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1

Infrared Protein Crystallography  

DOE Green Energy (OSTI)

We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO{sub 2}. Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

J Sage; Y Zhang; J McGeehan; R Ravelli; M Weik; J van Thor

2011-12-31T23:59:59.000Z

2

E-Science and Protein Crystallography  

SciTech Connect

Dr. Zoe Fisher is the instrument scientist for the Protein Crystallography Station (PCS) at the Los Alamos Neutron Science Center's (LANSC) Lujan Neutron Scattering Center. She helps schedule researchers who intend to use the instrument to collect data, and provides in depth support for their activities. Users submit proposals for beam/instrument time via LANSCE proposal review system. In 2012, there were about 20 proposals submitted for this instrument. The instrument scientists review the proposals online. Accepted proposals are scheduled via an aggregate calendar which takes into account staff and resource availability, and the scientist is notified via email when their proposal is accepted and their requested time is scheduled. The entire PCS data acquisition and processing workflow is streamlined through various locally developed and commercial software packages. One 24 hour period produces one 200 Mb file, giving a total of maybe 2-5 Gb of data for the entire run. This data is then transferred to a hard disk in Dr. Fisher's office where she views the data with the customer and compresses the data to a text format which she sends them. This compression translates the data from an electron density to structural coordinates, which are the products submitted to a protein structure database. As noted above, the raw experimental data is stored onsite at LANSCE on workstations maintained by the instrument scientist. It is extraordinarily rare for anyone to request this data, although the remote possibility of an audit by a funding organization motivates its limited preservation. The raw data is not rigorously backed up, but only stored on a single hard drive. Interestingly, only about 50% of the experimental data actually ends up deposited and described in peer reviewed publications; the data that is not published tends to either not be viable structures or is calibration data. Dr. Fisher does protein crystallography research using both neutron and x-ray scattering techniques. Many of the major funders as well as the major journals dealing with protein crystallography require deposition of the structural data in the Protein Data Bank (PDB). Files formatted for the PDB are automatically generated when the data is compressed. The header files in the PDB included experimental conditions of the experiment as well as experimental methods. Depending on the completeness and how 'hot' of a topic, it may not be needed to contact the original experimenter about using the data. Having said that, not all of the data is accurate and does requires some back and forth with the creators of the data. The RCSB PDB staff at Rutgers University goes through all submissions and works with the submitters to verify that the data meets their minimum standards of completeness and robustness. The Protein Data Bank (PDB) was initially created by Walter Hamilton at Brookhaven National Laboratory in 1971 after discussions about the value of scientists having access to structural biology data. Originally a partnership between Brookhaven and the Cambridge Crystallographic Data Center, the idea was conceived as a global initiative, which is certainly has become with partner sites in the US, Europe, and Japan. The PDB now contains structures determined from many different experimental techniques (Berman et al. 2012). Deposited structures are assigned a unique ID, and the structures are embargoed until the publication that references and describes them is published. The PDB staff often monitors these publications and takes the initiative to release protein structures when papers describing them are published. Dr. Fisher records setup and experimental details in word documents and inserts printed copies into paper lab notebooks. These details appear in the final published papers and the header files for structures in the PDB. Analysis of data collected at the PCS is performed with a combination of locally developed tools and commercial products which are capable of outputting data suitable for importing into the PDB. While the original output data from the

Miller, Laniece E. [Los Alamos National Laboratory; Powell, James E. Jr. [Los Alamos National Laboratory

2012-08-09T23:59:59.000Z

3

E-Science and Protein Crystallography  

Science Conference Proceedings (OSTI)

Dr. Zoe Fisher is the instrument scientist for the Protein Crystallography Station (PCS) at the Los Alamos Neutron Science Center's (LANSC) Lujan Neutron Scattering Center. She helps schedule researchers who intend to use the instrument to collect data, and provides in depth support for their activities. Users submit proposals for beam/instrument time via LANSCE proposal review system. In 2012, there were about 20 proposals submitted for this instrument. The instrument scientists review the proposals online. Accepted proposals are scheduled via an aggregate calendar which takes into account staff and resource availability, and the scientist is notified via email when their proposal is accepted and their requested time is scheduled. The entire PCS data acquisition and processing workflow is streamlined through various locally developed and commercial software packages. One 24 hour period produces one 200 Mb file, giving a total of maybe 2-5 Gb of data for the entire run. This data is then transferred to a hard disk in Dr. Fisher's office where she views the data with the customer and compresses the data to a text format which she sends them. This compression translates the data from an electron density to structural coordinates, which are the products submitted to a protein structure database. As noted above, the raw experimental data is stored onsite at LANSCE on workstations maintained by the instrument scientist. It is extraordinarily rare for anyone to request this data, although the remote possibility of an audit by a funding organization motivates its limited preservation. The raw data is not rigorously backed up, but only stored on a single hard drive. Interestingly, only about 50% of the experimental data actually ends up deposited and described in peer reviewed publications; the data that is not published tends to either not be viable structures or is calibration data. Dr. Fisher does protein crystallography research using both neutron and x-ray scattering techniques. Many of the major funders as well as the major journals dealing with protein crystallography require deposition of the structural data in the Protein Data Bank (PDB). Files formatted for the PDB are automatically generated when the data is compressed. The header files in the PDB included experimental conditions of the experiment as well as experimental methods. Depending on the completeness and how 'hot' of a topic, it may not be needed to contact the original experimenter about using the data. Having said that, not all of the data is accurate and does requires some back and forth with the creators of the data. The RCSB PDB staff at Rutgers University goes through all submissions and works with the submitters to verify that the data meets their minimum standards of completeness and robustness. The Protein Data Bank (PDB) was initially created by Walter Hamilton at Brookhaven National Laboratory in 1971 after discussions about the value of scientists having access to structural biology data. Originally a partnership between Brookhaven and the Cambridge Crystallographic Data Center, the idea was conceived as a global initiative, which is certainly has become with partner sites in the US, Europe, and Japan. The PDB now contains structures determined from many different experimental techniques (Berman et al. 2012). Deposited structures are assigned a unique ID, and the structures are embargoed until the publication that references and describes them is published. The PDB staff often monitors these publications and takes the initiative to release protein structures when papers describing them are published. Dr. Fisher records setup and experimental details in word documents and inserts printed copies into paper lab notebooks. These details appear in the final published papers and the header files for structures in the PDB. Analysis of data collected at the PCS is performed with a combination of locally developed tools and commercial products which are capable of outputting data suitable for importing into the PDB. While the original output data from the

Miller, Laniece E. [Los Alamos National Laboratory; Powell, James E. Jr. [Los Alamos National Laboratory

2012-08-09T23:59:59.000Z

4

High resolution electron crystallography of protein molecules  

Science Conference Proceedings (OSTI)

Electron diffraction data and high resolution images can now be used to obtain accurate, three-dimensional density maps of biological macromolecules. These density maps can be interpreted by building an atomic-resolution model of the structure into the experimental density. The Cowley-Moodie formalism of dynamical diffraction theory has been used to validate the use of kinematic diffraction theory, strictly the weak phase object approximation, in producing such 3-D density maps. Further improvements in the preparation of very flat specimens and in the retention of diffraction to a resolution of 0.2 nm or better could result in electron crystallography becoming as important a technique as x-ray crystallography currently is for the field of structural molecular biology.

Glaeser, R.M. [California Univ., Berkeley, CA (United States). Dept. of Molecular and Cell Biology]|[Lawrence Berkeley Lab., CA (United States); Downing, K.H. [Lawrence Berkeley Lab., CA (United States)

1993-06-01T23:59:59.000Z

5

Protein Energy Landscapes Determined by 5-Dimensional Crystallography  

E-Print Network (OSTI)

Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be determined from the same set of X-ray data. We demonstrate here how barriers of activation can be determined solely from five-dimensional crystallography [5]. Directly linking molecular structures with barriers of activation between them allows for gaining insight into the structural nature of the barrier. We analyze comprehensive time series of crystal-lographic data at 14 different temperature settings and determine entropy and enthalpy contributions to the barriers of activation. 100 years after the discovery of X-ray scattering, we advance X-ray structure determination to a new frontier, the determination of energy landscapes.

Schmidt, Marius; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

2013-01-01T23:59:59.000Z

6

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

DOE Patents (OSTI)

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

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

1997-01-01T23:59:59.000Z

7

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

DOE Patents (OSTI)

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

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

1997-01-28T23:59:59.000Z

8

Direct detection of x-rays for protein crystallography  

DOE Patents (OSTI)

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

Atac, Muzaffer; McKay, Timothy

1997-12-01T23:59:59.000Z

9

NMR crystallography: The effect of deuteration on high resolution 13 state NMR spectra of a 7-TM protein  

E-Print Network (OSTI)

NMR crystallography: The effect of deuteration on high resolution 13 C solid state NMR spectra, and indirect, 9­17 ppm, dimensions). The measured 13 C NMR line-widths observed for both protonated. Introduction Perdeuteration has been used routinely in solution NMR for 13 C, 15 N labeled protein assignment

Watts, Anthony

10

Charge-coupled-device/fiberoptic taper array X-ray detector for protein crystallography  

SciTech Connect

A large area, charge-couple-device (CCD) based fiberoptic taper array detector (APS-1) has been installed at the insertion-device beamline of the Structural Biology Center at the ANL Advanced Photon Source. The detector is used in protein crystallography diffraction experiments, where the objective is to measure the position and intensity of X-ray Bragg peaks in diffraction images. Large imaging area, very high spatial resolution, high X-ray sensitivity, good detective quantum efficiency, low noise, wide dynamic range, excellent stability and short readout time are all fundamental requirements in this application. The APS-1 detector converts the two-dimensional X-ray patterns to a visible light images by a thin layer of X-ray sensitive phosphor. The phosphor coating is directly deposited on the large ends of nine fiberoptic tapers arranged in a 3x3 array. Nine, thermoelectrically cooled 1024 x 1024 pixel CCD`s image the patterns, demagnified by the tapers. After geometrical and uniformity corrections, the nine areas give a continuous image of the detector face with virtually no gaps between the individual tapers. The 18 parallel analog signal-processing channels and analog-to-digital converters assure short readout time and low readout noise.

Naday, I.; Ross, S.; Westbrook, E.M.; Zentai, G.

1997-03-01T23:59:59.000Z

11

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

SciTech Connect

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

12

Operational experience of a large area x-ray camera for protein crystallography.  

Science Conference Proceedings (OSTI)

After 3 years experience of operating very large area (210mm x 210mm) CCD-based detectors at the Advanced Photon Source, operational experience is reported. Four such detectors have been built, two for Structural Biology Center (APS-1 and SBC-2), one for Basic Energy Sciences Synchrotrons Radiation Center (Gold-2) at Argonne National Laboratory's Advanced Photon Source and one for Osaka University by Oxford Instruments, for use at Spring 8 (PX-21O). The detector is specifically designed as a high resolution and fast readout camera for macromolecular crystallography. Design trade-offs for speed and size are reviewed in light of operational experience and future requirements are considered. Operational data and examples of crystallography data are presented, together with plans for more development.

Joachimiak, A.; Jorden, A. R.; Loeffen, P. W.; Naday, I.; Sanishvili, R.; Westbrook, E. M.

1999-07-13T23:59:59.000Z

13

electronic reprint Crystallography  

E-Print Network (OSTI)

electronic reprint Journal of Applied Crystallography ISSN 0021-8898 Molsee: a Tcl/Tk-based program of Crystallography Printed in Great Britain ± all rights reserved Molsee: a Tcl/Tk-based program to control Rasmol molecules. In order to make it more user-friendly, Molsee, a Tcl/Tk-based graphical user interface front end

Luhua, Lai

14

Neutron proton crystallography station (PCS)  

SciTech Connect

The PCS (Protein Crystallography Station) at Los Alamos Neutron Science Center (LANSCE) is a unique facility in the USA that is designed and optimized for detecting and collecting neutron diffraction data from macromolecular crystals. PCS utilizes the 20 Hz spallation neutron source at LANSCE to enable time-of-flight measurements using 0.6-7.0 {angstrom} neutrons. This increases the neutron flux on the sample by using a wavelength range that is optimal for studying macromolecular crystal structures. The diagram below show a schematic of PCS and photos of the detector and instrument cave.

Fisher, Zoe [Los Alamos National Laboratory; Kovalevsky, Andrey [Los Alamos National Laboratory; Johnson, Hannah [Los Alamos National Laboratory; Mustyakimov, Marat [Los Alamos National Laboratory

2009-01-01T23:59:59.000Z

15

electronic reprint Crystallography  

E-Print Network (OSTI)

of Crystallography Author(s) of this paper may load this reprint on their own web site provided that this cover page a new software toolbox for the handling of the various parameterizations of atomic anisotropic analysis of a structure. Therefore, a library for the conversion between the different parameterizations

Grosse-Kunstleve, Ralf

16

Diamondoid Monolayers as Monochromatic Electron Source  

NLE Websites -- All DOE Office Websites (Extended Search)

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

17

Diamondoid Monolayers as Monochromatic Electron Source  

NLE Websites -- All DOE Office Websites (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.

18

Diamondoid Monolayers as Monochromatic Electron Source  

NLE Websites -- All DOE Office Websites (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.

19

Phasing Out the Phase Problem in Interfacial Crystallography  

NLE Websites -- All DOE Office Websites (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

20

Instrumentation upgrades for the Macromolecular Crystallography beamlines  

NLE Websites -- All DOE Office Websites (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

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

Design of a compact high-output monochromatic x-ray source for radiography applications  

Science Conference Proceedings (OSTI)

The distinct advantages of monochromatic x rays in medical imaging, especially in computed tomography (CT) and radiography with contrast agents (e.g. angiography), provide a great incentive for developing compact sources of monochromatic, or nearly monochromatic, ...

Tigran Bacarian / F. A. Dilmanian

2003-01-01T23:59:59.000Z

22

Introduction to Crystallography | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (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

23

Multiplicity of monochromatic solutions to x+y  

Science Conference Proceedings (OSTI)

For integers n>=1 and k>=0, let M"k(n) represent the minimum number of monochromatic solutions to x+y=0, M"k(n)=Cn^3(1+o"k(1)), where C=112(1+22)^2~0.005686. A structural result is ... Keywords: Asymptotics, Ramsey theory, Schur numbers

Wojciech Kosek; Aaron Robertson; Dusty Sabo; Daniel Schaal

2010-11-01T23:59:59.000Z

24

Statistics of Grain Boundary Crystallography in Surrogates for Oxide ...  

Science Conference Proceedings (OSTI)

Presentation Title, Statistics of Grain Boundary Crystallography in Surrogates for ... of TIG Welded and Laser-surface Melted SUS 304 for Nuclear Power Plants.

25

Fast microtomography using bright monochromatic x-rays  

Science Conference Proceedings (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

26

Proteins  

NLE Websites -- All DOE Office Websites (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

27

Enhancing access to research data: the challenge of crystallography  

Science Conference Proceedings (OSTI)

This paper describes an ongoing collaborative effort across digital library and scientific communities in the UK to improve access to research data. A prototype demonstrator service supporting the discovery and retrieval of detailed results of crystallography ... Keywords: Eprints.org, OAI-PMH, crystallography, dublin core, institutional repositories, metadata, scholarly communication

Monica Duke; Michael Day; Rachel Heery; Leslie A. Carr; Simon J. Coles

2005-06-01T23:59:59.000Z

28

Proposal Review Panels (Areas Other Than Crystallography)  

NLE Websites -- All DOE Office Websites (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

29

Resources for Macromolecular Crystallography | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (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 ]

30

Mao of HP-CAT Awarded Aminoff Prize in Crystallography  

NLE Websites -- All DOE Office Websites (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

31

SIBYLS - A SAXS and protein crystallography beamline at the ALS  

E-Print Network (OSTI)

Beamline at the ALS C.Trame*, A.A.MacDowell*, R.S.Celestre*,recently installed at the ALS that allows for a hard x-rayAdvanced Light Source (ALS) ring (1.9 GeV). The beamline is

2003-01-01T23:59:59.000Z

32

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

33

Virtual monochromatic imaging in dual-source dual-energy CT: Radiation dose and image quality  

Science Conference Proceedings (OSTI)

Purpose: To evaluate the image quality of virtual monochromatic images synthesized from dual-source dual-energy computed tomography (CT) in comparison with conventional polychromatic single-energy CT for the same radiation dose. Methods: In dual-energy CT, besides the material-specific information, one may also synthesize monochromatic images at different energies, which can be used for routine diagnosis similar to conventional polychromatic single-energy images. In this work, the authors assessed whether virtual monochromatic images generated from dual-source CT scanners had an image quality similar to that of polychromatic single-energy images for the same radiation dose. First, the authors provided a theoretical analysis of the optimal monochromatic energy for either the minimum noise level or the highest iodine contrast to noise ratio (CNR) for a given patient size and dose partitioning between the low- and high-energy scans. Second, the authors performed an experimental study on a dual-source CT scanner to evaluate the noise and iodine CNR in monochromatic images. A thoracic phantom with three sizes of attenuating rings was used to represent four adult sizes. For each phantom size, three dose partitionings between the low-energy (80 kV) and the high-energy (140 kV) scans were used in the dual-energy scan. Monochromatic images at eight energies (40 to 110 keV) were generated for each scan. Phantoms were also scanned at each of the four polychromatic single energy (80, 100, 120, and 140 kV) with the same radiation dose. Results: The optimal virtual monochromatic energy depends on several factors: phantom size, partitioning of the radiation dose between low- and high-energy scans, and the image quality metrics to be optimized. With the increase of phantom size, the optimal monochromatic energy increased. With the increased percentage of radiation dose on the low energy scan, the optimal monochromatic energy decreased. When maximizing the iodine CNR in monochromatic images, the optimal energy was lower than that when minimizing noise level. When the total radiation dose was equally distributed between low and high energy in dual-energy scans, for minimum noise, the optimal energies were 68, 71, 74, and 77 keV for small, medium, large, and extra-large (xlarge) phantoms, respectively; for maximum iodine CNR, the optimal energies were 66, 68, 70, 72 keV. With the optimal monochromatic energy, the noise level was similar to and the CNR was better than that in a single-energy scan at 120 kV for the same radiation dose. Compared to an 80 kV scan, however, the iodine CNR in monochromatic images was lower for the small, medium, and large phantoms. Conclusions: In dual-source dual-energy CT, optimal virtual monochromatic energy depends on patient size, dose partitioning, and the image quality metric optimized. With the optimal monochromatic energy, the noise level was similar to and the iodine CNR was better than that in 120 kV images for the same radiation dose. Compared to single-energy 80 kV images, the iodine CNR in virtual monochromatic images was lower for small to large phantom sizes.

Yu Lifeng; Christner, Jodie A.; Leng Shuai; Wang Jia; Fletcher, Joel G.; McCollough, Cynthia H. [Department of Radiology, Mayo Clinic, Rochester, Minnesota 55905 (United States)

2011-12-15T23:59:59.000Z

34

Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines  

E-Print Network (OSTI)

Recent major improvements to the ALS Sector 5 Macromolecularthe Advanced Light Source (ALS)) was initially conceivedwhich together formed the ALS Macromolecular Crystallography

2008-01-01T23:59:59.000Z

35

JBluIce-EPICS control system for macromolecular crystallography.  

SciTech Connect

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

36

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.

37

A population global optimization algorithm to solve the image alignment problem in electron crystallography  

Science Conference Proceedings (OSTI)

Knowledge of the structure of biological specimens is critical to understanding their function. Electron crystallography is an electron microscopy (EM) approach that derives the 3D structure of specimens at high-resolution, even at atomic detail. Prior ... Keywords: Electron crystallography, Electron microscope tomography, Evolutionary algorithms, Global optimization, Image alignment, Stochastic optimization

P. M. Ortigosa; J. L. Redondo; I. Garca; J. J. Fernndez

2007-04-01T23:59:59.000Z

38

New Paradigm for Macromolecular Crystallography Experiments at SSRL: Automated Crystal Screening And Remote Data Collection  

Science Conference Proceedings (OSTI)

Complete automation of the macromolecular crystallography experiment has been achieved at Stanford Synchrotron Radiation Lightsource (SSRL) through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers' home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallography experimentation.

Soltis, S.M.; Cohen, A.E.; Deacon, A.; Eriksson, T.; Gonzalez, A.; McPhillips, S.; Chui, H.; Dunten, P.; Hollenbeck, M.; Mathews, I.; Miller, M.; Moorhead, P.; Phizackerley, R.P.; Smith, C.; Song, J.; Bedem, H.van dem; Ellis, P.; Kuhn, P.; McPhillips, T.; Sauter, N.; Sharp, K.

2009-05-26T23:59:59.000Z

39

A proposal to search for a monochromatic component of solar axions using $^{57}$Fe  

E-Print Network (OSTI)

A new experimental scheme is proposed to search for almost monochromatic solar axions, whose existence has not been discussed heretofore. The axions would be produced when thermally excited $^{57}$Fe in the sun relaxes to its ground state and could be detected via resonant excitation of the same nuclide in a laboratory. A detailed calculation shows that the rate of the excitation is up to order 10 events/day/kg-$^{57}$Fe. The excitation can be detected efficiently using bolometers or liquid scintillators.

Shigetaka Moriyama

1995-04-18T23:59:59.000Z

40

A proposal to search for a monochromatic component of solar axions using $^{57}$Fe  

E-Print Network (OSTI)

A new experimental scheme is proposed to search for almost monochromatic solar axions, whose existence has not been discussed heretofore. The axions would be produced when thermally excited ^{57}Fe in the sun relaxes to its ground state and could be detected via resonant excitation of the same nuclide in a laboratory. A detailed calculation shows that the rate of the excitation is up to order 10 events/day/kg-^{57}Fe. The excitation can be detected efficiently using bolometers or liquid scintillators.

Moriyama, S

1995-01-01T23:59:59.000Z

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.


41

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

SciTech Connect

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

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

2012-05-04T23:59:59.000Z

42

Dual microchannel plate module for a gated monochromatic x-ray imager  

SciTech Connect

Development and testing of a dual microchannel plate (MCP) module to be used in the national Inertial Confinement Fusion (ICF) program has recently been completed. The MCP module is a key component of a new monochromatic x-ray imaging diagnostic which is designed around a 4 channel Kirkpatrick-Baez microscope and diffraction crystals which is located at University of Rochester`s Omega laser system. The MCP module has two separate MCP regions with centers spaced 53 mm apart. Each region contains a 25 mm MCP proximity focused to a P-11 phosphor coated fiberoptic faceplate. The two L/D = 40, MCPs have a 10.2 mm wide, 8 ohm stripline constructed of 500 nm Copper overcoated with 100 nm Gold. A 4 kV, 150 ps electrical pulse provides an optical gatewidth of 80 ps and spatial resolution has been measured at 20 1p/mm.

Oertel, J.A.; Archuleta, T.; Peterson, C.G. [and others

1996-06-01T23:59:59.000Z

43

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

SciTech Connect

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

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

2011-07-15T23:59:59.000Z

44

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

45

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

SciTech Connect

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

Ham, Kyungmin; Willson, Clinton S. (LSU)

2006-01-31T23:59:59.000Z

46

Refining structures against reflection rank: An alternative metric for electron crystallography.  

E-Print Network (OSTI)

1Refining structures against reflection rank: An alternative metric for electron crystallography. Alexander S. Eggeman and Paul A. Midgley * Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge, CB2 3QZ... it contains a combination of heavy, medium and light atoms and has a sufficiently complex structure to give a wide range of diffraction intensities and a highly non-monotonic variation of intensity with increasing scattering angle. The material occupies...

Eggeman, Alexander; Migley, Paul

47

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

48

Optical Performance of the GM/CA-CAT Canted Undulator Beam lines for Protein Crystallography  

SciTech Connect

A new macromolecular crystallographic facility developed by GM/CA-CAT is operational at the Advanced Photon Source (APS). The facility consists of three beamlines: two lines based on the first 'hard' dual canted undulators and one bending magnet beamline. The ID lines are operational, and the BM line is being commissioned. Both insertion device (ID) beamlines are independently tunable over a wide energy range. The inboard ID lines have been upgraded with a new insertion device to provide enhanced performance for MAD phasing experiments near the selenium and bromine K-edges. The ID line monochromators' crystals are indirectly, cryogenically cooled for improved performance and reliability. Focusing is achieved by long bimorph mirrors in a Kirkpatrick-Baez geometry. This paper describes the design of the beam lines and the optical characterization of the mirrors and monochromators.

Fischetti, Robert F.; Yoder, Derek W.; Xu Shenglan; Stepanov, Sergey; Makarov, Oleg; Benn, Richard; Corcoran, Stephen [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Diete, Wolfgang; Schwoerer-Boehing, Markus; Signorato, Riccardo; Schroeder, Leif [ACCEL Instruments GmbH, Friedrich-Ebert Strasse 1, D-51429 Bergisch Gladbach (Germany); Berman, Lonny [National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973 (United States); Viccaro, P. James [University of Chicago, CARS-CAT, Argonne National Laboratory, Argonne, IL 60439 (United States); Smith, Janet L. [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 (United States)

2007-01-19T23:59:59.000Z

49

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

E-Print Network (OSTI)

extensively on second-generation sources where the largerbrightness on third-generation sources requires slope errorsLight Source is a relatively low-energy, 3 rd generation

2004-01-01T23:59:59.000Z

50

Recent Major Improvements to the ALS Sector 5 MacromolecularCrystallography Beamlines  

Science Conference Proceedings (OSTI)

Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or smaller crystals, and on more rapidly screening larger numbers of candidate crystals; all of these requirements translate directly into a pressing need for increased flux, a tighter beam focus and faster detectors. With these growing demands in mind a major program of beamline and detector upgrades was initiated in 2004 with the goal of dramatically enhancing all aspects of beamline performance. Approximately $3 million in funding from diverse sources including NIH, LBL, the ALS, and the industrial and academic members of the beamline Participating Research Team (PRT), has been employed to develop and install new high performance beamline optics and to purchase the latest generation of CCD detectors. This project, which reached fruition in early 2007, has now fulfilled all of its original goals--boosting the flux on all three beamlines by up to 20-fold--with a commensurate reduction in exposure and data acquisition times for users. The performance of the Sector 5.0 beamlines is now comparable to that of the latest generation ALS superbend beamlines and, in the case of beamline 5.0.2, even surpasses it by a considerable margin. Indeed, the present performance of this beamline is now, once again, comparable to that envisioned for many MX beamlines planned or under construction on newer or higher energy machines.

Morton, Simon A.; Glossinger, James; Smith-Baumann, Alexis; McKean, John P.; Trame, Christine; Dickert, Jeff; Rozales, Anthony; Dauz,Azer; Taylor, John; Zwart, Petrus; Duarte, Robert; Padmore, Howard; McDermott, Gerry; Adams, Paul

2007-07-01T23:59:59.000Z

51

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

E-Print Network (OSTI)

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

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

2008-01-01T23:59:59.000Z

52

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

Science Conference Proceedings (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

53

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

NLE Websites -- All DOE Office Websites (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

54

Proteins  

NLE Websites -- All DOE Office Websites (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.

55

Proteins  

NLE Websites -- All DOE Office Websites (Extended Search)

characteristics. Applications for GFP range from monitoring the expression level of a target protein to performing more effective drug discovery. Engineered (in collaboration...

56

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

E-Print Network (OSTI)

70A prior to transfer to the ALS. The capillary fits snuglyCrystallography of Plutonium Complexes at ALS Beamline11.3.1 (ALS and College of Chemistry Small Molecule

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

2008-01-01T23:59:59.000Z

57

Proton induced quasi-monochromatic x-ray beams for soft x-ray spectroscopy studies and selective x-ray fluorescence analysis  

Science Conference Proceedings (OSTI)

We present the analytical features and performance of an x-ray spectroscopy end station of moderate energy resolution operating with proton-induced quasi-monochromatic x-ray beams. The apparatus was designed, installed and operated at the 5.5 MV Tandem VdG Accelerator Laboratory of the Institute of Nuclear Physics, N.C.S.R. 'Demokritos,' Athens. The setup includes a two-level ultrahigh vacuum chamber that hosts in the lower level up to six primary targets in a rotatable holder; there, the irradiation of pure element materials-used as primary targets-with few-MeV high current ({approx}{mu}A) proton beams produces intense quasi-monochromatic x-ray beams of selectable energy. In the chamber's upper level, a six-position rotatable sample holder hosts the targets considered for x-ray spectroscopy studies. The proton-induced x-ray beam, after proper collimation, is guided to the sample position whereas various filters can be also inserted along the beam's path to eliminate the backscattered protons or/and to absorb selectively components of the x-ray beam. The apparatus incorporates an ultrathin window Si(Li) spectrometer (FWHM 136 eV at 5.89 keV) coupled with low-noise electronics capable of efficiently detecting photons down to carbon K{alpha}. Exemplary soft x-ray spectroscopy studies and results of selective x-ray fluorescence analysis are presented.

Sokaras, D. [Institute of Nuclear Physics, N.C.S.R. Demokritos, Aghia Paraskevi, 15310 Athens (Greece); Zarkadas, Ch. [PANalytical B.V., 7600 AA Almelo (Netherlands); Fliegauf, R.; Beckhoff, B. [Physikalisch-Technische Bundesanstalt, Abbestrasse 2-12, 10587 Berlin (Germany); Karydas, A. G. [Institute of Nuclear Physics, N.C.S.R. Demokritos, Aghia Paraskevi, 15310 Athens (Greece); Nuclear Spectrometry and Applications Laboratory, IAEA Laboratories, A-2444 Seibersdorf (Austria)

2012-12-15T23:59:59.000Z

58

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

59

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

60

Powder Diffraction with Proteins  

Science Conference Proceedings (OSTI)

... Sum up similar scans (typically chi2 statistic, CC also useful) ... TotalCrystallography Large software investment http://fable.sourceforge.net ...

2013-06-07T23:59:59.000Z

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.


61

Materials Science/Crystallography  

Science Conference Proceedings (OSTI)

... R.247 Hydrogen Adsorbed in Mesoporous Carbons Brown, C ... Physical and Chemical Mechanisms Responsible for Carbon Sequestration in Soil ...

2004-08-17T23:59:59.000Z

62

MATERIALS SCIENCE/CRYSTALLOGRAPHY  

Science Conference Proceedings (OSTI)

... Volume Fraction Determination in Ni-Base Superalloys by ... Induced Stress Relaxation Around Welds in Steel ... Properties of Stir-Welded AL-6XN ...

2003-01-07T23:59:59.000Z

63

MATERIALS SCIENCE/CRYSTALLOGRAPHY  

Science Conference Proceedings (OSTI)

... Macromolecular Assemblies of Natural Peptide-Amphiphiles ... Uranium Hydride in Uranium Metal Matrix ... 102 Development of Gas-loading Capability ...

2003-01-07T23:59:59.000Z

64

electronic reprint Crystallography  

E-Print Network (OSTI)

were implemented in a Chemkin-type kinetic mechanism to simulate a high-T (1500 K) pyrolitic the species involved in the pathways. Kinetic simulation results in a high-temperature pyrolysis environment. Thermochim. Acta 1990, 168, 179. (60) Lewis, I. C. Carbon 1982, 20, 519. (61) Dobbins, R. A.; Govatzidakis, G

Vocadlo, Lidunka

65

electronic reprint Crystallography  

E-Print Network (OSTI)

. Yao, K. Gouhara, N. Kato, Thermochim. Acta 88, 143 (1985). 58. G. Dolino, F. Mogeon, P. Bastie, Phys flux measurements at a depth of 8 cm. Conditional sampling (filled octa- gons) was simulated from

Vocadlo, Lidunka

66

Materials Science/Crystallography  

Science Conference Proceedings (OSTI)

... Understanding the ormation of Methane Hydrate F ... J.247 agnetic Excitation Spectrum in Spin ... eutron Vibrational Spectroscopy of Organic Materials ...

2003-11-12T23:59:59.000Z

67

electronic reprint Crystallography  

E-Print Network (OSTI)

software for the singular value decomposition of time-resolved crystallographic data Yi Zhao and Marius(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover and interpretation, numerical analysis and other related sub- jects are also covered. The journal is the primary

Schmidt, Marius

68

TUTORIALS: Software for Crystallography  

Science Conference Proceedings (OSTI)

Jul 8, 2007 ... The software runs in your web browser in the form of Java applets. Currently the site has applets on: Three dimensional visualization of the 14...

69

electronic reprint Crystallography  

E-Print Network (OSTI)

-plate single-crystal silicon sample holders for neutron powder diffraction studies of highly absorbing ­ all rights reserved Flat-plate single-crystal silicon sample holders for neutron powder diffraction 459, Station 18, Chalk River Laboratories, Chalk River, Ontario, Canada K0J 1J0. Correspondence e

Ryan, Dominic

70

Materials Science/Crystallography  

Science Conference Proceedings (OSTI)

... R.441, Alinger, M.441, Wirth, B.183 PV Steel Microstructure Evaluation SANS and SAXS Determination of the Dispersion in Organic Solvents of ...

2003-11-12T23:59:59.000Z

71

Single-crystal Raman spectroscopy and X-ray crystallography at beamline X26-C of the NSLS  

E-Print Network (OSTI)

Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of mystery density, i.e. ambiguous or unknown features within the electron density maps, especially at 2A ? resolutions typical of most macromolecular structures. Beamline X26-C at the

Deborah Stoner-ma; John M. Skinner; Dieter K. Schneider; Matt Cowan; Robert M. Sweet; Allen M. Orville

2010-01-01T23:59:59.000Z

72

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

E-Print Network (OSTI)

The three dimensional structure of a protein is important for its function. When misfolded, a protein may be rendered inactive or adapt a conformation that could be toxic. Studying protein folding requires an understanding of protein conformation. Traditionally, protein conformation has been studied using x-ray crystallography and nuclear magnetic resonance (NMR). X-ray crystallography is limited in the analysis of crystallized proteins and is computationally intensive. NMR deals with proteins in solution but reports only an average of conformation and the technique severely suffers from spectral overlapping due to the thousands of resonances of the protein. More recently, mass spectrometry has been employed not only to elucidate primary structures but also gather information on the three-dimensional conformation of proteins. In this study, a mass spectrometric-based approach is used to study the changes in conformation of cytochrome c and the green fluorescent protein when subjected to aqueous-organic solvent systems. The technique involved trypsin digestion and generation of peptide mass maps. For cytochrome c, the experiments were done with ethanol, methanol and acetonitrile to gain insights on naturation and denaturation. An apparent solvent effect to the rate of digestion and propensity for missed cleavages attributed to weakening of hydrophobic interactions and strengthening of intramolecular hydrogen bonding was observed. For the green fluorescent protein, sulfolane, a known supercharging agent, was used to gain insights on the effect of supercharging to protein conformation. Addition of 2.0% sulfolane shifted the charge state envelope of the protein towards lower m/z while adding lower amounts of sulfolane enhanced lower charge states while broadening the charge state envelope. The time course study showed different patterns of digestion dependent on solvent conditions implying changes in conformation. Furthermore, absorbance and fluorescence measurements suggested that addition of sulfolane protects the fluorophore from quenching. The activity of trypsin is not affected by addition of low amounts of sulfolane.

Tuvilla, Mavreen Rose

2013-05-01T23:59:59.000Z

73

ANIMATION: Crystallography: Gamma Prime - TMS  

Science Conference Proceedings (OSTI)

Feb 9, 2007 ... This 21-second animation demonstrates the crystal structure of gamma prime in nickel based superalloys. SOURCE: Bhadeshia, H. K. D. H....

74

Neutron crystallography aids drug design  

NLE Websites -- All DOE Office Websites (Extended Search)

shatters records in first year of accelerated shipping effort Evolutionary theory, web-search technology combine for DNA analysis Northern New Mexico College Foundation honors...

75

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

76

Diamondoid Monolayers as Monochromatic Electron Source  

NLE Websites -- All DOE Office Websites (Extended Search)

on a large array of nanosized electron emitters can replace current liquid-crystal and plasma technologies. FEDs hold forth the promise of sharper images, wider fields of view,...

77

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

78

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

79

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

80

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

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

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

82

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

83

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (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.

84

The determination of protonation states in proteins  

Science Conference Proceedings (OSTI)

The protonation states of aspartic acids and glutamic acids as well as histidine are investigated in four X-ray cases: Ni,Ca concanavalin A at 0.94 {angstrom}, a thrombin-hirugen binary complex at 1.26 {angstrom} resolution and two thrombin-hirugen-inhibitor ternary complexes at 1.32 and 1.39 {angstrom} resolution. The truncation of the Ni,Ca concanavalin A data at various test resolutions between 0.94 and 1.50 {angstrom} provided a test comparator for the 'unknown' thrombin-hirugen carboxylate bond lengths. The protonation states of aspartic acids and glutamic acids can be determined (on the basis of convincing evidence) even to the modest resolution of 1.20 {angstrom} as exemplified by our X-ray crystal structure refinements of Ni and Mn concanavalin A and also as indicated in the 1.26 {angstrom} structure of thrombin, both of which are reported here. The protonation-state indication of an Asp or a Glu is valid provided that the following criteria are met (in order of importance). (i) The acidic residue must have a single occupancy. (ii) Anisotropic refinement at a minimum diffraction resolution of 1.20 {angstrom} (X-ray data-to-parameter ratio of 3.5:1) is required. (iii) Both of the bond lengths must agree with the expectation (i.e. dictionary values), thus allowing some relaxation of the bond-distance standard uncertainties required to 0.025 {angstrom} for a '3' determination or 0.04 {angstrom} for a '2' determination, although some variation of the expected bond-distance values must be allowed according to the microenvironment of the hydrogen of interest. (iv) Although the F{sub o}-F{sub c} map peaks are most likely to be unreliable at the resolution range around 1.20 {angstrom}, if admitted as evidence the peak at the hydrogen position must be greater than or equal to 2.5 and in the correct geometry. (v) The atomic B factors need to be less than 10 {angstrom}2 for bond-length differentiation; furthermore, the C=O bond can also be expected to be observed with continuous 2F{sub o}-F{sub c} electron density and the C-OH bond with discontinuous electron density provided that the atomic B factors are less than approximately 20 {angstrom}{sup 2} and the contour level is increased. The final decisive option is to carry out more than one experiment, e.g. multiple X-ray crystallography experiments and ideally neutron crystallography. The complementary technique of neutron protein crystallography has provided evidence of the protonation states of histidine and acidic residues in concanavalin A and also the correct orientations of asparagine and glutamine side chains. Again, the truncation of the neutron data at various test resolutions between 2.5 and 3.0 {angstrom}, even 3.25 and 3.75 {angstrom} resolution, examines the limits of the neutron probe. These various studies indicate a widening of the scope of both X-ray and neutron probes in certain circumstances to elucidate the protonation states in proteins.

Ahmed, H.U.; Blakeley, M.P.; Cianci, M.; Cruickshank, D.W. J.; Hubbard, J.A.; Helliwell, J.R. (EMBL); (SCF); (Manchester); (GSK)

2008-09-17T23:59:59.000Z

85

Computational tools for experimental determination and theoretical prediction of protein structure  

SciTech Connect

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

O`Donoghue, S.; Rost, B.

1995-12-31T23:59:59.000Z

86

Protein Structure  

NLE Websites -- All DOE Office Websites (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!

87

Instrumentation upgrades for the Macromolecular Crystallography...  

NLE Websites -- All DOE Office Websites (Extended Search)

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...

88

MATERIALS SCIENCE/CRYSTALLOGRAPHY Bond-Valence ...  

Science Conference Proceedings (OSTI)

... Institut, Germany 85McClellan Nuclear Radiation Center ... of Puerto Ric 243NIST, Occupational Health and Safety Division 244University of ...

2002-03-20T23:59:59.000Z

89

The crystallography of three flavor quark matter  

E-Print Network (OSTI)

The nature of cold three-flavor quark matter at the large (but not asymptotic) densities relevant to neutron star phenomenology is not resolved. The gapless CFL phase, which was previously believed to have the lowest free ...

Sharma, Rishi, Ph. D. Massachusetts Institute of Technology

2007-01-01T23:59:59.000Z

90

Identification of DNA-Binding Proteins and Protein-Protein ...  

Science Conference Proceedings (OSTI)

The regulation may be either activation, stimulation, inhibition or suppression. ... genes is mediated by well-coordinated proteinprotein interactions between...

91

Beamline 5.0.1  

NLE Websites -- All DOE Office Websites (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

92

Beamline 5.0.3  

NLE Websites -- All DOE Office Websites (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

93

Beamline 5.0.2  

NLE Websites -- All DOE Office Websites (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

94

Beamline 5.0.3  

NLE Websites -- All DOE Office Websites (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

95

Beamline 5.0.2  

NLE Websites -- All DOE Office Websites (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

96

Beamline 5.0.3  

NLE Websites -- All DOE Office Websites (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

97

Beamline 5.0.2  

NLE Websites -- All DOE Office Websites (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

98

Beamline 5.0.1  

NLE Websites -- All DOE Office Websites (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

99

Beamline 5.0.2  

NLE Websites -- All DOE Office Websites (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

100

Beamline 5.0.2  

NLE Websites -- All DOE Office Websites (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

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

Beamline 5.0.3  

NLE Websites -- All DOE Office Websites (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

102

Beamline 5.0.2  

NLE Websites -- All DOE Office Websites (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

103

Beamline 5.0.3  

NLE Websites -- All DOE Office Websites (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

104

Beamline 5.0.3  

NLE Websites -- All DOE Office Websites (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

105

Beamline 5.0.1  

NLE Websites -- All DOE Office Websites (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

106

Beamline 5.0.1  

NLE Websites -- All DOE Office Websites (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

107

Beamline 5.0.1  

NLE Websites -- All DOE Office Websites (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

108

Beamline 5.0.1  

NLE Websites -- All DOE Office Websites (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

109

Beamline 5.0.3  

NLE Websites -- All DOE Office Websites (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

110

Structure of the Antiviral Assembly Inhibitor CAP-1 Complex with the HIV-1 CA Protein  

DOE Green Energy (OSTI)

The CA domain of the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein plays critical roles in both the early and late phases of viral replication and is therefore an attractive antiviral target. Compounds with antiviral activity were recently identified that bind to the N-terminal domain of CA (CA{sup N}) and inhibit capsid assembly during viral maturation. We have determined the structure of the complex between CA{sup N} and the antiviral assembly inhibitor N-(3-chloro-4-methylphenyl)-N'-{l_brace}2-[({l_brace}5-[(dimethylamino)-methyl]-2-furyl{r_brace}-methyl)-sulfanyl]ethyl{r_brace}-urea (CAP-1) using a combination of NMR spectroscopy and X-ray crystallography. The protein undergoes a remarkable conformational change upon CAP-1 binding, in which Phe32 is displaced from its buried position in the protein core to open a deep hydrophobic cavity that serves as the ligand binding site. The aromatic ring of CAP-1 inserts into the cavity, with the urea NH groups forming hydrogen bonds with the backbone oxygen of Val59 and the dimethylamonium group interacting with the side-chains of Glu28 and Glu29. Elements that could be exploited to improve binding affinity are apparent in the structure. The displacement of Phe32 by CAP-1 appears to be facilitated by a strained main-chain conformation, which suggests a potential role for a Phe32 conformational switch during normal capsid assembly.

Kelly,B.; Kyere, S.; Kinde, I.; Tang, C.; Howard, B.; Robinson, H.; Sundquist, W.; Summers, M.; Hill, C.

2007-01-01T23:59:59.000Z

111

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites  

E-Print Network (OSTI)

Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97 % of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

Gregory A. Ross; Garrett M. Morris; Philip C. Biggin

2011-01-01T23:59:59.000Z

112

Shotgun protein sequencing.  

Science Conference Proceedings (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

113

Essential proteins discovery from weighted protein interaction networks  

Science Conference Proceedings (OSTI)

Identifying essential proteins is important for understanding the minimal requirements for cellular survival and development. Fast growth in the amount of available protein-protein interactions has produced unprecedented opportunities for detecting protein ... Keywords: centrality, essential protein, protein interaction network

Min Li; Jianxin Wang; Huan Wang; Yi Pan

2010-05-01T23:59:59.000Z

114

Mining from proteinprotein interactions  

Science Conference Proceedings (OSTI)

Proteins are important cellular molecules, and interacting protein pairs provide biologically important information, such as functional relationships. We focus on the problem of predicting physically interacting protein pairs. This is an important problem ... Keywords: Biological Data Mining, Industry Specific Applications, Machine Learning

Hiroshi Mamitsuka

2012-09-01T23:59:59.000Z

115

J. Synchrotron Rad. (1999). 6, 50 A shutterphotodiode combination for UV  

E-Print Network (OSTI)

to shutter the beam. In our work this is to protect radiation-sensitive samples from unnecessary exposure. 50 Laboratory Notes # 1999 International Union of Crystallography Journal of Synchrotron Radiation for monochromatic radiation. Of course, the photodiode must intercept the beam, as our shutter does in its closed

116

Function of proteins  

NLE Websites -- All DOE Office Websites (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.

117

Distinguishing multiple chemotaxis Y protein conformations with laser-polarized 129Xe NMR  

E-Print Network (OSTI)

al. 1998. Crystallography & NMR system: A new software suiteand Pelton, J.G. 2000. NMR Structure of Activated CheY. J.hyperpolarized xenon-129 NMR. J. Am. Chem. Soc. 121: 9370

Lowery, Thomas J.; Doucleff, Michealeen; Ruiz, E. Janette; Rubin, Seth M.; Pines, Alexander; Wemmer, David E.

2005-01-01T23:59:59.000Z

118

Acid Stability of the Hemagglutinin Protein Regulates H5N1 Influenza Virus Pathogenicity  

SciTech Connect

Highly pathogenic avian influenza viruses of the H5N1 subtype continue to threaten agriculture and human health. Here, we use biochemistry and x-ray crystallography to reveal how amino-acid variations in the hemagglutinin (HA) protein contribute to the pathogenicity of H5N1 influenza virus in chickens. HA proteins from highly pathogenic (HP) A/chicken/Hong Kong/YU562/2001 and moderately pathogenic (MP) A/goose/Hong Kong/437-10/1999 isolates of H5N1 were found to be expressed and cleaved in similar amounts, and both proteins had similar receptor-binding properties. However, amino-acid variations at positions 104 and 115 in the vestigial esterase sub-domain of the HA1 receptor-binding domain (RBD) were found to modulate the pH of HA activation such that the HP and MP HA proteins are activated for membrane fusion at pH 5.7 and 5.3, respectively. In general, an increase in H5N1 pathogenicity in chickens was found to correlate with an increase in the pH of HA activation for mutant and chimeric HA proteins in the observed range of pH 5.2 to 6.0. We determined a crystal structure of the MP HA protein at 2.50 {angstrom} resolution and two structures of HP HA at 2.95 and 3.10 {angstrom} resolution. Residues 104 and 115 that modulate the acid stability of the HA protein are situated at the N- and C-termini of the 110-helix in the vestigial esterase sub-domain, which interacts with the B loop of the HA2 stalk domain. Interactions between the 110-helix and the stalk domain appear to be important in regulating HA protein acid stability, which in turn modulates influenza virus replication and pathogenesis. Overall, an optimal activation pH of the HA protein is found to be necessary for high pathogenicity by H5N1 influenza virus in avian species.

DuBois, Rebecca M.; Zaraket, Hassan; Reddivari, Muralidhar; Heath, Richard J.; White, Stephen W.; Russell, Charles J. (Tennessee-HSC); (SJCH)

2012-12-10T23:59:59.000Z

119

Effects of ancillary ligands on selectivity of protein labeling with platinum(II) chloro complexes  

SciTech Connect

Potassium (2,6-pyridinedicarboxylato)chloroplatinate(II) was synthesized. The molecular structure of the complex in (n-Bu){sub 4}N(Pt(dipic)Cl){center dot}0.5H{sub 2}O was determined by x-ray crystallography. The (Pt(dipic)Cl){sup {minus}} is essentially planar and contains a Pt(II) atom, a tridentate dipicolinate dianion ligand, and a unidentate Cl{sup {minus}} ligand. The bis(bidentate) complex trans-(Pt(dipic){sub 2}){sup 2{minus}} was also observed by {sup 1}H NMR. A red gel-like substance was observed when the yellow aqueous solution of K(Pt(dipic)Cl) was cooled or concentrated. The K(Pt(dipic)Cl) molecules form stacks in the solid state and gel-like substance but remain monomeric over a wide range of concentrations and temperatures. The reactivity and selectivity of(Pt(dipic)Cl){sup {minus}} toward cytochromes c from horse and tuna were studied. The new transition-metal reagent is specific for methionine residues. Di(2-pyridyl-{beta}-ethyl)sulfidochloroplatinum(II) chloride dihydrate was also synthesized. This complex labels histidine and methionine residues in cytochrome c. The ancillary ligands in these platinum(II) complexes clearly determine the selectivity of protein labeling. 106 refs., 10 figs., 11 tabs.

Zhou, Xia-Ying.

1990-02-01T23:59:59.000Z

120

Mining and analysing scale-free protein protein interaction network  

Science Conference Proceedings (OSTI)

Protein protein interaction network is essential to understand the fundamental processes that govern cell biology. In this paper, we integrate information extraction and data mining techniques to extract and mine the scale-free protein protein interaction ... Keywords: bioinformatics, biomedical literature, chromatin proteins, clustering, computational biology, data mining, information extraction, information retrieval, protein protein interaction, scale-free network graph

Xiaohua Hu

2005-04-01T23:59:59.000Z

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.


121

Soy Protein Products  

Science Conference Proceedings (OSTI)

This book will provide an overview of the key benefits of soy protein products in an easily understood format. ...

122

Highly thermostable fluorescent proteins  

DOE Patents (OSTI)

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

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

2011-03-22T23:59:59.000Z

123

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

E-Print Network (OSTI)

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

Fernndez Surez, Marta

2008-01-01T23:59:59.000Z

124

DNA's Role with Proteins  

NLE Websites -- All DOE Office Websites (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!

125

Protein from algae  

SciTech Connect

A review considering potential nutrient sources for algal culture, basic requirements for algal production, composition and nutritional value of algae, algae as human food, algal protein for animal feed, and current and future production of microalgae.

Grisanti, N.E.; Oswald, W.J.

1978-01-01T23:59:59.000Z

126

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

SciTech Connect

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

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

2012-04-24T23:59:59.000Z

127

Impact of Synchrotron Radiation on Macromolecular Crystallography: a Personal View  

SciTech Connect

The introduction of synchrotron radiation sources almost four decades ago has led to a revolutionary change in the way that diffraction data from macromolecular crystals are being collected. Here a brief history of the development of methodologies that took advantage of the availability of synchrotron sources are presented, and some personal experiences with the utilization of synchrotrons in the early days are recalled.

Dauter, Z.; Jaskolski, M; Wlodawer, A

2010-01-01T23:59:59.000Z

128

Texture, Crystallography, and Deformation Effects in Titanium Alloys  

Science Conference Proceedings (OSTI)

Oct 9, 2012... and specially textured beta grains that form under certain conditions ... distribution after compression in the alpha + beta phase field in a set...

129

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

130

Conference on New Frontiers in Neutron Macromolecular Crystallography  

NLE Websites -- All DOE Office Websites (Extended Search)

systems being studied by x-ray diffraction. The advent of the Spallation Neutron Source (SNS) with over an order of magnitude increase in neutron flux, in combination with advances...

131

Stanford Synchrotron Radiation Lightsource Extension Application for Macromolecular Crystallography Proposals  

E-Print Network (OSTI)

SSRL Users' Organization Meeting Thursday, January 27, 2011 The Users' Executive Committee (UEC) met in SSRL Building 137, 3rd Floor Conference Room, with several members participating will co-organize the next users' conference and serve as Chair next year. Strategic planning: SSRL

Wechsler, Risa H.

132

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

133

Morphology and Crystallography of Annealing Twins in Austenite  

Science Conference Proceedings (OSTI)

P1-04: 3D Microstructural Characterization of Uranium Oxide as a Surrogate Nuclear ... P1-15: Gating System Optimisation Design Study of a Cast Automobile ... P2-27: Characterization of Carbonate Rocks through X-ray Microtomography.

134

APS User News, Issue 59  

NLE Websites -- All DOE Office Websites (Extended Search)

of protein crystallography and a special executive session with directors of biology CATs on strategic planning for the future of biological research at APS and how the upgrade...

135

Cellulose binding domain proteins  

DOE Patents (OSTI)

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

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

1998-01-01T23:59:59.000Z

136

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

DOE Green Energy (OSTI)

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

Lee, Seok-Yong

2003-04-10T23:59:59.000Z

137

Stabilized polyacrylic saccharide protein conjugates  

DOE Patents (OSTI)

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

Callstrom, Matthew R. (Columbus, OH); Bednarski, Mark D. (Berkeley, CA); Gruber, Patrick R. (St. Paul, MN)

1996-01-01T23:59:59.000Z

138

Stabilized polyacrylic saccharide protein conjugates  

DOE Patents (OSTI)

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

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

1996-02-20T23:59:59.000Z

139

Visualizing the protein sequence universe  

Science Conference Proceedings (OSTI)

Modern biology is experiencing a rapid increase in data volumes that challenges our analytical skills and existing cyberinfrastructure. Exponential expansion of the Protein Sequence Universe (PSU), the protein sequence space, together with the costs ... Keywords: azure, blast, cog, computational bioinformatics, data visualization, data-enabled life sciences, delsa, em, hadoop, hive, mapreduce, mpi, multidimensional scaling, needleman-wunsch, protein annotation, protein sequence universe, psu, sammon, sequence similarity, twister, uniprot, uniref

Larissa Stanberry, Roger Higdon, Winston Haynes, Natali Kolker, William Broomall, Saliya Ekanayake, Adam Hughes, Yang Ruan, Judy Qiu, Eugene Kolker, Geoffrey Fox

2012-06-01T23:59:59.000Z

140

Computational Studies of Protein Folding  

Science Conference Proceedings (OSTI)

The authors describe the state of the art in the field of protein structure prediction. They also introduce Prospector

2001-01-01T23:59:59.000Z

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

NMR Spectroscopy Protein-NMR  

E-Print Network (OSTI)

Keywords NMR Spectroscopy Protein-NMR Physical Organic Chemistry » Prof. Dr. Stefan Berger The research group of Prof. Dr. Stefan Berger focuses its work on: 1. Protein-NMR for the genera- tion of Protein-Structures. This includes application of all mod- ern 3D NMR pulse sequences for fully 15 N and 13

Schüler, Axel

142

A randomized global optimization method for protein-protein docking  

E-Print Network (OSTI)

Apr 10, 2003... set of constants found this way was then consistently used to dock several other complexes obtained from the Brookhaven Protein Database.

143

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

144

High throughput protein production screening  

DOE Patents (OSTI)

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

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

2009-09-08T23:59:59.000Z

145

Molecular Simulations of the Effect of Cholesterol on Membrane-Mediated Protein-Protein Interactions  

E-Print Network (OSTI)

5 Molecular Simulation of the Effect of Cholesterol Protein-Properties . . . . . . . . iii 3 Molecular Simulation StudyProtein-Protein In- 4 Molecular Simulation Study of the

de Meyer, Frdrick Jean-Marie

2010-01-01T23:59:59.000Z

146

Expression of multiple proteins in transgenic plants  

DOE Patents (OSTI)

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

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

2002-01-01T23:59:59.000Z

147

Protein structure classification by structural transformatio  

Science Conference Proceedings (OSTI)

Protein structure classification plays an important role in understanding the relationships among structure and sequence. Recently, as the number of known protein structure are increasing steeply, automatic classification is highly required. This paper ... Keywords: Brookhaven Protein Data Bank, automatic classification, molecular biophysics, primitive operations, protein folds, protein structure classification, secondary structural elements, sequence, structural transformation

T. Ohkawa; D. Namihira; N. Komoda; A. Kidera; H. Nakamura

1996-11-01T23:59:59.000Z

148

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

149

Optimal contact map alignment of proteinprotein interfaces  

E-Print Network (OSTI)

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

Pulim, Vinay

150

Molecular characterization and evolutionary plasticity of protein-protein interfaces  

E-Print Network (OSTI)

.2.1 Protein modelling pipeline . . . . . . . . . . . . . . . . . . 159 5.2.2 Software for predicting the effects of nsSNPs on protein structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 5.2.3 Software for predicting the effects of ns... ) cannot have inter-molecular hydrogen-bonds(B)(scratched environments). . . . . . . . . . . . . 137 4.5 Distribution of ratios of alignment length to mean constituent se- quence length for the original BATON parameter sets (grey) and the latest parameter...

Bickerton, George Richard James

151

The Primary Nonlinear Dynamics of Modal and Nonmodal Perturbations of Monochromatic InertiaGravity Waves  

Science Conference Proceedings (OSTI)

The breaking of an inertiagravity wave (IGW), initiated by its leading normal modes (NMs) or singular vectors (SVs), and the resulting small-scale eddies are investigated by means of direct numerical simulations of a Boussinesq fluid ...

Ulrich Achatz

2007-01-01T23:59:59.000Z

152

The Effects of Wave Energy Converters on a Monochromatic Wave Climate  

E-Print Network (OSTI)

in wave energy converters as a possible means of providing renewable energy, the effects of a wave energy The interest in renewable energies is currently increasing due to the reported rise in global temperature is that of wave energy. The research is multifaceted and includes research on the efficiency of wave energy

Fox-Kemper, Baylor

153

Modal and Nonmodal Perturbations of Monochromatic High-Frequency Gravity Waves: Primary Nonlinear Dynamics  

Science Conference Proceedings (OSTI)

The primary nonlinear dynamics of high-frequency gravity waves (HGWs) perturbed by their most prominent normal modes (NMs) or singular vectors (SVs) in a rotating Boussinesq fluid have been studied by direct numerical simulations (DNSs), with ...

Ulrich Achatz

2007-06-01T23:59:59.000Z

154

Protein and Co-Products Division  

Science Conference Proceedings (OSTI)

Protein and Co-Products division include professionals interested in proteins and co-products from biomaterial for food, feed, and industrial applications as well as extraction, separation, purification, and characterization technologies. Protein and Co-Pr

155

Methods and applications in computational protein design  

E-Print Network (OSTI)

In this thesis, we summarize our work on applications and methods for computational protein design. First, we apply computational protein design to address the problem of degradation in stored proteins. Specifically, we ...

Biddle, Jason Charles

2010-01-01T23:59:59.000Z

156

Soy Protein Products - Electronic Version  

Science Conference Proceedings (OSTI)

Soybeans as Functional Foods and Ingredients is written to serve as a reference for food product developers, food technologists, nutritionists, plant breeders, academic and government professionals... Soy Protein Products - Electronic Version eChapters F

157

Predicting Continuous Epitopes in Proteins  

Science Conference Proceedings (OSTI)

The ability to predict antigenic sites on proteins is crucial for the production of synthetic peptide vaccines and synthetic peptide probes of antibody structure. Large number of amino acid propensity scales based on various properties of the antigenic ...

Reeti Tandon; Sudeshna Adak; Brion Sarachan; William FitzHugh; Jeremy Heil; Vaibhav A. Narayan

2005-08-01T23:59:59.000Z

158

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

159

Protein Flips Lipids Across Membranes  

NLE Websites -- All DOE Office Websites (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.

160

Drosophila huntingtin-interacting protein 14 is a presynaptic protein required for photoreceptor synaptic transmission and expression of the palmitoylated proteins synaptosome-associated protein 25 and cysteine string protein  

E-Print Network (OSTI)

and early death in cysteine string protein mutants ofProtein 25 and Cysteine String Protein R. Steven Stowers andSNAP-25 and cysteine string protein. In non-neuronal cells

Stowers, R Steven; Isacoff, Ehud Y

2007-01-01T23:59:59.000Z

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.


161

LANSCE | Lujan Center | Instruments | PCS  

NLE Websites -- All DOE Office Websites (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 Å 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

162

Decomposition of overlapping protein complexes: A graph ...  

E-Print Network (OSTI)

Apr 26, 2006 ... tion (COD), that given a protein interaction network iden- tifies its ... show that the COD method opens a new avenue for the analysis of protein...

163

Lesquerella fendleri Protein Fractionation and Characterization  

Science Conference Proceedings (OSTI)

tionate plant protein is to separate protein into water-soluble albumin, salt- soluble globulin, ethanol-soluble prolamin, and alkali-soluble glutelin. More basic...

164

Prediction and integration of regulatory and protein-protein interactions  

Science Conference Proceedings (OSTI)

Knowledge of transcriptional regulatory interactions (TRIs) is essential for exploring functional genomics and systems biology in any organism. While several results from genome-wide analysis of transcriptional regulatory networks are available, they are limited to model organisms such as yeast [1] and worm [2]. Beyond these networks, experiments on TRIs study only individual genes and proteins of specific interest. In this chapter, we present a method for the integration of various data sets to predict TRIs for 54 organisms in the Bioverse [3]. We describe how to compile and handle various formats and identifiers of data sets from different sources, and how to predict the TRIs using a homology-based approach, utilizing the compiled data sets. Integrated data sets include experimentally verified TRIs, binding sites of transcription factors, promoter sequences, protein sub-cellular localization, and protein families. Predicted TRIs expand the networks of gene regulation for a large number of organisms. The integration of experimentally verified and predicted TRIs with other known protein-protein interactions (PPIs) gives insight into specific pathways, network motifs, and the topological dynamics of an integrated network with gene expression under different conditions, essential for exploring functional genomics and systems biology.

Wichadakul, Duangdao; McDermott, Jason E.; Samudrala, Ram

2009-04-20T23:59:59.000Z

165

Systematic characterization of protein glycosylation of bacteria cell surface proteins  

NLE Websites -- All DOE Office Websites (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:

166

Protein Flips Lipids Across Membranes  

NLE Websites -- All DOE Office Websites (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.

167

Protein Flips Lipids Across Membranes  

NLE Websites -- All DOE Office Websites (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.

168

SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION  

SciTech Connect

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

JOHN C WALKER

2011-11-01T23:59:59.000Z

169

Recombinant fluorescent protein microsphere calibration standard  

SciTech Connect

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

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

2001-01-01T23:59:59.000Z

170

Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set  

Science Conference Proceedings (OSTI)

Recent techniques increase rapidly the amount of our knowledge on interactions between proteins. The interpretation of these new information depends on our ability to retrieve known substructures in the data, the Protein-Protein Interactions (PPIs) networks. ... Keywords: Graph query, pattern matching, dynamic programming, protein-protein interactions networks.

Guillaume Blin; Florian Sikora; Stephane Vialette

2010-10-01T23:59:59.000Z

171

Inference of protein-protein interactions by using co-evolutionary information  

Science Conference Proceedings (OSTI)

The mirror tree is a method to predict protein-protein interaction by evaluating the similarity between distance matrices of proteins. It is known, however, that predictions by the mirror tree method include many false positives. We suspected that the ... Keywords: co-evolution, partial correlation coefficient, projection operation, protein-protein

Tetsuya Sato; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh

2007-07-01T23:59:59.000Z

172

Cellulose binding domain fusion proteins  

DOE Patents (OSTI)

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

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

1998-01-01T23:59:59.000Z

173

Cellulose binding domain fusion proteins  

DOE Patents (OSTI)

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

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

1998-02-17T23:59:59.000Z

174

First Knot Discovered in Ancient Bacterium Protein  

NLE Websites -- All DOE Office Websites (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

175

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

E-Print Network (OSTI)

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

Chen, Tsan-Chou Scott

2012-01-01T23:59:59.000Z

176

Proteins  

NLE Websites -- All DOE Office Websites (Extended Search)

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...

177

Contributions to the analysis of proteins  

E-Print Network (OSTI)

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

Sharifi Sedeh, Reza

2011-01-01T23:59:59.000Z

178

PERSPECTIVE Directed Evolution of Novel Protein Functions  

E-Print Network (OSTI)

PERSPECTIVE Directed Evolution of Novel Protein Functions Huimin Zhao1,2 1 Department of Chemical.interscience.wiley.com). DOI 10.1002/bit.21455 ABSTRACT: Directed evolution has been successfully used to engineer proteins for basic and applied biological research. However, engineering of novel protein functions by directed

Zhao, Huimin

179

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.

Clemons, Gisela K. (Berkeley, CA)

1997-01-01T23:59:59.000Z

180

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, Philip D.; Wander, Marc J.

2012-09-11T23:59:59.000Z

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

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

182

Active Sites by Computational Protein Design  

Science Conference Proceedings (OSTI)

We have developed an automated method to design active sites into protein scaffolds using computational protein design techniques. We search through the amino acid sequence and conformation spaces by optimising protein stability and ligand binding. We use an all?atom force field

Pablo Tortosa; Alfonso Jaramillo

2006-01-01T23:59:59.000Z

183

Binding of Proteins to Copolymers of Varying  

E-Print Network (OSTI)

based on the free energy of transfer of hydro- carbons from aqueous solution to apolar solvent), hydro- phobic interactions between protein and stationary phase polymer are central to the protein of concrete evidence. However, in some cases, hydro- phobic contribution to protein­polymer interactions may

Dubin, Paul D.

184

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

185

Detecting Protein-Protein Interaction Decoys using Fast Free Energy Calculations  

E-Print Network (OSTI)

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

186

Essential Latent Knowledge for Protein-Protein Interactions: Analysis by an Unsupervised Learning Approach  

Science Conference Proceedings (OSTI)

Protein-protein interactions play a number of central roles in many cellular functions, including DNA replication, transcription and translation, signal transduction, and metabolic pathways. A recent increase in the number of protein-protein interactions ... Keywords: Biology and genetics, machine learning, data mining, mining methods and algorithms.

Hiroshi Mamitsuka

2005-04-01T23:59:59.000Z

187

Tubulin and microtubule associated proteins  

SciTech Connect

Active oxygen species including superoxide radicals, hydrogen peroxide and hydroxyl radicals are continuously being produced during respiration in cells, as well as during ionizing radiation or metabolism of various chemicals. Since these species are unstable and highly reactive, they are assumed to affect various biological phenomena such as mutation, cancer and aging. This book reviews the protection mechanisms that respiring organisms have evolved against these active oxygen species and the associated new genes mvrA and mvrB. This book presents a discussion of tubulin and microtubule associated proteins.

Foster, K.E. (Univ. of Kent (GB))

1989-01-01T23:59:59.000Z

188

The Plexus Model for the Inference of Ancestral Multidomain Proteins  

Science Conference Proceedings (OSTI)

Interactions of protein domains control essential cellular processes. Thus, inferring the evolutionary histories of multidomain proteins in the context of their families can provide rewarding insights into protein function. However, methods to infer ... Keywords: Proteins, domains, plexus, graphs, phylogeny.

John Wiedenhoeft; Roland Krause; Oliver Eulenstein

2011-07-01T23:59:59.000Z

189

Bacteria Modified to Secrete Biologically Active Protein for ...  

Manufacturing proteins for bioenergy production, therapeutic biologics and research tools; Rapid, high throughput production of proteins on a commercial scale ;

190

Expression of Stable Isotopically Labeled Proteins for Use as ...  

Science Conference Proceedings (OSTI)

Expression of Stable Isotopically Labeled Proteins for Use as Internal Standards for Mass Spectrometric Quantitation of Clinical Protein Biomarkers. ...

2013-03-13T23:59:59.000Z

191

Year 2 Report: Protein Function Prediction Platform  

SciTech Connect

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

192

DIP: The Database of Interacting Proteins  

DOE Data Explorer (OSTI)

The DIP Database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. By interaction, the DIP Database creators mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organisation and complexity of the protein interaction network at the cellular level. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. It is a relational database that can be searched by protein, sequence, motif, article information, and pathBLAST. The website also serves as an access point to a number of projects related to DIP, such as LiveDIP, The Database of Ligand-Receptor Partners (DLRP) and JDIP. Users have free and open access to DIP after login. [Taken from the DIP Guide and the DIP website] (Specialized Interface) (Registration Required)

International Molecular Interaction Exchange (IMEx) Consortium

193

Computational Method for Detecting and Enhancing Protein ...  

Technology Marketing Summary ORNL researchers have developed a method that uses simulation and experimental data to detect, analyze, and manipulate protein activity.

194

Statistical Mechanics Model for Protein Folding  

E-Print Network (OSTI)

We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition function of a protein obeying two-stage-like folding kinetics. Using the statistical mechanics model of solvation of hydrophobic hydrocarbons we obtain the partition function of infinitely diluted solution of proteins in water environment. The calculated dependencies of the protein heat capacities upon temperature are compared with the corresponding results of experimental measurements for staphylococcal nuclease and metmyoglobin.

Yakubovich, A V; Greiner, W

2010-01-01T23:59:59.000Z

195

Fast Dynamics in Stabilization of Proteins  

Science Conference Proceedings (OSTI)

Proteins can be effective agents for catalysis and biochemical signaling, but to provide an appreciable shelf life, as needed in fields like ...

196

Understanding Protein Solution Phase Behavior via Coarse ...  

Science Conference Proceedings (OSTI)

... folding problem: the intrinsic free energy of folding ... a general framework for modeling proteins in ... Our general approach builds upon the predictions ...

2013-02-14T23:59:59.000Z

197

Synthesizing Membrane Proteins Using In Vitro Methodology ...  

Scientists at Argonne National Laboratory have created an in vitro , cell-free system and method for producing several types of protein: membrane ...

198

Incorporating multiple genomic features with the utilization of interacting domain patterns to improve the prediction of protein-protein interactions  

Science Conference Proceedings (OSTI)

Protein-protein interaction (PPI) networks play an outstanding role in the organization of life. Parallel to the growth of experimental techniques on determining PPIs, the emergence of computational methods has greatly accelerated the time needed for ... Keywords: Gene ontology annotation, Genomic features, Interacting domain patterns, Protein-protein interaction-filter, Protein-protein interactions prediction

Rosfuzah Roslan; Razib M. Othman; Zuraini A. Shah; Shahreen Kasim; Hishammuddin Asmuni; Jumail Taliba; Rohayanti Hassan; Zalmiyah Zakaria

2010-10-01T23:59:59.000Z

199

Soy Protein ProductsChapter 3 Protein Quality and Human Nutrition  

Science Conference Proceedings (OSTI)

Soy Protein Products Chapter 3 Protein Quality and Human Nutrition Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry EB488804B9D11995A2463507F5B3CE67 AOCS Press Downloadable pdf of Ch

200

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

E-Print Network (OSTI)

Magnaporthe grisea is a notorious pathogenic fungus that causes rice blast disease worldwide. Proteins secreted by the fungus are likely candidates for being effectors that are potentially recognized by determinants of resistance or susceptibility in host plants. However, knowledge of the role of secreted proteins of M. grisea is still limited. In this study, I identified 29 proteins that were secreted into culture filtrates from M. grisea strains expressing candidate proteins. I confirmed secretion of these proteins and tested them for elicitor activity on plants. Among them, I studied two groups: cell wall degrading enzymes (CWDEs) and small cysteine-rich proteins. Cysteine-rich proteins have been shown in other systems to function as elicitors. Initially, I expressed and purified proteins in M. grisea to obtain proteins by a homologous expression system. Although this was effective for a number of proteins, the need for greater amounts of protein led me to express several proteins in the Pichia pastoris system. Several candidate proteins were purified and found to induce symptoms on rice and maize. Hypothetical proteins MG10424.4 and MG09998.4 were both found to have elicitor activity. Lipase MG07016.4 did not induce response of plants and we concluded that the lipase activity of MG07016.4 does not function as an elicitor. I also purified a small cysteine-rich protein, which belongs to the group of cluster 180 proteins in M. grisea, MG10732.4 from P. pastoris. It is able to cause yellowing symptoms and hydrogen peroxide production in plants and it might contain elicitor activity.

Shang, Yue

2003-05-01T23:59:59.000Z

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

Identifying the nature of the interface in protein-protein complexes  

Science Conference Proceedings (OSTI)

The role of molecular recognition is critical to the proper self-assembly of biological macromolecules and their function. Shape complementarity of the mutual recognition interfaces is one of the important factors that guide this interaction. The lock-and-key ... Keywords: data mining, nature of protein interfaces, protein-protein complex

Pralay Mitra

2010-02-01T23:59:59.000Z

202

Coupling between motor proteins determines dynamic behaviors of motor protein assemblies  

E-Print Network (OSTI)

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

203

Mechanisms ?of? change ?in ?protein ?architecture  

E-Print Network (OSTI)

of query sequence not present in the protein family and delete states allow for deletions of conserved residues in the protein family from the query sequence. The transition to the J state allows for multiple hits of the model to a single query sequence...

Buljan, Marija

2011-01-11T23:59:59.000Z

204

Bayesian Nonparametric Methods for Protein Structure Prediction  

E-Print Network (OSTI)

The protein structure prediction problem consists of determining a proteins three-dimensional structure from the underlying sequence of amino acids. A standard approach for predicting such structures is to conduct a stochastic search of conformation space in an attempt to find a conformation that optimizes a scoring function. For one subclass of prediction protocols, called template-based modeling, a new protein is suspected to be structurally similar to other proteins with known structure. The solved related proteins may be used to guide the search of protein structure space. There are many potential applications for statistics in this area, ranging from the development of structure scores to improving search algorithms. This dissertation focuses on strategies for improving structure predictions by incorporating information about closely related template protein structures into searches of protein conformation space. This is accomplished by generating density estimates on conformation space via various simplifications of structure models. By concentrating a search for good structure conformations in areas that are inhabited by similar proteins, we improve the efficiency of our search and increase the chances of finding a low-energy structure. In the course of addressing this structural biology problem, we present a number of advances to the field of Bayesian nonparametric density estimation. We first develop a method for density estimation with bivariate angular data that has applications to characterizing protein backbone conformation space. We then extend this model to account for multiple angle pairs, thereby addressing the problem of modeling protein regions instead of single sequence positions. In the course of this analysis we incorporate an informative prior into our nonparametric density estimate and find that this significantly improves performance for protein loop prediction. The final piece of our structure prediction strategy is to connect side-chain locations to our torsion angle representation of the protein backbone. We accomplish this by using a Bayesian nonparametric model for dependence that can link together two or more multivariate marginals distributions. In addition to its application for our angular-linear data distribution, this dependence model can serve as an alternative to nonparametric copula methods.

Lennox, Kristin Patricia

2010-08-01T23:59:59.000Z

205

Dynamic Phase Transitions in Coupled Motor Proteins  

E-Print Network (OSTI)

The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that there are two dynamic regimes, depending on the interaction between the particles. For strong interactions the motor proteins move as one tight cluster, while for weak interactions there is no correlation in the motion of the proteins, and the particle separation increases steadily with time. The boundary between two dynamic phases is specified by a critical interaction that has a non-zero value only for the coupling of the asymmetric motor proteins, and it depends on the temperature and the transitions rates. At the critical interaction there is a change in a slope for the mean velocities and a discontinuity in the dispersions of the motor proteins as a function of the interaction energy.

Evgeny B. Stukalin; Anatoly B. Kolomeisky

2005-09-16T23:59:59.000Z

206

Antimicrobial protein protects grapevines from pathogen  

NLE Websites -- All DOE Office Websites (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

207

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

208

Research Article: Bacterial protein structures reveal phylum dependent divergence  

Science Conference Proceedings (OSTI)

Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series ... Keywords: ?FSS, ?SeqID, COG, Evolution, FSS, Function, PDB, Proteins, Sequence, Split, Split+1, Starburst, Structure, ZAA and ZBB, ZAB

Matthew D. Shortridge; Thomas Triplet; Peter Revesz; Mark A. Griep; Robert Powers

2011-02-01T23:59:59.000Z

209

Protein Structure Suggests Role as Molecular Adapter  

NLE Websites -- All DOE Office Websites (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.

210

On the optimal contact potential of proteins  

E-Print Network (OSTI)

We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition for the native structure achieving the lower bound leads to the contact energy matrix that is a scalar multiple of the native contact matrix, i.e., the so-called Go potential. We also derive spectral relations between contact matrix and energy matrix, and approximations related to one-dimensional protein structures. Implications for protein structure prediction are discussed.

Kinjo, Akira R

2008-01-01T23:59:59.000Z

211

Toby of XSD to Chair U.S. National Committee for Crystallography  

NLE Websites -- All DOE Office Websites (Extended Search)

letter from Richard E. Bissell, Executive Director of Policy and Global Affairs for the National Academies, notes that the USNCCr "promotes the advancement of the...

212

Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography  

E-Print Network (OSTI)

in Blu-Ice. Figure 7: SSRL Web-Ice interface displaying theTable 1: Programs used by Web-Ice for data analysis. ProgramWeb-Ice: Integrated Data Collection and Analysis for

Gonzalez, Ana

2008-01-01T23:59:59.000Z

213

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

SciTech Connect

In this paper we discuss the pivotal role played by Sir John Pendry in the development of Low Energy Electron Diffraction (LEED) during the past three decades; the earliest understanding on the physics of LEED to the development of sophisticated methods for the structural solution of complex surfaces.

Somorjai, Gabor A.; Rous, P.J.

2007-10-15T23:59:59.000Z

214

Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography  

E-Print Network (OSTI)

results. A summary list is also available in Blu-Ice.Figure 7: SSRL Web-Ice interface displaying the summarizedTable 1: Programs used by Web-Ice for data analysis. Program

Gonzalez, Ana

2008-01-01T23:59:59.000Z

215

Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography  

E-Print Network (OSTI)

in Blu-Ice. Figure 7: SSRL Web-Ice interface displaying theRadiation Laboratory (SSRL), and subsequently adapted forsystems Blu-Ice / DCSS at SSRL (McPhillips et al. , 2002)

Gonzalez, Ana

2008-01-01T23:59:59.000Z

216

Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines  

E-Print Network (OSTI)

Source is a national user facility operated by Lawrencecontrol environment for users. This facility was immediatelyto our users. Detectors and endstation facilities The

2008-01-01T23:59:59.000Z

217

Real-Time Observation of Cuprates Structural Dynamics by Ultrafast Electron Crystallography  

E-Print Network (OSTI)

The phonon-mediated attractive interaction between carriers leads to the Cooper pair formation in conventional superconductors. Despite decades of research, the glue holding Cooper pairs in high-temperature superconducting ...

Carbone, F.

218

Pocket protein family function in mesenchymal tissue development and tumorigenesis  

E-Print Network (OSTI)

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

Landman, Allison Simone

2009-01-01T23:59:59.000Z

219

Protein structure alignment using elastic shape analysis  

Science Conference Proceedings (OSTI)

In this paper we present a method for flexible protein structure alignment based on elastic shape analysis of backbones, in a manner that can incorporate different characteristics of the backbones. In particular, it can include the backbone geometry, ...

Wei Liu; Anuj Srivastava; Jinfeng Zhang

2010-08-01T23:59:59.000Z

220

Purification of recombinant proteins with magnetic nanoclusters  

E-Print Network (OSTI)

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

Ditsch, Andre (Andre Paul)

2005-01-01T23:59:59.000Z

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.


221

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

222

Protein Structure Suggests Role as Molecular Adapter  

NLE Websites -- All DOE Office Websites (Extended Search)

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...

223

Inferring evolutionary scenarios for protein domain compositions  

Science Conference Proceedings (OSTI)

Essential cellular processes are controlled by functional interactions of protein domains, which can be inferred from their evolutionary histories. Methods to reconstruct these histories are challenged by the complexity of reconstructing macroevolutionary ...

John Wiedenhoeft; Roland Krause; Oliver Eulenstein

2010-05-01T23:59:59.000Z

224

Green fluorescent protein as a mechanical sensor  

E-Print Network (OSTI)

Inquiry into intracellular and cytoskeletal mechanics requires an intracellular mechanical sensor to verify models of sub-cellular structure dynamics. To this end, the green fluorescent protein (GFP) is considered as a ...

Muso, Taro M. (Taro Michael)

2007-01-01T23:59:59.000Z

225

Computer Simulations of Protein Dynamics and Thermodynamics  

Science Conference Proceedings (OSTI)

The computational challenges of producing realistic biomedical simulations are reviewed. Techniques for applying classical mechanics simulation methods to proteins and ways to solve Newton's equations are discussed. Two recent applications of these methods ...

David Case

1993-10-01T23:59:59.000Z

226

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

227

IAPSAP, International Association for Protein Structure Analysis  

NLE Websites -- All DOE Office Websites (Extended Search)

19th Methods in Protein Structure Analysis Meeting June 25-28, 2012 Ottawa, Ontario, Canada Held in conjunction with the China Canada Systems Biology Symposium The goal of this...

228

Exo-endo cellulase fusion protein  

DOE Patents (OSTI)

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

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

2012-01-17T23:59:59.000Z

229

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

230

Genetic noise control via protein oligomerization  

Science Conference Proceedings (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

231

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

E-Print Network (OSTI)

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

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

2010-01-01T23:59:59.000Z

232

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

NLE Websites -- All DOE Office Websites (Extended Search)

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

233

The Molecular Structure of a Key Viral Protein  

NLE Websites -- All DOE Office Websites (Extended Search)

have determined the molecular structure of a viral protein, the parainfluenza virus 5 fusion (F) protein. The parainfluenza virus 5 is part of a family of viruses...

234

Free energy functions in protein structural stability and folding kinetics.  

E-Print Network (OSTI)

??The accuracy of the theoretical description of protein folding and protein interactions is directly related to the accuracy of free energy functions developed for describing (more)

Morozov, Alexandre V., 1973-

2009-01-01T23:59:59.000Z

235

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

236

New Crystal Structures Lift Fog around Protein Folding  

NLE Websites -- All DOE Office Websites (Extended Search)

Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular...

237

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

NLE Websites -- All DOE Office Websites (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...

238

Genetic Incorporation of Noncanonical Amino Acids into Proteins for Protein Function Investigation  

E-Print Network (OSTI)

With the objective to functionalize proteins for the understanding of their biological roles and developing protein-based biosensors, I have been developing methods to synthesize proteins with defined modifications and applying them to study protein functional roles and generate proteins with new properties. These methods rely on the read-through of an in-frame stop codon in mRNA by a nonsense suppressor tRNA specifically acylated with a noncanoncial amino acid (NAA) by a unique aminoacyl-tRNA synthetase and the genetic incorporation of this NAA at the stop codon site. NAAs either provide chemical handles for site-specific manipulation or mimic the posttranslational modifications, which are critical for understanding cellular regulations and signal transduction. The pyrrolysine synthetase (PylRS) has been wildly used to incorporate NAAs into proteins in E. coli. Taking advantage of PylRS, I have developed method to genetically incorporate ketone-containing N-?-acetyl-L-lysine analog, 2-amino-8-oxononanoic acid (KetoK), into proteins for their site-specific modifications and used it to mimic the protein lysine acetylation process. I have also modified the ribosome in order to improve the amber suppression efficiency and therefore to achieve incorporation of multiple copies of NAA into one protein. By overexpressing a truncated ribosomal protein, L11C, I have demonstrated 5-fold increase of amber suppression level in E. coli, leading to higher expression levels for proteins incorporated with NAAs. I have also demonstrated this method can be applied successfully to incorporate at least 3 NAAs into one protein in E. coli. With the success of incorporating multiple NAAs into one protein, I have further introduced two distinct NAAs into one protein simultaneously. This is done by using a wild type or evolved PylRS-pylTUUA pair and an evolved M. jannaschii tyrosyl-tRNA synthetase (MjTyrRS)-tRNACUA pair. By suppressing both UAG and UAA stop codons in one mRNA, a protein incorporated with two NAAs is synthesized with a decent yield. There is of great interest to incorporate new NAAs into proteins, which is done by library selection. By introducing both positive and negative selective markers into one plasmid, I have developed a one-plasmid selection method. In this method, the positive and negative selections are accomplished by in a single type of cells hosting a single selection plasmid.

Huang, Ying

2012-05-01T23:59:59.000Z

239

Statistical Thermodynamics of Membrane Bending-Mediated ProteinProtein Attractions  

E-Print Network (OSTI)

ABSTRACT Highly wedge-shaped integral membrane proteins, or membrane-adsorbed proteins can induce long-ranged deformations. The strain in the surrounding bilayer creates relatively long-ranged forces that contribute to interactions with nearby proteins. In contrast, to direct short-ranged interactions such as van der Waals, hydrophobic, or electrostatic interactions, both local membrane Gaussian curvature and protein ellipticity can induce forces acting at distances of up to a few times their typical radii. These forces can be attractive or repulsive, depending on the proteins shape, height, contact angle with the bilayer, and a pre-existing local membrane curvature. Although interaction energies are not pairwise additive, for sufficiently low protein density, thermodynamic properties depend only upon pair interactions. Here, we compute pair interaction potentials and entropic contributions to the two-dimensional osmotic pressure of a collection of noncircular proteins. For flat membranes, bending rigidities of ?100k BT, moderate ellipticities, and large contact angle proteins, we find thermally averaged attractive interactions of order k BT. These interactions may play an important role in the intermediate stages of protein aggregation. Numerous biological processes where membrane bending-mediated interactions may be relevant are cited, and possible experiments are discussed.

Tom Chou; Ken S. Kim; George Oster

2001-01-01T23:59:59.000Z

240

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

SciTech Connect

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

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

A Novel Shape Complementarity Scoring Function for Protein-Protein Docking  

E-Print Network (OSTI)

been a wealth of research on protein-protein docking, described in several reviews.13­19 Predictive: Zhiping Weng, Dept. of Biomedical Engineer- ing, Boston University, 44 Cummington Street, Boston, MA 02215 are composed of the same number of receptor atoms (top; dark disks) and ligand atoms (bottom; light disks

Weng, Zhiping

242

Modeling sequence and function similarity between proteins for protein functional annotation  

Science Conference Proceedings (OSTI)

A common task in biological research is to predict function for proteins by comparing sequences between proteins of known and unknown function. This is often done using pair-wise sequence alignment algorithms (e.g. BLAST). A problem with this approach ... Keywords: bioinformatics, biostatistics, multiple sequence alignment

Roger Higdon; Brenton Louie; Eugene Kolker

2010-06-01T23:59:59.000Z

243

Detecting disease genes based on semi-supervised learning and protein-protein interaction networks  

Science Conference Proceedings (OSTI)

Objective: Predicting or prioritizing the human genes that cause disease, or ''disease genes'', is one of the emerging tasks in biomedicine informatics. Research on network-based approach to this problem is carried out upon the key assumption of ''the ... Keywords: Disease gene neighbours, Disease-causing gene prediction, Multiple data resources integration, Protein-protein interaction network, Semi-supervised learning

Thanh-Phuong Nguyen; Tu-Bao Ho

2012-01-01T23:59:59.000Z

244

An analysis pipeline for the inferenceof protein-protein interaction networks  

Science Conference Proceedings (OSTI)

We present an integrated platform that is used for the reconstruction and analysis of protein-protein interaction networks inferred from Mass Spectrometry (MS) bait-prey experiment data. At the heart of this pipeline is the Software Environment for Biological Network Inference (SEBINI), an interactive environment for the deployment and testing of network inference algorithms that use high-throughput data. 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. For integration, comparison and analysis of the inferred protein-protein interactions with interaction evidence obtained from multiple public sources, the pipeline connects to the Collective Analysis of Biological Interaction Networks (CABIN) software. Incorporating BEPro3 into SEBINI and automatically feeding the resulting inferred network into CABIN, we have created a structured workflow for protein-protein network inference and supplemental analysis from sets of MS bait-prey experiments.

Taylor, Ronald C. [Pacific Northwest National Laboratory (PNNL); Singhal, Mudita [Pacific Northwest National Laboratory (PNNL); Daly, Don S. [Pacific Northwest National Laboratory (PNNL); Gilmore, Jason [Pacific Northwest National Laboratory (PNNL); Cannon, Bill [Pacific Northwest National Laboratory (PNNL); Domico, Kelly [Pacific Northwest National Laboratory (PNNL); White, Amanda M. [Pacific Northwest National Laboratory (PNNL); Auberry, Deanna L [ORNL; Auberry, Kenneth J [ORNL; Hooker, Brian [Pacific Northwest National Laboratory (PNNL); Hurst, Gregory {Greg} B [ORNL; McDermott, Jason [Pacific Northwest National Laboratory (PNNL); McDonald, W Hayes [ORNL; Pelletier, Dale A [ORNL; Schmoyer, Denise D [ORNL; Wiley, Steven [Pacific Northwest National Laboratory (PNNL)

2009-09-01T23:59:59.000Z

245

Annual Meeting 2010 Hot Topic on High-Protein Diets  

Science Conference Proceedings (OSTI)

High-Protein Diets and Weight Management Organizer: Nicolas Deak, Solae LLC, USA; and Charles Schasteen, Solae LLC, USA. State-of-the-art research will show proteins key role in weight management, the satiety in high-protein diets, mechanism(s) o

246

Protein and Co-Products Division Newsletter 10/12  

Science Conference Proceedings (OSTI)

Read the November newsletter from the Protein and Co-Products Division. Protein and Co-Products Division Newsletter 10/12 Protein and Co-Products Division biomaterial division divisions membership physiochemistry Protein and Co-Products Division Waste ma

247

NIST Quantifies Low Levels of 'Heart Attack Risk' Protein  

Science Conference Proceedings (OSTI)

NIST Quantifies Low Levels of 'Heart Attack Risk' Protein. For Immediate Release: November 3, 2009. ...

2012-10-02T23:59:59.000Z

248

ET Kinetics of Bifunctional Redox Protein Maquettes  

NLE Websites -- All DOE Office Websites (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

249

Robust expression of a bioactive mammalian protein in chlamydomonas chloroplast  

DOE Patents (OSTI)

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

Mayfield, Stephen P. (Cardiff, CA)

2010-03-16T23:59:59.000Z

250

Protein Synthesis Initiation Factors: Phosphorylation and Regulation  

SciTech Connect

The initiation of the synthesis of proteins is a fundamental process shared by all living organisms. Each organism has both shared and unique mechanisms for regulation of this vital process. Higher plants provide for a major amount of fixation of carbon from the environment and turn this carbon into food and fuel sources for our use. However, we have very little understanding of how plants regulate the synthesis of the proteins necessary for these metabolic processes. The research carried out during the grant period sought to address some of these unknowns in the regulation of protein synthesis initiation. Our first goal was to determine if phosphorylation plays a significant role in plant initiation of protein synthesis. The role of phosphorylation, although well documented in mammalian protein synthesis regulation, is not well studied in plants. We showed that several of the factors necessary for the initiation of protein synthesis were targets of plant casein kinase and showed differential phosphorylation by the plant specific isoforms of this kinase. In addition, we identified and confirmed the phosphorylation sites in five of the plant initiation factors. Further, we showed that phosphorylation of one of these factors, eIF5, affected the ability of the factor to participate in the initiation process. Our second goal was to develop a method to make initiation factor 3 (eIF3) using recombinant methods. To date, we successfully cloned and expressed 13/13 subunits of wheat eIF3 in E. coli using de novo gene construction methods. The final step in this process is to place the subunits into three different plasmid operons for co-expression. Successful completion of expression of eIF3 will be an invaluable tool to the plant translation community.

Karen S. Browning

2009-06-15T23:59:59.000Z

251

Structural determination of intact proteins using mass spectrometry  

DOE Patents (OSTI)

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

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

2008-05-06T23:59:59.000Z

252

Compositions and methods for improved protein production  

DOE Patents (OSTI)

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

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

2012-07-10T23:59:59.000Z

253

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

254

Facilitated diffusion of proteins on chromatin  

E-Print Network (OSTI)

We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor, and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.

O. Benichou; C. Chevalier; B. Meyer; R. Voituriez

2010-06-24T23:59:59.000Z

255

BioPPISVMExtractor: A protein-protein interaction extractor for biomedical literature using SVM and rich feature sets  

Science Conference Proceedings (OSTI)

Protein-protein interactions play a key role in various aspects of the structural and functional organization of the cell. Knowledge about them unveils the molecular mechanisms of biological processes. However, the amount of biomedical literature regarding ... Keywords: Conditional random fields, Information extraction, Protein-protein interaction, Support vector machines, Text mining

Zhihao Yang; Hongfei Lin; Yanpeng Li

2010-02-01T23:59:59.000Z

256

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

E-Print Network (OSTI)

The aim of this study is to further our understanding of the forces that contribute to protein stability and to investigate how site-directed mutagenesis might be used for increasing protein stability. Eleven proteins ranging from 36 to 370 residues have been studied here. A 36-residue VHP and a 337-residue VlsE were used as model systems for studying the contribution of the hydrophobic effect on protein stability. Mutations were made in both proteins which replaced bulky hydrophobic side chains with smaller ones. All variants were less stable than their wild-type proteins. For VHP, the destabilizing effects of mutations were smaller when compared with similar mutations reported in the literature. For VlsE, a similarity was observed. This different behavior was investigated and reconciled by the difference in hydrophobicity and cavity modeling for both proteins. Therefore, the stabilizing mechanism of the hydrophobic effect appears to be similar for both proteins. Eight proteins were used as model systems for studying the effects of mutating non-proline and non-glycine residues to statistically favored proline and glycine residues in ?-turns. The results suggest that proline mutations generally increase protein stability, provided that the replaced residues are solvent exposed. The glycine mutations, however, only have a stabilizing effect when the wild-type residues have ?, ? angles in the L? region of Ramachandran plot. Nevertheless, this strategy still proves to be a simple and efficient way for increasing protein stability. Finally, using a combination of eight previously identified stabilizing mutations; we successfully designed two RNase Sa variants (7S, 8S) that have both much higher Tms and conformational stabilities than wild-type protein over the entire pH range studied. Further studies of the heat capacity change upon unfolding (?Cps) for both proteins and their variants suggest that residual structure may exist in the denatured state of the 8S variant. An analysis of stability curves for both variants suggests that they achieve their stabilization through different mechanisms, partly attributed to the different role of their denatured states. The 7S variants may have a more rigid denatured state and the 8S variant may have a compact denatured state in comparison with that of wild-type RNase Sa.

Fu, Hailong

2009-05-01T23:59:59.000Z

257

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

E-Print Network (OSTI)

??From opportunistic protist Cryptosporidium parvum we identified and functionally assayed a fatty acyl-CoA-binding protein (ACBP) gene. The CpACBP1 gene encodes a protein of 268 aa (more)

Zeng, Bin

2009-01-01T23:59:59.000Z

258

Modeling the flexibility of alpha helices in protein interfaces : structure based design and prediction of helix-mediated protein-protein interactions  

E-Print Network (OSTI)

Protein-protein interactions play an essential role in many biological functions. Prediction and design of these interactions using computational methods requires models that can be used to efficiently sample structural ...

Apgar, James R. (James Reasoner)

2008-01-01T23:59:59.000Z

259

Performance characteristics needed for protein crystal diffraction x-ray detectors.  

Science Conference Proceedings (OSTI)

During the 1990's, macromolecular crystallography became progressively more dependent on synchrotrons X-ray sources for diffraction data collection. Detectors of this diffraction data at synchrotrons beamlines have evolved over the decade, from film to image phosphor plates, and then to CCD systems. These changes have been driven by the data quality and quantity improvements each newer detector technology provided. The improvements have been significant. It is likely that newer detector technologies will be adopted at synchrotron beamlines for crystallographic diffraction data collection in the future, but these technologies will have to compete with existing CCD detector systems which are already excellent and are getting incrementally better in terms of size, speed, efficiency, and resolving power. Detector development for this application at synchrotrons must concentrate on making systems which are bigger and faster than CCDs and which can capture weak data more efficiently. And there is a need for excellent detectors which are less expensive than CCD systems.

Westbrook, E. M.

1999-09-21T23:59:59.000Z

260

Extracellular Proteins Promote Zinc Sulfide Aggregation  

NLE Websites -- All DOE Office Websites (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.

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

Protein and Co-Products Division List  

Science Conference Proceedings (OSTI)

Name AffiliationCity, State, CountryProtein & Co-Products Division2013 Members194 Members as of October 1, 2013Agarwal, RavindraPondicherry UniversityPondicherry, TN, IndiaAlla, SurendraJawaharlal Nehru Technological UniversityVikarabad,AP, IndiaAlsharari,

262

Bayesian Segmentation of Protein Secondary Structure  

E-Print Network (OSTI)

We present a novel method for predicting the secondary structure of a protein from its amino acid sequence. Most existing methods predict each position in turn based on a local window of residues, sliding this window along the length of the sequence. In contrast, we develop a probabilistic model of protein sequence/structure relationships in terms of structural segments, and formulate secondary structure prediction as a general Bayesian inference problem. A distinctive feature of our approach is the ability to develop explicit probabilistic models for -helices, -strands, and other classes of secondary structure, incorporating experimentally and empirically observed aspects of protein structure such as helical capping signals, side chain correlations, and segment length distributions. Our model is Markovian in the segments, permitting ef# cient exact calculation of the posterior probability distribution over all possible segmentations of the sequence using dynamic programming. The optimal segmentation is computed and compared to a predictor based on marginal posterior modes, and the latter is shown to provide signi# cant improvement in predictive accuracy. The marginalization procedure provides exact secondary structure probabilities at each sequence position, which are shown to be reliable estimates of prediction uncertainty. We apply this model to a database of 452 nonhomologous structures, achieving accuracies as high as the best currently available methods. We conclude by discussing an extension of this framework to model nonlocal interactions in protein structures, providing a possible direction for future improvements in secondary structure prediction accuracy.

Scott C. Schmidler; Jun S. Liu; Douglas L. Brutlag

2000-01-01T23:59:59.000Z

263

Molecular Nanosprings for Protein-Based Nanorobotics  

E-Print Network (OSTI)

Molecular Nanosprings for Protein-Based Nanorobotics Mustapha Hamdi 1 , Antoine Ferreira 1 antoine.ferreira@ensi-bourges.fr , mavro@coe.neu.edu This paper presents a molecular mechanics study using a molecular dynamics software (NAMD2) for characterization of molecular elastic joints for bio nanorobotic

Mavroidis, Constantinos

264

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

E-Print Network (OSTI)

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

Ryan, Jeremy Adam

2005-01-01T23:59:59.000Z

265

Extracellular Proteins Promote Zinc Sulfide Aggregation  

NLE Websites -- All DOE Office Websites (Extended Search)

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

266

Extracellular Proteins Promote Zinc Sulfide Aggregation  

NLE Websites -- All DOE Office Websites (Extended Search)

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

267

Photon Sciences | About Photon Sciences | What About Proteins?  

NLE Websites -- All DOE Office Websites (Extended Search)

What About Proteins? What About Proteins? « Back Lub dub, lub dub, lub dub. Every time your heart beats, proteins are creating the electrical current that tells muscles to contract and pump blood through that organ. You may think of proteins simply as food, but protein molecules in the body are responsible for many specialized functions. They are the true workhorses of the cell. Scientists use NSLS to "look" at proteins, visualizing their structure in three dimensions to learn how they work. For example, discovering protein structures from pathogens such as HIV or tuberculosis can help us understand how drugs interact with them. This can lead to the development of better medicines. Two remarkable 3D structures describing proteins in the body have been the focus of Nobel Prize-winning research at NSLS.

268

Protein structure prediction by a data-level parallel algorithm  

Science Conference Proceedings (OSTI)

We have developed a software system, PHI-PSI, on the Connection Machine that uses a parallel algorithm to retrieve and use information from a database of 112 known protein structures (selected from the Brookhaven Protein Databank) to ...

X. Zhang; D. Waltz; J. P. Mesirov

1989-08-01T23:59:59.000Z

269

Engineering Mammalian Cells for Improved Recombinant Protein Production  

E-Print Network (OSTI)

The production of recombinant glycoproteins from mammalian cell cultures requires robust processes that can achieve high protein yield while ensuring the efficacy of these proteins as human therapeutics. We describe two ...

Wong, Niki S.C.

270

Protein and Co-Products Division Student Poster Competition  

Science Conference Proceedings (OSTI)

Protein and Co-Products Division created the award to stimulate additional interest in the submission of quality student poster presentations at the AOCS Annual Meeting & Expo. Protein and Co-Products Division Student Poster Competition Divisions

271

Energetics of [alpha]-helix formation in peptides and proteins  

E-Print Network (OSTI)

This thesis focuses on the energetics of !-helix formation in peptides and proteins. The [alpha]-helix is the most prevalent type of secondary structure found in proteins, and has arguably dominated our thinking about ...

Schubert, Christian Reinhold

2009-01-01T23:59:59.000Z

272

Fragile X mental retardation protein and synaptic plasticity  

E-Print Network (OSTI)

Loss of the translational repressor FMRP causes Fragile X syndrome. In healthy neurons, FMRP modulates the local translation of numerous synaptic proteins. Synthesis of these proteins is required for the maintenance and ...

Sidorov, Michael Samuel

273

BIOINFORMATICS APPLICATIONS NOTE PIVOT: Protein Interactions VisualizatiOn Tool  

E-Print Network (OSTI)

algorithms to explore the relationships among distant proteins (see Datasets, Linking Distant Proteins below the layout mechanism dynamically places the others. Datasets: PIVOT allows the user to visually explore

Shamir, Ron

274

Recombinant Proteins in Milk A Bioreactor That Eats Hay  

Science Conference Proceedings (OSTI)

Recombinant Proteins in Milk A Bioreactor That Eats Hay. Purpose: The mammary gland has exceptional capacity for secretion. ...

2011-10-25T23:59:59.000Z

275

Cellulosic Fiber Composites Using Protein Hydrolysates and Methods ...  

Technology Marketing Summary This technology relates to cellulosic fiber composites using protein hydrolysates. Description Cellulosic fiber composites currently use ...

276

A Study of Hierarchical and Flat Classification of Proteins  

Science Conference Proceedings (OSTI)

Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially ... Keywords: Protein classification, hierarchical classification, multiclass classification.

Arthur Zimek; Fabian Buchwald; Eibe Frank; Stefan Kramer

2010-07-01T23:59:59.000Z

277

Sequence space and the ongoing expansion of the protein universe  

E-Print Network (OSTI)

each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of diver- gence of distant protein sequences be very strong, as evidenced by conservative proteins from distant organisms that retain substantial

Dean, Matthew D.

278

Photoswitchable method for the ordered attachment of proteins to surfaces  

DOE Patents (OSTI)

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

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

2011-07-05T23:59:59.000Z

279

An overview of protein-folding techniques: issues and perspectives  

Science Conference Proceedings (OSTI)

The importance of protein folding has been recognised for many years. Almost a half century ago, Linus Pauling discovered two quite simple, regular arrangements of amino acids the ?-helix and the ?-sheet that are found ... Keywords: algorithms, bioinformatics, computational biology, folding mechanism, kinetics, protein folding, protein structure prediction, sequence, tertiary structure

Abdur Rahman; Albert Y. Zomaya

2005-04-01T23:59:59.000Z

280

Subunit interactions and protein-DNA interactions of the Drosophila melanogaster small nuclear RNA activating protein complex  

E-Print Network (OSTI)

fusion protein, prepare 20ml of HEMG wash buffer and store it in the refrigerator so it will be cold

Titus, Mitchell

2007-01-01T23:59:59.000Z

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.


281

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

DOE Green Energy (OSTI)

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

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

2005-06-17T23:59:59.000Z

282

Gene encoding herbicide safener binding protein  

DOE Patents (OSTI)

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

Walton, Jonathan D. (East Lansing, MI); Scott-Craig, John S. (East Lansing, MI)

1999-01-01T23:59:59.000Z

283

ProMAT: protein microarray analysis tool  

SciTech Connect

Summary: ProMAT is a software tool for statistically analyzing data from ELISA microarray experiments. The software estimates standard curves, sample protein concentrations and their uncertainties for multiple assays. ProMAT generates a set of comprehensive figures for assessing results and diagnosing process quality. The tool is available for Windows or Mac, and is distributed as open-source Java and R code. Availability: ProMAT is available at http://www.pnl.gov/statistics/ProMAT. ProMAT requires Java version 1.5.0 and R version 1.9.1 (or more recent versions) which are distributed with the tool.

White, Amanda M.; Daly, Don S.; Varnum, Susan M.; Anderson, Kevin K.; Bollinger, Nikki; Zangar, Richard C.

2006-04-04T23:59:59.000Z

284

TIGRFAMS: The TIGRFAMs database of protein families  

DOE Data Explorer (OSTI)

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

285

Toward a comparative study of protein crystallization in microfluidic chambers using vapor diffusion and batch techniques  

Science Conference Proceedings (OSTI)

Using microfluidics for protein crystallization gives numerous advantages compared with classical techniques, as much reduced protein consumption, improved control accuracy and high parallelism. We propose here novel systems for the screening of protein ... Keywords: Microfluidic, Nanotechnology, Protein crystallization, Structural biology

M. Lounaci; P. Rigolet; G. Velve Casquillas; H. W. Huang; Y. Chen

2006-04-01T23:59:59.000Z

286

Determining protein interaction specificity of native and designed bZIP family transcription factors  

E-Print Network (OSTI)

Protein-protein interactions are important for almost all cellular functions. Knowing which proteins interact with one another is important for understanding protein function as well as for being able to disrupt their ...

Reinke, Aaron W

2012-01-01T23:59:59.000Z

287

Protein Solubility, Digestibility and Fractionation after Germination of Sorghum Varieties  

E-Print Network (OSTI)

The changes in crude protein, free amino acids, amino acid composition, protein solubility, protein fractionation and protein digestibility after germination of sorghum were investigated. Sorghum varieties (Dorado, Shandaweel-6, Giza-15) were soaked for 20 h followed by germination for 72 h; the results revealed that crude protein and free amino acids in raw sorghum varieties ranged from 10.62 to 12.46 % and 0.66 to 1.03 mg/g, respectively. Shandaweel-6 was the highest variety in crude protein and free amino acids content. After germination, crude protein was decreased and free amino acids were increased. There was an increase in content of valine and phenylalanine amino acids after germination. On the other hand, there was a decrease in most of amino acids after germination. After germination protein solubility was significantly increased. Regarding protein fractions, there was an increase in albumin, globulin and kafirin proteins and a decrease in cross linked kafirin and cross linked glutelin after germination.

Abd El-moneim M. R. Afify; Hossam S. El-beltagi; Samiha M. Abd El-salam; Azza A. Omran

2011-01-01T23:59:59.000Z

288

A protein sequence meta-functional signature for calcium binding residue prediction  

Science Conference Proceedings (OSTI)

The diversity of characterized protein functions found amongst experimentally interrogated proteins suggests that a vast array of unknown functions remains undiscovered. These protein functions are imparted by specific geometric distributions of amino ... Keywords: Calcium, Functional signature, Protein binding site, Protein function prediction, Protein sequence analysis

Jeremy A. Horst; Ram Samudrala

2010-10-01T23:59:59.000Z

289

Drosophila huntingtin-interacting protein 14 is a presynaptic protein required for photoreceptor synaptic transmission and expression of the palmitoylated proteins synaptosome-associated protein 25 and cysteine string protein  

E-Print Network (OSTI)

and cysteine string protein (CSP) were mislocalized and/orDlg (4F3), 1:50; mouse anti-CSP (6D6), 1:50; mouse anti-in mammals. SNAP-25 and CSP expression are altered in dHIP14

Stowers, R Steven; Isacoff, Ehud Y

2007-01-01T23:59:59.000Z

290

Stable Isotope, Site-Specific Mass Tagging For Protein Identification  

NLE Websites -- All DOE Office Websites (Extended Search)

Stable Isotope, Site-Specific Mass Tagging For Protein Stable Isotope, Site-Specific Mass Tagging For Protein Identification Stable Isotope, Site-Specific Mass Tagging For Protein Identification Proteolytic peptide mass mapping as measured by mass spectrometry provides an important method for the identification of proteins, which are usually identified by matching the measured and calculated m/z values of the proteolytic peptides. Available for thumbnail of Feynman Center (505) 665-9090 Email Stable Isotope, Site-Specific Mass Tagging For Protein Identification Proteolytic peptide mass mapping as measured by mass spectrometry provides an important method for the identification of proteins, which are usually identified by matching the measured and calculated m/z values of the proteolytic peptides. A unique identification is, however, heavily

291

Cornell researchers take step in deciphering what proteins look like  

NLE Websites -- All DOE Office Websites (Extended Search)

Ealick Research Group Ealick Research Group Cornell researchers take step in deciphering what proteins look like through discovery of new family member important in making DNA Nov. 3, 2004 ITHACA, N.Y. -- Cornell University researchers, who are trying to understand how proteins evolve and function by looking at their structural features, have uncovered the crystal structure of a protein involved in making the building blocks of DNA correctly. The protein is AIRs kinase, and to the researchers' surprise, its shape is similar to other members of the riboside kinase family, proteins that are important in making DNA and RNA, the molecules that make up genes. As a result, the research group now has nine members of the riboside kinase family that are thought to have evolved from a common protein ancestor.

292

New Crystal Structures Lift Fog around Protein Folding  

NLE Websites -- All DOE Office Websites (Extended Search)

New Crystal Structures Lift Fog New Crystal Structures Lift Fog around Protein Folding New Crystal Structures Lift Fog around Protein Folding Print Wednesday, 25 July 2012 00:00 Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab, Stanford University, and the Massachusetts Institute of Technology has deciphered the crystal structure of a critical control element within chaperonin, the protein complex responsible for the correct folding of other proteins.

293

BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Fusion  

NLE Websites -- All DOE Office Websites (Extended Search)

Fusion Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose Xinhao Ye & Zhiguang Zhu & Chenming Zhang & Y.-H. Percival Zhang Received: 31 March 2011 / Revised: 2 May 2011 / Accepted: 3 May 2011 # Springer-Verlag (outside the USA) 2011 Abstract Clostridium thermocellum cellodextrin phosphor- ylase (CtCDP), a single-module protein without an apparent carbohydrate-binding module, has reported activities on soluble cellodextrin with a degree of polymerization (DP) from two to five. In this study, CtCDP was first discovered to have weak activities on weakly water-soluble cellohep- taose and insoluble regenerated amorphous cellulose (RAC). To enhance its activity on solid cellulosic materials, four cellulose binding modules, e.g., CBM3 (type A) from C. thermocellum

294

DAPS: Database of Aligned Protein Structures  

DOE Data Explorer (OSTI)

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

Mallick, Parag; Rice, Danny; Eisenberg, David

295

Heat capacity and compactness of denatured proteins  

E-Print Network (OSTI)

One of the striking results of protein thermodynamics is that the heat capacity change upon denaturation is large and positive. This change is generally ascribed to the exposure of non-polar groups to water on denaturation, in analogy to the large heat capacity change for the transfer of small non-polar molecules from hydrocarbons to water. Calculations of the heat capacity based on the exposed surface area of the completely unfolded denatured state give good agreement with experimental data. This result is difficult to reconcile with evidence that the heat denatured state in the absence of denaturants is reasonably compact. In this work, sample conformations for the denatured state of truncated CI2 are obtained by use of an effective energy function for proteins in solution. The energy function gives denatured conformations that are compact with radii of gyration that are slightly larger than that of the native state. The model is used to estimate the heat capacity, as well as that of the native state, at 300 and 350 K via finite enthalpy differences. The calculations show that the heat capacity of denaturation can have large positive contributions from non-covalent intraprotein interactions because these interactions change more with temperature in non-native conformations than in the native state. Including this contribution, which has been neglected in empirical surface area models, leads to heat capacities of unfolding for compact denatured states that are consistent with the experimental heat capacity data. Estimates of the stability curve of CI2 made with the effective energy function support the present model. # 1999 Elsevier Science B.V. All rights reserved.

Themis Lazaridis; Martin Karplus

1999-01-01T23:59:59.000Z

296

Structure and Function of Microbial Metal-Reduction Proteins  

SciTech Connect

In this project, we proposed (i) identification of metal-reduction genes, (ii) development of new threading techniques and (iii) fold recognition and structure prediction of metal-reduction proteins. However, due to the reduction of the budget, we revised our plan to focus on two specific aims of (i) developing a new threading-based protein structure prediction method, and (ii) developing an expert system for protein structure prediction.

Xu, Ying; Crawford, Oakly H.; Xu, Dong; Larimer, Frank W.; Uberbacher, Edward C.; Zhou, Jizhong

2009-09-02T23:59:59.000Z

297

Recombinant HT{sub m4} gene, protein and assays  

DOE Patents (OSTI)

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

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

1996-09-03T23:59:59.000Z

298

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

Science Conference Proceedings (OSTI)

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

Jae-Hyung Lee

2007-12-01T23:59:59.000Z

299

New Crystal Structures Lift Fog around Protein Folding  

NLE Websites -- All DOE Office Websites (Extended Search)

New Crystal Structures Lift Fog around Protein Folding Print New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab, Stanford University, and the Massachusetts Institute of Technology has deciphered the crystal structure of a critical control element within chaperonin, the protein complex responsible for the correct folding of other proteins. Chaperonins promote the proper folding of newly translated proteins and proteins that have been stress-denatured-meaning they've lost their structure-by encapsulating them inside a protective chamber formed from two rings of molecular complexes stacked back-to-back. There are two classes of chaperonins, group I found in prokaryotes and group II found in eukaryotes and archaea (organisms with no cell membrane or internal membrane-bound organelles). Much of the basic architecture has been evolutionarily preserved (conserved) across these two classes but they do differ in how the protective chamber is opened to accept proteins and closed to fold them. Whereas group I chaperonins require a detachable ring-shaped molecular lid to open and close the chamber, group II chaperonins have a built-in lid.

300

A bacterial factory for the production of MEMBRANE PROTEINS  

Office of Technology Transfer A bacterial factory for the production of MEMBRANE PROTEINS Cell membranes are important biological structures as they ...

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

Structures for Three Membrane Transport Proteins Yield Functional...  

NLE Websites -- All DOE Office Websites (Extended Search)

to the guardians at old-time city gates who controlled the flux of "goods" through the city walls, specialized membrane transport proteins catalyze the flow across cell...

302

A macromolecular delivery vehicle for protein-based vaccines: Acid ...  

... methane, was designed as the key acid-cleavable crosslinking monomer used to prepare acid-degradable protein-loaded microgels by inverse ...

303

Three Frontiers in the Thermodynamics of Protein Solutions  

E-Print Network (OSTI)

Three frontiers in the thermodynamics of protein solutions*the broad high- way of thermodynamics. ACKNOWLEDGMENTS ForThe great virtue of thermodynamics is its generality, its

Prausnitz, John M; Foose, Loddie

2007-01-01T23:59:59.000Z

304

Three Frontiers in the Thermodynamics of Protein Solutions  

E-Print Network (OSTI)

is the broad highway of thermodynamics. Acknowledgments: ForThree Frontiers in the Thermodynamics of Protein SolutionsThe great virtue of thermodynamics is its generality, its

Prausnitz, John; Hagar, Loddie

2008-01-01T23:59:59.000Z

305

Improved Processes for the Production of Proteins and ...  

Summary. Researchers at PNNL have developed an improved process for the production of proteins and chemicals in fungal bioprocesses. The technology is ...

306

High-Pressure Protein Digestion System - PNNL: Available ...  

Summary. Researchers at PNNL have developed a system that utilizes high pressure to reduce the time of protein fractionation and improve peptide ...

307

Phenylpropanoid related regulatory protein-regulatory region associations  

SciTech Connect

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

Apuya, Nestor (Culver City, CA); Bobzin, Steven Craig (Malibu, CA); Park, Joon-Hyun (Oak Park, CA); Doukhanina, Elena (Newbury Park, CA)

2012-01-03T23:59:59.000Z

308

Soy Protein ProductsChapter 1 Historical Aspects  

Science Conference Proceedings (OSTI)

Soy Protein Products Chapter 1 Historical Aspects Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry AOCS Press Downloadable pdf of Chapter 1 Historical Aspects from the book ...

309

MTBreg: The Database of Conditionally Regulated Proteins in Mycobacterium Tuberculosis  

DOE Data Explorer (OSTI)

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

Kaufman, Markus; Pal, Debnath; Eisenberg, David

310

Large Scale Quantum-mechanical Calculations of Proteins, Nanomaterials...  

NLE Websites -- All DOE Office Websites (Extended Search)

Large Scale Quantum-mechanical Calculations of Proteins, Nanomaterials and Other Large Systems Event Sponsor: Leadership Computing Facility Seminar Start Date: Dec 5 2013 - 2:00pm...

311

Sending a Message: How Receptors Talk to G Proteins | Advanced...  

NLE Websites -- All DOE Office Websites (Extended Search)

An Understanding of Elastin's Properties Springs Forth Visualizing the Flow of Molten Rock through Seabed Mantle How Dinosaurs Put Proteins into Long-Term Storage Plutonium...

312

Expression Screening of Fusion Partners from an E. coli Genome for Soluble Expression of Recombinant Proteins in a Cell-Free Protein Synthesis System  

E-Print Network (OSTI)

While access to soluble recombinant proteins is essential for a number of proteome studies, preparation of purified functional proteins is often limited by the protein solubility. In this study, potent solubility-enhancing ...

Ahn, Jin Ho

313

Investigation of the kinetics of protein folding and the ensemble of conformations in non-native states of proteins by liquid NMR spectroscopy  

E-Print Network (OSTI)

For a complete description of protein folding dynamics and the structure of the folded state, of unfolded and of non-native states of proteins and the kinetics of protein folding from the unfolded state to the folded state ...

Wirmer, Julia

2005-01-01T23:59:59.000Z

314

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

E-Print Network (OSTI)

as they mediate almost all cellular functions, including cell signalling, proliferation, differentiation, DNA repair and immunity. As we endeavour to gain a systems level description of these processes, it is clear that we require a greater comprehension... drug targets [2]. Much optimism followed the discovery from alanine scanning studies that a small proportion of interface residues - the so-called hot- spots - contribute the majority of the free energy of binding, thereby making protein interactions...

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

2011-07-29T23:59:59.000Z

315

Facilitating protein solubility by use of peptide extensions  

DOE Patents (OSTI)

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

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

2013-09-17T23:59:59.000Z

316

Review: Protein knots and fold complexity: Some new twists  

Science Conference Proceedings (OSTI)

The current knowledge on topological knots in protein structure is reviewed, considering in turn, knots with three, four and five strand crossings. The latter is the most recent to be identified and has two distinct topological forms. The knot observed ... Keywords: Fold complexity, Protein knots

William R. Taylor

2007-06-01T23:59:59.000Z

317

Protein and Energy Supplementation to Beef Cows Grazing  

E-Print Network (OSTI)

with a higher energy content. Urea Usage in Protein Supplements Nonprotein nitrogen (NPN) in the form of urea) if it is not possible to correct the short supply of energy by reducing stocking rates. Typically, energy supplementsProtein and Energy Supplementation to Beef Cows Grazing New Mexico Rangelands Cooperative Extension

Castillo, Steven P.

318

Cold shock and regulation of surface protein trafficking convey sensitization  

E-Print Network (OSTI)

Cold shock and regulation of surface protein trafficking convey sensitization to inducers of stage and GPEET procyclins. Here we show that a cold shock of T > 15°C is sufficient to reversibly induce high of the EP mRNA is necessary and sufficient for the increased expression. During cold shock, EP protein

Arnold, Jonathan

319

An expert system to predict protein thermostability using decision tree  

Science Conference Proceedings (OSTI)

Protein thermostability information is closely linked to commercial production of many biomaterials. Recent developments have shown that amino acid composition, special sequence patterns and hydrogen bonds, disulfide bonds, salt bridges and so on are ... Keywords: Bioinformatics, Decision Tree, Expert system, Machine learning, Protein thermostability

Li-Cheng Wu; Jian-Xin Lee; Hsien-Da Huang; Baw-Juine Liu; Jorng-Tzong Horng

2009-07-01T23:59:59.000Z

320

PERSPECTIVE Automated protein structure calculation from NMR data  

E-Print Network (OSTI)

PERSPECTIVE Automated protein structure calculation from NMR data Mike P. Williamson ? C. Jeremy completely automatic structure determination of small pro- teins of\\15 kDa, from NMR spectra to structure, particu- larly by structural genomics consortia. Keywords NMR structure calculation of proteins Á

Craven, Jeremy

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

Electrorheological crystallization of proteins and other molecules  

DOE Patents (OSTI)

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

Craig, G.D.; Rupp, B.

1996-06-11T23:59:59.000Z

322

Electrorheological crystallization of proteins and other molecules  

DOE Patents (OSTI)

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

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

1996-01-01T23:59:59.000Z

323

Construction of artificial pigment-protein antennae  

DOE Green Energy (OSTI)

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

Sibbald, J.

1997-01-10T23:59:59.000Z

324

Proteins' Amazing Origami Powers: Insight for Potential Disease Treatments  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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

325

Shedding Light on Protein Drug Interactions | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

Science Highlights Archives: 2013 | 2012 | 2011 | 2010 Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Shedding Light on Protein Drug Interactions JANUARY 23, 2008 Bookmark and Share In this e-coli cell, the proteins (shown in blue) crowd around ribosomes (purple). These regions have a high concentration of protein, typically greater than 30 percent, which limits the ensemble of states into which the proteins can bend themselves. Download hi-res image.) Proteins, the biological molecules that are involved in virtually every action of every organism, may themselves move in surprising ways, according to a recent study carried out at the Biophysics Collaborative Access Team x-ray beamline 18-ID at the Advanced Photon Source, a national user

326

Zoomable map of poplar proteins | ornl.gov  

NLE Websites -- All DOE Office Websites (Extended Search)

'Zoomable' map of poplar proteins offers new view of bioenergy crop 'Zoomable' map of poplar proteins offers new view of bioenergy crop January 29, 2013 An extensive molecular map of poplar tree proteins from Oak Ridge National Laboratory offers new insight into the plant's biological processes. Knowing how poplar trees alter their proteins to change and adapt to environmental surroundings could help bioenergy researchers develop plants better suited to biofuel production. The study is featured on the cover of January's Molecular and Cellular Proteomics. Researchers seeking to improve production of ethanol from woody crops have a new resource in the form of an extensive molecular map of poplar tree proteins, published by a team from the Department of Energy's Oak Ridge National Laboratory (DOE ORNL). Populus, a fast-growing perennial tree, holds potential as a bioenergy crop

327

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

Protein Bridges DNA Base and Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Wednesday, 28 October 2009 00:00 Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

328

The functions of tryptophan residues in membrane proteins  

SciTech Connect

Membrane proteins in general have a significantly higher Trp content than do soluble proteins. This is especially true for the M and L subunits of the photosynthetic reaction center from purple bacteria. The Trp residues are located mostly in the segments that connect the transmembrane helices. Further, they are concentrated at the periplasmic side of the complex. Within the protein subunits, many form hydrogen bonds with carbonyl oxygens of the main chain, thereby stabilizing the protein. On the surface of the molecule, they are correctly positioned to form hydrogen bonds with the lipid head groups while their hydrophobic rings are immersed in the lipid part of the bilayer. We suggest that Trp residues are involved in the translocation of protein through the membrane and that following translocation, Trp residues serve as anchors on the periplasmic side of the membrane.

Schiffer, M.; Chang, C.H.; Stevens, F.J.

1994-08-01T23:59:59.000Z

329

Automating the determination of 3D protein structure  

SciTech Connect

The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

Rayl, K.D.

1993-12-31T23:59:59.000Z

330

A thermodynamic model for agglomeration of DNA-looping proteins  

E-Print Network (OSTI)

In this paper, we propose a thermodynamic mechanism for the formation of transcriptional foci via the joint agglomeration of DNA-looping proteins and protein-binding domains on DNA: The competition between the gain in protein-DNA binding free energy and the entropy loss due to DNA looping is argued to result in an effective attraction between loops. A mean-field approximation can be described analytically via a mapping to a restricted random-graph ensemble having local degree constraints and global constraints on the number of connected components. It shows the emergence of protein clusters containing a finite fraction of all looping proteins. If the entropy loss due to a single DNA loop is high enough, this transition is found to be of first order.

Sumedha; Martin Weigt

2008-01-09T23:59:59.000Z

331

A novel family of small proteins that affect plant development  

Science Conference Proceedings (OSTI)

The DVL genes represent a new group of plant proteins that influence plant growth and development. Overexpression of DVL1, and other members of the DVL family, causes striking phenotypic changes. The DVL proteins share sequence homology in their C-terminal half. Point mutations in the C-terminal domain show it is necessary and deletion studies demonstrate the C-terminal domain is sufficient to confer the overexpression phenotypes. The phenotypes observed, and the conservation of the protein sequence in the plant kingdom, does suggest the DVL proteins have a role in modulating plant growth and development. Our working hypothesis is the DVL proteins function as regulators of cellular signaling pathways that control growth and development.

John Charles Walker

2011-04-29T23:59:59.000Z

332

Temperature dependence of the radiation inactivation of proteins  

Science Conference Proceedings (OSTI)

The radiation inactivation method allows determination of the relative molecular mass (Mr) of proteins by exposure to high doses of ionizing radiation. The analysis by target theory of biological activity decay curves yields the size of the protein. A correction factor for Mr has been routinely used in the literature when irradiation is conducted at low temperature. Since the radiation inactivation of proteins is affected by temperature, we propose a general equation which relates Mr of a protein to D37,t, the dose in megarads at a given temperature t (in degree C) where 37% of its initial biological activity remains log Mr = 5.89 - log D37,t - 0.0028t. It is concluded that temperature affects the amount of absorbed radiation energy required to inactivate 1 mol of protein.

Beauregard, G.; Potier, M.

1985-10-01T23:59:59.000Z

333

Promoters and proteins from Clostridium thermocellum and uses thereof  

DOE Patents (OSTI)

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

Wu, J. H. David; Newcomb, Michael

2012-11-13T23:59:59.000Z

334

Towards an understanding of protein-protein interaction network hierarchies. Analysis of DnaN (?)-binding peptide motifs in members of protein families interacting with the eubacterial processivity clamp, the ? subunit of DNA Polymerase III  

Science Conference Proceedings (OSTI)

The consensus pentapeptide QL[SD]LF is a major component in the interaction of a number of families of proteins with the eubacterial DNA-clamp protein, DnaN (the ?-subunit of DNA Polymerase III holoenzyme). Rankings of the motifs were established ... Keywords: DNA polymerase III, protein-protein interaction, sliding clamp

Brian P. Dalrymple; Gene Wijffels; Kritaya Kongsuwan; Phil Jennings

2003-01-01T23:59:59.000Z

335

High-Resolution Design of a Protein Loop  

DOE Green Energy (OSTI)

Despite having irregular structure, protein loops often adopt specific conformations that are critical to protein function. Most studies in de novo protein design have focused on creating proteins with regular elements of secondary structure connected by very short loops or turns. To design longer protein loops that adopt specific conformations, we have developed a protocol within the Rosetta molecular modeling program that iterates between optimizing the sequence and conformation of a loop in search of low-energy sequence-structure pairs. We have tested the procedure by designing 10-residue loops for the connection between the second and third strand in the {beta}-sandwich protein tenascin. Three low-energy designs from 7,200 flexible backbone trajectories were selected for experimental characterization. All three designs, called LoopA, LoopB, and LoopC, adopt stable folded structures. High-resolution crystal structures of LoopA and LoopB have been solved. LoopB adopts a structure very similar to the design model (0.46 Angstroms rmsd), and all but one of the side chains are modeled in the correct rotamers. LoopA crystallized at low pH in a structure that differs dramatically from our design model. It forms a strand-swapped dimer mediated by hydrogen bonds to protonated glutamic acids. Gel filtration indicates that the protein is not a dimer at neutral pH. These results suggest that the high-resolution design of protein loops is possible; however, they also highlight how small changes in protein energetics can dramatically perturb the low free energy structure of a protein.

Hu,X.; Wang, H.; Ke, H.; Kuhlman, B.

2007-01-01T23:59:59.000Z

336

Clusters of proteins in bio-membranes: insights into the roles of interaction potential shapes and of protein diversity  

E-Print Network (OSTI)

It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range repulsive forces between proteins, specific to these systems. In this paper, we carry on our investigation, by Monte Carlo simulations, of different aspects of cluster phases of proteins in bio-membranes. First, we compare different long-range potentials (including notably three-body terms) to demonstrate that the existence of cluster phases should be quite generic. Furthermore, a real membrane contains hundreds of different protein species that are far from being randomly distributed in these nano-domains. We take this protein diversity into account by modulating protein-protein interaction potentials both at short and longer range. We confirm theoretical predictions in terms of biological cluster specialization by deciphering how clusters recruit only a few protein species. In this respect, we highlight that cluster phases can turn out to be an advantage at the biological level, for example by enhancing the cell response to external stimuli.

Nicolas Meilhac; Nicolas Destainville

2011-06-07T23:59:59.000Z

337

Role of Entropy in Protein Thermostability: Folding Kinetics of a Hyperthermophilic Cold Shock Protein at High Temperatures Using 19  

E-Print Network (OSTI)

and hyperthermophilic cold shock proteins at ambient temperature extend to their temperature depen- dence: the lower The conservation of the temperature dependences of folding and unfolding in this family of small cold shockRole of Entropy in Protein Thermostability: Folding Kinetics of a Hyperthermophilic Cold Shock

Schuler, Ben

338

Improved application of the oscillating method for the isoelectric point determination of protein: Potential connection with protein data banks  

Science Conference Proceedings (OSTI)

The oscillating method (OM) for the theoretical determination of the pI values, one by one, of proteins and other macromolecules has been previously published [Sillero and Maldonado, Comput. Biol. Med 36 (2006) 157-166]. An improved application of the ... Keywords: Acid-base residues, Electric charge, PH, PI theoretical determination, PICAL, Proteins, Visual basic

Andrs Maldonado; Francisco Vara; Antonio Sillero

2008-01-01T23:59:59.000Z

339

Fifth Annual Meeting of the Advanced Light Source User`s Association  

SciTech Connect

This report discusses the following topics: ALS Project Status; Accelerator Commissioning; Experimental Systems: Supersmooth Optics and Ultra-Precise Undulators; Planning for Users and User Services; ALS Scientific Program; High Resolution Core-Level Photoemission; Photoelectron Diffraction and Holography; Soft X-Ray Emission Spectroscopy of Solids at the NSLS and the ALS; Gas-Phase Spectrometry; Spectromicroscopy; X-Ray Dichroism Experiments Using Circular Polarization; Magnetic Circular X-Ray Dichroism and MCXD Microscopy; Applications of Soft X-Ray Optics to Sub-Micron Silicon Device Technology; Bend Magnet Microprobe; Protein Crystallography: Recent Developments and Plans for the ALS; and Applications of High-Brightness Synchrotron Radiation to Protein Crystallography.

Not Available

1993-10-01T23:59:59.000Z

340

Lipid ion channels and the role of proteins  

E-Print Network (OSTI)

Synthetic lipid membranes in the absence of proteins can display quantized conduction events for ions that are virtually indistinguishable from those of protein channel. By indistinguishable we mean that one cannot decide based on the current trace alone whether conductance events originate from a membrane, which does or does not contain channel proteins. Additional evidence is required to distinguish between the two cases, and it is not always certain that such evidence can be provided. The phenomenological similarities are striking and span a wide range of phenomena: The typical conductances are of equal order and both lifetime distributions and current histograms are similar. One finds conduction bursts, flickering, and multistep-conductance. Lipid channels can be gated by voltage, and can be blocked by drugs. They respond to changes in lateral membrane tension and temperature. Thus, they behave like voltage-gated, temperature-gated and mechano-sensitive protein channels, or like receptors. Lipid channels are remarkably under-appreciated. However, the similarity between lipid and protein channels poses an eminent problem for the interpretation of protein channel data. For instance, the Hodgkin-Huxley theory for nerve pulse conduction requires a selective mechanism for the conduction of sodium and potassium ions. To this end, the lipid membrane must act both as a capacitor and as an insulator. Non-selective ion conductance by mechanisms other than the gated protein-channels challenges the proposed mechanism for pulse propagation. ... Some important questions arise: Are lipid and protein channels similar due a common mechanism, or are these similarities fortuitous? Is it possible that both phenomena are different aspects of the same phenomenon? Are lipid and protein channels different at all? ... (abbreviated)

Lars D. Mosgaard; Thomas Heimburg

2013-07-11T23:59:59.000Z

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

Microsoft Word - lois for 2011_v2.doc  

NLE Websites -- All DOE Office Websites (Extended Search)

Letters of Intent Letters of Intent 2011 Call for Beamline Development Proposals National Synchrotron Light Source II 1. High-energy x-ray micro-mapping of materials for advanced energy and structural engineering applications beamline (HEX) Spokesperson: Mark Croft, Rutgers University Source: Superconducting wiggler 2. Synchrotron-based discoveries for Chemical Biology (HIT) Marc Allaire, Brookhaven National Laboratory Undulator 3. NSLS-II Beamline for Combined High Magnetic Field and High Pressure Materials Studies (HMP) Trevor Tyson, New Jersey Institute of Technology Dipole wiggler 4. High-energy macromolecular crystallography (HMX) Vivian Stojanoff, Brookhaven National Laboratory 5. Monochromatic/White Beam X-ray Topography and High Resolution Diffraction Beamline at NSLS-II (HXT)

342

Structure and activity of protein-nanoparticle conjugates: towards a strategy for optimizing the interface  

E-Print Network (OSTI)

Nanoparticle-protein conjugates have a variety of applications in imaging, sensing, assembly and control. The nanoparticle-protein interface is made of numerous complex interactions between protein side-chains and the ...

Aubin-Tam, Marie-Eve

2008-01-01T23:59:59.000Z

343

Protein and Co-Products Division April 201/span>3 Newsletter  

Science Conference Proceedings (OSTI)

Read the Protein and Co-Products Division April 201/span>3 Newsletter. Protein and Co-Products Division April 201/span>3 Newsletter Protein and Co-Products Division Newsletter April 201/span>3 ...

344

Protein and Co-Products Division October 201/span>3 Newsletter  

Science Conference Proceedings (OSTI)

Read the Protein and Co-Products Division October 201/span>3 Newsletter. Protein and Co-Products Division October 201/span>3 Newsletter Protein and Co-Products Division Newsletter October 201/span>3 ...

345

Computational studies of tau protein : implications for the pathogenesis and treatment of neurodegenerative diseases  

E-Print Network (OSTI)

Tau protein is the primary constituent of protein aggregates known as neurofibrillary tangles, a pathological hallmark of Alzheimer's disease (AD). Previous studies suggest that tau protein may play a contributing role in ...

Huang, Austin V., 1980-

2009-01-01T23:59:59.000Z

346

Methods and constructs for expression of foreign proteins in photosynthetic organisms  

DOE Patents (OSTI)

A method for expressing and purifying foreign proteins in photosynthetic organisms comprising the simultaneous expression of both the heterologous protein and a means for compartmentalizing or sequestering of the protein.

Laible, Philip D. (Villa Park, IL); Hanson, Deborah K. (Downers Grove, IL)

2002-01-01T23:59:59.000Z

347

Effect of microtubule-associated protein tau in dynamics of single-headed motor proteins KIF1A  

E-Print Network (OSTI)

Intracellular transport based on molecular motors and its regulation are crucial to the functioning of cells. Filamentary tracks of the cells are abundantly decorated with non-motile microtubule-associated proteins, such as tau. Motivated by experiments on kinesin-tau interactions [Dixit et al. Science 319, 1086 (2008)] we developed a stochastic model of interacting single-headed motor proteins KIF1A that also takes into account the interactions between motor proteins and tau molecules. Our model reproduce experimental observations and predicts significant effects of tau on bound time and run length which suggest an important role of tau in regulation of kinesin-based transport.

J. Sparacino; M. G. Faras; P. W. Lamberti

2013-02-11T23:59:59.000Z

348

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

349

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

350

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

351

Synthetic scaffolds and protein assemblies for engineering applications  

E-Print Network (OSTI)

S-layer proteins, which naturally self-assemble on the exterior of cells, provide an interesting basis for the creation of synthetic scaffolds. In this thesis, I created a plasmid which produces a recombinant form of a ...

Norville, Julie Erin, 1980-

2004-01-01T23:59:59.000Z

352

Theoretical Study on Catalysis by Protein Enzymes and Ribozyme  

NLE Websites -- All DOE Office Websites (Extended Search)

Theoretical Study on Theoretical Study on Catalysis by Protein Enzymes and Ribozyme Theoretical Study on Catalysis by Protein Enzymes and Ribozyme 2000 NERSC Annual Report 17shkarplus.jpg The energetics were determined for three mechanisms proposed for TIM catalyzed reactions. Results from reaction path calculations suggest that the two mechanisms that involve an enediol intermediate are likely to occur, while the direct intra-substrate proton transfer mechanism (in green) is energetically unfavorable due to the presence of His95 in the active site. Principal Investigator: Martin Karplus, Harvard University Research Objectives The goal of this project is to develop a greater understanding of the mechanisms involved in enzyme catalysis and related protein functions. We are studying two types of enzymes: proteins and a nucleic acid (hammerhead

353

Protein Puzzles and Scientific Solutions | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Protein Puzzles and Scientific Solutions Protein Puzzles and Scientific Solutions Protein Puzzles and Scientific Solutions January 8, 2014 - 1:45pm Addthis This 3-D rendering of a lysozyme molecule shows two gadolinium atoms bound to it. Researchers soaked lysozyme crystals in a solution containing the metal gadolinium to help improve imaging quality in an experiment at SLAC's Linac Coherent Light Source (LCLS) X-ray laser. The experiment proved that LCLS can resolve the lysozyme structure without using data obtained earlier, and researchers hope to use similar techniques to reconstruct important unsolved proteins. | Photo credit: Max Planck Society. This 3-D rendering of a lysozyme molecule shows two gadolinium atoms bound to it. Researchers soaked lysozyme crystals in a solution containing the

354

How the Membrane Protein AmtB Transports Ammonia  

NLE Websites -- All DOE Office Websites (Extended Search)

How the Membrane Protein AmtB Transports Ammonia Print How the Membrane Protein AmtB Transports Ammonia Print Membrane proteins provide molecular-sized entry and exit portals for the various substances that pass into and out of cells. While life scientists have solved the structures of protein channels for ions, uncharged solutes, and even water, up to now they have only been able to guess at the precise mechanisms by which gases (such as NH3, CO2, O2, NO, N2O, etc.) cross biological membranes. But, with the first high-resolution structure of a bacterial ammonia transporter (AmtB), determined by a team in the Stroud group from the University of California, San Francisco, it is now known that this family of transporters conducts ammonia by stripping off the proton from the ammonium (NH4+) cation and conducting the uncharged NH3 "gas."

355

Robust, High-Throughput Analysis of Protein Structures  

NLE Websites -- All DOE Office Websites (Extended Search)

Robust, High-Throughput Analysis of Protein Structures Print Robust, High-Throughput Analysis of Protein Structures Print Scientists have developed a fast and efficient way to determine the structure of proteins, shortening a process that often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling genomic-scale protein-structure characterization. Coupling brilliant x rays from one of the superconducting bend magnets at the ALS to liquid-handling robotics has enabled the collection of 96 samples in 4 hours. Importantly, the sample format and the amount of material required are practical for most biological problems. The beamline's high-throughput capability is set to have a large impact on many fields that require genomic-scale information, such as Berkeley Lab's bioenergy efforts and cancer biology studies.

356

Protein Thermostability Calculations Using Alchemical Free Energy Simulations  

E-Print Network (OSTI)

Protein Thermostability Calculations Using Alchemical Free Energy Simulations Daniel Seeliger by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchem- ical free energy simulations, such as free energy perturbation or thermodynamic integration

de Groot, Bert

357

Insights into protein function from evolutionary and conformational dynamics  

E-Print Network (OSTI)

The volume of protein structure data has grown rapidly over the past 30 years, leaving a wake of facts that still require explanation. We endeavored to answer a few open questions on the structure-function relationship of ...

Bransford, Philip W

2011-01-01T23:59:59.000Z

358

Protein Structure Could Lead to Better Treatments for HIV, Early...  

NLE Websites -- All DOE Office Websites (Extended Search)

Highlights rss feed Protein Structure Could Lead to Better Treatments for HIV, Early Aging APRIL 9, 2013 Bookmark and Share Ribbon diagram of the Ste24p protease. Researchers...

359

20 petaflops simulation of proteins suspensions in crowding conditions  

Science Conference Proceedings (OSTI)

We present performance results for the simulation of proteins suspensions in crowding conditions obtained with MUPHY, a computational platform for multi-scale simulations of real-life biofluidic problems. Previous versions of MUPHY have ...

Massimo Bernaschi, Mauro Bisson, Massimiliano Fatica, Simone Melchionna

2013-11-01T23:59:59.000Z

360

Nanofluidic devices for rapid analysis of DNA and proteins  

E-Print Network (OSTI)

Direct analysis of biologically-relevant entities such as nucleic acids and proteins offers the potential to outperform conventional analysis techniques and diagnostic methods through enhancements in speed, accuracy, and ...

Fu, Jianping, Ph. D. Massachusetts Institute of Technology

2007-01-01T23:59:59.000Z

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.


361

Materiomics: biological protein materials, from nano to macro  

E-Print Network (OSTI)

Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain ...

Cranford, Steven Wayne

362

Molecular Computations for the Stabilization of Therapeutic Proteins  

E-Print Network (OSTI)

Molecular computations based on quantum mechanics and statistical mechanics have been applied to the understanding and quantification of processes leading to the degradation of therapeutic proteins. In particular, we focus ...

Trout, Bernhardt L.

363

Soy Protein ProductsChapter 7 Regulations Regarding Usage  

Science Conference Proceedings (OSTI)

Soy Protein Products Chapter 7 Regulations Regarding Usage Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry AOCS Press Downloadable pdf of Chapter 7 Regulations Regarding Usage from the

364

SLAC National Accelerator Laboratory - Giant Virus, Tiny Protein...  

NLE Websites -- All DOE Office Websites (Extended Search)

A big payoff from tiny crystals The protein structure experiments were led by Chapman and Arizona State's John Spence and Petra Fromme. They chose as their target Photosystem I, a...

365

NMR structure of hypothetical protein MG354 from Mycoplasma genitalium  

E-Print Network (OSTI)

Bicelle-based liquid crystals for NMR measurement of dipolarbasic pH values. J Biomol NMR 1999;13:187-191. Kraulis PJ.Prot-00430-2004-R1 NMR structure of hypothetical protein

Pelton, Jeffrey G.; Shi, Jianxia; Yokotoa, Hisao; Kim, Rosalind; Wemmer, David E.

2005-01-01T23:59:59.000Z

366

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

E-Print Network (OSTI)

Protein-protein interactions (PPIs) are attractive targets because of their therapeutic potential. One approach to design small molecules that can disrupt the PPIs is to use structural information of proteins. With this approach, triazole-based peptidomimetics that mimic beta-turn hot-spot regions in neurotrophins were synthesized. The monovalent mimics were assembled into bivalent mimics via a combinatorial method. Three different bivalent mimics were prepared for different studies. Bivalent mimics with long-linkers bound to TrkA or TrkC receptor and showed partial antagonism for the receptors. Other mimics were conjugated with cytotoxic compounds and they were used for TrkC targeted drug delivery. The last group of bivalent mimics previously showed targeted delivery effects for pancreatic cancer cells. In this study, we synthesized Eu-chelated bivalent mimics to perform a competitive binding assay for pancreatic cancer cells. Previous research in our group focused on design of secondary structures' mimics on rigid scaffolds as "minimalist mimics." We sought to establish structural design criteria for the minimalist mimics, and we wanted to propose that sets of such compounds could mimic local pairs of amino acids in any secondary structures as "universal peptidomimetics." Thus, we designed five compounds, such as oxazoline-, pyrrole-, dyine- "kinked" and "linear" bistrizole-based peptidomimetics, and performed molecular modelings, DFT calculations, and QMD for them to validate our hypothesis. On the concepts of "minimalist mimics" and "universal peptidomimetics," we developed the C alpha ? C beta vector matching program to evaluate preferred orientations of C alpha - C beta coordinates for secondary structures. We applied the program to omegatides and pyrrolinone-pyrrolidine oligomers. The compounds matched better with strands than for helices. We expanded the C alpha ? C beta vector matching idea to a method that ranks preferred conformations of small molecules on any combination of three interface side-chains in all structurally characterized PPIs. We developed a PDB mining program (explores key orientation, EKO) to do this, and EKO applied to pyrrolinone-pyrrolidine oligomers to find targets. EKO found several interesting targets, such as AICAR Tfase, GAPDH, and HIV-1 protease. HIV-1 dimerization inhibition and Zhang-Poorman kinetic assays were performed to validate our hypothesis, and the results showed that pyrrolinone-pyrrolidine derivatives inhibited HIV-1 dimerization.

Ko, Eunhwa

2012-05-01T23:59:59.000Z

367

Protein Activity that Protects Our DNA - Research Highlights | ORNL Neutron  

NLE Websites -- All DOE Office Websites (Extended Search)

Neutrons help shed light on critical protein activity that protects our DNA Neutrons help shed light on critical protein activity that protects our DNA "New study provides a framework for understanding how protein works and how it stimulates the DNA processing machines" Research Contact: Walter Chazin Illustration of the change in architecture of the essential eukaryotic ssDNA binding protein RPA as it engages progressively longer segments of ssDNA. Small-angle x-ray scattering data are displayed in the background for the DNA binding core of RPA in its DNA-free state (green) and when engaged on 10 (yellow), 20 (red, and 30 (blue) nucleotide ssDNA substrates. Overlaid molecular surfaces and ribbon representations of the three distinct architectural states of RPA are shown, one for the DNA-free protein and the two others for the initial and fully ssDNA-engaged modes, revealing the progressive compaction of the protein as it binds to the substrate. The RPA70 subunit is colored in blue, RPA32 in green, and RPA14 in red, with ssDNA displayed as a yellow ribbon.

368

Structures for Three Membrane Transport Proteins Yield Functional Insights  

NLE Websites -- All DOE Office Websites (Extended Search)

Structures for Three Membrane Structures for Three Membrane Transport Proteins Yield Functional Insights Structures for Three Membrane Transport Proteins Yield Functional Insights Print Wednesday, 27 January 2010 00:00 Cells depend on contact with their outside environment in order to thrive. Two examples illustrate why: In one, information needed to guide cellular processes is constantly transmitted across cell membranes by specialized proteins, and in the other, maintaining the right gradient of ions across the membrane is a process critical to the life and death of a cell. Membrane transport proteins-functioning either as channels or transporters-are the gatekeepers that control contact with the world outside the cell by catalyzing the flow of ions and molecules across cell membranes. Malfunctioning transport proteins can lead to cancer, inflammatory, and neurological diseases. Despite their importance in cell function and in a multitude of physiological processes such as sensing pain, there are still many unknowns about how they function. Recently, in an impressive series of three papers in Nature and Science, researchers at the Oregon Health and Science University delineated the structures of three transporter proteins, one of which had never before been characterized structurally in such detail. The structures were solved using ALS Beamlines 5.0.2, 8.2.1, and 8.2.2.

369

Prediction of Protein Function Using Statistically Significant Sub-Structure Discovery.  

E-Print Network (OSTI)

??Proteins perform a vast number of functional roles. The number of protein structures available for analysis continues to grow and, with the development of methods (more)

Lucas, Craig

2007-01-01T23:59:59.000Z

370

The mechanics of SR protein phosphorylation by the splicing kinases SRPK1 and Clk/Sty  

E-Print Network (OSTI)

SAN DIEGO The Mechanics of SR protein Phosphorylation by theTHE DISSERTATION The Mechanics of SR protein Phosphorylationproject would have altered mechanics with SRPK1 catalysis

Hagopian, Jonathan Charles

2008-01-01T23:59:59.000Z

371

Investigating amino acid residue-level damage using novel proteomic approaches, with application to wool proteins.  

E-Print Network (OSTI)

??Damage to wool is derived from the modification of its constituent proteins, as the dry matter of wool is principally made up of protein. A (more)

Grosvenor, Anita J.

372

Protein Stabilized Latex Polymer Emulsions, Methods of Making, and Adhesives Containing Such Emulsions  

The invention relates to the stabilization of latex polymer emulsions with soy proteins, and to adhesives formed from the protein-stabilized latex ...

373

The characterization of Csp (Cold Shock Protein) from the Antarctic archaeon, Methanogenium frigidum.  

E-Print Network (OSTI)

??Cold shock proteins (Csp) are small acidic proteins that fold into ?-barrel structures with five anti-parallel ?-strands and are involved in essential cellular processes. Upon (more)

Giaquinto, Laura

2006-01-01T23:59:59.000Z

374

Towards understanding of Nipah virus attachment protein assembly and the role of protein affinity and crowding for membrane curvature events.  

SciTech Connect

Pathogenic viruses are a primary threat to our national security and to the health and economy of our world. Effective defense strategies to combat viral infection and spread require the development of understanding of the mechanisms that these pathogens use to invade the host cell. We present in this report results of our research into viral particle recognition and fusion to cell membranes and the role that protein affinity and confinement in lipid domains plays in membrane curvature in cellular fusion and fission events. Herein, we describe 1) the assembly of the G attachment protein of Nipah virus using point mutation studies to define its role in viral particle fusion to the cell membrane, 2) how lateral pressure of membrane bound proteins induce curvature in model membrane systems, and 3) the role of membrane curvature in the selective partitioning of molecular receptors and specific affinity of associated proteins.

Stachowiak, Jeanne C.; Hayden, Carl C.; Negrete, Oscar A.; Davis, Ryan Wesley; Sasaki, Darryl Yoshio

2013-10-01T23:59:59.000Z

375

Coev2Net: a computational framework for boosting confidence in high-throughput protein-protein interaction datasets  

E-Print Network (OSTI)

Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a ...

Hosur, Raghavendra

376

Protein Molecular Structures and Protein Fraction Profiles of New Co-Products of BioEthanol Production: A Novel Approach  

SciTech Connect

The objectives of this study were to determine the protein molecular structures of the new coproducts from bioethanol production, quantify protein structure amide I to II and {alpha}-helix to {beta}-sheet spectral peak intensity ratio, and illustrate multivariate molecular spectral analyses as a novel research tool for rapid characterization of protein molecular structures in bioethonal bioproducts. The study demonstrated that the grains had a significantly higher ratio of {alpha}-helix to {beta}-sheet in the protein structure than their coproducts produced from bioethanol processing (1.38 vs 1.03, P < 0.05). There were significant differences between wheat and corn (1.47 vs 1.29, P < 0.05) but no difference between wheat dried distiller grains with solubles (DDGS) and corn DDGS (1.04 vs 1.03, P > 0.05). The grains had a significantly higher ratio of protein amide I to II in the protein structure than their coproducts produced from bioethanol processing (4.58 vs 2.84, P < 0.05). There were no significant differences between wheat and corn (4.61 vs 4.56, P > 0.05), but there were significant differences between wheat DDGS and corn DDGS (3.08 vs 2.21, P < 0.05). This preliminary study indicated that bioethanol processing changes protein molecular structures, compared with original grains. Further study is needed with a large set of the new bioethanol coproducts to quantify protein molecular structures ({alpha}-helix to {beta}-sheet ratio; amide I to II ratio) of the bioethanol coproducts in relation to nutrient supply and availability in animals.

Yu, P.; Niu, Z; Damiran, D

2010-01-01T23:59:59.000Z

377

Digestion of protein in the equine small and large intestines  

E-Print Network (OSTI)

Four mature pony geldings weighing an average of 134 kg and fitted with ileal cannulas were used in two 4X4 Latin square experiments to determine the digestibility of forage and soybean meal protein in different segments of the equine digestive tract. Chromic oxide was fed in both trials to measure ileal flow and fecal excretion. Digestion and absorption of nitrogen was determined from changes in nitrogen:chromium ratios, and true digestion of nitrogen was computed by regression analyses. In trial 1, four diets containing varying ratios of chopped bermudagrass and alfalfa hays were fed. True total tract nitrogen digestibility was 89.6%. True digestibility of forage nitrogen in the small intestine was 40.5% in this trial, while true postileal digestibility was 78.1%. These data indicate that almost 90% of forage protein was digested over the total digestive tract. Approximately 45% of the digestible forage nitrogen was digested prececally with the remaining nitrogen being digested postileally. Thus, when ponies were fed all forage diets the lower tract was a major site for protein digestion. In trial 2, a basal, corn-based diet and three diets with soybean meal as the primary source of protein were formulated to contain approximately 5%, 9.5%, 14% and 16.5% crude protein as fed. True total tract digestion of nitrogen was 95.3%. True digestibility of feed (SBM) nitrogen in the small intestine over the range of linearity was 72.2%, while true digestibility of nitrogen reaching the large intestine was 89.8%. These data indicate that the protein in soybean meal was almost completely digested in the equine digestive tract. Further, while results from this trial indicate there may be an upper limit to the quantity of SBM nitrogen digested in the small intestine from a meal, approximately 75% of the digestible SBM protein was digested prececally when nitrogen intake was less than approximately 125 mg/kg body weight/feeding.

Farley, Eleanor Baker

1995-01-01T23:59:59.000Z

378

From Protein Structure to Function: Ring Cycle for Dilating and  

NLE Websites -- All DOE Office Websites (Extended Search)

From Protein Structure to From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore Print Wednesday, 28 August 2013 00:00 Nuclear pore complexes (NPCs) act as the central gatekeepers for selective transport between the cytoplasm and the nucleus. They allow the exchange of selected proteins and ribonucleoproteins, while preventing the transport of material not meant to cross the nuclear envelope. The NPC transport channel is the largest and most complex transport conduit in the eukaryotic kingdom and it is likely composed of only 3 out of 30 nuclear pore complex proteins (nups). Researchers from the Howard Hughes Medical Institute at the Rockefeller University have determined crystal structures of interacting domains of these centrally located channel nups, Nup54, Nup58, and Nup62, using data collected at ALS Beamline 8.2.1. These structures allowed them to elucidate the molecular mechanism that underlies large-scale diameter changes of NPCs and propose a 'ring cycle' for dilating and constricting NPCs from 10-50 nm. The ring cycle would provide a method to adjust transport activities to cellular demands with a rapid response time.

379

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-Print Network (OSTI)

Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and function of complex macromolecules. This is reasoned by the interdisciplinary character of the associated questions ranging from the molecular origin of the loss of biological functionality as, for example, in Alzheimer's disease to the development of organic circuits for biosensory applications. In this lecture, we focus on the analysis of mesoscopic models for protein folding, aggregation, and hybrid systems of soft and solid condensed matter. The simplicity of the coarse-grained models allows for a more universal description of the notoriously difficult problem of protein folding. In this approach, classifications of structure formation processes with respect to the conformational pseudophases are possible. This is similar in aggregation and adsorption processes, where the individual folding propensity is influenced by external forces. The main problem in studies of conformational transitions is that the sequences of amino acids proteins are built up of are necessarily of finite length and, therefore, a thermodynamic limit does not exist. Thus, structural transitions are not phase transitions in the strict thermodynamic sense and the analysis of pseudouniversal aspects is intricate, as apparently small-system effects accompany all conformational transitions and cannot be neglected.

Michael Bachmann; Wolfhard Janke

2007-10-25T23:59:59.000Z

380

An extremal optimization search method for the protein folding problem: the go-model example  

Science Conference Proceedings (OSTI)

The protein folding problem consists of predicting the functional (native)structure of the protein given its linear sequence of amino acids. Despite extensive progress made in understanding the process of protein folding, this problem still remains ... Keywords: extremal optimization, go-model, protein folding

Alena Shmygelska

2007-07-01T23:59:59.000Z

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.


381

Highly accurate and consistent method for prediction of helix and strand content from primary protein sequences  

Science Conference Proceedings (OSTI)

Objective:: One of interesting computational topics in bioinformatics is prediction of secondary structure of proteins. Over 30 years of research has been devoted to the topic but we are still far away from having reliable prediction methods. A critical ... Keywords: Bioinformatics, Composition moment vector, Composition vector, Primary protein sequence, Protein content prediction, Proteomics, Secondary protein structure

Jishou Ruan; Kui Wang; Jie Yang; Lukasz A. Kurgan; Krzysztof Cios

2005-09-01T23:59:59.000Z

382

Nucleic acid encoding a self-assembling split-fluorescent protein system  

DOE Patents (OSTI)

The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

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

2011-06-07T23:59:59.000Z

383

Crystal Structure of a Protein Kinase A Complex  

NLE Websites -- All DOE Office Websites (Extended Search)

Crystal Structure of a Protein Kinase A Complex Print Crystal Structure of a Protein Kinase A Complex Print Protein kinase A (PKA) is an enzyme that regulates processes as diverse as growth, memory, and metabolism. In its unactivated state, PKA exists as a tetrameric complex of two catalytic subunits and a regulatory subunit dimer, but when the intracellular signaling molecule cyclic adenosine monophosphate (cAMP) binds to the regulatory subunit, it facilitates dissociation and activation of the catalytic subunits. While separate structures of these subunits were previously known, a group from the University of California, San Diego, is the first to determine (to a resolution of 2.0 Å) the structure of the PKA catalytic subunits bound to the regulatory subunit. The structure of the complex clarifies the mechanism for PKA inhibition, and its comparison with the structure of cAMP bound to the regulatory subunit hints at how cAMP binding drives its activation.

384

Large Scale Quantum-mechanical Calculations of Proteins, Nanomaterials and  

NLE Websites -- All DOE Office Websites (Extended Search)

Large Scale Quantum-mechanical Calculations of Proteins, Nanomaterials and Large Scale Quantum-mechanical Calculations of Proteins, Nanomaterials and Other Large Systems Event Sponsor: Leadership Computing Facility Seminar Start Date: Dec 5 2013 - 2:00pm Building/Room: Building 240/Room 4301 Location: Argonne National Laboratory Speaker(s): Dmitri G. Fedorov Speaker(s) Title: National Institute of Advanced Industrial Science and Technology (AIST) Host: Yuri Alexeev Our approach to large scale calculations is based on fragmenting a molecular system into pieces, and performing quantum-mechanical calculations of these fragments and their pairs in the fragment molecular orbital method (FMO). After a brief summary of the methodology, some typical applications to protein-ligand complexes, chemical reactions in explicit solvent, and nanomaterials (silicon nanowires, zeolites.

385

Crystal Structure of a Protein Kinase A Complex  

NLE Websites -- All DOE Office Websites (Extended Search)

Crystal Structure of a Protein Kinase A Complex Print Crystal Structure of a Protein Kinase A Complex Print Protein kinase A (PKA) is an enzyme that regulates processes as diverse as growth, memory, and metabolism. In its unactivated state, PKA exists as a tetrameric complex of two catalytic subunits and a regulatory subunit dimer, but when the intracellular signaling molecule cyclic adenosine monophosphate (cAMP) binds to the regulatory subunit, it facilitates dissociation and activation of the catalytic subunits. While separate structures of these subunits were previously known, a group from the University of California, San Diego, is the first to determine (to a resolution of 2.0 Å) the structure of the PKA catalytic subunits bound to the regulatory subunit. The structure of the complex clarifies the mechanism for PKA inhibition, and its comparison with the structure of cAMP bound to the regulatory subunit hints at how cAMP binding drives its activation.

386

Past MPSA Meetings, IAPSAP, International Association for Protein Structure  

NLE Websites -- All DOE Office Websites (Extended Search)

Past MPSA Meetings Past MPSA Meetings The MPSA conferences began in 1974 with a small workshop in Boston, MA, USA organized by Richard A. Laursen, Boston University, for the purpose of exchanging information on the then new chemistry for sequencing proteins by removing amino acids from the amino terminus one at a time. This chemical scheme was developed principally by Pehr Edman, at the Rockefeller Institute, the University of Lund, Sweden, and finally at the St. Vincent School of Medical Research in Melbourne, Australia. Subsequent workshops have been held approximately every two years and have alternated between Europe, Japan and the United States. As techniques for protein analysis increased in the early 1990s, the workshops expanded in scope and size to emphasize additional aspects of protein structure analysis as well as chemistries related to primary sequence analysis.

387

Crystal Structure of a Protein Kinase A Complex  

NLE Websites -- All DOE Office Websites (Extended Search)

Crystal Structure of a Protein Kinase A Complex Print Crystal Structure of a Protein Kinase A Complex Print Protein kinase A (PKA) is an enzyme that regulates processes as diverse as growth, memory, and metabolism. In its unactivated state, PKA exists as a tetrameric complex of two catalytic subunits and a regulatory subunit dimer, but when the intracellular signaling molecule cyclic adenosine monophosphate (cAMP) binds to the regulatory subunit, it facilitates dissociation and activation of the catalytic subunits. While separate structures of these subunits were previously known, a group from the University of California, San Diego, is the first to determine (to a resolution of 2.0 Å) the structure of the PKA catalytic subunits bound to the regulatory subunit. The structure of the complex clarifies the mechanism for PKA inhibition, and its comparison with the structure of cAMP bound to the regulatory subunit hints at how cAMP binding drives its activation.

388

Translationally Controlled Tumor Protein Protects against DNA Damage in Low  

NLE Websites -- All DOE Office Websites (Extended Search)

Translationally Controlled Tumor Protein Protects against DNA Damage in Low Translationally Controlled Tumor Protein Protects against DNA Damage in Low Dose γ-Irradiated Cells Edouard Azzam New Jersey Medical School Cancer Center Abstract We have previously shown that exposure to low dose/low dose rate γ-rays can protect normal human and rodent cells against oxidative/clastogenic damages induced spontaneously or by a subsequent challenge dose of ionizing radiation. To gain insight into the mechanisms underlying these effects, we used amine-specific isobaric tags for relative and absolute quantitation (iTRAQ)-based approach to identify induced proteolytic events. Intriguingly, the Translationally Controlled Tumor Protein (TCTP) was significantly up-regulated after 10cGy (0.2cGy/h) but not after 4 Gy (1 Gy/min) in several strains of normal human fibroblasts maintained in 2- or

389

Scientists ratchet up understanding of cellular protein factory  

NLE Websites -- All DOE Office Websites (Extended Search)

Understanding of cellular protein factory Understanding of cellular protein factory Scientists ratchet up understanding of cellular protein factory The research could aid in development of new antibiotics used to fight multidrug resistant superbugs such as MRSA found in many U.S. hospitals. December 2, 2010 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics and new materials. Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics and new materials.

390

Order parameter prediction from molecular dynamics simulations in proteins  

E-Print Network (OSTI)

A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter -- a reduced descriptor for the major subset of degrees of freedom -- that can be used to aid sampling for the large conformational change. We present a novel way to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that ma...

Perilla, Juan R

2011-01-01T23:59:59.000Z

391

Degradation of the E. coli small heat-shock proteins by the AAA+ protease lon : significance to protein quality-control  

E-Print Network (OSTI)

The refolding and elimination of damaged and aggregated proteins requires the concerted effort of several branches of the protein quality-control network. This network includes refolding chaperones, disaggregases, holdases ...

Bissonnette, Sarah Ayano

2010-01-01T23:59:59.000Z

392

Fast computational methods for predicting protein structure from primary amino acid sequence  

SciTech Connect

The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

Agarwal, Pratul Kumar (Knoxville, TN)

2011-07-19T23:59:59.000Z

393

Investigating insect molecular responses to two plant defense proteins and characterizing a novel insecticidal protein from Arabidopsis  

E-Print Network (OSTI)

The molecular interaction between plants and insects is dynamic and multifaceted. We are interested in understanding the molecular mechanism that insects utilize to overcome plant defense proteins, as well as discovering novel plant insecticidal proteins. Three projects were developed. First, we evaluated the effects of soybean cysteine protease inhibitor (soyacystatin N, scN) on the growth and development in southern corn rootworm. Both subtractive suppressed hybridization (SSH) and cDNA microarray analyses were used to uncover the changes of gene expression profiles in southern corn rootworm under the scN challenge. The counterdefense-related genes were identified, suggesting that southern corn rootworm deployed several regulatory mechanisms to overcome the dietary scN. Second, to identify and confirm insecticidal properties of vegetative storage protein 2 in Arabidopsis (AtVSP2), the gene was cloned and expressed in E.coli. This protein showed acid phosphatase activity. Feeding assay indicated that AtVSP increased the mortality and delayed the development of two coleopteran and one dipteran insects. Third, to identify the molecular mechanism of this novel insecticidal protein, P element mutagenesis was utilized to generate AtVSP resistant mutants (VRs). Two balanced VR mutants and their revertants were generated, and can be used to further characterize the genetic loci of P element inserted in the mutants.

Liu, Yilin

2005-12-01T23:59:59.000Z

394

High-Resolution Differential Ion Mobility Spectrometry of a Protein  

SciTech Connect

Use of elevated electric fields and helium-rich gases has recently enabled differential IMS with resolving power up to R ~ 300. Here we applied that technique to proteins (namely, mass-selected ubiquitin ions), achieving R up to ~80 and separating many previously mixed conformers. While still limited by conformational multiplicity within each observed feature, this resolution is some four times the highest previously reported using either conventional or differential IMS. The capability for fine resolution of protein conformers may open new avenues for variant separation in top-down proteomics.

Shvartsburg, Alexandre A.; Smith, Richard D.

2013-01-17T23:59:59.000Z

395

Directed transport as a mechanism for protein folding in vivo  

E-Print Network (OSTI)

We propose a model for protein folding in vivo based on a Brownian-ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different type of obstacles. This model solves Levinthal's paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.

Gonzalez-Candela, Ernesto

2009-01-01T23:59:59.000Z

396

Directed transport as a mechanism for protein folding in vivo  

E-Print Network (OSTI)

We propose a model for protein folding in vivo based on a Brownian-ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different type of obstacles. This model solves Levinthal's paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.

Ernesto Gonzalez-Candela; Victor Romero-Rochin

2009-09-23T23:59:59.000Z

397

Photoconversion of organic materials into single-cell protein  

DOE Patents (OSTI)

A process is described for converting organic materials (such as biomass wastes) into sterile, high-grade bacterial protein suitable for use an animal feed or human food supplements. In a preferred embodiment the process involves thermally gasifying the organic material into primarily carbon monoxide, hydrogen and nitrogen products, followed by photosynthetic bacterial assimilation of the gases into cell material, which can be as high as 65% protein. The process is ideally suited for waste recycling and for food production under zero-gravity or extra-terrestrial conditions.

Weaver, Paul F. (13130 W. 66th Pl., Golden, CO 80401)

2001-01-01T23:59:59.000Z

398

Divinyl ether synthase gene and protein, and uses thereof  

DOE Patents (OSTI)

The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.

Howe, Gregg A. (East Lansing, MI); Itoh, Aya (Tsuruoka, JP)

2011-09-13T23:59:59.000Z

399

Photoconversion of organic materials into single-cell protein  

DOE Patents (OSTI)

A process is described for converting organic materials (such as biomass wastes) into sterile, high-grade bacterial protein suitable for use an animal feed or human food supplements. In a preferred embodiment the process involves thermally gasifying the organic material into primarily carbon monoxide, hydrogen and nitrogen products, followed by photosynthetic bacterial assimilation of the gases into cell material, which can be high as 65% protein. The process is ideally suited for waste recycling and for food production under zero-gravity or extra-terrestrial conditions.

Weaver, P.F.

1991-12-31T23:59:59.000Z

400

From Protein Structure to Function: Ring Cycle for Dilating and  

NLE Websites -- All DOE Office Websites (Extended Search)

From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore Print From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore Print Nuclear pore complexes (NPCs) act as the central gatekeepers for selective transport between the cytoplasm and the nucleus. They allow the exchange of selected proteins and ribonucleoproteins, while preventing the transport of material not meant to cross the nuclear envelope. The NPC transport channel is the largest and most complex transport conduit in the eukaryotic kingdom and it is likely composed of only 3 out of 30 nuclear pore complex proteins (nups). Researchers from the Howard Hughes Medical Institute at the Rockefeller University have determined crystal structures of interacting domains of these centrally located channel nups, Nup54, Nup58, and Nup62, using data collected at ALS Beamline 8.2.1. These structures allowed them to elucidate the molecular mechanism that underlies large-scale diameter changes of NPCs and propose a 'ring cycle' for dilating and constricting NPCs from 10-50 nm. The ring cycle would provide a method to adjust transport activities to cellular demands with a rapid response time.

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

Length control of microtubules by depolymerizing motor proteins  

E-Print Network (OSTI)

In many intracellular processes, the length distribution of microtubules is controlled by depolymerizing motor proteins. Experiments have shown that, following non-specific binding to the surface of a microtubule, depolymerizers are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. We develop a quantitative model to study the depolymerizing action of such a generic motor protein, and its possible effects on the length distribution of microtubules. We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the length distribution is, in general, non-monotonic with a single peak. However, for highly processive motors and large motor densities, this distribution effectively becomes an exponential decay. Our findings suggest that such motor proteins may be selectively used by the cell to ensure precise control of MT lengths. The model is also used to analyze experimental observations of motor-induced depolymerization.

Bindu S. Govindan; Manoj Gopalakrishnan; Debashish Chowdhury

2007-09-24T23:59:59.000Z

402

From Protein Structure to Function: Ring Cycle for Dilating and  

NLE Websites -- All DOE Office Websites (Extended Search)

From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore Print From Protein Structure to Function: Ring Cycle for Dilating and Constricting the Nuclear Pore Print Nuclear pore complexes (NPCs) act as the central gatekeepers for selective transport between the cytoplasm and the nucleus. They allow the exchange of selected proteins and ribonucleoproteins, while preventing the transport of material not meant to cross the nuclear envelope. The NPC transport channel is the largest and most complex transport conduit in the eukaryotic kingdom and it is likely composed of only 3 out of 30 nuclear pore complex proteins (nups). Researchers from the Howard Hughes Medical Institute at the Rockefeller University have determined crystal structures of interacting domains of these centrally located channel nups, Nup54, Nup58, and Nup62, using data collected at ALS Beamline 8.2.1. These structures allowed them to elucidate the molecular mechanism that underlies large-scale diameter changes of NPCs and propose a 'ring cycle' for dilating and constricting NPCs from 10-50 nm. The ring cycle would provide a method to adjust transport activities to cellular demands with a rapid response time.

403

Contrasting HIV phylogenetic relationships and V3 loop protein similarities  

Science Conference Proceedings (OSTI)

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

Korber, B. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Myers, G. [Los Alamos National Lab., NM (United States)

1992-12-31T23:59:59.000Z

404

Contrasting HIV phylogenetic relationships and V3 loop protein similarities  

Science Conference Proceedings (OSTI)

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

Korber, B. (Los Alamos National Lab., NM (United States) Santa Fe Inst., NM (United States)); Myers, G. (Los Alamos National Lab., NM (United States))

1992-01-01T23:59:59.000Z

405

Electrostatics Controls the Formation of Amyloid Superstructures in Protein Aggregation  

E-Print Network (OSTI)

density for a cluster composed of N protein monomers: 2 3/1 3/222 4 )1( 4 )1( 4 )1()( a enN Na enN R enN N cr c r c r pi ? pi ? pi ?? ?= ?= ?= (2.15) Where a = monomer radius R = cluster radius 3 ?? ??? ? = a RN and nce charge per monomer...

Foder, Vito; Zaccone, Alessio; Lattuada, Marco; Donald, Athene M.

2013-09-05T23:59:59.000Z

406

Go-ing for the prediction of protein folding mechanisms  

E-Print Network (OSTI)

of Chemistry, Faculty of Science, Kobe University, Kobe, 657-8501, Japan Protein folding has been a long-lived could be relatively simple. These three ingredients are linked together with an almost one-line free work (8, 9). The surprise of the three papers is that apparently one can have both simplicity and fair

Takada, Shoji

407

Protein kinase and phosphatase activities of thylakoid membranes  

DOE Green Energy (OSTI)

Dephosphorylation of the 25 and 27 kDa light-harvesting Chl a/b proteins (LHCII) of the thylakoid membranes is catalyzed by a phosphatase which differs from previously reported thylakoid-bound phosphatases in having an alkaline pH optimum (9.0) and a requirement for Mg/sup 2 +/ ions. Dephosphorylation of the 8.3 kDa psb H gene product requires a Mg/sup 2 +/ ion concentration more than 200 fold higher than that for dephosphorylation of LHC II. The 8.3 kDa and 27 kDa proteins appear to be phosphorylated by two distinct kinases, which differ in substrate specificity and sensitivity to inhibitors. The plastoquinone antagonist 2,5-dibromo-3-methyl-6-isopropyl-benzoquinone (DBMIB) inhibits phosphorylation of the 27 kDa LHC II much more readily than phosphorylation of the 8.3 kDa protein. A similar pattern of inhibition is seen for two synthetic oligopeptides (MRKSATTKKAVC and ATQTLESSSRC) which are analogs of the phosphorylation sites of the two proteins. Possible modes of action of DBMIB are discussed. 45 refs., 7 figs., 3 tabs.

Michel, H.; Shaw, E.K.; Bennett, J.

1987-01-01T23:59:59.000Z

408

Probabilistic annotation of protein sequences based on functional classifications  

E-Print Network (OSTI)

? ? ??? = N 1 *))(( * ))(( )( )( ???? ? ? cYN N N N cYN j j j jj = ))(( ))(( )( )( ???? ? ? ? ?? cN cN j j j . (S5) We find that ))( | ( )( ccP j j ? ? ??? is simply the ratio between two numbers: i) the number of proteins truly...

Levy, Emmanuel D; Ouzounis, Christos A; Gilks, Walter R; Audit, Benjamin

2005-12-14T23:59:59.000Z

409

Soy Protein ProductsChapter 6 Uses in Food Systems  

Science Conference Proceedings (OSTI)

Soy Protein Products Chapter 6 Uses in Food Systems Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry 92B3B17CCACD0D1166530AEA8D994D92 AOCS Press Downloadable pdf of Chapter 6 Uses in

410

Protein structure prediction enhanced with evolutionary diversity : SPEED.  

SciTech Connect

For naturally occurring proteins, similar sequence implies similar structure. Consequently, multiple sequence alignments (MSAs) often are used in template-based modeling of protein structure and have been incorporated into fragment-based assembly methods. Our previous homology-free structure prediction study introduced an algorithm that mimics the folding pathway by coupling the formation of secondary and tertiary structure. Moves in the Monte Carlo procedure involve only a change in a single pair of {phi},{psi} backbone dihedral angles that are obtained from a Protein Data Bank-based distribution appropriate for each amino acid, conditional on the type and conformation of the flanking residues. We improve this method by using MSAs to enrich the sampling distribution, but in a manner that does not require structural knowledge of any protein sequence (i.e., not homologous fragment insertion). In combination with other tools, including clustering and refinement, the accuracies of the predicted secondary and tertiary structures are substantially improved and a global and position-resolved measure of confidence is introduced for the accuracy of the predictions. Performance of the method in the Critical Assessment of Structure Prediction (CASP8) is discussed.

DeBartolo, J.; Hocky, G.; Wilde, M.; Xu, J.; Freed, K. F.; Sosnick, T. R.; Univ. of Chicago; Toyota Technological Inst. at Chicago

2010-03-01T23:59:59.000Z

411

Preserving Genome Integrity: The DdrA Protein  

E-Print Network (OSTI)

, the action of DdrA may overlap with the activity of at least one other protein, and while each redundant activity is functional in rich medium, only DdrA is functional in cultures held in MgSO4. Alternatively simply by preventing the massive genomic degradation evident in Figure 5B. In a rich medium, active DNA

Raines, Ronald T.

412

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops  

Science Conference Proceedings (OSTI)

Several applications in biology - e.g., incorporation of protein flexibility in ligand docking algorithms, interpretation of fuzzy X-ray crystallographic data, and homology modeling - require computing the internal parameters of a flexible fragment (usually, ... Keywords: Biology and genetics, Robotics

Peggy Yao; Ankur Dhanik; Nathan Marz; Ryan Propper; Charles Kou; Guanfeng Liu; Henry van den Bedem; Jean-Claude Latombe; Inbal Halperin-Landsberg; Russ B. Altman

2008-10-01T23:59:59.000Z

413

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters  

E-Print Network (OSTI)

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters Michael S. Lee1,2,3 , Rajkumar. Methodology/Principal Findings: The pipeline consists of a Perl core that integrates more than 20 individual-delimited, and hypertext markup language (HTML) formats. So far, the pipeline has been used to study viral and bacterial

414

Methods of use of cellulose binding domain proteins  

DOE Patents (OSTI)

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

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

1997-09-23T23:59:59.000Z

415

Prolinks: A Database of Protein Functional Linkages Derived from Coevolution  

DOE Data Explorer (OSTI)

Prolinks makes dozens of genome data files available for download and is a a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. [From About Prolinks Database 2.0 at http://prolinks.doe-mbi.ucla.edu/cgi_files/functionator/about.html] Users may search the database using a unique identifier number from any of several, well known resources or by various characteristics for specific proteins within specific genomes. Results include amino acid sequences, homologs, phylogenetic profiles, COGs (Clusters of Orthologous Groups of proteins), and KEGG information (Kyoto Encyclopedia of Genes and Genomes). When the Prolinks inferences are run, color graphs of linkages are generated. (Specialized Interface)

Bowers, Peter M.; Pelligrini, Matteo; Thompson, Mike J.; Fierro, Joe; Yeates, Todd O.; Eisenberg, David

416

Methods of use of cellulose binding domain proteins  

SciTech Connect

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

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

1997-01-01T23:59:59.000Z

417

RESEARCH ARTICLES Effective Energy Function for Proteins in Solution  

E-Print Network (OSTI)

for use with a slightly modified version of the CHARMM 19 polar hydro- gen potential energy function.26RESEARCH ARTICLES Effective Energy Function for Proteins in Solution Themis Lazaridis1 and Martin solvent-exclusion model for the solvation free energy is developed. It is based on theoretical

Lazaridis, Themis

418

Structural alignment of largesize proteins via lagrangian relaxation  

Science Conference Proceedings (OSTI)

We illustrate a new approach to the Contact Map Overlap problem for the comparison of protein structures. The approach is based on formulating the problem as an integer linear program and then relaxing in a Lagrangian way a suitable set of constraints. ...

Alberto Caprara; Giuseppe Lancia

2002-04-01T23:59:59.000Z

419

Protein Science (1997). 6:1849-1857. Cambridge University Press. Printed in the USA. Copyright 0 1997 The Protein Society  

E-Print Network (OSTI)

of several en- zymes utilizing such methods have led to functional insights. For instance, the very high protein, is a complicated task. The simplest method is to com- pare the net charge of the molecules of this surface element is kept fixed in both sets of calculations (see Methods). As summarized in Table 1

Raychaudhuri, Soumya

420

Molecular Characterization of Radial Spoke Subcomplex Containing Radial Spoke Protein 3 and Heat Shock Protein 40 in Sperm Flagella of the Ascidian Ciona intestinalis  

E-Print Network (OSTI)

Members of the heat-shock protein (HSP)40 regulate the protein folding activity of HSP70 proteins and help the functional specialization of this molecular chaperone system in various types of cellular events. We have recently identified Hsp40 as a component of flagellar axoneme in the ascidian Ciona intestinalis, suggesting a correlation between Hsp40 related chaperone system and flagellar function. In this study, we have found that Ciona 37-kDa Hsp40 is extracted from KCl-treated axonemes with 0.5 M KI solution and comigrates with radial spoke protein (RSP)3 along with several proteins as a complex through gel filtration and ion exchange columns. Peptide mass fingerprinting with matrix-assisted laser desorption ionization/time of flight/mass spectrometry revealed that other proteins in the complex include a homolog of sea urchin spokehead protein (homolog of RSP4/6), a membrane occupation and recognition nexus repeat protein with sequence similarity with meichroacidin, and a functionally unknown 33-kDa protein. A spoke head protein, LRR37, is not included in the complex, suggesting that the complex constructs the stalk of radial spoke. Immunoelectron microscopy indicates that Hsp40 is localized in the distal portion of spoke stalk, possibly at the junction between spoke head and the stalk.

Yuhkoh Satouh; Potturi Padma; Toshifusa Toda; Nori Satoh; Hiroyuki Ide; Kazuo Inaba

2004-01-01T23:59:59.000Z

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

The Collagen Protein Viewed at Unprecedented Detail | Advanced Photon  

NLE Websites -- All DOE Office Websites (Extended Search)

Assembling Nanoparticles the Easy DNA-Way Assembling Nanoparticles the Easy DNA-Way Better, cleaner fuel injectors for automobiles? Poxvirus Potency Uncovered in New Atomic Map Striking Nano Gold Oldest Known Magnet's Secrets Revealed Under High Pressures Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed The Collagen Protein Viewed at Unprecedented Detail FEBRUARY 26, 2008 Bookmark and Share A view of a rat tail tendon using second-harmonic generation microscopy. The collagen fibers show up in green and red. The structure and behavior of one of the most common proteins in our bodies has been resolved at a level of detail never before seen, thanks to new research performed at the Advanced Photon Source (APS) at the U.S.

422

Regulation of Nuclear Localization of Signaling Proteins by Cytokinin  

SciTech Connect

Cytokinins are a class of mitogenic plant hormones that play an important role in most aspects of plant development, including shoot and root growth, vascular and photomorphogenic development and leaf senescence. A model for cytokinin perception and signaling has emerged that is similar to bacterial two-component phosphorelays. In this model, binding of cytokinin to the extracellular domain of the Arabidopsis histidine kinase (AHKs) receptors induces autophosphorylation within the intracellular histidine-kinase domain. The phosphoryl group is subsequently transferred to cytosolic Arabidopsis histidine phosphotransfer proteins (AHPs), which have been suggested to translocate to the nucleus in response to cytokinin treatment, where they then transfer the phosphoryl group to nuclear-localized response regulators (Type-A and Type-B ARRs). We examined the effects of cytokinin on AHP subcellular localization in Arabidopsis and, contrary to expectations, the AHPs maintained a constant nuclear/cytosolic distribution following cytokinin treatment. Furthermore, mutation of the conserved phosphoacceptor histidine residue of the AHP, as well as disruption of multiple cytokinin signaling elements, did not affect the subcellular localization of the AHP proteins. Finally, we present data indicating that AHPs maintain a nuclear/cytosolic distribution by balancing active transport into and out of the nucleus. Our findings suggest that the current models indicating relocalization of AHP protein into the nucleus in response to cytokinin are incorrect. Rather, AHPs actively maintain a consistent nuclear/cytosolic distribution regardless of the status of the cytokinin response pathway.

Kieber, J.J.

2010-05-01T23:59:59.000Z

423

Toluene 4-Monooxygenase and its Complex with Effector Protein T4moD  

Science Conference Proceedings (OSTI)

Toluene 4-monooxygenase (T4MO) is a multiprotein diiron enzyme complex that catalyzes the regiospecific oxidation of toluene to p-cresol. Catalytic function requires the presence of a small protein, called the effector protein. Effector protein exerts substantial control on the diiron hydroxylase catalytic cycle through protein-protein interactions. High-resolution crystal structures of the stoichometric hydroxylase and effector protein complex described here reveal how protein-protein interactions and reduction of the diiron center produce an active site configuration poised for reaction with O{sub 2}. Further information from crystal structures of mutated isoforms of the hydroxylase and a peroxo adduct is combined with catalytic results to give a fuller picture of the geometry of the enzyme-substrate complex used for the high fidelity oxidation of hydrocarbon substrates.

Bailey, Lucas J.; Fox, Brian G. (UW)

2012-10-16T23:59:59.000Z

424

Enzyme-based reporters for mapping proteome and imaging proteins in living cells  

E-Print Network (OSTI)

Each eukaryotic cell is exquisitely divided into organellar compartments whose functions are uniquely defined by the set of proteins they possess. For each individual protein, precise targeting to a specific sub-cellular ...

Zou, Peng, 1985-

2013-01-01T23:59:59.000Z

425

FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein...  

NLE Websites -- All DOE Office Websites (Extended Search)

FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein Structure Data Taken at ALS FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein Structure Data...

426

Size-dependent mechanical properties of beta-structures in protein materials  

E-Print Network (OSTI)

Protein materials such as spider silk can be exceptionally strong, and they can stretch tremendously before failure. Notably, silks are made entirely of proteins, which owe their structure and stability to weak molecular ...

Keten, Sinan

2010-01-01T23:59:59.000Z

427

The development of novel excipients for the stabilization of proteins against aggregation  

E-Print Network (OSTI)

Although protein based therapeutics is the fastest growing sector of the pharmaceutical industry, production costs remain incredibly high and rapid commercialization of new protein drug candidates are not being fully ...

Schneider, Curtiss P. (Curtiss Paul)

2011-01-01T23:59:59.000Z

428

Characterization of UNUSUAL LATERAL ORGANS : a miRNA regulated F-Box protein  

E-Print Network (OSTI)

between ULO and the HD-ZIP proteins in planta. Anotherof homodomain-leucine zipper (HD-Zip) proteins. Plant SignalKANADI and class III HD-Zip gene families regulate embryo

Smith, Peter Thomas

2009-01-01T23:59:59.000Z

429

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes  

E-Print Network (OSTI)

The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions ...

Lin, Michael F.

430

Temperature-jump 2D IR spectroscopy to study protein conformational dynamics  

E-Print Network (OSTI)

Temperature-jump (T-jump) two-dimensional infrared spectroscopy (2D IR) is developed, characterized, and applied to the study of protein folding and association. In solution, protein conformational changes span a wide range ...

Jones, Kevin C. (Kevin Chapman)

2012-01-01T23:59:59.000Z

431

Natural -sheet proteins use negative design to avoid edge-to-edge aggregation  

E-Print Network (OSTI)

of proteins almost all have severe problems of insol- ubility and aggregation (3­6); many designs originally surveys their properties in all classes of all- structure. Methods Coordinate files are from the Protein

Richardson, David

432

A Robust and Rapid Method of Producing Soluble, Stable, and Functional G-Protein Coupled Receptors  

E-Print Network (OSTI)

Membrane proteins, particularly G-protein coupled receptors (GPCRs), are notoriously difficult to express. Using commercial E.coli cell-free systems with the detergent Brij-35, we could rapidly produce milligram quantities ...

Baaske, Philipp

433

Understanding the functions of HMGB proteins in the mechanism of action of cisplatin  

E-Print Network (OSTI)

High mobility group box (HMGB) proteins are DNA-binding proteins that regulate many important DNA-related processes. They are known to recognize the major lesion present in cisplatin-modified DNA, and have been assumed to ...

Park, Semi, Ph. D. Massachusetts Institute of Technology

2012-01-01T23:59:59.000Z

434

Investigating asparagine-linked glycosylation substrate : specificity and effects on protein folding  

E-Print Network (OSTI)

N-linked glycosylation is a ubiquitous form of protein modification whereby a preassembled oligosaccharide is covalently attached the asparagine side chain of an acceptor protein. This process involves numerous enzymes, ...

Chen, Mark M

2009-01-01T23:59:59.000Z

435

Methods for validating the presence of and characterizing proteins deposited onto an array  

DOE Patents (OSTI)

A method of determining if proteins have been transferred from liquid-phase protein fractions to an array comprising staining the array with a total protein stain and imaging the array, optionally comparing the staining with a standard curve generated by staining known amounts of a known protein on the same or a similar array; a method of characterizing proteins transferred from liquid-phase protein fractions to an array including staining the array with a post-translational modification-specific (PTM-specific) stain and imaging the array and, optionally, after staining the array with a PTM-specific stain and imaging the array, washing the array, re-staining the array with a total protein stain, imaging the array, and comparing the imaging with the PTM-specific stain with the imaging with the total protein stain; stained arrays; and images of stained arrays.

Schabacker, Daniel S. (Naperville, IL)

2010-09-21T23:59:59.000Z

436

Mucin granule-associated proteins in human bronchial epithelial cells: the airway goblet cell "granulome"  

E-Print Network (OSTI)

of cysteine string protein (CSP) in regulated exocytosis.Cysteine string protein [CSP]) and cytoskeletal (actin,that MARCKS, HSP70, CSP and hCLCA1 were present on the

Raiford, Kimberly L; Park, Joungjoa; Lin, Ko-Wei; Fang, Shijing; Crews, Anne L; Adler, Kenneth B

2011-01-01T23:59:59.000Z

437

A CD19/Fc fusion protein for detection of anti-CD19 chimeric antigen receptors  

E-Print Network (OSTI)

Oliveira et al. : A CD19/Fc fusion protein for detection ofof the CD19-IgG 1 Fc fusion was performed under denatur- ingOpen Access A CD19/Fc fusion protein for detection of anti-

De Oliveira, Satiro N; Wang, Jiexin; Ryan, Christine; Morrison, Sherie L; Kohn, Donald B; Hollis, Roger P

2013-01-01T23:59:59.000Z

438

2D IR spectroscopy and computational modeling : application to protein folding and binding  

E-Print Network (OSTI)

In this thesis, dynamics experiments are developed that can be used to study protein conformational changes such as folding and binding. Every functional motion of a protein is inextricably linked to conformational dynamics. ...

Ganim, Ziad

2010-01-01T23:59:59.000Z

439

Cross-linking proteins with bimetallic tetracarboxylate compounds of transition metals  

DOE Patents (OSTI)

Stable cross-linked complexes of transition-metal tetracarboxylates and proteins are formed. The preferred transition-metal is rhodium. The protein may be collagen or an enzyme such as a proteolytic enzyme.

Kostic, Nenad M. (Ames, IA); Chen, Jian (Ames, IA)

1991-03-05T23:59:59.000Z

440

ATP-Induced Shape Change in a Model Protein Complexed in ...  

Science Conference Proceedings (OSTI)

ATP-Induced Shape Change in a Model Protein Complexed in Chaperonins. The role of molecular chaperones in mediating ...

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

Vacuum deposition of non-protein materials for use in antibody detection assays  

DOE Patents (OSTI)

An apparatus and method for detecting antibodies specific to non-protein antigens. The apparatus is an immunological plate containing a plurality of plastic projections coated with a non-protein material. Assays utilizing the plate are capable of stabilizing the non-protein antigens with detection levels for antibodies specific to the antigens on a nanogram level. A screening assay with the apparatus allows for early detection of exposure to non-protein materials. 10 figs.

Barrick, C.W.; Clarke, S.M.; Nordin, C.W.

1990-02-02T23:59:59.000Z

442

Cellulosic Fiber Composites Using Protein Hydrolysates and Methods of Making Same  

This technology relates to cellulosic fiber composites using protein hydrolysates. Cellulosic fiber composites currently use petroleum-derived binders ...

443

A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank  

E-Print Network (OSTI)

diffe n GC biases, for thre singl -dom in proteins, ys-ozym (PDB cod 31z , circl s), p osphocarrier prot in Hpr (PDB code 1op , d amonds), and myoglobin (PDB c de 1a6g,squar s), a d f r th small tw -do ins protein ATP s n-thase ? un t (ATPE, PDB cod... is the same for all sites, times the site-specific distributions due to the selection process, Eq. (6), ?i(a) ? wAA(a) exp[-?i h(a)], (10) The factor wAA(a) is obtained as the sum of the expected frequencies of its codons under mutation alone, wCOD(n) = f(n1...

Bastolla, Ugo; Porto, Markus; Roman, H Eduardo; Vendruscolo, Michele

2006-05-31T23:59:59.000Z

444

An overview of recent developments in the interpretation and prediction of fast internal protein dynamics  

E-Print Network (OSTI)

in proteins, and a variety of new NMR techniques have been developed to access internal mobility in proteins the description of overall dynamics and its possible coupling to internal mobility, the introduction of models Introduction Over the past decades, structures of proteins have been intensely studied, new folds

445

High-Order Membrane Complexes from Activated G-Protein Subunits  

NLE Websites -- All DOE Office Websites (Extended Search)

High-Order Membrane Complexes from Activated G-Protein Subunits Print High-Order Membrane Complexes from Activated G-Protein Subunits Print Many physiological processes initiated in response to external (extracellular) signals such as hormones, neurotransmitters, or light are regulated by a complex dance involving GTP-binding (G) proteins: G-protein-coupled receptors (GPCRs), proteins integral to the cell membrane, sense the signal and activate G proteins in the cellular cytoplasm, but enzymes such as G-protein-coupled receptor kinase 2 (GRK2) inhibit the activity of the G proteins. A joint University of Michigan-University of Illinois, Chicago, team has determined the first structure of a particular G-protein-GRK2 complex. The structure in combination with previous structures of related G-protein complexes shows how Nature has evolved the G-protein structure to not only propagate activation signals but at the same time also directly respond to regulatory proteins that control the duration of the signal.

446

High-Order Membrane Complexes from Activated G-Protein Subunits  

NLE Websites -- All DOE Office Websites (Extended Search)

High-Order Membrane Complexes from Activated G-Protein Subunits Print High-Order Membrane Complexes from Activated G-Protein Subunits Print Many physiological processes initiated in response to external (extracellular) signals such as hormones, neurotransmitters, or light are regulated by a complex dance involving GTP-binding (G) proteins: G-protein-coupled receptors (GPCRs), proteins integral to the cell membrane, sense the signal and activate G proteins in the cellular cytoplasm, but enzymes such as G-protein-coupled receptor kinase 2 (GRK2) inhibit the activity of the G proteins. A joint University of Michigan-University of Illinois, Chicago, team has determined the first structure of a particular G-protein-GRK2 complex. The structure in combination with previous structures of related G-protein complexes shows how Nature has evolved the G-protein structure to not only propagate activation signals but at the same time also directly respond to regulatory proteins that control the duration of the signal.

447

Comparative analysis of the Epstein-Barr virus encoded nuclear proteins of EBNA-3 family  

Science Conference Proceedings (OSTI)

It is known that the EBNA-3 family proteins (EBNA-3, -4 and -6, alternative nomenclature EBNA-3A, B and C correspondingly) show a limited sequence similarity. We have analyzed EBNA-3 proteins both at the primary sequence and secondary structure levels. ... Keywords: Charge clusters, EBNA3 family proteins, Praline rich domain, Secondary structure analysis, Stonin homology domain

Surya Pavan Yenamandra; Ramakrishna Sompallae; George Klein; Elena Kashuba

2009-11-01T23:59:59.000Z

448

Directed evolution methods for improving polypeptide folding and solubility and superfolder fluorescent proteins generated thereby  

DOE Patents (OSTI)

The current invention provides methods of improving folding of polypeptides using a poorly folding domain as a component of a fusion protein comprising the poorly folding domain and a polypeptide of interest to be improved. The invention also provides novel green fluorescent proteins (GFPs) and red fluorescent proteins that have enhanced folding properties.

Waldo, Geoffrey S. (Santa Fe, NM)

2007-09-18T23:59:59.000Z

449

Nuclear export of proteins and RNAs Sara Nakielny and Gideon Dreyfuss*  

E-Print Network (OSTI)

420 Nuclear export of proteins and RNAs Sara Nakielny and Gideon Dreyfuss* Our understanding, signal-mediated export pathways. Nuclear export signals have been identified in several proteins, the majority of which are RNA-binding proteins. Nuclear export of RNA molecules is likely to be driven

Dreyfuss, Gideon

450

Protein Phosphatase 5 Mediates Lipid Metabolism Through Reciprocal Control of Glucocorticoid and PPAR Receptors  

E-Print Network (OSTI)

.sanchez@utoledo.edu Keywords: Protein phosphatase, TPR proteins, glucocorticoid receptor, peroxisome proliferator-activated) and peroxisome proliferator-activated (PPAR) receptors are antagonists of lipid metabolism. Result: Protein phosphatase 5 (PP5) dephosphorylates GR and PPAR to reciprocally control their activities. Conclusion: PP5

Brand, Paul H.

451

Radiation chemistry of amino acids, peptides and proteins in relation to the radiation sterilization of high-protein foods  

SciTech Connect

An important source of information on the question of whether or not toxic or other deleterious substances are formed in the radiation sterilization of foods is the chemical study of reaction products and reaction mechanisms in the radiolysis of individual food components. The present evaluation of the radiation chemistry of amino acids, peptides, and proteins outlines the various radiation-induced processes which lead to amino acid degradation and to the synthesis of amino acid derivatives of higher molecular weight. Among the latter are the ..cap alpha..,..cap alpha..'-diamino dicarboxylic acids which are formed as major products in the radiolysis of peptides both in aqueous solution and in the solid state. The ..cap alpha..,..cap alpha..'-diamino acids are of particular interest as irradiation products because they represent a class of compounds not normally encountered in plant and animal protein sources. Such compounds have, however, been isolated from certain types of bacteria and bacterial products. All of the available data strongly suggest that the ..cap alpha..,..cap alpha..'-diamino acids are produced in significant yield in the radiation sterilization of high protein foods. The importance of initiating extensive chemical and biological studies of these and of other high molecular weight products in irradiated food is emphasized.

Garrison, W. M.

1981-12-01T23:59:59.000Z

452

A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq  

E-Print Network (OSTI)

The SMc01113/YbeY protein, belonging to the UPF0054 family, is highly conserved in nearly every bacterium. However, the function of these proteins still remains elusive. Our results show that SMc01113/YbeY proteins share ...

Pandey, Shree P.

453

Proteomic investigation of protein interactions and post-translational modifications of the Pfh1 helicase and yeast telomerase holoenzymes.  

E-Print Network (OSTI)

??In this thesis I describe a targeted proteomics approach to study in vivo protein interactions and post-translational modifications of protein complexes involved in the maintenance (more)

McDonald, Karin Rainey

2012-01-01T23:59:59.000Z

454

Impact of C-reactive protein (CRP) on surfactant function  

Science Conference Proceedings (OSTI)

Plasma levels of the acute-phase reactant, C-reactive protein (CRP), increase up to one thousand-fold as a result of trauma or inflammation. CRP binds to phosphorylcholine (PC) in a calcium-ion dependent manner. The structural homology between PC and the major phospholipid component of surfactant, dipalmitoyl phosphatidylcholine (DPPC), led to the present study in which we examined if CRP levels might be increased in patients with adult respiratory distress syndrome (ARDS), and subsequently interfere with surfactant function. Our results showed that CRP levels in the bronchoalveolar fluid (BALF) was increased in patients with ARDS (97.8 +/- 84.2 micrograms/mg total protein vs. 4.04 +/- 2.2 micrograms/mg total protein in normals). Our results show that CRP binds to liposomes containing DPPC and phosphatidylglycerol (PG). As a result of this interaction, CRP inhibits the surface activity of a PG-DPPC mixture when tested with a Wilhelmy surfactometer or with the Enhorning pulsating bubble apparatus. Furthermore, the surface activity of a clinically used surfactant replacement, Surfactant TA (2 mg/ml), was also severely impaired by CRP in a dose-dependent manner (doses used ranging from 24.5 to 1,175 micrograms/ml). In contrast, human serum albumin (HSA) at 500 and 900 micrograms/ml had no inhibitory effect on Surfactant TA surface activity. These results suggest that CRP, although not an initiating insult in ARDS, may contribute to the subsequent abnormalities of surfactant function and thus the pathogenesis of the pulmonary dysfunction seen in ARDS.

Li, J.J.; Sanders, R.L.; McAdam, K.P.; Hales, C.A.; Thompson, B.T.; Gelfand, J.A.; Burke, J.F. (Shriners Burns Institute, Boston, MA (USA))

1989-12-01T23:59:59.000Z

455

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy  

SciTech Connect

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.

King, Neil P.; Sheffler, William; Sawaya, Michael R.; Vollmar, Breanna S.; Sumida, John P.; Andr, Ingemar; Gonen, Tamir; Yeates, Todd O.; Baker, David (UWASH); (UCLA); (HHMI); (LIT)

2012-10-24T23:59:59.000Z

456

CV1995  

NLE Websites -- All DOE Office Websites (Extended Search)

Norma Edith Cope Duke Beamline Scientist, Protein Crystallographer Norma Edith Cope Duke Beamline Scientist, Protein Crystallographer University of Calgary B. Science 1982 Chemistry University of Calgary B. Arts 1983 English University of Calgary Ph.D. Science 1989 Physical Chemistry Yale University Post-Doc 1990 Protein Crystallography University of Alberta Post-Doc 1995 Protein Crystallography Positions and Employment 2004-present Scientist, level 706; Argonne National Laboratory 1998-2004 Scientist, level 705; Argonne National Laboratory 1995-1998 Visiting Scientist, Argonne National Laboratory Other Experience and Professional Memberships 1983-1988 Studentship; Alberta Heritage Fund for Medical Research (AHFMR) 1983-present Member, American Crystallographic Association (ACA) 1999 D.O.E. Review Committee, Dept. of Educational Programs, Oakridge National

457

An angiogenin-binding protein from endothelial cells  

SciTech Connect

A 42-kDa bovine protein that binds bovine angiogenin (angiogenin binding protein (AngBP)) has been identified as a dissociable cell-surface component of calf pulmonary artery endothelial cells and a transformed bovine endothelial cell line, GM7373. {sup 125}I-Ang can be crosslinked efficiently to AngBP by a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbo-diimide. Bovine ribonuclease A competes with the binding of {sup 125}I-Ang to AngBP, but lysozyme does not. Direct binding to AngBP of {sup 125}I-labeled bovine ribonuclease A is, however, much weaker than that of {sup 125}I-Ang. Two enzymatically active derivatives of angiogenin cleaved at residues 60-61 and 67-68, respectively, fail to induce angiogenesis and also bind to AngBP only weakly. AngBP has been isolated by treatment of cells with heparan sulfate, affinity chromatography on angiogenin-Sepharose of the material dissociated from the cell surface, and gel filtration HPLC. The results suggest that AngBP has the characteristics of a receptor that may likely function in angiogenesis.

Hu, Guofu; Chang, Sooik; Riordan, J.F.; Vallee, B.L. (Harvard Medical School, Boston, MA (United States))

1991-03-15T23:59:59.000Z

458

Fermentation of soybean hulls to ethanol while retaining protein value  

Science Conference Proceedings (OSTI)

Soybean hulls were evaluated as a resource for production of ethanol by the simultaneous saccharification and fermentation (SSF) process, and no pretreatment of the hulls was found to be needed to realize high ethanol yields with S. cerevisiae D5A. The impact of cellulase, -glucosidase and pectinase dosages were determined at a 15% biomass loading, and ethanol concentrations of 25-30 g/L were routinely obtained, while under these conditions corn stover, wheat straw, and switchgrass produced 3-4 times lower ethanol yields. Removal of carbohydrates also concentrated the hull protein to over 25% w/w from the original roughly 10%. Analysis of the soybean hulls before and after fermentation showed similar amino acid profiles including an increase in the essential amino acids lysine and threonine in the residues. Thus, eliminating pretreatment should assure that the protein in the hulls is preserved, and conversion of the carbohydrates to ethanol with high yields produces a more concentrated and valuable co-product in addition to ethanol. The resulting upgraded feed product from soybean hulls would likely to be acceptable to monogastric as well as bovine livestock.

Mielenz, Jonathan R [ORNL; Wyman, Professor Charles E [University of California, Riverside; John, Bardsley [Dartmouth College

2009-01-01T23:59:59.000Z

459

Structure and Biochemical Characterization of Protein Acetyltransferase from Sulfolobus solfataricus  

Science Conference Proceedings (OSTI)

The Sulfolobus solfataricus protein acetyltransferase (PAT) acetylates ALBA, an abundant nonspecific DNA-binding protein, on Lys{sup 16} to reduce its DNA affinity, and the Sir2 deacetylase reverses the modification to cause transcriptional repression. This represents a 'primitive' model for chromatin regulation analogous to histone modification in eukaryotes. We report the 1.84-{angstrom} crystal structure of PAT in complex with coenzyme A. The structure reveals homology to both prokaryotic GNAT acetyltransferases and eukaryotic histone acetyltransferases (HATs), with an additional 'bent helix' proximal to the substrate binding site that might play an autoregulatory function. Investigation of active site mutants suggests that PAT does not use a single general base or acid residue for substrate deprotonation and product reprotonation, respectively, and that a diffusional step, such as substrate binding, may be rate-limiting. The catalytic efficiency of PAT toward ALBA is low relative to other acetyltransferases, suggesting that there may be better, unidentified substrates for PAT. The structural similarity of PAT to eukaryotic HATs combined with its conserved role in chromatin regulation suggests that PAT is evolutionarily related to the eukaryotic HATs.

Brent, Michael M.; Iwata, Ayaka; Carten, Juliana; Zhao, Kehao; Marmorstein, Ronen; (UPENN)

2009-09-02T23:59:59.000Z

460

The effects of added wheat proteins on processing and quality of wheat flour tortillas  

E-Print Network (OSTI)

Specific proteins improve quality of flour for breadmaking but protein composition in tortilla flour has not been investigated. Selected wheat protein fractions can separately modify dough resistance and extensibility. This may yield tortillas with increased diameter, opacity and stability. Tortillas were prepared using laboratory-scale, commercial equipment with fixed processing parameters. Dough and tortilla properties were evaluated using a texture analyzer and subjective methods. Tortillas were stored in plastic bags at 22?C for 28 days. The effects of ten wheat proteins (donated by Midwest Grain Products, Inc; at 3.0 baker's percent) on processing and quality of flour tortillas were determined. Mixograph parameters varied but were not significantly affected by added wheat proteins. Dough absorption, mixing time, and cysteine level were adjusted slightly to attain uniform dough for tortillas. Wheat protein fractions added to pastry, tortilla and bread flours did not significantly affect tortilla weight, moisture, pH, opacity or specific volume, except for glutenin and vital wheat gluten, which decreased opacity in pastry flour tortillas. Protein fractions yielding improved tortilla properties and stability were FP600, FP6000, FP5000 and Gliadin in pastry and tortilla flour. Addition levels of selected wheat proteins were evaluated in weak protein tortilla formulas. Addition of 1% FP5000 or PF6000 improved tortilla stability. Calcium peroxide was added to the formula to better incorporate added protein fractions in a reduced-oxidized dough system. A combination of 7.5 ppm calcium peroxide with 1% Gliadin resulted in tortillas with improved shelf stability. Bread-making quality of wheat flour is correlated with the insoluble polymeric protein fraction. The insoluble polymeric proteins in flour correlated with smaller diameter and improved rollability score at 12 days of storage for tortillas made from different wheat flours. The insoluble proteins correlated only with tortilla stability for tortillas prepared with added wheat protein fractions to flours with different protein strengths. Several wheat protein fractions improve storage stability of tortillas, while retaining good tortilla properties. This was not related to the insoluble protein amount; however the more insoluble proteins in flour caused smaller diameter tortillas.

Pascut, Simina

2002-01-01T23:59:59.000Z

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.


461

Glycoprotein and protein markers for strain differentiation and growth environment or media attribution  

SciTech Connect

Recent experience with Bacillus spore characterization has demonstrated that protein markers can provide potentially vital identifying and bioforensic information. The masses of constitutively expressed proteins and their peptide fragments can be used to identify bacterial isolates. Protein marker mass variation information reflects the underlying amino acid sequence variation to provide complementary information to genetic sequence analysis. Protein markers (identified by mass or sequence) that are conserved or variable can be readily selected. In contrast, genetic primers, as used in PCR, target conserved genetic regions. Furthermore, protein markers are relatively stable compared to nucleic acids and may remain in samples for longer periods of time. This is important to consider when the source, age and condition of samples may vary in a forensic investigation. Examples of constitutively expressed proteins that have been extensively characterized include the exosporium BclA and BclB proteins and small acid soluble proteins (SASPs). Finally, gene expression (usually assessed at the mRNA level) can vary in response to different environmental conditions. As a result, the profile of protein markers of the organism also reflects the culture environment. Mass spectrometric tools can be used to access the same information on culture-related protein expression variation. However, unlike genetic methods, with proteomic methodology there is the potential to define exactly which medium was employed for organism growth. This potential could provide additional clues for forensic attribution

Wunschel, David S.; Fox, Alvin; Wahl, Karen L.

2012-01-01T23:59:59.000Z

462

The Sorcerer II Global Ocean Sampling Expedition: Expanding theUniverse of Protein Families  

SciTech Connect

Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature.

Yooseph, Shibu; Sutton, Granger; Rusch, Douglas B.; Halpern,Aaron L.; Williamson, Shannon J.; Remington, Karin; Eisen, Jonathan A.; Heidelberg, Karla B.; Manning, Gerard; Li, Weizhong; Jaroszewski, Lukasz; Cieplak, Piotr; Miller, Christopher S.; Li, Huiying; Mashiyama, Susan T.; Joachimiak, Marcin P.; van Belle, Christopher; Chandonia, John-Marc; Soergel, David A.; Zhai, Yufeng; Natarajan, Kannan; Lee, Shaun; Raphael,Benjamin J.; Bafna, Vineet; Friedman, Robert; Brenner, Steven E.; Godzik,Adam; Eisenberg, David; Dixon, Jack E.; Taylor, Susan S.; Strausberg,Robert L.; Frazier, Marvin; Venter, J.Craig

2006-03-23T23:59:59.000Z

463

Assaying protein import into mitochondria using fluorescence spectroscopy  

E-Print Network (OSTI)

Most proteins residing in the mitochondrial matrix are synthesized in the cytosol and post-translationally imported into the mitochondrial matrix. The matrix-targeted preproteins traverse the outer mitochondrial membrane (OM) via the Translocase of the Outer Membrane (TOM) complex, and the inner mitochondrial membrane (IM) via the Translocase of the Inner Membrane 23 (TIM23) complex. A novel system was set up to examine the import of matrix-targeted preproteins into mitochondria using fluorescence spectroscopy. The fluorescent probe 6-(7-nitrobenz-2-oxa-1,3-diazol-4- yl)aminohexanoic acid (NBD) was site-specifically incorporated into different positions along the model matrix protein Su9-DHFR. The fluorescent-labeled polypeptides were either fully imported into isolated mitochondria or were arrested along the translocation pathway by the binding of methotrexate (MTX) to the DHFR moiety, creating NBDSu9- DHFR?MTX import intermediates. The NBD-Su9-DHFR polypeptides were able to be fully imported into the mitochondrial matrix in the absence of MTX, and were inaccessible to externally-added iodide ion quenchers. Treatment of the mitochondria with the pore-forming antibiotic alamethicin allowed the iodide ion quenchers access to the matrix through pores in the inner membrane (IM). After Alamethicin treatment the fully-imported NBD-Su9-DHFR polypeptides were accessible to the externally-added iodide ions. The extent of collisional quenching of the NBD fluorophores by the iodide ions was measured as the Stern-Volmer quenching constant, Ksv. Ksv values were obtained for the NBD-Su9-DHFR polypeptides in the presence of MTX (import intermediates) or in the absence of MTX (fully-imported). The Ksv values for NBD-Su9- DHFR import intermediates were similar, despite the location of the NBD probe along the translocation pathway. These Ksv values were similar to those obtained for the fullyimported NBD-Su9-DHFR polypeptides (-MTX). The locations of the varying probe positions along the import pathway were addressed using chemical crosslinking of Su9- DHFR Cys mutants. The use of fluorescence spectroscopy, in association with chemical crosslinking, to analyze the mitochondrial protein import pathways will prove a useful tool to probe the environment of the nascent chain as it is crossing the import pathway (the TOM, TIM23 complexes).

Cargill, Holly Beth

2003-05-01T23:59:59.000Z

464

Statistical-mechanical lattice models for protein-DNA binding in chromatin  

E-Print Network (OSTI)

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quant...

Teif, Vladimir B

2010-01-01T23:59:59.000Z

465

Fermentation of soybean hulls to ethanol while preserving protein value  

NLE Websites -- All DOE Office Websites (Extended Search)

Fermentation Fermentation of soybean hulls to ethanol while preserving protein value Jonathan R. Mielenz a,b, * , John S. Bardsley a,c , Charles E. Wyman a,d a Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, United States b BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States c Mascoma Corporation, Lebanon, NH 03766, United States d Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92507, United States a r t i c l e i n f o Article history: Received 12 August 2008 Received in revised form 11 February 2009 Accepted 11 February 2009 Available online 27 March 2009 Keywords: Ethanol SSF Biomass Agricultural residue Animal feed a b s t r a c t Soybean hulls were evaluated as a resource for production of ethanol by the simultaneous saccharifica- tion and fermentation (SSF) process, and no pretreatment

466

Process for foaming aqueous protein-containing blasting agents  

SciTech Connect

A process is provided for foaming blasting agents which cosists of (1) passing a thickened protein-containing water-bearing blasting agent through a number of orifices at a pressure of about 40 to 160, preferably 125 to 140 psi into a suction chamber in order to form a number of streams of thickened explosive and create a vacuum in the area where the blasting agent exists; (2) simultaneously incorporating gas into the thickened explosive in the suction chamber so as to cause an intimate admixture of the gas with the thickened explosive; and (3) thereafter reducing the velocity of the thickened explosive by subsequently passing it through an enlarged opening, and recovering the resulting foamed, thickened blasting agent. (6 claims)

Adams, P.E.; Fearnow, P.W.

1972-07-18T23:59:59.000Z

467

A Master equation approach to modeling an artificial protein motor  

E-Print Network (OSTI)

Linear bio-molecular motors move unidirectionally along a track by coordinating several different processes, such as fuel (ATP) capture, hydrolysis, conformational changes, binding and unbinding from a track, and center-of-mass diffusion. A better understanding of the interdependencies between these processes, which take place over a wide range of different time scales, would help elucidate the general operational principles of molecular motors. Artificial molecular motors present a unique opportunity for such a study because motor structure and function are a priori known. Here we describe use of a Master equation approach, integrated with input from Langevin and molecular dynamics modeling, to stochastically model a molecular motor across many time scales. We apply this approach to a specific concept for an artificial protein motor, the Tumbleweed.

Kuwada, Nathan J; Linke, Heiner

2010-01-01T23:59:59.000Z

468

A Master equation approach to modeling an artificial protein motor  

E-Print Network (OSTI)

Linear bio-molecular motors move unidirectionally along a track by coordinating several different processes, such as fuel (ATP) capture, hydrolysis, conformational changes, binding and unbinding from a track, and center-of-mass diffusion. A better understanding of the interdependencies between these processes, which take place over a wide range of different time scales, would help elucidate the general operational principles of molecular motors. Artificial molecular motors present a unique opportunity for such a study because motor structure and function are a priori known. Here we describe use of a Master equation approach, integrated with input from Langevin and molecular dynamics modeling, to stochastically model a molecular motor across many time scales. We apply this approach to a specific concept for an artificial protein motor, the Tumbleweed.

Nathan J. Kuwada; Gerhard A. Blab; Heiner Linke

2010-04-07T23:59:59.000Z

469

Modifying Proteins to Combat Disease | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

Higher Temperature at the Earth's Core Higher Temperature at the Earth's Core Clues about Rheumatoid Arthritis Damage Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Modifying Proteins to Combat Disease JANUARY 22, 2013 Bookmark and Share Structure of the human PRMT5:MEP50 hetero-octameric complex bound to a substrate peptide and a cofactor analog. Cartoon representations of the PRMT5 monomers are colored blue, green, wheat, and yellow, while the MEP50 molecules are in red. Highlighted in stick representation are the substrate peptide derived from histone H3 in magenta, and the cofactor analog in orange. Transmitting from one generation to the next the genetic message encoded in

470

Interfacial instability and DNA fork reversal by repair proteins  

E-Print Network (OSTI)

A repair protein like RecG moves the stalled replication fork in the direction from the zipped to the unzipped state of DNA. It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating towards the unzipped side. In this scenario, an ordinary helicase destabilizes the zipped state locally near the interface and the fork propagates towards the zipped side. The softening of the interface can be produced by the aromatic interaction, predicted from crystal structure, between RecG and the nascent broken base pairs at the Y-fork. A numerical analysis of the model also reveals the possibility of a stop and go type motion.

Somendra M. Bhattacharjee

2009-09-03T23:59:59.000Z

471

Comparison of soy protein concentrates produced by membrane filtration and acid precipitation  

E-Print Network (OSTI)

The recovery of proteins using ultrafiltration (UF) process is an attractive alternative compared to conventional acid precipitation method. The mild processing condition, which leads to less protein denaturation, may be one of major virtues of this method. This research was directed to identify such assumptions of the products. Three soy protein concentrates were obtained in this study. Full-fat soybean flour and hexane-defatted soybean flour were dispersed into distilled water (1:8) at 60?C, respectively. A series of operations including pH adjustment (8.0), agitation (250 rpm, 30 min), sonication (40 dB, 20 min), homogenization (3 min), and centrifugation (3,000 x g, 15 min) were followed. For the membrane processing, the ultrafiltration cartridge used molecular weight cut-off 100,000 daltons. Acid-precipitated protein (at pH 4.5) was produced from hexane-defatted soybean flour following the identical procedures as above. Protein content of the membrane-processed product from full-fat soybean flour was 63.5% and that of the acid precipitated product was 71.9%. All samples were comparable in their functional properties. Nitrogen solubility at pH 7.0 was exhibited better in the protein produced by membrane filtration than the protein produced by acid precipitation due to protein denaturation. Also the membrane-processed soy protein showed good heat coagulation, emulsifying stability, and foaming stability. Amino acid patterns were similar to the typical one of soy proteins. However, relatively low lysine, threonine and valine contents in the acid-precipitated protein were noteworthy. The sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) patterns were almost comparable among samples. In appearance, the acid-precipitated protein was light and slightly greenish tint.

Kim, Hyun Jung

2003-01-01T23:59:59.000Z

472

Apolipoprotein A-I mutant proteins having cysteine substitutions and polynucleotides encoding same  

DOE Patents (OSTI)

Functional Apolipoprotein A-I mutant proteins, having one or more cysteine substitutions and polynucleotides encoding same, can be used to modulate paraoxonase's arylesterase activity. These ApoA-I mutant proteins can be used as therapeutic agents to combat cardiovascular disease, atherosclerosis, acute phase response and other inflammatory related diseases. The invention also includes modifications and optimizations of the ApoA-I nucleotide sequence for purposes of increasing protein expression and optimization.

Oda, Michael N. (Benicia, CA); Forte, Trudy M. (Berkeley, CA)

2007-05-29T23:59:59.000Z

473

Method for early detection of infectious mononucleosis by identifying Inmono proteins  

DOE Patents (OSTI)

Early detection of infectious mononucleosis is carried out using a sample of human blood by isolating and identifying the presence of Inmono proteins in the sample from a two-dimensional protein map with the proteins being characterized by having isoelectric banding as measured in urea of about -16 to -17 with respect to certain isoelectric point standards and molecular mass of about 70 to 75 K daltons as measured in the presence of sodium dodecylsulfate containing polyacrylamide gels, the presence of the Inmono proteins being correlated with the existence of infectious mononucleosis.

Willard, Karen E. (Woodridge, IL)

1984-01-01T23:59:59.000Z

474

Isolation and characterization of a new zinc-binding protein from albacore tuna plasma  

SciTech Connect

The protein responsible for sequestering high levels of zinc in the plasma of the albacore tuna (Thunnus alalunga) has been isolated by sequential chromatography. The glycoprotein has a molecular weight of 66,000. Approximately 8.2% of its amino acid residues are histidines. Equilibrium dialysis experiments show it to bind 3 mol of zinc/mol of protein. The stoichiometric constant for the association of zinc with a binding site containing three histidines was determined to be 10/sup 9.4/. This protein is different from albumin and represents a previously uncharacterized zinc transport protein.

Dyke, B.; Hegenauer, J.; Saltman, P.; Laurs, R.M.

1987-06-02T23:59:59.000Z

475

Soybeans: Chemistry, Production, Processing, and UtilizationChapter 8 Soybean Proteins  

Science Conference Proceedings (OSTI)

Soybeans: Chemistry, Production, Processing, and Utilization Chapter 8 Soybean Proteins Food Science Health Nutrition Biochemistry Processing Soybeans eChapters Food Science & Technology Health - Nutrition - Biochemistry Processing

476

Effect of Heat Treating Alfalfa Hay on Chemical Composition and Ruminal In Vitro Protein Degradation1  

E-Print Network (OSTI)

Conventional (unshredded) and shredded alfalfa hays were heated in either a forced-air oven or a steam pressure cooker at different times and temperatures to determine the effect of heat treatment on chemical composition and ruminal protein degradability. Rates of protein degradation and extents of protein escape were estimated using a ruminal inhibitor in vitro system. Both rates and extents were corrected for the proportion of total N in ADIN. Estimated net protein escape (total escape minus ADIN-bound CP) of unshredded and shredded hays was increased by oven or steam heating. Optimal oven treatments, as indicated by the greatest increase in net protein escape, were 120 min at 150C and 60 min at 160'C. Net protein escapes of shredded hay were greater than unshredded hay when neither was heated and when hays were heated to the same extent. Equivalent protein protection was obtained by oven heating for 120 min at 140'C, 60 rnin at 150"C, and 30 rnin at lWC, which gave net protein escapes of 55, 54, and 54% for shredded hay and 44, 45, and 43% for unshredded hay, respectively. Similar protein protection was obtained at lower

J. H. Yang; A. Broderick; R. G. Koegel

1992-01-01T23:59:59.000Z

477

Alpha-helical Protein Networks Are Self-protective and Flaw-tolerant  

Science Conference Proceedings (OSTI)

Presentation Title, Alpha-helical Protein Networks Are Self-protective and Flaw- ... Bulk Metallic Glass Composites: A New High-Performance Structural Material.

478

Molecular simulations of beta-amyloid protein near hydrated lipids (PECASE).  

Science Conference Proceedings (OSTI)

We performed molecular dynamics simulations of beta-amyloid (A{beta}) protein and A{beta} fragment(31-42) in bulk water and near hydrated lipids to study the mechanism of neurotoxicity associated with the aggregation of the protein. We constructed full atomistic models using Cerius2 and ran simulations using LAMMPS. MD simulations with different conformations and positions of the protein fragment were performed. Thermodynamic properties were compared with previous literature and the results were analyzed. Longer simulations and data analyses based on the free energy profiles along the distance between the protein and the interface are ongoing.

Thompson, Aidan Patrick; Han, Kunwoo (Texas A& M University, College Station, TX); Ford, David M. (Texas A& M University, College Station, TX)

2005-12-01T23:59:59.000Z

479

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold  

SciTech Connect

The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew; Carrico, Chris; Kalyuzhniy, Oleksandr; Chen, Lei; Schroeter, Alexandria; Huang, Po-Ssu; McLellan, Jason S.; Kwong, Peter D.; Baker, David; Strong, Roland K.; Schief, William R. (UWASH); (FHCRC); (NIAID)

2012-02-07T23:59:59.000Z

480

Xenopus CENP-A assembly into chromatin requires base excision repair proteins  

E-Print Network (OSTI)

Remodelling the paternal chromatin at fertilization inEarly disruption of centromeric chromatin organization ingene encoding a novel chromatin- associated protein in

Zeitlin, Samantha G

2005-01-01T23:59:59.000Z

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.


481

Computational modeling of protein-biomolecule interactions with application to mechanotransduction and antibody maturation  

E-Print Network (OSTI)

Cell survival, growth, differentiation, migration, and communication all depend on the appropriate combination of specific interactions between proteins and biomolecules. Therefore, understanding the molecular mechanisms ...

Zyto, Aurore

2008-01-01T23:59:59.000Z

482

Processing and characterization of sorghum protein concentrates using extrusion-enzyme liquefaction.  

E-Print Network (OSTI)

??Sorghum grain (Sorghum bicolor) is safe for consumption by individuals afflicted with celiac disease, and its proteins can be used as a supplement in gluten-free (more)

Stonestreet, Normell Jhoe de Mesa

2011-01-01T23:59:59.000Z

483

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

E-Print Network (OSTI)

fits snugly into the brass pin and secured with wax. Thisbetween facilities. f) A close-up of the brass holding pin.The goniometer head with the brass holding post that mounts

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

2008-01-01T23:59:59.000Z

484

Dynamic and collective analysis of membrane protein interaction network based on gene regulatory network model  

Science Conference Proceedings (OSTI)

Membrane protein interactions are vitally important for every process in a living cell. Information about these interactions can improve our understanding of diseases and provide the basis to revolutionize therapeutic treatments. However, current experimental ... Keywords: Bio-network, Dynamic and collective control, Gene regulatory network, Membrane protein interaction network, Robustness, Scale free distributing, Small-world network

Yong-Sheng Ding; Yi-Zhen Shen; Li-Hong Ren; Li-Jun Cheng

2012-12-01T23:59:59.000Z

485

A motion sensor interactive interface for viewing and manipulating protein structural data in 3D  

Science Conference Proceedings (OSTI)

We propose a fun, interactive way to view and alter protein structural data by hand via motion sensors and voice activation. This will enable users to freely zoom, rotate, and view a protein through a friendly hands-on experience. Multiple view and rotation ...

Robyn Moncrief; William Gobber

2012-08-01T23:59:59.000Z

486

Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies  

Science Conference Proceedings (OSTI)

The recent explosion in procurement and availability of high-dimensional gene- and protein-expression profile datasets for cancer diagnostics has necessitated the development of sophisticated machine learning tools with which to analyze them. A major ... Keywords: Bioinformatics (genome or protein) databases, Clustering, classification, and association rules, Data and knowledge visualization, Data mining, Feature extraction or construction

George Lee; Carlos Rodriguez; Anant Madabhushi

2008-07-01T23:59:59.000Z

487

A simple model for evolution of proteins towards the global minimum of free energy  

E-Print Network (OSTI)

A simple model for evolution of proteins towards the global minimum of free energy Tamar Kaffe-Abramovich and Ron Unger Background: Proteins seem to have their native structure in a global minimum of free energy is in the global minimum of free energy. The aim of this study is to investigate such evolutionary processes

Unger, Ron

488

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation  

E-Print Network (OSTI)

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP, we show that the entropy component of our free energy estimates can useful in distinguishing native

Xing, Eric P.

489

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation  

E-Print Network (OSTI)

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP, we show that the entropy compo- nent of our free energy estimates can be useful in distinguishing

Langmead, Christopher James

490

Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path  

E-Print Network (OSTI)

Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path Gregg Lois be calculated from measurements of the free energy. We test these predictions against numerical simulations folding problem (2­4). Each protein conformation has a free energy that determines its probability

Gelfond, Michael

491

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief  

E-Print Network (OSTI)

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation H Detection, Free Energy, Probabilistic Graphical Models #12;Abstract We present a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP). The accuracy and utility

492

An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies  

Science Conference Proceedings (OSTI)

Fanconi Anemia (FA) is a rare autosomal genetic disease with multiple birth defects and severe childhood complications for its patients. The lack of sequence homology of the entire FA Complementation Group proteins in such as FANCC, FANCG, FANCA makes ... Keywords: disease target, fanconi anemia, protein interaction network, proteomics

Jake Yue Chen; Sarah L. Pinkerton; Changyu Shen; Mu Wang