements from known x-ray crystallography data. This result is an important step toward realizing in-vivo observations of single-molecular conformational changes in membrane proteins.

Okumura, Yasuaki [Department of Biomolecular Science and Technology, Shinshu University, Ueda, Nagano 386-8567 (Japan); Life and Environmental Science Div., Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan); CREST-Sasaki Team, Japan Science and Technology Corporation (JST), Tachikawa 190-0012 (Japan); Oka, Toshihiko [Life and Environmental Science Div., Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan); Taniguchi, Yoshio [Department of Biomolecular Science and Technology, Shinshu University, Ueda, Nagano 386-8567 (Japan); Sasaki, Yuji C. [Life and Environmental Science Div., Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan); CREST-Sasaki Team, Japan Science and Technology Corporation (JST), Tachikawa 190-0012 (Japan)

2004-05-12T23:59:59.000Z

125

Protein Structure  

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

Protein Structure Protein Structure Name: Chris Location: N/A Country: N/A Date: N/A Question: what are the four levels or structure of protien Replies: Hi Chris... as you must know proteins are made of amino acids arranged in polypeptide chains, and the order of them in these chains is called primary structure. The regular way in which the polypeptide chains are arranged in space to form a protein molecule is called secondary structure. The arrangement of the three-dimensional structure of the polypeptide chain in space is the tertiary structure. The arrangement of the combination of two or more polypeptide chains constitutes the quartenary structure. Quite simple, isn't? If you just remember that the molecular weights of proteins range usually from 10,000 to 100,000 daltons (one dalton is the weight of one hydrogen atom) and that 20 different amino-acids in a chain 100 amino acids long can be arranged in far more than 10 to its 100 potency ( number 1 followed by 100 zeroes) ways!

126

High efficiency quasi-monochromatic infrared emitter  

SciTech Connect (OSTI)

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.

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

127

Manipulating and Visualizing Proteins  

E-Print Network [OSTI]

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

Simon, Horst D.

2003-01-01T23:59:59.000Z

128

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

SciTech Connect (OSTI)

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.

Barends, Thomas, R.M.

2013-11-25T23:59:59.000Z

129

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

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

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.

Barends, Thomas, R.M.

130

Predicting protein folding pathways  

Science Journals Connector (OSTI)

......never for 1MBC. Protein Acylphosphatase...transition state ensemble with a marked...it is highly disordered relative to rest...superfamily domain protein (PDB 1WIT; 93...transition state ensemble in two-state proteins. Proteins, 43......

Mohammed J. Zaki; Vinay Nadimpally; Deb Bardhan; Chris Bystroff

2004-08-01T23:59:59.000Z

131

Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray  

SciTech Connect (OSTI)

Diffracted X-ray tracking (DXT) enables the tilting and twisting motions of single protein molecules to be monitored with micro- to milliradian resolution using a highly brilliant X-ray source with a wide energy bandwidth. We have developed a technique to monitor single molecules using gold nanocrystals attached to individual protein molecules using the BL28B2 beamline at SPring-8. In this paper we present the installation of a single toroidal X-ray mirror at BL28B2 to focus X-rays in an energy range of 10–20 keV (?E/E = 82% for an X-ray with a wide energy bandwidth). With this beamline we tracked diffraction spots from gold nanocrystals over a wide angle range than that using quasi-monochromatic X-rays. Application of the wide angle DXT technique to biological systems enabled us to observe the on-site motions of single protein molecules that have been functionalized in vivo. We further extend the capability of DXT by observing the fractional tilting and twisting motions of inner proteins under various conditions. As a proof of this methodology and to determine instrumental performance the intramolecular motions of a human serum albumin complex with 2-anthracenecarboxylic acid was investigated using the BL28B2 beamline. The random tilting and twisting intramolecular motions are shown to be directly linked to the movement of individual protein molecules in the buffer solution.

Ichiyanagi, Kouhei; Sasaki, Yuji C. [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 609 Kiban Building 5-1-5 Kashiwanoha, Kahiwashi, Chiba 277-8561 (Japan) [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 609 Kiban Building 5-1-5 Kashiwanoha, Kahiwashi, Chiba 277-8561 (Japan); Japan Science and Technology Agency, CREST, CREST, Sasaki-Team, 609 Kiban Building, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Sekiguchi, Hiroshi; Hoshino, Masato; Kajiwara, Kentaro; Senba, Yasunori; Ohashi, Haruhiko; Ohta, Noboru [Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan)] [Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Hoshisashi, Kentaro; Jae-won, Chang; Tokue, Maki; Matsushita, Yufuku [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 609 Kiban Building 5-1-5 Kashiwanoha, Kahiwashi, Chiba 277-8561 (Japan)] [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 609 Kiban Building 5-1-5 Kashiwanoha, Kahiwashi, Chiba 277-8561 (Japan); Nishijima, Masaki; Inoue, Yoshihisa [Department of Applied Chemistry and Office for University-Industry Collaboration, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)] [Department of Applied Chemistry and Office for University-Industry Collaboration, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yagi, Naoto [Japan Science and Technology Agency, CREST, CREST, Sasaki-Team, 609 Kiban Building, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan) [Japan Science and Technology Agency, CREST, CREST, Sasaki-Team, 609 Kiban Building, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan)

2013-10-15T23:59:59.000Z

132

Discover protein sequence signatures from protein-protein interaction data  

E-Print Network [OSTI]

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

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

2005-11-23T23:59:59.000Z

133

Shotgun protein sequencing.  

SciTech Connect (OSTI)

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.

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

2009-06-01T23:59:59.000Z

134

Natively Disordered Proteins  

Science Journals Connector (OSTI)

Proteins can exist in at least three forms: ... random coil-like or gas-like). The protein trinity hypothesis has two components: (i) a given native protein can be in any one of the ... and data mining were used ...

Dr Pedro Romero; Zoran Obradovic; A. Keith Dunker

2004-06-01T23:59:59.000Z

135

Function of proteins  

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

Function of proteins Function of proteins Name: Collins Location: N/A Country: N/A Date: N/A Question: What is the function of proteins in your body? Replies: Proteins have many functions. They serve as enzymatic catalysts, are used as transport molecules (hemoglobin transports oxygen) and storage molecules (iron is stored in the liver as a complex with the protein ferritin); they are used in movement (proteins are the major component of muscles); they are needed for mechanical support (skin and bone contain collagen-a fibrous protein); they mediate cell responses (rhodopsin is a protein in the eye which is used for vision); antibody proteins are needed for immune protection; control of growth and cell differentiation uses proteins (hormones). These are just a few examples of the many, many functions of proteins.

136

Slide 1  

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

FRONTIER MACROMOLECULAR CRYSTALLOGRAPHY (FMX) SCIENTIFIC SCOPE BEAMLINE CHARACTERISTICS Micro crystal diffraction often required to yield structures: Membrane protein (L), amyloid...

137

Enriched Protein-Protein Interactions from Biomedical Text  

E-Print Network [OSTI]

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

Edinburgh, University of

138

Protein-protein interaction Functional Genomics  

E-Print Network [OSTI]

., (2007) Molecular Systems Biology ­ ~300 purifications · E. coli ­ Butland G et al., (2005) Nature ­ 857 ­ Krogan et al., (2006) · 547 complexes, 2600 bait protein, 4000 prey proteins · Human ­ Ewing RB et al of the effects of the individual strains · Highly functional interaction ­ Collins SR et al. (2007) Nature test

Spang, Rainer

139

Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

Nothing is solid about proteins. Governing rules and established laws are constantly ... old belief that the unique function of a protein is determined by its unique structure, which ... unique amino acid sequenc...

Vladimir N. Uversky

2014-01-01T23:59:59.000Z

140

Optimization Approaches to Protein Folding.  

E-Print Network [OSTI]

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

Yoon, Hyun-suk

2006-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

Electrostatics in intrinsically disordered proteins.  

E-Print Network [OSTI]

??Protein-protein interactions are fundamental to many biological processes. A large proportion of proteins have been identified as partially or entirely disordered in their native state.… (more)

Wong, Eric Tsz Chung

2012-01-01T23:59:59.000Z

142

Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

Abstract Many biologically active proteins fail to form unique three-dimensional (3D) structures under physiological conditions, either along their entire lengths or locally. These proteins are known as intrinsically disordered proteins (IDPs) among several other names. The discovery of these proteins challenged the traditional protein structure paradigm, according to which a unique well-defined structure was required for the correct function of a protein and therefore a unique structure defines a unique function of a protein. \\{IDPs\\} are structurally and functionally very different from ordered proteins, and therefore require special experimental and computational tools for identification and analyses. They are highly abundant in nature; and, in any given organism, they constitute a functionally broad and densely populated unfoldome. They possess a number of crucial biological functions that complement the functional repertoire of structured (ordered) proteins. They are very important players in cell signaling, protein–protein interaction networks and gene regulation networks. Their signaling activities are modulated by numerous posttranslational modifications and, in multicellular eukaryotes, by alternative splicing. Some \\{IDPs\\} in some cases can fold into a specific 3D structure after binding to natural partners. These proteins are tightly controlled inside the cell and their dysregulation and misbehavior is frequently associated with the development of various pathological conditions.

V.N. Uversky

2013-01-01T23:59:59.000Z

143

Simulations of Protein Folding  

E-Print Network [OSTI]

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.

Michael Cahill; Mark Fleharty; Kevin Cahill

1999-09-17T23:59:59.000Z

144

Using Superfolder Green Fluorescent Protein for Periplasmic Protein Localization Studies  

Science Journals Connector (OSTI)

...Microbial Cell Biology Using Superfolder Green Fluorescent Protein for Periplasmic Protein...hampered by problems with the export of green fluorescent protein (GFP). Here we show...problems with the export of functional green fluorescent protein (GFP) (9). When...

Thuy Dinh; Thomas G. Bernhardt

2011-07-15T23:59:59.000Z

145

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

E-Print Network [OSTI]

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

Jager, M; Michalet, X; Weiss, Shimon

2005-01-01T23:59:59.000Z

146

Seafood proteins and preparation of protein concentrates  

Science Journals Connector (OSTI)

Seafoods namely fish, crustaceans and molluscs are important ... in human nutrition. Approximately 11-27% of seafoods consist of crude proteins. However, contribution ... contribute to the overall content of NPN ...

F. Shahidi

1994-01-01T23:59:59.000Z

147

Virus structure: Crystallography attacks the cold  

Science Journals Connector (OSTI)

... unique reflections, were collected using a synchrotron X-ray source - the Cornell High Energy Synchroton Source. Synchrotron radiation is an extremely bright source of X rays. X-ray exposure ...

Don C. Wiley

1985-09-12T23:59:59.000Z

148

New opportunities in biological and chemical crystallography  

Science Journals Connector (OSTI)

This article, now updated, was originally published in Indian J. Phys. [(2001), A84, 1-11] which in turn was based on the Professor K. Banerjee Birth Centennial Medal lecture of the author given in Calcutta in September 2000.

Helliwell, J.R.

2001-12-24T23:59:59.000Z

149

Automation of sample mounting for macromolecular crystallography  

Science Journals Connector (OSTI)

A sample holder standard for use with robotic sample changers is defined. The standard includes a system for sample identification, tracking and management of data flow in a macromolecular structure-determination pipeline. A robotic sample changer designed for use with the sample standard is described.

Cipriani, F.

2006-09-19T23:59:59.000Z

150

Nanostructure, Chemistry and Crystallography of Iron Nitride...  

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

of hybrid-electric and battery electric vehicles may increase worldwide demand for rare earth elements and certain other materials. It is likely that future supply of these...

151

Microcrystallization techniques for serial femtosecond crystallography...  

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

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

152

Protein kinesis: The dynamics of protein trafficking and stability  

SciTech Connect (OSTI)

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.

NONE

1995-12-31T23:59:59.000Z

153

Protein folding tames chaos  

E-Print Network [OSTI]

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...

Xia, Kelin

2013-01-01T23:59:59.000Z

154

Beamline 5.0.1  

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

1 Print 1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available

155

Beamline 5.0.2  

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

2 Print 2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving power (E/ΔE) 7,000 Divergence at sample 3.0(h) x 0.4 (v) mrad (user selectable) Spot size 25-125 µm (user selectable) Endstations Standard hutch Characteristics Single axis, air bearing goniometer; CCD detector, low-temperature system

156

Beamline 5.0.2  

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

2 Print 2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving power (E/ΔE) 7,000 Divergence at sample 3.0(h) x 0.4 (v) mrad (user selectable) Spot size 25-125 µm (user selectable) Endstations Standard hutch Characteristics Single axis, air bearing goniometer; CCD detector, low-temperature system

157

Beamline 5.0.3  

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

3 Print 3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available; automated sample mounting system

158

Beamline 5.0.2  

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

2 Print 2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving power (E/ΔE) 7,000 Divergence at sample 3.0(h) x 0.4 (v) mrad (user selectable) Spot size 25-125 µm (user selectable) Endstations Standard hutch Characteristics Single axis, air bearing goniometer; CCD detector, low-temperature system

159

Beamline 5.0.3  

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

3 Print 3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available; automated sample mounting system

160

Beamline 5.0.3  

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

3 Print 3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available; automated sample mounting system

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

Beamline 5.0.1  

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

1 Print 1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available

162

Beamline 5.0.1  

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

1 Print 1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available

163

Beamline 5.0.1  

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

1 1 Beamline 5.0.1 Print Tuesday, 20 October 2009 08:32 Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules

164

Beamline 5.0.1  

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

1 Print 1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available

165

Beamline 5.0.3  

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

3 Print 3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available; automated sample mounting system

166

Beamline 5.0.1  

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

1 Print 1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12.7 keV (fixed) Monochromator Si(220) Asymmetric cut single crystal Measured flux 1.50 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Resolving power (E/ΔE) ~10,000 Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available

167

Beamline 5.0.3  

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

3 3 Beamline 5.0.3 Print Tuesday, 20 October 2009 08:36 Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available; automated sample mounting system

168

Beamline 5.0.2  

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

2 Print 2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving power (E/ΔE) 7,000 Divergence at sample 3.0(h) x 0.4 (v) mrad (user selectable) Spot size 25-125 µm (user selectable) Endstations Standard hutch Characteristics Single axis, air bearing goniometer; CCD detector, low-temperature system

169

Beamline 5.0.3  

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

3 Print 3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available; automated sample mounting system

170

Beamline 5.0.2  

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

5.0.2 5.0.2 Beamline 5.0.2 Print Tuesday, 20 October 2009 08:35 Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving power (E/ΔE) 7,000 Divergence at sample 3.0(h) x 0.4 (v) mrad (user selectable) Spot size 25-125 µm (user selectable) Endstations Standard hutch Characteristics

171

Beamline 5.0.3  

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

3 3 Beamline 5.0.3 Print Tuesday, 20 October 2009 08:36 Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm-period wiggler (W11) Energy range 12,700 eV(fixed) Monochromator Asymmetric cut single crystal Si(220) Measured flux 2.4 x 1011 photons/s at 400-mA ring current, with 1.5-mrad divergence and 100-µm pinhole collimator Divergence at sample 3.0 (h) x 0.4 (v) mrad (user selectable) Spot size 100 µm Endstations Standard hutch Detectors 3 x 3 CCD array (ADSC Q315R) Sample format Single crystals of biological molecules Sample preparation Support labs available; automated sample mounting system

172

Beamline 5.0.2  

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

2 Print 2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Proposal cycle Proposals for Structural Biology Beamlines (2-month cycle) Source characteristics 11.4-cm period wiggler (W11) Energy range 5-16 keV Monochromator Double-crystal, Si(111) liquid N2 cooled Measured flux at 12.4 keV 8.0 x 1011 photons/s at 400-mA ring current, with 1.5-mrad convergence and 100-µm pinhole collimator Resolving power (E/ΔE) 7,000 Divergence at sample 3.0(h) x 0.4 (v) mrad (user selectable) Spot size 25-125 µm (user selectable) Endstations Standard hutch Characteristics Single axis, air bearing goniometer; CCD detector, low-temperature system

173

Protein folding and heteropolymers  

E-Print Network [OSTI]

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.

T. Garel; H. Orland; E. Pitard

1997-06-12T23:59:59.000Z

174

Proteins at interfaces.  

E-Print Network [OSTI]

??Protein adsorption is a fundamental and ubiquitous phenomenon, which has severe implications in the fields of biomaterials as well as bio- and nanotechnology, e.g., in… (more)

Evers, Florian

2010-01-01T23:59:59.000Z

175

Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments  

E-Print Network [OSTI]

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

Haspel, Nurit

176

Protein Science (1992), I , 322-328. Cambridge University Press. Printed in the USA. Copyright 0 1992 The Protein Society  

E-Print Network [OSTI]

of Crystallography, Birkbeck College, Malet Street, 'Department of Medicinal Chemistry, Pfizer Inc., Central Research-(R)(statine-like) hydroxyl of the tetrahedral carbonyl hydrateis hydrogen-bonded to bothactive-site aspartates 32 and 215 in the position occupiedby a wa- ter in the native enzyme. The second hydroxyloxygen of the hydrateis hydrogen

Sali, Andrej

177

Biophysics of protein evolution and evolutionary protein biophysics  

Science Journals Connector (OSTI)

...neglects the dynamic nature of proteins. Recent advances in experimental...the dynamic properties of proteins [173,248-250] and...for the construction of ensembles of diverse conformations of disordered proteins based on NMR and other...

2014-01-01T23:59:59.000Z

178

DNA's Role with Proteins  

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

DNA's Role with Proteins DNA's Role with Proteins Name: Hans Location: N/A Country: N/A Date: N/A Question: Is it sure that the most important information of living cells is stored in the DNA? DNA seems to be nothing more than an inventory of useful proteins and a tool to create those proteins. Could it be that more important operational know how of how these proteins interact to build a living organism is actually located in the rest of the cell? So that the rest of the cell is the most important inheritance, whereas DNA merely takes care of the genetic variation? Replies: DNA is the entire library of protein information for an organism. All seven types of protein. It is true that in developmental stages of an organism that the presence and absences of certain proteins and other chemicals generated by proteins will influence what the DNA in a "particular" cell will express. Hence, you can start out with one cell and end up with a complex organism. You may have heard some of this information with the cloning activities that have been going on lately. All the inheritance comes from the DNA, but what parts of the DNA expression may be dictated by the cells special characteristics developed upon specializing. In that way the liver cells will only do "liver" things and the kidney cells will only do "kidney" things, BUT they use the same DNA information to operate, just a different portion of the same DNA that pertains to their particular "job". If you can convince a cell that it does not have a special job anymore, then you can develop the entire organism from this cell with the right signals; this is what cloning techniques have done!

179

Protein Folding Simulation in CCP  

Science Journals Connector (OSTI)

A protein is a list of linked units called aminoacids. There are 20 different kinds of aminoacids and the typical length of a protein is 100–500 units. The Protein Structure Prediction Problem (PSP) is the pro...

Alessandro Dal Palů; Agostino Dovier; Federico Fogolari

2004-01-01T23:59:59.000Z

180

Structural Characterization of Disordered States of Proteins.  

E-Print Network [OSTI]

??Disordered states of proteins include the biologically functional intrinsically disordered proteins and the unfolded states of folded proteins which are important for protein folding and… (more)

Marsh, Joseph Arthur

2010-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

Viruses and viral proteins  

Science Journals Connector (OSTI)

The X-ray structures of viruses and viral proteins currently available are providing high-resolution snapshots of viral molecular machineries, expanding our vision of the virus world and giving crucial information on potential targets for future antiviral therapies.

Verdaguer, N.

2014-10-14T23:59:59.000Z

182

Protein folding and cosmology  

E-Print Network [OSTI]

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.

González-Diáz, P F

1997-01-01T23:59:59.000Z

183

Protein folding and cosmology  

E-Print Network [OSTI]

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.

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

1997-06-04T23:59:59.000Z

184

Protein Folding and Assembly  

Science Journals Connector (OSTI)

Abstract In order to carry out their biological functions, most polypeptide chains must fold into stable three-dimensional structures, for it is the precise spatial distribution of chemical groups within a protein that gives the molecule its ability to interact specifically with other molecules and, in the case of an enzyme, catalyze a chemical reaction. In many cases, individual polypeptide chains must also assemble into larger structures containing additional proteins or nucleic acids. The folding of many proteins is reversible, so that the native structure can be disrupted by a change in temperature or addition of a chemical denaturant, and the unfolded protein can then be induced to refold and assemble by returning it to physiological conditions. Experiments of this type demonstrate that the information specifying the native structure of a protein resides in its amino acid sequence, and in vitro studies have provided important insights into the energetic factors that drive folding and assembly and the kinetic mechanisms of these processes. Folding in vivo is often facilitated by transient interactions with other proteins, molecular chaperones. Folding may also compete with the formation of aberrant aggregates in vivo, sometimes leading to pathological conditions such as amyloid diseases.

D.P. Goldenberg

2013-01-01T23:59:59.000Z

185

Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction  

E-Print Network [OSTI]

Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction of Biochemistry and Molecular Biology University College London Darwin Building, Gower Street London WC1E 6BT, UK: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins

Teichmann, Sarah

186

Structures of Domains I and IV from YbbR are Representative of a Widely Distributed Protein Family  

SciTech Connect (OSTI)

YbbR domains are widespread throughout Eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. Although the precise role of these domains remains undefined, the location of the multiple YbbR domain-encoding ybbR gene in the Bacillus subtilis glmM operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. To further characterize the YbbR domains, structures of two of the four domains (I and IV) from the YbbR-like protein of Desulfitobacterium hafniense Y51 were solved by solution nuclear magnetic resonance and X-ray crystallography. The structures show the domains to have nearly identical topologies despite a low amino acid identity (23%). The topology is dominated by {beta}-strands, roughly following a 'figure 8' pattern with some strands coiling around the domain perimeter and others crossing the center. A similar topology is found in the C-terminal domain of two stress-responsive bacterial ribosomal proteins, TL5 and L25. Based on these models, a structurally guided amino acid alignment identifies features of the YbbR domains that are not evident from naive amino acid sequence alignments. A structurally conserved cis-proline (cis-Pro) residue was identified in both domains, though the local structure in the immediate vicinities surrounding this residue differed between the two models. The conservation and location of this cis-Pro, plus anchoring Val residues, suggest this motif may be significant to protein function.

A Barb; J Cort; J Seetharaman; S Lew; H Lee; T Acton; L Tong; G Montelione; J Prestegard; et al.

2011-12-31T23:59:59.000Z

187

New trends in protein expression In order to benefit from the wealth of genomics data and to  

E-Print Network [OSTI]

-ray and neu- tron crystallography, NMR, electron microscopy and tomography, small angle X-ray and neutron scattering, mass spectroscopy and advanced light microscopy techniques. Common to all these tech- niques

Sussman, Joel L.

188

Protein folding: concepts and perspectives  

Science Journals Connector (OSTI)

...In this review, the main concepts of protein folding, as deduced from both theoretical and experimental...

J. M. Yon

1997-07-01T23:59:59.000Z

189

INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION  

E-Print Network [OSTI]

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

Halligan, Daniel

190

Computer Simulations of Protein Folding  

E-Print Network [OSTI]

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

Sorin, Eric J.

191

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

E-Print Network [OSTI]

[16) Green Fluorescent Protein Chimeras to Probe Protein-Protein Interactions By SANG-HYUN PARK and RONALD T. RAINES Introduction Green fluorescent protein (GFP) from the jellyfish Aequorea victoria. These properties include high thermal stability and resis- tance to detergents, organic solvents, and proteases

Raines, Ronald T.

192

Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein  

E-Print Network [OSTI]

-Azhar University, Cairo, Egypt {lixue, rjordan, yasser, ddobbs, honavar}@iastate.edu ABSTRACT Computational protein-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface efficiency of docking) [2]. In this study, we test whether knowledge of predicted interface residues can also

Honavar, Vasant

193

Predicting mostly disordered proteins by using structure-unknown protein data  

Science Journals Connector (OSTI)

Predicting intrinsically disordered proteins is important in structural biology because they ... We know the structures of far more ordered proteins than disordered proteins. The structural distribution of proteins

Kana Shimizu; Yoichi Muraoka; Shuichi Hirose; Kentaro Tomii…

2007-03-01T23:59:59.000Z

194

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

E-Print Network [OSTI]

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

Bigelow, Stephen

195

Molecular Origin of Electron Paramagnetic Resonance Line Shapes on [beta]-Barrel Membrane Proteins: The Local Solvation Environment Modulates Spin-Label Configuration  

SciTech Connect (OSTI)

In this work, electron paramagnetic resonance (EPR) spectroscopy and X-ray crystallography were used to examine the origins of EPR line shapes from spin-labels at the protein-lipid interface on the {beta}-barrel membrane protein BtuB. Two atomic-resolution structures were obtained for the methanethiosulfonate spin-label derivatized to cysteines on the membrane-facing surface of BtuB. At one of these sites, position 156, the label side chain resides in a pocket formed by neighboring residues; however, it extends from the protein surface and yields a single-component EPR spectrum in the crystal that results primarily from fast rotation about the fourth and fifth bonds linking the spin-label to the protein backbone. In lipid bilayers, site 156 yields a multicomponent spectrum resulting from different rotameric states of the labeled side chain. Moreover, changes in the lipid environment, such as variations in bilayer thickness, modulate the EPR spectrum by modulating label rotamer populations. At a second site, position 371, the labeled side chain interacts with a pocket on the protein surface, leading to a highly immobilized single-component EPR spectrum that is not sensitive to hydrocarbon thickness. This spectrum is similar to that seen at other sites that are deep in the hydrocarbon, such as position 170. This work indicates that the rotameric states of spin-labels on exposed hydrocarbon sites are sensitive to the environment at the protein-hydrocarbon interface, and that this environment may modulate weak interactions between the labeled side chain and the protein surface. In the case of BtuB, lipid acyl chain packing is not symmetric around the {beta}-barrel, and EPR spectra from labeled hydrocarbon-facing sites in BtuB may reflect this asymmetry. In addition to facilitating the interpretation of EPR spectra of membrane proteins, these results have important implications for the use of long-range distance restraints in protein structure refinement that are obtained from spin-labels.

Freed, Daniel M.; Khan, Ali K.; Horanyi, Peter S.; Cafiso, David S. (UV)

2012-01-20T23:59:59.000Z

196

Identifying protein-protein interactions of a cell cycle regulator  

E-Print Network [OSTI]

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

Amos, Joseph Edward

2013-02-22T23:59:59.000Z

197

Neutron Diffraction Studies of Proteins  

Science Journals Connector (OSTI)

20 November 1980 research-article Neutron Diffraction Studies of Proteins G. A. Bentley S. A. Mason Neutrons interact differently with protein crystals...hydrogen or deuterium atoms diffract neutrons relatively more strongly, but in addition...

1980-01-01T23:59:59.000Z

198

Autoproteolysis in hedgehog protein biogenesis  

Science Journals Connector (OSTI)

...ARTICLE Autoproteolysis in hedgehog Protein Biogenesis John J. Lee, Stephen C. Ekker, Doris P. von Kessler, Jeffery A. Porter, Benjamin 1. Sun, Philip A. Beachy* Extracellular signaling proteins encoded by the hedgehog (hh) multigene family...

JJ Lee; SC Ekker; DP von Kessler; JA Porter; BI Sun; PA Beachy

1994-12-02T23:59:59.000Z

199

Simplified Models of Protein Folding  

Science Journals Connector (OSTI)

Protein folding is one of the most basic physico-...1...]. As in all theoretical endeavors, the degree of simplification in modeling protein behavior depends on the questions to be addressed. The motivations for ...

Hue Sun Chan

2005-01-01T23:59:59.000Z

200

Simulated annealing in protein folding  

Science Journals Connector (OSTI)

Proteins are the fundamental molecules of living cells. They are roughly linear chains of subunits called amino acids. There are 20 biologically interesting amino acids, and thus a protein molecule can be thou...

Avner Friedman

1992-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

A Novel Topology for Representing Protein Folds  

E-Print Network [OSTI]

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

Segal, Mark R

2009-01-01T23:59:59.000Z

202

Hydration dynamics near a model protein surface  

E-Print Network [OSTI]

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

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

2003-01-01T23:59:59.000Z

203

Protein synthesis in the dendrite  

Science Journals Connector (OSTI)

...April 2002 research-article Protein synthesis in the dendrite Shao Jun Tang Erin M...understood. One mechanism is synaptic protein synthesis. According to this idea, messenger...dendrite, information about the synaptic synthesis of specific proteins in a physiological...

2002-01-01T23:59:59.000Z

204

Petaflop Computing for Protein Folding  

E-Print Network [OSTI]

"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

Izaguirre, JesĂşs A.

205

Hydrophobic tint of knot proteins  

Science Journals Connector (OSTI)

Protein structures having knotted configurations in their native fold, have great impact in their function. Protein knot localization has become possible in single molecule experiments though they are identified in their structure level. Signal processing ... Keywords: Fourier transform, cross correlation, hydrophobicity, knot protein, spectral analysis

P. Lissy Anto; S. Nair Achuthsankar

2010-02-01T23:59:59.000Z

206

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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

Thirumalai, Devarajan

207

Challenging Proteins Principles and Methods  

E-Print Network [OSTI]

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

Jacobsen, Steve

208

Protein domain organisation: adding order  

E-Print Network [OSTI]

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

Kummerfeld, Sarah K; Teichmann, Sarah A

2009-01-29T23:59:59.000Z

209

Mathematical methods for protein science  

SciTech Connect (OSTI)

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.

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

1997-12-31T23:59:59.000Z

210

IMPROVING SEQUENCE ALIGNMENTS FOR INTRINSICALLY DISORDERED PROTEINS  

E-Print Network [OSTI]

IMPROVING SEQUENCE ALIGNMENTS FOR INTRINSICALLY DISORDERED PROTEINS PREDRAG RADIVOJAC, ZORAN sequence alignments for intrinsically disordered proteins. For 55 disordered protein families we measure and discriminate related disordered proteins whose average sequence identity with the other family members is below

Radivojac, Predrag

211

Ontological foundation for protein data models  

Science Journals Connector (OSTI)

In this paper we proposed a Protein Ontology to integrate protein data and information from various Protein Data Sources. Protein Ontology provides the technical and scientific infrastructure and knowledge to allow description and analysis of relationships ...

Amandeep S. Sidhu; Tharam S. Dillon; Elizabeth Chang

2005-10-01T23:59:59.000Z

212

On the rough folding landscape of green fluorescent protein  

E-Print Network [OSTI]

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

Andrews, Benjamin Thomas

2008-01-01T23:59:59.000Z

213

Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1  

Science Journals Connector (OSTI)

Femtosecond X-ray crystallography allows structural analysis of a difficult-to-crystallize fusion protein that is a potential component of a candidate HIV-1 subunit vaccine.

Lee, H.-H.

2014-08-20T23:59:59.000Z

214

ALS Activity Report 2004  

E-Print Network [OSTI]

Science U3 Protein Crystallography 4.2.2 MagneticMagnetic microscopy, spectromicroscopy Surface and materials science,and external magnetic field. Science Highlights / Nano and

Tamura Ed., Lori S.

2005-01-01T23:59:59.000Z

215

Slide 1  

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

HIGHLY AUTOMATED BEAMLINE FOR MACROMOLECULAR CRYSTALLOGRAPHY (AMX) SCIENTIFIC SCOPE BEAMLINE CHARACTERISTICS Atomic structures from x-ray diffraction of proteins and their...

216

Better models by discarding data?  

Science Journals Connector (OSTI)

Making the most of hard-won data in protein crystallography: to keep or not to keep, that is the question.

Diederichs, K.

2013-06-15T23:59:59.000Z

217

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

SciTech Connect (OSTI)

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.

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

2006-01-01T23:59:59.000Z

218

Hydrodynamic Description of Protein Folding  

Science Journals Connector (OSTI)

A hydrodynamic description of protein folding is proposed and illustrated with a lattice protein model, which has a free energy surface (FES) typical of proteins with two-state folding kinetics. The flows from the unfolded to the native state are concentrated in a limited region of the FES. The rest is occupied by a flow “vortex”, which does not lead to the native state. In contrast with intermediates that are associated with local minima, the vortex is not visible on the FES. The hydrodynamic interpretation thus provides new insights into the mechanism of protein folding and can be a useful complement to standard analyses.

Sergei F. Chekmarev; Andrey Yu. Palyanov; Martin Karplus

2008-01-11T23:59:59.000Z

219

Protein detection system  

DOE Patents [OSTI]

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.

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

220

Manipulating Protein Adsorption using a Patchy Protein-Resistant Brush  

Science Journals Connector (OSTI)

Toward the development of surfaces for the precise manipulation of proteins, this study explores the fabrication and protein-interactive behavior of a new type of surface containing extremely small (on the order of 10 nm or less) flat adhesive “patches” ...

Saugata Gon; Marina Bendersky; Jennifer L. Ross; Maria M. Santore

2010-06-17T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

Mechanisms of binding diversity in protein disorder : molecular recognition features mediating protein interaction networks.  

E-Print Network [OSTI]

??Indiana University-Purdue University Indianapolis (IUPUI) Intrinsically disordered proteins are proteins characterized by lack of stable tertiary structures under physiological conditions. Evidence shows that disordered proteins… (more)

Hsu, Wei-Lun

2014-01-01T23:59:59.000Z

222

E-Print Network 3.0 - analyse protein-protein interactions Sample...  

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

use only. Not for reproduction, distribution or commercial use. Summary: on four interrelated aspects of protein-protein and protein-nucleic acid interactions. Section 2...

223

Convergent evolution of protein structure  

E-Print Network [OSTI]

Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP by N. Siew D. Fischer Predicting the three-dimensional structure of a protein from its amino acid of Structure Prediction) blind prediction experiments aim to assess the prediction capabilities in the field

Fischer, Daniel

224

Chloroplast ribosomes and protein synthesis.  

Science Journals Connector (OSTI)

...1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene...protein-encoding genes, rp116 and rps3, of the marine macro-algae, Gracilaria tenuistipitata...of the plastid encoded rp122 protein in marine macroalgae, Gracilaria tenuistipitata...

E H Harris; J E Boynton; N W Gillham

1994-12-01T23:59:59.000Z

225

Introduction to Grid computing Protein folding  

E-Print Network [OSTI]

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

Boyar, Joan

226

Fusion Protein Products Screen Purify Detect Cleave  

E-Print Network [OSTI]

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

Lebendiker, Mario

227

Do viral proteins possess unique biophysical features?  

E-Print Network [OSTI]

for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, Indiana 46202Do viral proteins possess unique biophysical features? Nobuhiko Tokuriki1 , Christopher J. Oldfield of proteins to fit their environ- ment. We hypothesize that highly thermostable proteins and viral proteins

Tawfik, Dan S.

228

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

E-Print Network [OSTI]

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

Zhu, L; Kaback, HR; Dalbey, RE

2013-01-01T23:59:59.000Z

229

ANCHOR: web server for predicting protein binding regions in disordered proteins  

Science Journals Connector (OSTI)

......involved in protein-protein interactions. Disordered binding regions...segments differ from protein interaction sites of globular proteins due to their distinct...flexible structural ensemble in isolation and...indicative of disordered binding regions......

Zsuzsanna Dosztányi; Bálint Mészáros; István Simon

2009-10-15T23:59:59.000Z

230

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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.

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

2010-07-18T23:59:59.000Z

231

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...

232

Improvement of the Protein Quality of Corn With Soybean Protein  

Science Journals Connector (OSTI)

In most Central American countries, lime-treated corn provides 31% of the total protein and 45% of the energy intake, and beans 24% of the ... quality and quantity, as well as in energy. To overcome these deficie...

Ricardo Bressani; Luiz G. Elías…

1978-01-01T23:59:59.000Z

233

Protein MAS NMR methodology and structural analysis of protein assemblies  

E-Print Network [OSTI]

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. ...

Bayro, Marvin J

2010-01-01T23:59:59.000Z

234

Optimized Null Model for Protein Structure Networks  

E-Print Network [OSTI]

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

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

2009-01-01T23:59:59.000Z

235

A motion planning approach to protein folding  

E-Print Network [OSTI]

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...

Song, Guang

2004-09-30T23:59:59.000Z

236

Mutagenic effects on protein folding and stability  

E-Print Network [OSTI]

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 ...

Anderson, Thomas Anthony, 1973-

2002-01-01T23:59:59.000Z

237

Principles of Chaperone-Mediated Protein Folding  

Science Journals Connector (OSTI)

...Principles of Chaperone-Mediated Protein Folding F. Ulrich Hartl The recent discovery...coordinated pathway of cellular protein folding. Principles of chaperone-mediated protein folding. | The recent discovery of molecular...

1995-01-01T23:59:59.000Z

238

Pathway and Stability of Protein Folding  

Science Journals Connector (OSTI)

...research-article Pathway and Stability of Protein Folding Alan R. Fersht Mark Bycroft...experimental approach to the problem of protein folding and stability which measures...helices. Pathway and stability of protein folding. | We describe an experimental...

1991-01-01T23:59:59.000Z

239

Models of Cooperativity in Protein Folding  

Science Journals Connector (OSTI)

...research-article Models of Cooperativity in Protein Folding Hue Sun Chan Sarina Bromberg...two-state cooperativity of protein folding? Since the 1950s, three main...Models of cooperativity in protein folding. | What is the basis for the...

1995-01-01T23:59:59.000Z

240

Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches  

Science Journals Connector (OSTI)

...small ligands or protein-binding partners...conformational ensemble for docking will...intrinsically disordered proteins (IDPs), which...conformational ensembles in biomolecular...predictors of mostly disordered proteins. Biochemistry...

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Metal-directed protein self-assembly  

E-Print Network [OSTI]

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

Salgado. Eric N.

2010-01-01T23:59:59.000Z

242

Towards a Molecular Understanding of Protein Solubility  

E-Print Network [OSTI]

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

Kramer, Ryan 1984-

2011-05-31T23:59:59.000Z

243

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

E-Print Network [OSTI]

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

244

Adhesives from modified soy protein  

DOE Patents [OSTI]

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.

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

2008-08-26T23:59:59.000Z

245

Elastic energy of proteins and the stages of protein folding  

E-Print Network [OSTI]

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^{\

Lei, Jinzhi

2010-01-01T23:59:59.000Z

246

Combining in vivo and in silico screening for protein stability  

E-Print Network [OSTI]

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

Barakat, Nora Hisham

2007-01-01T23:59:59.000Z

247

Extending the theoretical framework of protein folding dynamics  

E-Print Network [OSTI]

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

Yang, Sichun

2006-01-01T23:59:59.000Z

248

Journal Article: Simplified Protein Models: Predicting Folding...  

Office of Scientific and Technical Information (OSTI)

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

249

Search for: "protein folding" | DOE PAGES  

Office of Scientific and Technical Information (OSTI)

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

250

Antimicrobial protein protects grapevines from pathogen  

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

protein protects grapevines from pathogen Engineered grapevines produce a hybrid antimicrobial protein to block infection. February 21, 2012 Grapevines Goutam Gupta,...

251

Protein secretion in Bacillus species.  

Science Journals Connector (OSTI)

...relatively early, was the need for a proton motive force in protein export (211...by Bacillus amyloliquefaciens requires proton motive force. J. Bacteriol. 164:712-716...266. Ribes, V., K. Romisch, A. Giner, B. Dobberstein, and D. Tollervey...

M Simonen; I Palva

1993-03-01T23:59:59.000Z

252

Protein Folding Sculpting Evolutionary Change  

E-Print Network [OSTI]

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, ...

Lindquist, Susan

253

Turbulent phenomena in protein folding  

Science Journals Connector (OSTI)

Protein folding and hydrodynamic turbulence are two long-standing challenges, in molecular biophysics and fluid dynamics, respectively. The theories of these phenomena have been developed independently and used different formalisms. Here we show that the protein folding flows can be surprisingly similar to turbulent fluid flows. Studying a benchmark model protein (an SH3 domain), we have found that the flows for the slow folding trajectories of the protein, in which a partly formed N- and C-terminal ? sheet hinders the RT loop from attaching to the protein core, have many properties of turbulent flows of a fluid. The flows are analyzed in a three-dimensional (3D) space of collective variables, which are the numbers of native contacts between the terminal ? strands, between the RT loop and the protein core, and the rest of the native contacts. We have found that the flows have fractal nature and are filled with 3D eddies; the latter contain strange attractors, at which the tracer flow paths behave as saddle trajectories. Two regions of the space increment have been observed, in which the flux variations are self-similar with the scaling exponent h=1/3, in surprising agreement with the Kolmogorov inertial range theory of turbulence. In one region, the cascade of protein rearrangements is directed from larger to smaller scales (net folding), and in the other, it is oppositely directed (net unfolding). Folding flows for the fast trajectories are essentially “laminar” and do not have the property of self-similarity. Based on the results of our study, we infer, and support this inference by simulations, that the origin of the similarity between the protein folding and turbulent motion of a fluid is in a cascade mechanism of structural transformations in the systems that underlies these phenomena.

Igor V. Kalgin and Sergei F. Chekmarev

2011-01-31T23:59:59.000Z

254

Protein Flips Lipids Across Membranes  

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

Protein Flips Lipids Across Protein Flips Lipids Across Membranes Protein Flips Lipids Across Membranes Print Wednesday, 26 October 2005 00:00 Found ubiquitously in both bacteria and humans, membrane proteins of the adenosine triphosphate (ATP)-binding cassette (ABC) transporter family have been implicated in both antibiotic and cancer-drug resistance. The mechanisms used by these proteins to expel toxins from cells therefore represent key targets for the development of drugs designed to combat the growing problem of multidrug resistance. Toward this end, researchers from The Scripps Research Institute have succeeded in crystallizing MsbA-an ABC transporter protein-together with a substrate (the molecule to be transported) and a hydrolyzed (spent) form of the nucleotide ATP, the transporter's source of chemical energy. The resulting molecular complex is caught at a moment following the transporter's "power stroke," the force-generating part of the transport cycle. This snapshot suggests a mechanism by which the substrate molecule gets flipped head-over-tail from one side of the membrane to the other, on its way out of the cell.

255

Fast events in protein folding  

SciTech Connect (OSTI)

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.

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

1996-04-01T23:59:59.000Z

256

Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump–probe experiment  

Science Journals Connector (OSTI)

...usually done in protein crystallography...scatter off the protein solution. Initially...information from disordered ensembles of molecules...structure of a disordered ensemble of photoexcited...photoactive yellow protein from nanoseconds...

2014-01-01T23:59:59.000Z

257

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

DOE Patents [OSTI]

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.

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

258

3.2 Energetics of Protein Folding  

Science Journals Connector (OSTI)

Protein is only marginally stable as a result of a small net difference between large contributions of stabilizing and destabilizing forces. This article reviews the contribution of various energetic factors such as the hydrophobic effect, hydrogen bonding, electrostatic interaction, and conformation entropy to protein folding. Based on our current understanding of the protein-folding energetic, strategies to improve protein stability are discussed.

K.-B. Wong; T.-H. Yu; C.-H. Chan

2012-01-01T23:59:59.000Z

259

Flavors of Protein Disorder Slobodan Vucetic,1  

E-Print Network [OSTI]

Flavors of Protein Disorder Slobodan Vucetic,1 Celeste J. Brown,2* A. Keith Dunker,2** and Zoran-4660 ABSTRACT Intrinsically disordered proteins are characterized by long regions lacking 3-D struc- ture showed that protein predictors trained on disorder from one type of protein often achieve poor accuracy

Vucetic, Slobodan

260

Advanced Review Ordered and disordered proteins  

E-Print Network [OSTI]

Advanced Review Ordered and disordered proteins as nanomaterial building blocks Nithya Srinivasan on intrinsically disordered proteins, using nucleoporin and neurofilament proteins as case studies. A key theme and Sanjay Kumar Proteins possess a number of attractive properties that have contributed to their recent

Kumar, Sanjay

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Intrinsically Disordered Protein A. Keith Dunker1  

E-Print Network [OSTI]

Intrinsically Disordered Protein A. Keith Dunker1 , J. David Lawson1 , Celeste J. Brown1 , Pedro, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those proteins having disordered regions of length = 50 consecutive residues. Keywords: disordered protein

Obradovic, Zoran

262

Thermodynamics of Protein Folding Erik Sandelin  

E-Print Network [OSTI]

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

Sandelin, Erik

263

272 Dispatch Protein folding: Chaperones get Hip  

E-Print Network [OSTI]

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

Craig, Elizabeth A

264

Systematic characterization of protein glycosylation of bacteria cell surface proteins  

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

Bacteria cell Bacteria cell Insoluble fraction Glycoprotein Enrichment Integrated top-down and bottom-up Glycoprotein & Glycopeptide Step 1: Glycoproteome profile Glycans HILIC-FTICR-MS/MS (Sequencing ) Step 2: Glycan profile NMR (structure recognization) Data Interpretation Databases De Novo and other algorithms Step 3: Glycoinformatics Glycan database Glycoprotein database Hydrolysis graphitized carbon cloumn Schematic Representation of Proposed Platform for Bacterial Glycoproteome Characterization EMSL Research and Capability Development Proposals Systematic characterization of protein glycosylation of bacteria cell surface proteins Project start date: July 2011 Principal Investigator: Si Wu Mass Spectrometry and Magnet Resonance Group, EMSL, PNNL Co-investigators:

265

Protein Flips Lipids Across Membranes  

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

Protein Flips Lipids Across Membranes Print Protein Flips Lipids Across Membranes Print Found ubiquitously in both bacteria and humans, membrane proteins of the adenosine triphosphate (ATP)-binding cassette (ABC) transporter family have been implicated in both antibiotic and cancer-drug resistance. The mechanisms used by these proteins to expel toxins from cells therefore represent key targets for the development of drugs designed to combat the growing problem of multidrug resistance. Toward this end, researchers from The Scripps Research Institute have succeeded in crystallizing MsbA-an ABC transporter protein-together with a substrate (the molecule to be transported) and a hydrolyzed (spent) form of the nucleotide ATP, the transporter's source of chemical energy. The resulting molecular complex is caught at a moment following the transporter's "power stroke," the force-generating part of the transport cycle. This snapshot suggests a mechanism by which the substrate molecule gets flipped head-over-tail from one side of the membrane to the other, on its way out of the cell.

266

Protein Flips Lipids Across Membranes  

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

Protein Flips Lipids Across Membranes Print Protein Flips Lipids Across Membranes Print Found ubiquitously in both bacteria and humans, membrane proteins of the adenosine triphosphate (ATP)-binding cassette (ABC) transporter family have been implicated in both antibiotic and cancer-drug resistance. The mechanisms used by these proteins to expel toxins from cells therefore represent key targets for the development of drugs designed to combat the growing problem of multidrug resistance. Toward this end, researchers from The Scripps Research Institute have succeeded in crystallizing MsbA-an ABC transporter protein-together with a substrate (the molecule to be transported) and a hydrolyzed (spent) form of the nucleotide ATP, the transporter's source of chemical energy. The resulting molecular complex is caught at a moment following the transporter's "power stroke," the force-generating part of the transport cycle. This snapshot suggests a mechanism by which the substrate molecule gets flipped head-over-tail from one side of the membrane to the other, on its way out of the cell.

267

Characterization of protein folding intermediates  

SciTech Connect (OSTI)

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.

Kim, P.S.

1986-01-01T23:59:59.000Z

268

Denaturant-Induced Conformational Transitions in Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

Intrinsically disordered proteins (IDPs) differ from ordered proteins at several levels: structural, functional, and...

Paolo Neyroz; Stefano Ciurli…

2012-01-01T23:59:59.000Z

269

A phenomenological model of protein folding  

E-Print Network [OSTI]

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.

Danielsson, Ulf H; Niemi, Antti J

2009-01-01T23:59:59.000Z

270

Method for removing atomic-model bias in macromolecular crystallography  

DOE Patents [OSTI]

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.

Terwilliger, Thomas C. (Santa Fe, NM)

2006-08-01T23:59:59.000Z

271

Operation of the Australian Store.Synchrotron for macromolecular crystallography  

Science Journals Connector (OSTI)

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.

Meyer, G.R.

2014-09-30T23:59:59.000Z

272

Room-temperature macromolecular serial crystallography using synchrotron radiation  

Science Journals Connector (OSTI)

The room-temperature structure of lysozyme is determined using 40000 individual diffraction patterns from micro-crystals flowing in liquid suspension across a synchrotron microfocus beamline.

Stellato, F.

2014-05-30T23:59:59.000Z

273

Instrumentation in X-ray crystallography: Past, present and future  

Science Journals Connector (OSTI)

...was intended that a radiation detector anywhere would...unacceptable under today's safety regulations. 458 U...specimen crystal and the radiation detector were rotated...milling machines. The radiation detector was no longer...and data-processing software as into the design and...

2001-01-01T23:59:59.000Z

274

The role of crystallography and nanostructures on metallic friction.  

SciTech Connect (OSTI)

In ductile metals, sliding contact is often accompanied by severe plastic deformation localized to a small volume of material adjacent to the wear surface. During the initial run-in period, hardness, grain structure and crystallographic texture of the surfaces that come into sliding contact undergo significant changes, culminating in the evolution of subsurface layers with their own characteristic features. Here, a brief overview of our ongoing research on the fundamental phenomena governing the friction-induced recrystallization in single crystal metals, and how these recrystallized structures with nanometer-size grains would in turn influence metallic friction will be presented. We have employed a novel combination of experimental tools (FIB, EBSD and TEM) and an analysis of the critical resolved shear stress (RSS) on the twelve slip systems of the FCC lattice to understand the evolution of these friction-induced structures in single crystal nickel. The later part of the talk deals with the mechanisms of friction in nanocrystalline Ni films. Analyses of friction-induced subsurfaces seem to confirm that the formation of stable ultrafine nanocrystalline layers with 2-10 nm grains changes the deformation mechanism from the traditional dislocation mediated one to that is predominantly controlled by grain boundaries, resulting in significant reductions in the coefficient friction.

Michael, Joseph Richard; Prasad, Somuri V.; Battaile, Corbett Chandler; Majumdar, Bhaskar Sinha (New Mexico Institute of Mining & Technology, Socorro, NM); Kotula, Paul Gabriel

2010-06-01T23:59:59.000Z

275

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

E-Print Network [OSTI]

analysis of small molecules and materials (not macromolecules) using x-ray and neutron elastic scattering analysis of small molecules and materials using x-ray and neutron elastic scattering 2) Production) Interaction of x-rays and neutrons with mater a. Coherent elastic scattering, incoherent elastic scattering

Sherrill, David

276

Scaling Up: Towards a Federation of Crystallography Data  

E-Print Network [OSTI]

: The Museums, Libraries and Archives Council, the Joint Information Systems Committee (JISC) of the Higher and Further Education Funding Councils, as well as by project funding from the JISC and the European Union) ...................................................................................17 4.7 Science & Technology Facilities Council (STFC

Rzepa, Henry S.

277

Making sense of Miley p10 Crystallography 101 p30  

E-Print Network [OSTI]

engineering fraternity, Theta Tau. At Buffalo SPRING 2014 1 #12;2 SPRING 2014 At Buffalo #12;At Buffalo SPRING for alumni and friends of the State University of New York at Buffalo Spring 2014 Story on page 22 In 1998 on a single piece of evidence. A bite mark. #12;1 SPRING 2014 At Buffalo Mesmerized fans crowd a Plexiglas

Sachs, Frederick

278

Serial time-resolved crystallography of photosystem II using...  

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

Source: Nature Year: 2014 Volume: Published online 09 July 2014 Pages: ABSTRACT: Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to...

279

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

E-Print Network [OSTI]

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

Bigelow, Stephen

280

Protein folding in the ER.  

SciTech Connect (OSTI)

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.

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

1999-10-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Tailoring Peptidomimetics for Targeting Protein–Protein Interactions  

Science Journals Connector (OSTI)

...designed by computer modeling approaches of the target-binding...complexed with Smac. Simulation revealed 4 residues...Hammerhead: fast, fully automated docking of flexible...by molecular dynamics simulation.Proteins 1999;35...hormones-a focus on rapid, nongenomic effects...

Omar N. Akram; David J. DeGraff; Jonathan H. Sheehan; Wayne D. Tilley; Robert J. Matusik; Jung-Mo Ahn; and Ganesh V. Raj

2014-07-01T23:59:59.000Z

282

SINGLE CELL PROTEIN | The Algae  

Science Journals Connector (OSTI)

Abstract Algae, as source of single-cell protein (SCP), is a term that refers to either microscopic single-cell true algae or prokaryotic cyanobacteria, and their growth is based on the use of carbon dioxide and light energy (autotrophic growth). In contrast with other SCP-producing organisms, algae are grown in many cases by processes resembling traditional agriculture, because they depend on large areas and sunlight radiation; on the other hand, modern production techniques include growth inside photobioreactors. Moreover, macroscopic algae are used widely as source of food, but they hardly can fit the SCP definition because of their multicellular nature and low protein content.

M. García-Garibay; L. Gómez-Ruiz; A.E. Cruz-Guerrero; E. Bárzana

2014-01-01T23:59:59.000Z

283

Crystallography -Teacher's Notes Crystallography is a technique employed in all of the major scientific disciplines, so there are examples of  

E-Print Network [OSTI]

and green technology for a clean environment. Examples include studies of: · hydrogen absorption in new. It is owned and operated by the Science and Technology Facilities Council. ISIS produces beams of neutrons for areas as varied as energy, nanotechnology, materials processing, drug design and pharmaceuticals, bio-technology

Zharkova, Valentina V.

284

First Knot Discovered in Ancient Bacterium Protein  

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

First Knot Discovered in Ancient Bacterium Protein First Knot Discovered in Ancient Bacterium Protein The first knotted protein from the most ancient type of single-celled organism, an archaebacterium, has been discovered by researchers from Argonne National Laboratory and the University of Toronto using the Advanced Photon Source (APS) at Argonne. It is one of the few times that a knot has been seen in any protein structure. Protein folding theory previously held that forming a knot was beyond the ability of a protein. Image of knotted protein. The newly discovered knotted protein comes from a microorganism called Methanobacterium thermoautotrophicum. This organism is of interest to industry for its ability to break down waste products and produce methane gas. Scientists know which gene codes for the 268-amino acid protein, but

285

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

E-Print Network [OSTI]

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

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

2012-07-11T23:59:59.000Z

286

Building Biochips: A Protein Production Pipeline  

SciTech Connect (OSTI)

Protein arrays are emerging as a practical format in which to study proteins in high-throughput using many of the same techniques as that of the DNA microarray. The key advantage to array-based methods for protein study is the potential for parallel analysis of thousands of samples in an automated, high-throughput fashion. Building protein arrays capable of this analysis capacity requires a robust expression and purification system capable of generating hundreds to thousands of purified recombinant proteins. We have developed a method to utilize LLNL-I.M.A.G.E. cDNAs to generate recombinant protein libraries using a baculovirus-insect cell expression system. We have used this strategy to produce proteins for analysis of protein/DNA and protein/protein interactions using protein microarrays in order to understand the complex interactions of proteins involved in homologous recombination and DNA repair. Using protein array techniques, a novel interaction between the DNA repair protein, Rad51B, and histones has been identified.

de Carvalho-Kavanagh, M; Albala, J S

2004-02-09T23:59:59.000Z

287

Laboratory-Directed Protein Evolution  

Science Journals Connector (OSTI)

...protein engineering using alpha-phosphothioate nucleotides...III. 2002. Integrin alpha(v)beta3 targeted...generating estrogen receptor alpha and beta chimeras in...display selects for amylases with improved low pH starch-binding. J. Biotechnol...

Ling Yuan; Itzhak Kurek; James English; Robert Keenan

2005-09-01T23:59:59.000Z

288

3.9 Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

This chapter introduces intrinsically disordered proteins, which do not have rigid three-dimensional (3-D) structures under physiological conditions, but which nevertheless carry out numerous biological functions. Such proteins challenge the prevailing structure-function paradigm, according to which the unique 3-D structure of a protein is a prerequisite to its function. Here we argue that the prevailing paradigm needs to be expanded to include intrinsically disordered proteins and their new relationships among protein sequence, structure, and function. Since this extended paradigm opens new levels of understanding of the complex life of proteins, it represents a major breakthrough for biochemistry, biophysics, and molecular biology.

V.N. Uversky; A.K. Dunker

2012-01-01T23:59:59.000Z

289

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

290

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

E-Print Network [OSTI]

and disordered protein systems should not conform to a single dominant structure, and should only be described by appropriate ensembles.

Phillips, Aaron Hale

2010-01-01T23:59:59.000Z

291

Molecular Dynamics Simulations of Protein Folding  

Science Journals Connector (OSTI)

I illustrate the use of the replica exchange molecular dynamics (REMD) algorithm to study the folding of a small (57 amino acids) protein that folds into a three-helix bundle, protein A. The REMD is a triviall...

Angel E. Garcia

2008-01-01T23:59:59.000Z

292

Characterization of disordered proteins with ENSEMBLE  

Science Journals Connector (OSTI)

......STRUCTURAL BIOINFORMATICS Characterization of disordered proteins with ENSEMBLE Mickael Krzeminski 1 Joseph A. Marsh...data into the generation of structural ensembles of disordered protein states. ENSEMBLE makes use of a switching Monte-Carlo......

Mickaël Krzeminski; Joseph A. Marsh; Chris Neale; Wing-Yiu Choy; Julie D. Forman-Kay

2013-02-01T23:59:59.000Z

293

Characterization of disordered proteins with ENSEMBLE  

Science Journals Connector (OSTI)

Summary: ENSEMBLE is a computational approach for determining a set of conformations that represents the structural ensemble of a disordered protein based on input experimental data. The disordered protein can be an unfolded or intrinsically disordered ...

Mickaël Krzeminski; Joseph A. Marsh; Chris Neale; Wing-Yiu Choy; Julie D. Forman-Kay

2013-02-01T23:59:59.000Z

294

Archaic chaos: intrinsically disordered proteins in Archaea  

Science Journals Connector (OSTI)

Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure ... with recent improvements in the accuracy of intrinsic disorder

Bin Xue; Robert W Williams; Christopher J Oldfield; A Keith Dunker…

2010-05-01T23:59:59.000Z

295

Bioinformatics analysis of disordered proteins in prokaryotes  

Science Journals Connector (OSTI)

A significant number of proteins have been shown to be intrinsically disordered, meaning that they lack a fixed 3 ... . It has also been proven that a protein's disorder content is related to its function. We ......

Gordana M Pavlovi?-Lažeti?; Nenad S Miti?; Jovana J Kova?evi?…

2011-03-01T23:59:59.000Z

296

Intrinsic Fluorescence of Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

Resolution of the intrinsic emission properties of a protein by different fluorescence spectroscopy techniques is an ... on rotational movements of peptide chains or whole proteins. Here, we describe the details ...

Paolo Neyroz; Stefano Ciurli

2012-01-01T23:59:59.000Z

297

Nanomechanics of Proteins, Both Folded and Disordered  

Science Journals Connector (OSTI)

Single-molecule techniques have recently provided a versatile tool for imaging and manipulating protein molecules one at a time, enabling us ... , cell adhesion and signaling, neurodegeneration) and protein scien...

Rubén Hervás; Albert Galera-Prat…

2013-01-01T23:59:59.000Z

298

Sensitivity and Selectivity in Protein Sequence Comparison  

Science Journals Connector (OSTI)

Recent improvements in computer algorithms for comparing DNA and protein sequences have dramatically decreased the amount of time required to compare an unidentified sequence to a DNA or protein sequence libra...

William R. Pearson

1987-01-01T23:59:59.000Z

299

Seafood Protein in Human and Animal Nutrition  

Science Journals Connector (OSTI)

In the body, protein is used for the structural formation of cells and tissues, the production of various essential compounds such as enzymes, antibodies, hormones, and protein mediators for regulating fluid a...

Shi-Yen Shiau

1995-01-01T23:59:59.000Z

300

Topology to geometry in protein folding: -Lactoglobulin  

E-Print Network [OSTI]

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

Berry, R. Stephen

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

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

E-Print Network [OSTI]

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

Anderson, William David

2007-01-01T23:59:59.000Z

302

Struts, springs and crumple zones: protein structures under force  

E-Print Network [OSTI]

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

Dill, Jesse

2012-01-01T23:59:59.000Z

303

Computational Modeling of Protein Interactions at Multiple Lengthscales  

E-Print Network [OSTI]

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

Yap, Eng Hui

2010-01-01T23:59:59.000Z

304

Protein-Folding Landscapes in Multi-Chain Systems  

E-Print Network [OSTI]

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

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

2005-01-01T23:59:59.000Z

305

Protein-folding via divide-and-conquer optimization  

E-Print Network [OSTI]

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

Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

2004-01-01T23:59:59.000Z

306

The unfolded protein response during prostate cancer development  

E-Print Network [OSTI]

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

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

2009-01-01T23:59:59.000Z

307

Intermediates and the folding of proteins L and G  

E-Print Network [OSTI]

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

Brown, Scott; Head-Gordon, Teresa

2008-01-01T23:59:59.000Z

308

Automated data extraction from in situ protein stable isotope...  

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

data extraction from in situ protein stable isotope probing studies. Automated data extraction from in situ protein stable isotope probing studies. Abstract: Protein stable isotope...

309

Evaluation of physicochemical properties of modified algae protein adhesives.  

E-Print Network [OSTI]

??Algae proteins have similar amino acid compositions as conventional plant proteins, and are comparatively richer in the essential amino acids. Algae protein has the potential… (more)

Borgen, Kelly

2012-01-01T23:59:59.000Z

310

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

E-Print Network [OSTI]

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

Guo, Minghao

2014-01-01T23:59:59.000Z

311

Toy model for protein folding  

Science Journals Connector (OSTI)

A conceptually simple model for protein-folding phenomena has been created: it is two-dimensional and has only two different ‘‘amino acids.’’ Ground-state conformations have been determined for all of its flexible polypeptides containing seven or fewer monomers. This complete database displays a wide geometric variety of folded shapes and shows that single point mutations in some cases induce substantial folding modifications. Neural-network concepts have been employed to analyze results. The simplest static neural networks required to act as error-free read-only memories provide a way to visualize the logical structure of underlying folding principles. The topologies of optimal networks found thus far suggest that protein folding has a more complex cooperative character than has been embodied previously in theoretical approaches.

Frank H. Stillinger; Teresa Head-Gordon; Catherine L. Hirshfeld

1993-08-01T23:59:59.000Z

312

Protein folding using contact maps  

E-Print Network [OSTI]

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.

Michele Vendruscolo; Eytan Domany

1999-01-21T23:59:59.000Z

313

Protein Structures Revealed at Record Pace  

ScienceCinema (OSTI)

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.

Hura, Greg

2013-05-29T23:59:59.000Z

314

Protein Structures Revealed at Record Pace  

ScienceCinema (OSTI)

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.

Greg Hura

2010-01-08T23:59:59.000Z

315

JBS Protein Transduction Kit Cell Penetration  

E-Print Network [OSTI]

Manual JBS Protein Transduction Kit Cell Penetration Jena Bioscience GmbH | Löbstedter Str. 80-Proteoducin Cocktail of Cell Penetrating Peptides and proteins for internalization of peptides and proteins (CPP-C01S to transport a cargo into the nucleus. The Kit further contains compounds for increasing rate and efficiency

Lebendiker, Mario

316

How Nature Fine Tunes Protein Stability  

E-Print Network [OSTI]

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

Wickstrom, Megan

2007-07-14T23:59:59.000Z

317

EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS  

E-Print Network [OSTI]

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

Guibas, Leonidas J.

318

Amphiphiles for protein solubilization and stabilization  

DOE Patents [OSTI]

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.

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

2014-11-04T23:59:59.000Z

319

Erythropoietin binding protein from mammalian serum  

DOE Patents [OSTI]

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.

Clemons, G.K.

1997-04-29T23:59:59.000Z

320

Synthetic mimetics of protein secondary structure domains  

Science Journals Connector (OSTI)

...stable alpha-helix in a protein, are unable to achieve...entropic penalties, as a disordered chain of residues is...the Bcl-2 family of proteins, the HIV-1 capsid...completed the antenna ensemble (figure-9). Regardless...structural features of proteins. These turns generally...

2010-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

GREEN FLUORESCENT PROTEIN The green revolution  

E-Print Network [OSTI]

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

Stearns, Tim

322

Protein folding: not just another optimization  

E-Print Network [OSTI]

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

Karplus, Kevin

323

UNCORRECTED 3 Protein folding: Then and now  

E-Print Network [OSTI]

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

Dokholyan, Nikolay V.

324

Atomistic Protein Folding Simulations on the  

E-Print Network [OSTI]

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

Snow, Christopher

325

Disulfide-Linked Protein Folding Pathways  

E-Print Network [OSTI]

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

Bardwell, James

326

STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS  

E-Print Network [OSTI]

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

Dinner, Aaron

327

Intracellular Signaling by the Unfolded Protein  

E-Print Network [OSTI]

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

Mullins, Dyche

328

Approximate Inference and Protein-Folding  

E-Print Network [OSTI]

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

Weiss, Yair

329

Extracellular secretion of recombinant proteins  

DOE Patents [OSTI]

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.

Linger, Jeffrey G.; Darzins, Aldis

2014-07-22T23:59:59.000Z

330

LANSCE | Lujan Center | Instruments | PCS  

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

Protein Crystallography Station | PCS Protein Crystallography Station | PCS Structural Enzymology The Protein Crystallography Station (PCS) at LANSCE is a high performance beam line that is funded by DOE OBER. It forms the core of a capability for joint neutron and X-ray macromolecular structure and function determination. The PCS is the first protein crystallography beam line to be built at a spallation neutron source and is still the only resource of its kind in North America. The beam-line exploits the pulsed nature of spallation neutrons and a large electronic detector in order to efficiently collect wavelength resolved Laue patterns using all available neutrons in the white beam (0.7 - 7 Ă… wavelength band). Neutron crystallography is a powerful technique for locating H atoms that can be hard to detect using X-rays. The PCS therefore provides unique

331

Part 1: Protein Dynamics Folded protein at physiologic or room temperature samples wide range of  

E-Print Network [OSTI]

protein molecule is likely to differ significantly from average structure - folded protein is an ensemble(unfolded state) 2 Aside 1: What disordered states are relevant to understand protein folding? compact denatured Protein Motions within Folded State Ensemble high energy costs of deformations of bond lengths, angles

Chan, Hue Sun

332

Translocation of Proteins Across the Endoplasmic Reticulum II . Signal Recognition Protein (SRP) Mediates the  

E-Print Network [OSTI]

Translocation of Proteins Across the Endoplasmic Reticulum II . Signal Recognition Protein (SRP-extracted but was restored by an 11S protein (SRP, Signal Recognition Protein) previously purified from the salt- extract of microsomal vesicles (Walter and Blobel , 1980. Proc. Nat/ . Acad. Sci . U. S. A. 77 :7112-7116) . SRP

Walter, Peter

333

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

E-Print Network [OSTI]

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

Dinner, Aaron

334

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

335

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

336

Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system  

Science Journals Connector (OSTI)

In this study, the amount of protein synthesized using an in vitro protein synthesis system composed of only highly purified components (the PURE system) was optimized. By varying the concentrations of each system component, we determined the component concentrations that result in the synthesis of 0.38 mg/mL green fluorescent protein (GFP) in batch mode and 3.8 mg/mL GFP in dialysis mode. In dialysis mode, protein concentrations of 4.3 and 4.4 mg/mL were synthesized for dihydrofolate reductase and ?-galactosidase, respectively. Using the optimized system, the synthesized protein represented 30% (w/w) of the total protein, which is comparable to the level of overexpressed protein in Escherichia coli cells. This optimized reconstituted in vitro protein synthesis system may potentially be useful for various applications, including in vitro directed evolution of proteins, artificial cell assembly, and protein structural studies.

Yasuaki Kazuta; Tomoaki Matsuura; Norikazu Ichihashi; Tetsuya Yomo

2014-01-01T23:59:59.000Z

337

Review Protein Folding and Misfolding on Surfaces  

E-Print Network [OSTI]

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

Massimo Stefani

2008-01-01T23:59:59.000Z

338

Computational and experimental investigations of forces in protein folding  

E-Print Network [OSTI]

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...

Schell, David Andrew

2005-02-17T23:59:59.000Z

339

Protein folding using contact maps Michele Vendruscolo and Eytan Domany  

E-Print Network [OSTI]

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

Domany, Eytan

340

Glassy dynamics of protein folding  

Science Journals Connector (OSTI)

A coarse-grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis dynamics at low temperatures with the exponent ??1/4, in agreement with the best experimental results. The time dependent correlation functions for fluctuations about the native state, computed in the Gaussian approximation for real proteins, have also been found to have the same functional form. Our results indicate that the energy landscape exhibits universal features over a very large range of energies and is relatively independent of the specific dynamics.

Erkan Tüzel and Ay?e Erzan

2000-02-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

Is protein folding rate dependent on number of folding stages? Modeling of protein folding with ferredoxin-like fold  

Science Journals Connector (OSTI)

Statistical analysis of protein folding rates has been done for 84 proteins ... than those with two-state kinetics. The protein folding for six proteins with a ferredoxin-like...

O. V. Galzitskaya

2010-06-01T23:59:59.000Z

342

Annotation of PDB with respect to ``Disordered Regions'' in Proteins  

E-Print Network [OSTI]

Annotation of PDB with respect to ``Disordered Regions'' in Proteins Meeta Rani 1 Pedro Romero 2­peptide, protein­protein, protein­RNA and protein­DNA complexes. It has been suggested that disorder. Disordered regions in proteins can be random coil­like, molten globule­like or somewhere in be­ tween

Obradovic, Zoran

343

Dominant Pathways in Protein Folding  

E-Print Network [OSTI]

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.

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

2006-07-27T23:59:59.000Z

344

An analysis pipeline for the inference of protein-protein interaction networks  

Science Journals Connector (OSTI)

We present a platform for the reconstruction of protein-protein interaction networks inferred from Mass Spectrometry (MS) bait-prey data. The Software Environment for Biological Network Inference (SEBINI), an environment for the deployment of network inference algorithms that use high-throughput data, forms the platform core. Among the many algorithms available in SEBINI is the Bayesian Estimator of Probabilities of Protein-Protein Associations (BEPro3) algorithm, which is used to infer interaction networks from such MS affinity isolation data. Also, the pipeline incorporates the Collective Analysis of Biological Interaction Networks (CABIN) software. We have thus created a structured workflow for protein-protein network inference and supplemental analysis.

Ronald C. Taylor; Mudita Singhal; Don S. Daly; Jason Gilmore; William R. Cannon; Kelly Domico; Amanda M. White; Deanna L. Auberry; Kenneth J. Auberry; Brian S. Hooker; Greg Hurst; Jason E. McDermott

2009-01-01T23:59:59.000Z

345

10 - Regulator of G Protein Signaling Proteins as Drug Targets: Current State and Future Possibilities  

Science Journals Connector (OSTI)

Abstract Regulators of G protein signaling (RGS) proteins have emerged in the past two decades as novel drug targets in many areas of research. Their importance in regulating signaling via G protein-coupled receptors has become evident as numerous studies have been published on the structure and function of RGS proteins. A number of genetic models have also been developed, demonstrating the potential clinical importance of RGS proteins in various disease states, including central nervous system disorders, cardiovascular disease, diabetes, and several types of cancer. Apart from their classical mechanism of action as GTPase-activating proteins (GAPs), RGS proteins can also serve other noncanonical functions. This opens up a new approach to targeting RGS proteins in drug discovery as the view on the function of these proteins is constantly evolving. This chapter summarizes the latest development in RGS protein drug discovery with special emphasis on noncanonical functions and regulatory mechanisms of RGS protein expression. As more reports are being published on this group of proteins, it is becoming clear that modulation of GAP activity might not be the only way to therapeutically target RGS proteins.

Benita Sjögren

2011-01-01T23:59:59.000Z

346

Brownian Dynamics Simulation of Protein Solutions: Structural...  

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

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

347

Year 2 Report: Protein Function Prediction Platform  

SciTech Connect (OSTI)

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

Zhou, C E

2012-04-27T23:59:59.000Z

348

Protein Folding: Generalized-Ensemble Algorithms  

Science Journals Connector (OSTI)

We briefly review the development of generalized-ensemble optimization techniques and their application since publication of “Protein Folding: Generalized-Ensemble Algorithms” was published in...

Ulrich H. E. Hansmann

2009-01-01T23:59:59.000Z

349

Simulating Temperature Jumps for Protein Folding Studies.  

E-Print Network [OSTI]

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

Kim, Seonah

2007-01-01T23:59:59.000Z

350

Protein Engineering of Bacillus thuringiensis ?-Endotoxins  

Science Journals Connector (OSTI)

Protein engineering of insecticidal Bt ?-endotoxins is a ... including increased toxicity and binding affinity, enhanced ion-transport activity, and changes in insect specificity ... . The understanding and prope...

Dr. Alvaro M. Florez; Dr. Cristina Osorio…

2012-01-01T23:59:59.000Z

351

Controlling membrane protein folding using photoresponsive surfactant.  

E-Print Network [OSTI]

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

Chang, Chia Hao

2012-01-01T23:59:59.000Z

352

Knots and Swelling in Protein Folding  

E-Print Network [OSTI]

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.

Martin Lundgren; Antti J. Niemi

2009-06-26T23:59:59.000Z

353

Collaboration drives achievement in protein structure research  

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

AlumniLink November 2014 Collaboration drives achievement in protein structure research Alumni Link: Opportunities, News and Resources for Former Employees Latest...

354

Dominant Pathways in Protein Folding  

Science Journals Connector (OSTI)

We present a method to investigate the kinetics of protein folding and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. By writing the solution of the Fokker-Planck equation 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 simulated using a Go model. An initial collapsing phase driven by the initial configuration is followed by a rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This completely general method does not require the prior knowledge of any reaction coordinate and is an efficient tool to perform simulations of the entire folding process with available computers.

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

2006-09-06T23:59:59.000Z

355

Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms  

E-Print Network [OSTI]

Background: Protein-protein interactions play vital roles in nearly all cellular processes and are involved in the construction of biological pathways such as metabolic and signal transduction pathways. Although large-scale ...

Lin, Xiaotong; Liu, Mei; Chen, Xue-wen

2009-04-29T23:59:59.000Z

356

ProDDO: a database of disordered proteins from the Protein Data Bank (PDB)  

Science Journals Connector (OSTI)

......1996) and natively disordered (Dunker et al. , 1998...represent disorder in proteins. Molten globule structure...sequence adopts. The disordered ensemble of structures can involve...Certain regions of the proteins that may have weak Flexible......

Kim Lan Sim; Tomoyuki Uchida; Satoru Miyano

2001-04-01T23:59:59.000Z

357

Antigenic Characterization of an Intrinsically Unstructured Protein, Plasmodium falciparum Merozoite Surface Protein 2  

Science Journals Connector (OSTI)

...different conformational ensembles of MSP2 being analyzed...monomeric recombinant proteins showed them to be highly disordered in solution and largely...intrinsically unstructured proteins (1, 57). Consistent...regions. In the ensemble of equilibrium conformations...

Christopher G. Adda; Christopher A. MacRaild; Linda Reiling; Kaye Wycherley; Michelle J. Boyle; Vivian Kienzle; Paul Masendycz; Michael Foley; James G. Beeson; Raymond S. Norton; Robin F. Anders

2012-09-10T23:59:59.000Z

358

Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation  

Science Journals Connector (OSTI)

...essential state of numerous proteins, in which it is associated...feature of intrinsically disordered proteins (also called unstructured...structure, they adopt ensembles of rapidly interconverting...globules (100), and some disordered regions can become ordered...

Corinne Rancurel; Mahvash Khosravi; A. Keith Dunker; Pedro R. Romero; David Karlin

2009-07-29T23:59:59.000Z

359

Mean Net Charge of Intrinsically Disordered Proteins: Experimental Determination of Protein Valence by Electrophoretic Mobility Measurements  

Science Journals Connector (OSTI)

Under physiological conditions, intrinsically disordered proteins (IDPs) are unfolded, mainly because of ... charged residues of the same sign within the protein. Softwares have been designed to facilitate the co...

Ana Cristina Sotomayor-Pérez; Johanna C. Karst…

2012-01-01T23:59:59.000Z

360

Sequence homology between certain viral proteins and proteins related to encephalomyelitis and neuritis  

Science Journals Connector (OSTI)

...Although RNA segment 8 in influenza viruses codes for the two nonstructural proteins NS, and NS2, these proteins are found in the infected host...173, 736 (1971)]. 15. The single letter code ofabbreviations for amino acids is as follows...

U Jahnke; EH Fischer; EC Alvord Jr

1985-07-19T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins  

Science Journals Connector (OSTI)

......sought to produce a novel dataset of human nuclear-encoded mitochondrial proteins...sought to produce a novel dataset of nuclear-encoded proteins that are...sought to produce a novel dataset of nuclear-encoded proteins that are......

J. M. Cameron; T. Hurd; B. H. Robinson

2005-05-01T23:59:59.000Z

362

PROTEINS: Structure,Function, and Genetics 1:109-115 (1986) Protein Fluorescence Quenchingby Small Molecules  

E-Print Network [OSTI]

by a molecular dynamics simulation12 which displayed an extreme dependence of protein penetration rate Molecules: Protein Penetration Versus Solvent Exposure DorothyB. Calhoun,' Jane M. Vanderkooi,' Gary R the thesis that acrylamide and similar small molecules can penetrate into proteins on a nanosecond time scale

Englander, S. Walter

363

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

SciTech Connect (OSTI)

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

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

2011-12-31T23:59:59.000Z

364

Translocation of Proteins Across the Endoplasmic Reticulum III . Signal Recognition Protein (SRP) Causes Signal  

E-Print Network [OSTI]

Translocation of Proteins Across the Endoplasmic Reticulum III . Signal Recognition Protein (SRP-550) inhibitory effect of SRP selectively on the cel l -free translation of mRNA for secretory protein chain elongation . The Mr of the SRP-arrested nascent preprolactin chain was estimated to be 8

Walter, Peter

365

Chapter 4 - Regulators of G Protein Signaling Proteins as Targets for Drug Discovery  

Science Journals Connector (OSTI)

Signaling via G-protein-coupled receptors (GPCRs) is central for the function of biological systems. Many clinically used drugs target \\{GPCRs\\} directly or target molecules involved in GPCR signaling. As an alternative to targeting receptors directly, one could modulate signaling cascades downstream of receptor activation. In recent years, there has been substantial interest in a family of proteins called regulators of G protein signaling (RGS) proteins. They modulate GPCR signaling by accelerating GTP hydrolysis on active G? subunits, thereby reducing the amplitude and duration of signaling. Modulating RGS activity would be a useful strategy to control GPCR signaling. An RGS inhibitor would be expected to enhance GPCR signaling and could do so in a tissue- or pathway-specific manner. Apart from the central GAP (GTPase accelerating protein) activity, many RGS proteins also have other functions like regulating protein–protein interactions, subcellular localization of signaling molecules, and protein translation. It is clear that these proteins serve important functions in a number of physiological and pathophysiological processes, and they are emerging as potential drug targets. This chapter gives an overview of what is currently known about biological functions of RGS proteins based on in vivo and in vitro data. We also summarize the current status in targeting RGS proteins in drug discovery.

Benita Sjögren; Levi L. Blazer; Richard R. Neubig

2010-01-01T23:59:59.000Z

366

UA62784, a novel inhibitor of centromere protein E kinesin-like protein  

Science Journals Connector (OSTI)

...25). The mitotic kinesin motor proteins such as Eg5 and centromere...was filtered and washed with water, 1 N NaOH, 1 N HCl, and water...had 1 mug purified CENP-E motor protein (Cytoskeleton) with...next tested UA62784 for kinesin motor protein inhibition using a cell-free...

Meredith C. Henderson; Yeng-Jeng Y. Shaw; Hong Wang; Haiyong Han; Laurence H. Hurley; Gary Flynn; Robert T. Dorr; and Daniel D. Von Hoff

2009-01-01T23:59:59.000Z

367

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

SciTech Connect (OSTI)

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.

B Wallace; R Janes

2011-12-31T23:59:59.000Z

368

Nutritional geometry: gorillas prioritize non-protein energy while consuming surplus protein  

Science Journals Connector (OSTI)

...disparity enabled us to infer from geometrical...over non-protein energy (NPE) and test whether...relatives can help us to improve human health...and non-protein energy (NPE) by gorillas...Proteins analysis Energy Intake Female Fruit...Herbivory Male Nutritional Status Plant Leaves chemistry...

2011-01-01T23:59:59.000Z

369

NASA's Protein Crystal Work Gets Mixed Reviews  

Science Journals Connector (OSTI)

NASA's Protein Crystal Work Gets Mixed Reviews ... In a just released report, a National Research Council (NRC) task group agrees with NASA's critics that efforts to grow higher quality protein crystals in space have been incremental at best. ... Still, the task group offers NASA solace. ...

LOIS EMBER

2000-03-13T23:59:59.000Z

370

Biophysical characterization of protein folding and misfolding.  

E-Print Network [OSTI]

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

Schmittschmitt, Jason Peter

2004-09-30T23:59:59.000Z

371

Trafficking of Proteins through Plastid Stromules  

Science Journals Connector (OSTI)

...course of many experiments led us to conclude that transmission...thylakoid membranes in such bulbs readily distinguishes them...demonstrate trafficking of fluorescent protein from one plastid or...order to visualize movement of fluorescent protein. When the laser was...

Maureen R. Hanson; Amirali Sattarzadeh

2013-08-27T23:59:59.000Z

372

Solvent-induced forces in protein folding  

SciTech Connect (OSTI)

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.

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

1990-08-23T23:59:59.000Z

373

Exploring the mechanisms of protein folding  

E-Print Network [OSTI]

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,...

Xu, Ji; Ren, Ying; Li, Jinghai

2013-01-01T23:59:59.000Z

374

Antimicrobial protein protects grapevines from pathogen  

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

Antimicrobial protein protects grapevines from pathogen Antimicrobial protein protects grapevines from pathogen Antimicrobial protein protects grapevines from pathogen Engineered grapevines produce a hybrid antimicrobial protein to block infection. February 21, 2012 Grapevines Goutam Gupta, from the Lab's Bioscience Division and the Center for Bio-security Science, along with researchers at the University of California at Davis (UCD), and the U.S. Department of Agriculture's Agricultural Research Service, have created specially engineered grapevines that produce a hybrid antimicrobial protein that can block Xylella fastidiosa (Xf) infection. Get Expertise Researcher Goutam Gupta Bioscience Division and the Center for Bio-security Science Email "We wanted the plant to clear itself of the pathogen without relying on

375

Unusual biophysics of intrinsically disordered proteins  

Science Journals Connector (OSTI)

Abstract Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where \\{IDPs\\} possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of \\{IDPs\\} are covered. In addition to the peculiar sequence characteristics of \\{IDPs\\} these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. \\{IDPs\\} are also characterized by the “turned-out” response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some \\{IDPs\\} is associated with the awaking of the dormant disorder. It is possible that \\{IDPs\\} represent the “edge of chaos” systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.

Vladimir N. Uversky

2013-01-01T23:59:59.000Z

376

Protein Folding Challenge and Theoretical Computer Science Somenath Biswas  

E-Print Network [OSTI]

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

Biswas, Somenath

377

A Visual Analytics Approach for Protein Disorder Prediction  

E-Print Network [OSTI]

A Visual Analytics Approach for Protein Disorder Prediction Jaegul Choo and Fuxin Li and Keehyoung to the protein disorder prediction problem. Protein disorder is one of the most im- portant characteristics that the disorder within each protein is usually well separated linearly. However, if various proteins

Park, Haesun

378

Can Contact Potentials Reliably Predict Stability of Proteins?  

E-Print Network [OSTI]

; 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

Khatun, Jainab

379

Self-Organized Criticality in Proteins: Hydropathic Roughening Profiles of G-Protein Coupled Receptors  

E-Print Network [OSTI]

Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein conformational functionality is often dominated by long-range hydro(phobic/philic) interactions which both drive protein compaction and mediate protein-protein interactions. Superfamily transmembrane GPCR are the largest family of proteins in the human genome; their amino acid sequences form the largest data base for protein-membrane interactions. While there are now structural data on the heptad transmembrane structures of representatives of several heptad families, here we show that fresh insights into global and some local chemical trends in GPCR properties can be obtained accurately from sequences alone, especially by separating the extracellular and cytoplasmic loops from transmembrane segments. The global mediation of long-range water-protein interactions occurs in conjunction with modulation of these interactions by roughened interfaces. Hydropathic roughening profiles are defined here solely in terms of amino acid sequences, and knowledge of protein coordinates is not required. Roughening profiles both for GPCR and some simpler protein families display accurate and transparent connections to protein functionality.

J. C. Phillips

2010-11-18T23:59:59.000Z

380

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

SciTech Connect (OSTI)

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.

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

2003-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Protein Structure Suggests Role as Molecular Adapter  

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

Protein Structure Suggests Role Protein Structure Suggests Role as Molecular Adapter Protein Structure Suggests Role as Molecular Adapter Print Wednesday, 24 June 2009 00:00 To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the replisome. An essential step in replisome assembly is the loading of ring-shaped helicases (motor proteins) onto the separated strands of DNA. Dedicated ATP-fueled proteins regulate the loading; however, the mechanism by which these proteins recruit and deposit helicases has remained unclear. To better understand this process, researchers at the University of California, Berkeley, recently determined the structure of the ATPase region of DnaC, a bacterial helicase loader. The structure revealed that DnaC is a close cousin of DnaA, the protein thought to be responsible for unwinding DNA. Unexpectedly, the team further found that DnaC forms a right-handed helix similar to the state adopted by ATP-bound DnaA. These findings, together with biochemical studies, implicate DnaC as a molecular adapter that uses ATP-activated DnaA as a docking site for ensuring that DnaB (the ring-shaped helicase) is correctly deposited at the onset of replication.

382

Cotranslational protein folding with L-systems  

E-Print Network [OSTI]

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

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

383

Plasma Protein Concentrations in Interstitial Fluid from Human Aortas  

Science Journals Connector (OSTI)

22 December 1982 research-article Plasma Protein Concentrations in Interstitial...Eileen M. Staples The concentration of plasma proteins was examined in interstitial...quantitative immunoelectrophoresis for three plasma proteins covering a range of molecular...

1982-01-01T23:59:59.000Z

384

Trends in template/fragment-free protein structure prediction  

E-Print Network [OSTI]

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.

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

2011-01-01T23:59:59.000Z

385

Exploring zipping and assembly as a protein folding principle  

E-Print Network [OSTI]

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

Voelz, Vince A; Dill, Ken A

2007-01-01T23:59:59.000Z

386

Protein folding in the secretory pathway of animal cells  

Science Journals Connector (OSTI)

The exit of newly-synthesized proteins from the lumen of the endoplasmic reticulum (ER) is the rate-determining step in protein secretion. Only correctly-folded and fully-assembled proteins exit the ER and pro...

Robert B. Freedman; Carole Greenall; Nigel Jenkins; Mick F. Tuite

1995-01-01T23:59:59.000Z

387

PREDICTION OF BOUNDARIES BETWEEN INTRINSICALLY ORDERED AND DISORDERED PROTEIN REGIONS  

E-Print Network [OSTI]

PREDICTION OF BOUNDARIES BETWEEN INTRINSICALLY ORDERED AND DISORDERED PROTEIN REGIONS PREDRAG. Using proteins with both disordered and ordered regions collected through literature searches disordered protein is gaining increased attention in the biological community.1-4 Following the prior work

Obradovic, Zoran

388

Comprehensive large-scale assessment of intrinsic protein disorder  

Science Journals Connector (OSTI)

......GlobPlot: exploring protein sequences for globularity...Linding R , et al. Protein disorder prediction...structural mobility in NMR protein ensembles. Bioinformatics (2010...sequence-based prediction of disordered regions with multilayer......

Ian Walsh; Manuel Giollo; Tomás Di Domenico; Carlo Ferrari; Olav Zimmermann; Silvio C. E. Tosatto

2014-10-01T23:59:59.000Z

389

Intrinsic Disorder and Protein Function A. Keith Dunker,,  

E-Print Network [OSTI]

. For intrinsically disordered protein, the ensemble members have different (and typically dynamic) Ramachandran1 Intrinsic Disorder and Protein Function A. Keith Dunker,, * Celeste J. Brown, J. David Lawson disorder, protein structure- function, genomics, proteomics, and bioinformatics Abbreviations: circular

Obradovic, Zoran

390

DisProt: a database of protein disorder  

Science Journals Connector (OSTI)

......intrinsically disordered proteins or regions...as dynamic ensembles in which...intrinsically disordered proteins fail to form...instead as ensembles of conformations...intrinsically disordered proteins or regions...as dynamic ensembles in which......

Slobodan Vucetic; Zoran Obradovic; Vladimir Vacic; Predrag Radivojac; Kang Peng; Lilia M. Iakoucheva; Marc S. Cortese; J. David Lawson; Celeste J. Brown; Jason G. Sikes; Crystal D. Newton; A. Keith Dunker

2005-01-01T23:59:59.000Z

391

Exploiting Heterogeneous Sequence Properties Improves Prediction of Protein Disorder  

E-Print Network [OSTI]

Exploiting Heterogeneous Sequence Properties Improves Prediction of Protein Disorder Zoran disordered regions. Proteins 2005; Suppl 7:176­182. © 2005 Wiley-Liss, Inc. Key words: disorder prediction; intrinsically disor- dered; length dependent predictors INTRODUCTION Intrinsically disordered proteins

Obradovic, Zoran

392

ESpritz: accurate and fast prediction of protein disorder  

Science Journals Connector (OSTI)

......et al. Library of disordered patterns in 3D protein structures. PLoS...structural mobility in NMR protein ensembles. Bioinformatics...analysis of multiple protein fold recognition...sequence-based prediction of disordered regions with multilayer......

Ian Walsh; Alberto J. M. Martin; Tomŕs Di Domenico; Silvio C. E. Tosatto

2012-02-15T23:59:59.000Z

393

Proteins without 3D structure: definition, detection and beyond  

Science Journals Connector (OSTI)

......exist as dynamic ensembles within which atom...The intrinsically disordered proteins (IDPs), the most...predictions in CASP5. Proteins (2003) 53(Suppl...characterization of disordered protein ensembles. Curr. Opin. Struct......

Ferenc Orosz; Judit Ovádi

2011-06-01T23:59:59.000Z

394

Measuring and comparing structural fluctuation patterns in large protein datasets  

Science Journals Connector (OSTI)

......readily calculated from any ensemble of protein conformations, such as...comparing the conformational ensembles that characterise protein fluctuations. Each method...such as intrinsically disordered regions of a protein. 3.2.1 Overall performance......

Edvin Fuglebakk; Julián Echave; Nathalie Reuter

2012-10-01T23:59:59.000Z

395

Methods for Improving Protein Disorder Prediction Slobodan Vucetic1  

E-Print Network [OSTI]

Methods for Improving Protein Disorder Prediction Slobodan Vucetic1 , Predrag Radivojac3 , Zoran several methods for improving prediction of protein disorder. These include attribute con- struction from protein sequence, choice of classifier and postprocessing. While ensembles of neural networks achieved

Vucetic, Slobodan

396

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS DISORDER: ASSESSMENT  

E-Print Network [OSTI]

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS DISORDER: ASSESSMENT Assessment of disorder5 analysis of the possibility of predicting ``unstructured'' or ``disordered'' regions of proteins sequence. The interest in intrinsically disordered proteins (IDPs) has greatly increased, as it has become

Sussman, Joel L.

397

Disordered binding regions of Ewing’s sarcoma fusion proteins  

Science Journals Connector (OSTI)

A relationship was found between the amino acid (AA) composition, intrinsic protein disorder (IPD) and protein binding regions (PBRs) of the functional regions of Ewing’s sarcoma protein (EWS) and oncogenic EWS f...

R. Todorova

2014-01-01T23:59:59.000Z

398

Septin Self-Assembly: Plasticity and Protein Scaffolding  

E-Print Network [OSTI]

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

Garcia, III, Galo

2012-01-01T23:59:59.000Z

399

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...

400

THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES  

E-Print Network [OSTI]

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

Sosnick, Tobin R.

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

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

402

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping  

E-Print Network [OSTI]

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

Baker, David

403

Introducing Protein Folding Using Simple Models  

E-Print Network [OSTI]

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.

D. Thirumalai; D. K. Klimov

2001-01-04T23:59:59.000Z

404

Efficient inference of protein structural ensembles  

E-Print Network [OSTI]

It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a protein adopts (native state), but the entire ensemble of conformations the system can adopt. Such ensemble mod- els are necessary to understand intrinsically disordered proteins, enzyme catalysis, and signaling. We suggest that the most difficult aspect of generating such a model will be finding a small set of configurations to accurately model structural heterogeneity and present one way to overcome this challenge.

Lane, Thomas J; Beauchamp, Kyle A; Pande, Vijay S

2014-01-01T23:59:59.000Z

405

Constructing ensembles for intrinsically disordered proteins  

Science Journals Connector (OSTI)

The relatively flat energy landscapes associated with intrinsically disordered proteins makes modeling these systems especially problematic. A comprehensive model for these proteins requires one to build an ensemble consisting of a finite collection of structures, and their corresponding relative stabilities, which adequately capture the range of accessible states of the protein. In this regard, methods that use computational techniques to interpret experimental data in terms of such ensembles are an essential part of the modeling process. In this review, we critically assess the advantages and limitations of current techniques and discuss new methods for the validation of these ensembles.

Charles K Fisher; Collin M Stultz

2011-01-01T23:59:59.000Z

406

Nonlinear conformation of secondary protein folding  

E-Print Network [OSTI]

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.

Januar, M; Handoko, L T

2012-01-01T23:59:59.000Z

407

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

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

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

408

Application of a Laser-Wakefield Driven Monochromatic Photon Source to  

E-Print Network [OSTI]

) is a 100-TW, 30-fs pulsed Ti:sapphire laser system. Diocles routinely provides electron beams exhibiting

Umstadter, Donald

409

Monochromatic neutrinos generated by dark matter and the see-saw mechanism  

E-Print Network [OSTI]

We study a minimal extension of the Standard Model where a scalar field is coupled to the right handed neutrino responsible for the see-saw mechanism for neutrino masses. In the absence of other couplings, the scalar $A$ has a unique decay mode $A \\rightarrow \

Dudas, Emilian; Olive, Keith

2014-01-01T23:59:59.000Z

410

Diamond X-ray photodiode for white and monochromatic SR beams  

SciTech Connect (OSTI)

High-purity, single-crystal CVD diamond plates are screened for quality and instrumented into a sensor assembly for quantitative characterization of flux and position sensitivity. Initial investigations have yielded encouraging results and have led to further development. Several limiting complications are observed and discussed, as well as mitigations thereof. For example, diamond quality requirements for X-ray diodes include low nitrogen impurity and crystallographic defectivity. Thin electrode windows and electronic readout performance are ultimately also critical to device performance. Promising features observed so far from prototype devices include calculable responsivity, flux linearity, position sensitivity and timing performance. Recent results from testing in high-flux and high-speed applications are described.

Keister, J.W.; Heroux, A.; Smedley, J.; Muller, E. M.; Bohon, J.

2011-09-01T23:59:59.000Z

411

Monochromatic short pulse laser produced ion beam using a compact passive magnetic device  

SciTech Connect (OSTI)

High-intensity laser accelerated protons and ions are emerging sources with complementary characteristics to those of conventional sources, namely high charge, high current, and short bunch duration, and therefore can be useful for dedicated applications. However, these beams exhibit a broadband energy spectrum when, for some experiments, monoenergetic beams are required. We present here an adaptation of conventional chicane devices in a compact form (10 cm × 20 cm) which enables selection of a specific energy interval from the broadband spectrum. This is achieved by employing magnetic fields to bend the trajectory of the laser produced proton beam through two slits in order to select the minimum and maximum beam energy. The device enables a production of a high current, short duration source with a reproducible output spectrum from short pulse laser produced charged particle beams.

Chen, S. N.; Gauthier, M.; Higginson, D. P.; Dorard, S.; Marqučs, J.-R.; Fuchs, J. [LULI, École Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau (France)] [LULI, École Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau (France); Mangia, F.; Atzeni, S. [Dipartimento SBAI, Universitŕ di Roma “La Sapienza,” Roma (Italy)] [Dipartimento SBAI, Universitŕ di Roma “La Sapienza,” Roma (Italy); Riquier, R. [LULI, École Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau (France) [LULI, École Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau (France); CEA, DAM, DIF, F-91297 Arpajon (France)

2014-04-15T23:59:59.000Z

412

Internal energy flows and instantaneous field of a monochromatic paraxial light beam  

Science Journals Connector (OSTI)

It is known that the orbital angular momentum of a paraxial light beam is related to the rotational features of the instantaneous optical-frequency oscillation pattern within the beam...

Bekshaev, Aleksandr Ya

2012-01-01T23:59:59.000Z

413

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be  

Science Journals Connector (OSTI)

......mutations: regular protein secondary structure...intrinsically disordered) regions. Is...mutated native protein sequences into...sequence-like ensembles and monitored...intrinsically disordered) regions. Is...mutated native protein sequences into...sequence-like ensembles and monitored......

Christian Schaefer; Avner Schlessinger; Burkhard Rost

2010-03-01T23:59:59.000Z

414

Intrinsically Disordered Proteins in the Neurodegenerative Processes: Formation of Tau Protein Paired Helical Filaments and Their Analysis  

Science Journals Connector (OSTI)

1. Several intrinsically disordered proteins (IDPs) play principal role in the...?...-synuclein is involved in Parkinson's disease, prion protein in transmissible spongiform encephalopathies, and tau protein in A...

Rostislav Skrabana; Jozef Sevcik; Michal Novak

2006-11-01T23:59:59.000Z

415

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...

416

Protein-Based Nanomedicine Platforms for Drug Delivery. | EMSL  

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

Protein-Based Nanomedicine Platforms for Drug Delivery. Protein-Based Nanomedicine Platforms for Drug Delivery. Abstract: Drug delivery systems have been developed for many years,...

417

Stable Isotope, Site-Specific Mass Tagging For Protein Identification  

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

Stable Isotope, Site-Specific Mass Tagging For Protein Identification Stable Isotope, Site-Specific Mass Tagging For Protein Identification Proteolytic peptide mass mapping as...

418

Protein Folding Pathways Implementing Dihedral Angle Variable Speed  

Science Journals Connector (OSTI)

Protein folding remains as an impossible riddle biologist must ... requirements make it difficult to obtain clues regarding protein folding nature. The procedure presented in this paper...

Mikel Diez; Victor Petuya; Mónica Urizar…

2012-01-01T23:59:59.000Z

419

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

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

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

420

Ensemble FRET Methods in Studies of Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

The main structural characteristic of intrinsically disordered proteins (IDPs) or intrinsically disordered regions of globular proteins is that they exist as ensembles of multiple conformers which can continuousl...

Elisha Haas

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

DPROT: prediction of disordered proteins using evolutionary information  

Science Journals Connector (OSTI)

The association of structurally disordered proteins with a number of diseases has engendered ... the development of a computational method for predicting disordered proteins using sequence and profile composition...

Deepti Sethi; Aarti Garg; G. P. S. Raghava

2008-10-01T23:59:59.000Z

422

Determining a substitution matrix for the alignment of disordered proteins.  

E-Print Network [OSTI]

?? As the research of disordered proteins progresses and more disordered protein sequences are discovered, an optimal substitution matrix for the alignment of these sequences… (more)

Kim, Dong

2013-01-01T23:59:59.000Z

423

Amino acid treatment enhances protein recovery from sediment...  

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

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

424

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...

425

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

E-Print Network [OSTI]

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

De Micheli, Giovanni

426

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

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

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

427

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

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

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

428

Versatile Apoferritin Nanoparticle Labels for Assay of Protein...  

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

Versatile Apoferritin Nanoparticle Labels for Assay of Protein . Versatile Apoferritin Nanoparticle Labels for Assay of Protein . Abstract: A versatile bioassay label based on...

429

Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios  

E-Print Network [OSTI]

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

Berry, R. Stephen

430

SciTech Connect: Manipulating and Visualizing Proteins  

Office of Scientific and Technical Information (OSTI)

are working to make ProteinShop more applicable and adaptable to different protein folding methodologies. If users could manipulate structures from a biological point of...

431

DOE Science Showcase - Protein Folding | OSTI, US Dept of Energy...  

Office of Scientific and Technical Information (OSTI)

Science Showcase - Protein Folding Proteins are the main constitute of our bones, muscles, hair, skin and blood vessels, performing a vast array of functions such as catalyzing...

432

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...

433

Combining NMR, PRE, and EPR Methods For Homodimer Protein Structure...  

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

NMR, PRE, and EPR Methods For Homodimer Protein Structure Determination. Combining NMR, PRE, and EPR Methods For Homodimer Protein Structure Determination. Abstract: Homo-oligomer...

434

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...

435

More grapes, less wrath: hybrid antimicrobial protein protects...  

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

Hybrid antimicrobial protein protects grapevines from pathogen More grapes, less wrath: hybrid antimicrobial protein protects grapevines from pathogen Researchers has found a way...

436

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

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

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

437

Photovoltaic devices using photosynthetic protein complexes  

E-Print Network [OSTI]

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 ...

Das, Rupa, 1980-

2004-01-01T23:59:59.000Z

438

Telomere-associated proteins in Arabidopsis thaliana  

E-Print Network [OSTI]

. 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...

Surovtseva, Yulia V.

2009-05-15T23:59:59.000Z

439

IR laser-induced protein crystal transformation  

Science Journals Connector (OSTI)

A novel method and the associated instrumentation for improving crystalline order (higher resolution of X-ray diffraction and reduced mosaicity) of protein crystals by precisely controlled heating is demonstrated. Crystal transformation is optically controlled by a video system.

Kiefersauer, R.

2014-04-26T23:59:59.000Z

440

Prion protein in health and disease  

E-Print Network [OSTI]

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, ...

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

2008-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


441

Structural and Energetic Heterogeneity in Protein Folding  

E-Print Network [OSTI]

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.

Steven S. Plotkin; Jose N. Onuchic

2000-09-27T23:59:59.000Z

442

Proline peptide isomerization and protein folding  

Science Journals Connector (OSTI)

The unfolding-refolding of proteins is a cooperative process and, as judged by equilibrium properties, occurs in one step involving the native,N, and the unfoldedU, conformational states. Kinetic studies have sho...

A. Salahuddin

1984-10-01T23:59:59.000Z

443

Ensemble modeling of [beta]-sheet proteins  

E-Print Network [OSTI]

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 ...

O'Donnell, Charles William

2011-01-01T23:59:59.000Z

444

Enhanced sampling and applications in protein folding.  

E-Print Network [OSTI]

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

Zhang, Cheng

2013-01-01T23:59:59.000Z

445

Femtosecond X-ray protein nanocrystallography  

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

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

446

Energetics of protein charge transfer and photosynthesis  

E-Print Network [OSTI]

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

Matyushov, Dmitry

447

Genetic noise control via protein oligomerization  

SciTech Connect (OSTI)

Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamical role of protein-protein associations. We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch), integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast protein binding-unbinding kinetics, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its intrinsic switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced) state from randomly being induced (uninduced). The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of phenotypically important toggle switches, and nested positive feedback loops in general, is of direct implications to organism fitness. Finally, noise control through oligomerization suggests avenues for the design of robust synthetic gene circuits for engineering purposes.

Ghim, C; Almaas, E

2008-06-12T23:59:59.000Z

448

Positive modulator of bone morphogenic protein-2  

DOE Patents [OSTI]

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.

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

2009-01-27T23:59:59.000Z

449

Rhoptry protein 6 from Toxoplasma gondii is an intrinsically disordered protein  

Science Journals Connector (OSTI)

Abstract Rhoptry protein 6 (ROP6) from Toxoplasma gondii is a 480-amino acid protein with no homology to any reported excretory or secretory protein. Especially, unlike the many other rhoptry protein types, ROP6 does not have a kinase domain. The biochemical and biophysical properties of ROP6 are unknown. Here, we investigated its structure using an in silico analysis method and overexpression and purification using an Escherichia coli system. The protein was purified to more than 85% homogeneity using immobilized metal affinity chromatography in denaturing conditions. After purification, ROP6 showed slow migration in SDS–PAGE, including fast proteolysis. This implies that ROP6 has a high percentage of flexible regions or extended loop structures. Secondary structure prediction and prediction of intrinsically disordered regions by using various bioinformatics tools, indicated that approximately 60% of ROP6 is predicted to be intrinsically disordered or random coil regions. These observations indicate that ROP6 is an intrinsically disordered protein.

Won-Kyu Lee; Hye-Jin Ahn; Yeon Gyu Yu; Ho-Woo Nam

2014-01-01T23:59:59.000Z

450

Protein Folding: A Perspective From Statistical Physics  

E-Print Network [OSTI]

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^{\

Jinzhi Lei; Kerson Huang

2010-02-26T23:59:59.000Z

451

Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA  

E-Print Network [OSTI]

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

Simona Cocco; John F. Marko; Remi Monasson

2014-05-26T23:59:59.000Z

452

Solvent-induced forces in protein folding reflections on the protein folding problem  

Science Journals Connector (OSTI)

Abstract It is shown that the solvent induced forces on hydrophilic groups are the strongest ones. The relevance of this finding to protein folding is discussed.

Arieh Ben-Naim

2013-01-01T23:59:59.000Z

453

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

SciTech Connect (OSTI)

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.

Eliezer, D.

1994-06-01T23:59:59.000Z

454

Distribution of Protein Folds in the Three Superkingdoms of Life  

E-Print Network [OSTI]

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

455

Guide to Red Fluorescent Proteins and Biosensors for Flow Cytometry  

E-Print Network [OSTI]

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

Verkhusha, Vladislav V.

456

ProDy: Protein Dynamics Inferred from Theory and Experiments  

Science Journals Connector (OSTI)

......protein. Given a query protein, fast and flexible...and examples. 2.2 Protein from experiments The experimental data refer to ensembles of structures, X-ray...data due to unresolved disordered regions. In ProDy...Bahar, 2009). 2.3 Protein dynamics from theory......

Ahmet Bakan; Lidio M. Meireles; Ivet Bahar

2011-06-01T23:59:59.000Z

457

Intrinsic Protein Disorder in Complete Genomes A. Keith Dunker1  

E-Print Network [OSTI]

Intrinsic Protein Disorder in Complete Genomes A. Keith Dunker1 Zoran Obradovic2 dunker@disorder State University, Pullman, WA 99164-2752 Abstract Intrinsic protein disorder refers to segments or to whole proteins that fail to fold completely on their own. Here we predicted disorder on protein

Obradovic, Zoran

458

Sequence Complexity of Disordered Protein Pedro Romero,1#  

E-Print Network [OSTI]

Sequence Complexity of Disordered Protein Pedro Romero,1# Zoran Obradovic,1ÂĄ Xiaohong Li,1 Ethan C University, Pullman, Washington ABSTRACT Intrinsic disorder refers to seg- ments or to whole proteins proteins, these variously characterized intrinsically disordered seg- ments and proteins, and also

Obradovic, Zoran

459

THOUSANDS OF PROTEINS LIKELY TO HAVE LONG DISORDERED REGIONS  

E-Print Network [OSTI]

THOUSANDS OF PROTEINS LIKELY TO HAVE LONG DISORDERED REGIONS PEDRO ROMERO, ZORAN OBRADOVIC School of protein disorder using primary sequence information were developed and applied to the Swiss Protein Database. More than 15,000 proteins were predicted to contain disordered regions of at least 40 consecutive

Obradovic, Zoran

460

GlobPlot: exploring protein sequences for globularity and disorder  

E-Print Network [OSTI]

GlobPlot: exploring protein sequences for globularity and disorder Rune Linding*, Robert B. Russell within the query protein for order/globularity and disorder. We show examples with known proteins where important protein segments lie outside of globular domains in regions that are intrinsically disordered (2

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


461

INTRODUCTION Proteins must mature to their native confor-  

E-Print Network [OSTI]

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

Hebert, Daniel N.

462

Introduction Protein secretion is an essential process in prokaryotes and  

E-Print Network [OSTI]

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

Cheng, Chi-Hing Christina

463

Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics  

E-Print Network [OSTI]

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

Santiago, Juan G.

464

DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS  

E-Print Network [OSTI]

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

Langmead, Christopher James

465

FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

466

Cellular mechanisms of membrane protein folding William R Skach  

E-Print Network [OSTI]

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

Cai, Long

467

Evolutionary Monte Carlo for protein folding simulations Faming Lianga)  

E-Print Network [OSTI]

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

Liang, Faming

468

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

E-Print Network [OSTI]

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

Smith, J. MacGregor

469

Adaptive dimensionality reduction of stochastic differential equations for protein dynamics  

E-Print Network [OSTI]

. 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

Izaguirre, JesĂşs A.

470

Folding simulations of small proteins Seung-Yeon Kima  

E-Print Network [OSTI]

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

Lee, Jooyoung

471

Kinetics of Halide Release of Haloalkane Dehalogenase:? Evidence for a Slow Conformational Change  

Science Journals Connector (OSTI)

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands ... We thank the members of the Protein Crystallography and Molecular Dynamics groups from the University of Groningen for many stimulating discussions. ...

Joost P. Schanstra; Dick B. Janssen

1996-05-07T23:59:59.000Z

472

High-Yield Secretion of Multiple Client Proteins in Aspergillus  

SciTech Connect (OSTI)

Production of pure and high-yield client proteins is an important technology that addresses the need for industrial applications of enzymes as well as scientific experiments in protein chemistry and crystallization. Fungi are utilized in industrial protein production because of their ability to secrete large quantities of proteins. In this study, we engineered a high-expression-secretion vector, pEXPYR that directs proteins towards the extracellular medium in two Aspergillii host strains, examine the effect of maltose-induced over-expression and protein secretion as well as time and pH-dependent protein stability in the medium. We describe five client proteins representing a core set of hemicellulose degrading enzymes that accumulated up to 50-100 mg/L of protein. Using a recyclable genetic marker that allows serial insertion of multiple genes, simultaneous hyper-secretion of three client proteins in a single host strain was accomplished.

Segato, F.; Damasio, A. R. L.; Goncalves, T. A.; de Lucas, R. C.; Squina, F. M.; Decker, S. R.; Prade, R. A.

2012-07-15T23:59:59.000Z

473

A novel link prediction algorithm for reconstructing protein–protein interaction networks by topological similarity  

Science Journals Connector (OSTI)

......into the same complex in the set of predicted complexes and that in the set of known complexes, the prediction...denotes the cardinality of the set . As shown in Figure 3a, the...known protein complexes only covers of the proteins in the PPI network......

Chengwei Lei; Jianhua Ruan

2013-02-01T23:59:59.000Z

474

ClusPro: a fully automated algorithm for protein protein docking  

E-Print Network [OSTI]

possible to evaluate billions of putative complex structures covering a large set of the translationalClusPro: a fully automated algorithm for protein­ protein docking Stephen R. Comeau1 , David W.rcsb.org/pdb/). The docking algorithms evalu- ate billions of putative complexes, retaining a preset number with favorable

Vajda, Sandor

475

Replica exchange simulations of transient encounter complexes in protein–protein association  

Science Journals Connector (OSTI)

...the specific complex (S) and nonspecific complexes (NS1, NS2, and NS3) connected by a diffuse cloud of loosely bound...Protein coordinates are taken from the Protein Data Bank [ID codes 1VRC (24), 1J6T (25), and 3EZA (26) for IIA Man -HPr...

Young C. Kim; Chun Tang; G. Marius Clore; Gerhard Hummer

2008-01-01T23:59:59.000Z

476

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS PROTS: A fragment based protein  

E-Print Network [OSTI]

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

Zhang, Yang

477

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

E-Print Network [OSTI]

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

Cox, Michael M.

478

Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins  

E-Print Network [OSTI]

ensemble of the sequence in which a pair of residues is in contact. Lattice model proteins with a high (such as disordered proteins and proteins that are dependent on chaperonins for their folding) indicatesTrade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real

Unger, Ron

479

Translocation of Proteins Across the Endoplasmic Reticulum I . Signal Recognition Protein (SRP) Binds to In-Vitro-  

E-Print Network [OSTI]

Translocation of Proteins Across the Endoplasmic Reticulum I . Signal Recognition Protein (SRP protein, termed signal recognition protein (SRP), has been shown here (a) to inhibit translation-affinity binding as wel l as the selective translation- inhibitory effect were abol ished after modification of SRP

Walter, Peter

480

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

E-Print Network [OSTI]

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

Lathrop, Richard H.

Note: This page contains sample records for the topic "monochromatic protein crystallography" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins with Long Disordered Regions  

E-Print Network [OSTI]

Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins to functionalities of intrinsically disordered proteins and provides researchers with a novel tool that could be used Intrinsic disorder; protein structure; protein function; intrinsically disordered proteins; bioinformatics

Obradovic, Zoran

482

Dynamic interactions of proteins in complex networks  

SciTech Connect (OSTI)

Recent advances in techniques such as NMR and EPR spectroscopy have enabled the elucidation of how proteins undergo structural changes to act in concert in complex networks. The three minireviews in this series highlight current findings and the capabilities of new methodologies for unraveling the dynamic changes controlling diverse cellular functions. They represent a sampling of the cutting-edge research presented at the 17th Meeting of Methods in Protein Structure Analysis, MPSA2008, in Sapporo, Japan, 26-29 August, 2008 (http://www.iapsap.bnl.gov). The first minireview, by Christensen and Klevit, reports on a structure-based yeast two-hybrid method for identifying E2 ubiquitin-conjugating enzymes that interact with the E3 BRCA1/BARD1 heterodimer ligase to generate either mono- or polyubiquitinated products. This method demonstrated for the first time that the BRCA1/BARD1 E3 can interact with 10 different E2 enzymes. Interestingly, the interaction with multiple E2 enzymes displayed unique ubiquitin-transfer properties, a feature expected to be common among other RING and U-box E3s. Further characterization of new E3 ligases and the E2 enzymes that interact with them will greatly enhance our understanding of ubiquitin transfer and facilitate studies of roles of ubiquitin and ubiquitin-like proteins in protein processing and trafficking. Stein et al., in the second minireview, describe recent progress in defining the binding specificity of different peptide-binding domains. The authors clearly point out that transient peptide interactions mediated by both post-translational modifications and disordered regions ensure a high level of specificity. They postulate that a regulatory code may dictate the number of combinations of domains and post-translational modifications needed to achieve the required level of interaction specificity. Moreover, recognition alone is not enough to obtain a stable complex, especially in a complex cellular environment. Increasing evidence indicates that disordered domains can acquire structural features that modulate the binding and strength of the signaling cascade. Whereas the first two minireviews describe ways in which protein interactions are modulated, the third, by Tompa, focuses on the importance of protein disorder in a subset of amyloid proteins. It is apparent that within this group, part of the polypeptide chain remains disordered during amyloid formation. Moreover, the disordered segments have different amino acid composition and physicochemical characteristics, which suggests that they may play a role in amyloid stability. The disordered region may serve as a linker to connect the ordered core and a globular domain, maintaining the stability and structure of the globular domain and minimizing protein refolding upon amyloid formation. As techniques in protein chemistry advance, we are learning more and more about the mechanisms that regulate and are regulated by protein interactions. The three minireviews in this series offer a glimpse of the complex dynamics fundamental to protein-protein interactions. In the future, we expect that the knowledge gained will help to augment our ability to control complex pathologies and treat diverse diseases states.

Appella, E.; Anderson, C.

2009-10-01T23:59:59.000Z

483

The Colorful Journey of Green Fluorescent Protein  

Science Journals Connector (OSTI)

Though the story of GFP began millions of years ago when the jellyfish Aequorea aequorea (also commonly referred to as Aequorea victoria and Aequorea forskalea) successfully evolved a fluorescent protein species with the uncanny ability to convert the excited blue energy of the bioluminescent protein aequorin into the green light observed in nature, its journey to “Nature’s Scientific Contributors Hall of Fame” started much more recently, in 1961. ... This observation, which represents the initial discovery of GFP, was included as a footnote in a paper by Shimomura and Johnson (1) describing the purification and characterization of aequorin: “A protein giving solutions that look slightly greenish in sunlight though only yellowish under tungsten lights, and exhibiting a very bright, greenish fluorescence in the ultraviolet of a Mineralite, has also been isolated from the squeezates.” ... In fact, during my time there, he still tried to find time to carry out chemical syntheses, which usually happened during Christmas. ...

Jin Zhang

2009-02-20T23:59:59.000Z

484

ET Kinetics of Bifunctional Redox Protein Maquettes  

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

Kinetics of Bifunctional Redox Protein Maquettes Kinetics of Bifunctional Redox Protein Maquettes Mitchell W. Mutz, James F. Wishart and George L. McLendon Adv. Chem Ser. 254, Ch. 10, pp. 145-159 Abstract: We prepared three bifunctional redox protein maquettes based on 12-, 16-, and 20-mer three-helix bundles. In each case, the helix was capped with a Co(III) tris-bipyridyl electron acceptor and also functionalized with a C-terminal viologen (1-ethyl-1'-ethyl-4,4'-bipyridinium) donor. Electron transfer (ET) was initiated by pulse radiolysis and flash photolysis and followed spectrometrically to determined average, concentration-independent, first-order rates for the 16-mer and 20-mer maquettes. For the 16-mer bundle, the alpha-helical content was adjusted by the addition of urea or trifluoroethanol to solutions containing the metalloprotein. This

485

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

E-Print Network [OSTI]

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

Annunziata, Onofrio

486

Exploration of homodimer receptor: homodimer protein interactions  

Science Journals Connector (OSTI)

Homodimerisation is producing a proteinâ??protein complex composed of two identical molecules. Dimerisation is a phenomenon often occurring in the regulation of biochemical systems like signal transduction pathways. We investigated whether the existence of a homodimer-activated receptor and the activation of homodimer transducers correspond to a more general pattern in cell signalling. We developed a workflow to merge data from the Gene Ontology and the BIND database to produce a list of interactions between homodimer receptors and homodimer proteins. Finally, we found a prevalence of homodimerâ??homodimer interactions in signalling systems in human cells.

Julio Vera; Taesoo Kwon; Ulf Schmitz; Walter Kolch; Olaf Wolkenhauer

2009-01-01T23:59:59.000Z

487

Protein synthesis driven by dynamical stochastic transcription  

E-Print Network [OSTI]

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.

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

2014-06-12T23:59:59.000Z

488

Protein Folding in Contact Map Space  

Science Journals Connector (OSTI)

Changing a few contacts in a contact map corresponds to a large scale move in confrontation space; hence, one gains a lot by using the contact map representation for protein folding. We developed an efficient search procedure in the space of physical contact maps, which could identify the native fold as of the lowest free energy, provided on had a free energy function whose ground state is the native map. We prove rigorously that the widely used pairwise contact approximation to the free energy cannot stabilize even a single protein's native map. Testing the native map against a set of decoys obtained by gapless threading, one may be misled to the opposite conclusion.

M. Vendruscolo; R. Najmanovich; E. Domany

1999-01-18T23:59:59.000Z

489

Protein Folding as a Physical Stochastic Process  

E-Print Network [OSTI]

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.

Kerson Huang

2007-07-17T23:59:59.000Z

490

Preparation of white sunflower protein isolates  

E-Print Network [OSTI]

and selected functional properties, Proximate Analysis All samples were analyzed using the Official Methods of AOAC (1975) and AOCS (1957). Moisture and solid contents were determined by AOAC method 14. 004; ash, AOAC method 14. 006; crude nitrogen... and protein, AOCS method Aa 5-38; crude fat, AOCS method Aa 4-38; and crude fiber, AOCS method Ba 6-61. Materials Balances Materials balances and yields of solids and protein were calcu- lated for each fraction of the isolation procedure. These were...

Wen, Hwei-Mei

2012-06-07T23:59:59.000Z

491

Rigidity Analysis for Modeling Protein Motion  

E-Print Network [OSTI]

, it is not a rigid molecule. It can move and flex in response to changes in its environment such as temperature or the 11 presence of other proteins or chemicals. The atoms in a protein are connected by bonds. The lengths and angles of these bonds are not fixed... and evaluate the likelihood of observing that conformation under the given environmental conditions. In general, a potential energy function may be expressed as a summation 12 of various terms including bond length flexing, bond angle flexing, dihedral angle...

Thomas, Shawna L.

2010-07-14T23:59:59.000Z

492

1.17 - Protein Folding in the Endoplasmic Reticulum  

Science Journals Connector (OSTI)

Abstract The endoplasmic reticulum (ER) is the principal protein-folding organelle for secretory and membrane proteins. Proteins are folded, assembled, and post-translationally modified in the ER. Chaperones and folding enzymes assist in this process. Before exiting the ER, all proteins undergo quality control such that only properly folded proteins transit to the Golgi and cell surface. The ER is also the site for sterol and lipid synthesis. As a major synthetic organelle, the ER is extremely sensitive to perturbations in homeostasis. Accumulation of misfolded or unfolded proteins within the ER induces a signaling pathway termed the unfolded protein response (UPR), which acts to restore ER homeostasis. This article discusses the basic mechanisms of protein folding in the ER, the role of the key ER chaperones, induction of the UPR, ER-associated degradation, and human diseases caused by protein misfolding and aggregation.

N. Naidoo

2011-01-01T23:59:59.000Z

493

Extracellular Proteins Promote Zinc Sulfide Aggregation  

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

Extracellular Proteins Promote Extracellular Proteins Promote Zinc Sulfide Aggregation Extracellular Proteins Promote Zinc Sulfide Aggregation Print Wednesday, 26 September 2007 00:00 Researchers from the ALS, Berkeley Lab's National Center for Electron Microscopy (NCEM), and Lawrence Livermore National Laboratory analyzed biofilm samples rich in zinc sulfide and dominated by sulfate-reducing bacteria, which were collected from lead-zinc mine waters. The researchers were curious about the relationship of the organic material and metals, particularly how organics affect mobility, and its potential for bioremediation. It is known that some organics promote aggregation. Amine-bearing molecules, for example, can organize sulfide nanoparticles into semiconductor nanowires. The research team used a series of imaging techniques and detectors to analyze aggregates of biogenic zinc sulfide nanocrystals in the biofilms. Their examination yielded excellent results and some surprises. They were able to prove that natural organic matter promotes dense aggregation of the zinc sulfide nanocrystals into much larger spheroids and that the organic matter is preserved in nanometer-scale pores in the spheroids. What was not expected was the presence of proteins in the spheroids, making them a key component in aggregation and an example of extracellular biomineralization.

494

Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches  

Science Journals Connector (OSTI)

...design of small peptides and even mini-proteins [66] and indicates...78] or three-dimensional grid-based approaches such as VICE...LigSite [82] that search for grid points that are not situated...probe points installed in the grid to determine their atom environment...

2012-01-01T23:59:59.000Z

495

Type IV Pilin Proteins: Versatile Molecular Modules  

Science Journals Connector (OSTI)

...2012 review-article Reviews Type IV Pilin Proteins...adaptable functional plan. The type IV pilin is...substrates. In this review, we consider recent...adaptable functional plan. The type IV pilin is...substrates. In this review, we consider recent...

Carmen L. Giltner; Ylan Nguyen; Lori L. Burrows

2012-12-01T23:59:59.000Z

496

Collection of very low resolution protein data  

Science Journals Connector (OSTI)

Simple modifications to a MAR 345 detector which facilitate the collection of very low resolution data are described. With these modifications, the lowest order reflections from a poliovirus crystal (c = 377.1 ?) were observed, and measurement of all reflections in typical protein cells should be routine.

Miller, S.T.

1999-12-01T23:59:59.000Z

497

Energy use by biological protein transport pathways  

E-Print Network [OSTI]

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

Economou, Tassos

498

CORN GERM: A VALUABLE PROTEIN FOOD  

Science Journals Connector (OSTI)

...per cent. of the crop by dry milling and distilling,2 and a yield...value of the proteins of the corn germ has not been studied by...Scientist, 31: 142, 1943. 2 Corn germ made by the wet-milling process, due to leaching with...

H. H. MITCHELL; JESSIE R. BEADLES

1944-02-11T23:59:59.000Z

499

Critical aspects of hierarchical protein folding  

E-Print Network [OSTI]

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.

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

1998-01-13T23:59:59.000Z

500

PROTEIN INTERACTIONS AND DISEASE MARICEL KANN  

E-Print Network [OSTI]

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

Radivojac, Predrag