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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.


1

Protein crystallography with spallation neutrons  

SciTech Connect (OSTI)

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

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

2003-01-01T23:59:59.000Z

2

MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY  

E-Print Network [OSTI]

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

Quake, Stephen R.

3

Serial Femtosecond Crystallography of G Protein-Coupled Receptors  

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

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

Liu, Liu

4

Cryogenic Neutron Protein Crystallography: routine methods and potential benefits  

SciTech Connect (OSTI)

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

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

2014-01-01T23:59:59.000Z

5

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

SciTech Connect (OSTI)

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

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

2004-05-12T23:59:59.000Z

6

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

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

Atac, Muzaffer (Wheaton, IL); McKay, Timothy (Ann Arbor, MI)

1999-01-01T23:59:59.000Z

7

Media invited to join students in crystallography experiment  

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

skills to the test Monday in the Protein Crystallography Station at the Los Alamos Research Park. The students will learn about the history and theory of X-ray...

8

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

SciTech Connect (OSTI)

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

Wang, Hong; Kelley, M.A.

1989-02-07T23:59:59.000Z

9

Johann Deisenhofer, Crystallography, and Proteins  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-SeriesFlickrinformation forTechnologies |Jennifer DunnEnergyGarciaJobs

10

electronic reprint Crystallography  

E-Print Network [OSTI]

distributions from 1 to 100 nm, and shape and orientation distributions, in liquids, powders and bulk samples, aluminas, microemulsions, nucleic acids, proteins, mesoporous materials, inorganic polymers, coal samples

Gruner, Sol M.

11

An International Journal of MINERALOGY, CRYSTALLOGRAPHY, GEOCHEMISTRY,  

E-Print Network [OSTI]

, developed from the weathering of alumosilicate-rich parent rocks. These residual deposits are mainly formedAn International Journal of MINERALOGY, CRYSTALLOGRAPHY, GEOCHEMISTRY, ORE DEPOSITS, PETROLOGY

Boni, Maria

12

Nanostructure, Chemistry and Crystallography of Iron Nitride...  

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

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

13

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

SciTech Connect (OSTI)

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

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

2008-10-24T23:59:59.000Z

14

Lipidic phase membrane protein serial femtosecond crystallography  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-SeriesFlickrinformationPostdocsCenterCentera A B C D E F G H I J K L M N

15

A heat-driven monochromatic light source  

SciTech Connect (OSTI)

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

Stefani, F.; Lawless, J.L.

1989-04-01T23:59:59.000Z

16

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

Office of Scientific and Technical Information (OSTI)

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

17

The Development of the GCPCC Protein Crystallography Beamline at CAMD  

E-Print Network [OSTI]

as a simple synchrotron with a bending radius of 0.71 meters. For heat-load calculations, all five wiggler heat load on the first monochromator crystal by acting as a low pass filter. The wavelength is selected. The beamline design, with supporting calculations and ray tracing, is presented to substantiate the expected

Phillips, George N. Jr.

18

Neutron Macromolecular Crystallography (NMC) can provide accurate hydrogen atom  

E-Print Network [OSTI]

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

Pennycook, Steve

19

Monte Carlo Characterization of a Pulsed Laser-Wakefield Driven Monochromatic  

E-Print Network [OSTI]

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

Umstadter, Donald

20

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

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

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

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

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

E-Print Network [OSTI]

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

22

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

23

JBluIce-EPICS control system for macromolecular crystallography.  

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

24

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.

25

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

E-Print Network [OSTI]

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

Miao, Jianwei "John"

26

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

SciTech Connect (OSTI)

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

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

2014-09-15T23:59:59.000Z

27

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

28

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

E-Print Network [OSTI]

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

Najmabadi, Farrokh

29

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

E-Print Network [OSTI]

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

Danon, Yaron

30

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

E-Print Network [OSTI]

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

31

A Beam line for Macromolecular Crystallography in ALBA  

SciTech Connect (OSTI)

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

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

2007-01-19T23:59:59.000Z

32

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

33

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

SciTech Connect (OSTI)

We have theoretically demonstrated a new light-trapping mechanism to reduce emission from a photovoltaic (PV) cell used for a monochromatic light source, which improves limiting conversion efficiency determined by the detailed balance. A multilayered bandpass filter formed on the surface of a PV cell has been found to prevent the light generated inside by radiative recombination from escaping the cell, resulting in a remarkable decrease of the effective solid angle for the emission. We have clarified a guide to design a suitable configuration of the bandpass filter and achieved significant reduction of the emission. The resultant gain in monochromatic conversion efficiency in the radiative limit due to the optimally designed 18-layerd bandpass filters is as high as 6% under normally incident 1064?nm illumination of 10 mW/cm{sup 2?}??1?kW/cm{sup 2}, compared with the efficiency for the perfect anti-reflection treatment to the surface of a conventional solar cell.

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

2014-09-28T23:59:59.000Z

34

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

SciTech Connect (OSTI)

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

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

2010-01-01T23:59:59.000Z

35

Proteins  

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

Bioscience: Bioenergy, Biosecurity, and Health Proteins Protein Engineering, Structure, and Function Los Alamos scientists seek a comprehensive understanding of the structure...

36

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

SciTech Connect (OSTI)

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

Hall, G. N., E-mail: gareth.hall@imperial.ac.uk; Burdiak, G. C.; Suttle, L.; Stuart, N. H.; Swadling, G. F.; Lebedev, S. V.; Smith, R. A.; Patankar, S.; Suzuki-Vidal, F.; Grouchy, P. de; Harvey-Thompson, A. J.; Bennett, M.; Bland, S. N.; Pickworth, L.; Skidmore, J. [The Blackett Laboratory, Imperial College, London SW7 2BW (United Kingdom)

2014-11-15T23:59:59.000Z

37

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

E-Print Network [OSTI]

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

Rohrer, Gregory S.

38

PublishedbyManeyPublishing(c)IOMCommunicationsLtd Crystallography of Widmanstatten austenite in  

E-Print Network [OSTI]

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

Cambridge, University of

39

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

E-Print Network [OSTI]

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

Bourne, Philip E.

40

X-Ray Crystallography Facility Last update: June, 2006 410-413 Kasha Laboratory  

E-Print Network [OSTI]

X-Ray Crystallography Facility Last update: June, 2006 410-413 Kasha Laboratory Institute Badge/Ring Open the valve in building-chilled water X-Ray Generator Start-up & Shut-down Flowchart (Mar POWER on X-RAY panel Check vaccum- meter reading =

Weston, Ken

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

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

SciTech Connect (OSTI)

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

42

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

43

Proteins  

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

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

44

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

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

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45

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

SciTech Connect (OSTI)

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

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

2013-07-15T23:59:59.000Z

46

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

SciTech Connect (OSTI)

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

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

2013-11-15T23:59:59.000Z

47

Proteins  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedlesAdvanced Photon Source The SuperpowerrelatedProteins

48

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

E-Print Network [OSTI]

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

Agard, David

49

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

E-Print Network [OSTI]

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

Cavanagh, John

50

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

SciTech Connect (OSTI)

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

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

2012-10-15T23:59:59.000Z

51

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

SciTech Connect (OSTI)

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

Koestner, R.J.

1982-08-01T23:59:59.000Z

52

Hydrogen bond dynamics in the active site of photoactive yellow protein  

E-Print Network [OSTI]

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

Herschlag, Dan

53

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

SciTech Connect (OSTI)

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

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

2010-04-08T23:59:59.000Z

54

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

E-Print Network [OSTI]

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

Hisakazu Minakata; Shoichi Uchinami

2006-08-05T23:59:59.000Z

55

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

2005-07-19T23:59:59.000Z

56

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

57

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

SciTech Connect (OSTI)

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

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

2008-04-02T23:59:59.000Z

58

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

E-Print Network [OSTI]

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

Thirumalai, Devarajan

59

Multistable monochromatic laser solitons  

SciTech Connect (OSTI)

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

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

2010-05-15T23:59:59.000Z

60

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

SciTech Connect (OSTI)

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

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

2010-06-23T23:59:59.000Z

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

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

SciTech Connect (OSTI)

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

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

2012-12-15T23:59:59.000Z

62

electronic reprint Crystallography  

E-Print Network [OSTI]

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

Jacobsen, Steven D.

63

SMB, Macromolecular Crystallography  

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

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64

electronic reprint Crystallography  

E-Print Network [OSTI]

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

Ismagilov, Rustem F.

65

Macromolecular Crystallography - Beamline facilities  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fund Las ConchasTrail ofDensityTrainingand TechnicalSearch

66

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

SciTech Connect (OSTI)

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

Zhu, Liang Cong

2009-06-08T23:59:59.000Z

67

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

SciTech Connect (OSTI)

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

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

1990-11-01T23:59:59.000Z

68

Protein Characterisation by Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy  

SciTech Connect (OSTI)

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

Wallace, B.

2009-01-01T23:59:59.000Z

69

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

SciTech Connect (OSTI)

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

D Freed; P Horanyi; M Wiener; D Cafiso

2011-12-31T23:59:59.000Z

70

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

SciTech Connect (OSTI)

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

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

2010-09-27T23:59:59.000Z

71

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

SciTech Connect (OSTI)

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

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

2013-09-17T23:59:59.000Z

72

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

SciTech Connect (OSTI)

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

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

2011-09-15T23:59:59.000Z

73

Neutron crystallography aids drug design  

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

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74

Powder Diffraction Crystallography Instructional Materials  

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

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75

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

E-Print Network [OSTI]

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

76

Computational tools for experimental determination and theoretical prediction of protein structure  

SciTech Connect (OSTI)

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

77

High efficiency quasi-monochromatic infrared emitter  

SciTech Connect (OSTI)

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

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

2014-02-24T23:59:59.000Z

78

Diamondoid Monolayers as Monochromatic Electron Source  

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

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79

Diamondoid Monolayers as Monochromatic Electron Source  

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

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80

Diamondoid Monolayers as Monochromatic Electron Source  

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

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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

Diamondoid Monolayers as Monochromatic Electron Source  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phasesData FilesShape,Physics Diagnostics UWDiamondoid Monolayers as

82

Diamondoid Monolayers as Monochromatic Electron Source  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phasesData FilesShape,Physics Diagnostics UWDiamondoid Monolayers

83

Diamondoid Monolayers as Monochromatic Electron Source  

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

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84

Diamondoid Monolayers as Monochromatic Electron Source  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to UserProduct: CrudeOfficeNERSC Helps Develop Di-Jia

85

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

SciTech Connect (OSTI)

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

Barends, Thomas, R.M.

2013-11-25T23:59:59.000Z

86

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

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

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

Barends, Thomas, R.M.

87

Manipulating and Visualizing Proteins  

E-Print Network [OSTI]

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

Simon, Horst D.

2003-01-01T23:59:59.000Z

88

Discover protein sequence signatures from protein-protein interaction data  

E-Print Network [OSTI]

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

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

2005-11-23T23:59:59.000Z

89

Shotgun protein sequencing.  

SciTech Connect (OSTI)

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

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

2009-06-01T23:59:59.000Z

90

Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites  

SciTech Connect (OSTI)

Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak contact with the protein surface. Combined, the results provide a starting point for determining a motional model for R1 on membrane proteins, allowing quantification of nitroxide dynamics in the aliphatic environment of detergent and lipids. In addition, initial contributions to a rotamer library of R1 on membrane proteins are provided, which will assist in reliably modeling the R1 conformational space for pulsed dipolar EPR and NMR paramagnetic relaxation enhancement distance determination.

Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda (UV)

2010-12-07T23:59:59.000Z

91

Engineering novel fluorescent proteins  

E-Print Network [OSTI]

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

Shaner, Nathan Christopher

2006-01-01T23:59:59.000Z

92

Protein Dynamics and Biocatalysis  

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

Protein Dynamics and Biocatalysis Protein Dynamics and Biocatalysis 1998 Annual Report Grand Challenge Projects biocatalysis.gif A model of the Michaelis complex for the TEM-1...

93

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

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

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

94

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

SciTech Connect (OSTI)

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

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

2009-04-30T23:59:59.000Z

95

Protein Design Zhilei Chen  

E-Print Network [OSTI]

Protein Design Zhilei Chen Center for Biophysics and Computational Biology, University of Illinois of Illinois, Urbana, Illinois, U.S.A. INTRODUCTION Protein design refers to the ability to alter protein, and selectivity. To overcome this lim- itation, tailor-made biocatalysts must be developed by protein design

Zhao, Huimin

96

Protein Structure Analysis Iosif Vaisman  

E-Print Network [OSTI]

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

Vaisman, Iosif

97

COMPUTATIONAL METHODOLOGY IN CRYSTALLOGRAPHY: EVALUATION AND EXTENSION  

E-Print Network [OSTI]

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

Templeton Ed, D.

2011-01-01T23:59:59.000Z

98

COMPUTATIONAL METHODOLOGY IN CRYSTALLOGRAPHY: EVALUATION AND EXTENSION  

E-Print Network [OSTI]

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

Templeton Ed, D.

2011-01-01T23:59:59.000Z

99

Nanostructure, Chemistry and Crystallography of Iron Nitride...  

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

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

100

Resources for Macromolecular Crystallography | Advanced Photon Source  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassive Solar HomePromisingStories »Submitter ApropaneBacteria

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

Instrumentation upgrades for the Macromolecular Crystallography beamlines  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-SeriesFlickrinformation for and Novel ComputationalBeckyScience &

102

Microcrystallization techniques for serial femtosecond crystallography  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary)morphinanInformation Desert Southwest Regionat Cornell Batteries & Fuel Cells InDioxideusing Photosystem II

103

Protein- protein interaction detection system using fluorescent protein microdomains  

DOE Patents [OSTI]

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

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

2010-02-23T23:59:59.000Z

104

Enriched Protein-Protein Interactions from Biomedical Text  

E-Print Network [OSTI]

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

Edinburgh, University of

105

Protein Structure Analysis Iosif Vaisman  

E-Print Network [OSTI]

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

Vaisman, Iosif

106

Optimization Approaches to Protein Folding.  

E-Print Network [OSTI]

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

Yoon, Hyun-suk

2006-01-01T23:59:59.000Z

107

Simulations of Protein Folding  

E-Print Network [OSTI]

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

Michael Cahill; Mark Fleharty; Kevin Cahill

1999-09-17T23:59:59.000Z

108

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

E-Print Network [OSTI]

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

Fusco, Diana

109

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

E-Print Network [OSTI]

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

Jager, M; Michalet, X; Weiss, Shimon

2005-01-01T23:59:59.000Z

110

Protein folding tames chaos  

E-Print Network [OSTI]

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

Xia, Kelin

2013-01-01T23:59:59.000Z

111

Protein kinesis: The dynamics of protein trafficking and stability  

SciTech Connect (OSTI)

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

NONE

1995-12-31T23:59:59.000Z

112

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 ...

Fernández Suárez, Marta

2008-01-01T23:59:59.000Z

113

Protein folding and heteropolymers  

E-Print Network [OSTI]

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

T. Garel; H. Orland; E. Pitard

1997-06-12T23:59:59.000Z

114

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

E-Print Network [OSTI]

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

Sali, Andrej

115

Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments  

E-Print Network [OSTI]

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

Haspel, Nurit

116

Peptidomimetics to mimic protein-protein interactions  

E-Print Network [OSTI]

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

Xia, Zebin

2005-08-29T23:59:59.000Z

117

Interfacial rheology of globular proteins  

E-Print Network [OSTI]

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

Jaishankar, Aditya

2011-01-01T23:59:59.000Z

118

Protein folding and cosmology  

E-Print Network [OSTI]

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

González-Diáz, P F

1997-01-01T23:59:59.000Z

119

Protein folding and cosmology  

E-Print Network [OSTI]

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

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

1997-06-04T23:59:59.000Z

120

Cotton and Protein Interactions  

SciTech Connect (OSTI)

The adsorbent properties of important wound fluid proteins and cotton cellulose are reviewed. This review focuses on the adsorption of albumin to cotton-based wound dressings and some chemically modified derivatives targeted for chronic wounds. Adsorption of elastase in the presence of albumin was examined as a model to understand the interactive properties of these wound fluid components with cotton fibers. In the chronic non-healing wound, elastase appears to be over-expressed, and it digests tissue and growth factors, interfering with the normal healing process. Albumin is the most prevalent protein in wound fluid, and in highly to moderately exudative wounds, it may bind significantly to the fibers of wound dressings. Thus, the relative binding properties of both elastase and albumin to wound dressing fibers are of interest in the design of more effective wound dressings. The present work examines the binding of albumin to two different derivatives of cotton, and quantifies the elastase binding to the same derivatives following exposure of albumin to the fiber surface. An HPLC adsorption technique was employed coupled with a colorimetric enzyme assay to quantify the relative binding properties of albumin and elastase to cotton. The results of wound protein binding are discussed in relation to the porosity and surface chemistry interactions of cotton and wound proteins. Studies are directed to understanding the implications of protein adsorption phenomena in terms of fiber-protein models that have implications for rationally designing dressings for chronic wounds.

Goheen, Steven C.; Edwards, J. V.; Rayburn, Alfred R.; Gaither, Kari A.; Castro, Nathan J.

2006-06-30T23:59:59.000Z

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

Purine inhibitors of protein kinases, G proteins and polymerases  

DOE Patents [OSTI]

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

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

2001-07-03T23:59:59.000Z

122

The unfolded-protein-response  

E-Print Network [OSTI]

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

Walter, Peter

123

Computer Simulations of Protein Folding  

E-Print Network [OSTI]

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

Sorin, Eric J.

124

INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION  

E-Print Network [OSTI]

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

Halligan, Daniel

125

Protein sequence databases Rolf Apweiler1,  

E-Print Network [OSTI]

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

126

Expression of Recombinant Proteins in Microalgae  

E-Print Network [OSTI]

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

Mayfield, Stephen P.; Franklin, Scott E.

2003-01-01T23:59:59.000Z

127

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

E-Print Network [OSTI]

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

Raines, Ronald T.

128

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

SciTech Connect (OSTI)

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

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

2012-01-20T23:59:59.000Z

129

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

130

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.; Doi, R.

1998-11-17T23:59:59.000Z

131

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

E-Print Network [OSTI]

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

Bigelow, Stephen

132

Annotation Transfer Between Genomes: ProteinProtein Interologs and  

E-Print Network [OSTI]

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

Gerstein, Mark

133

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

134

A Novel Topology for Representing Protein Folds  

E-Print Network [OSTI]

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

Segal, Mark R

2009-01-01T23:59:59.000Z

135

Hydration dynamics near a model protein surface  

E-Print Network [OSTI]

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

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

2003-01-01T23:59:59.000Z

136

Protein Dynamics Hit the Big Screen  

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

Protein Dynamics Hit the Big Screen Protein Dynamics Hit the Big Screen Now playing at a supercomputer near you: proteins in action June 29, 2005 Contact: Dan Krotz,...

137

Fluorescent Protein Applications in Microscopy  

E-Print Network [OSTI]

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

Straight, Aaron

138

Petaflop Computing for Protein Folding  

E-Print Network [OSTI]

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

Izaguirre, Jesús A.

139

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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

Thirumalai, Devarajan

140

Challenging Proteins Principles and Methods  

E-Print Network [OSTI]

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

Jacobsen, Steve

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

Protein subcellular localization assays using split fluorescent proteins  

DOE Patents [OSTI]

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

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

2009-09-08T23:59:59.000Z

142

Protein domain organisation: adding order  

E-Print Network [OSTI]

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

Kummerfeld, Sarah K; Teichmann, Sarah A

2009-01-29T23:59:59.000Z

143

Mathematical methods for protein science  

SciTech Connect (OSTI)

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

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

1997-12-31T23:59:59.000Z

144

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

E-Print Network [OSTI]

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

145

On the rough folding landscape of green fluorescent protein  

E-Print Network [OSTI]

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

Andrews, Benjamin Thomas

2008-01-01T23:59:59.000Z

146

Protein Dynamics and Biocatalysis  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProtein

147

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

E-Print Network [OSTI]

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

148

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

SciTech Connect (OSTI)

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

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

2006-01-01T23:59:59.000Z

149

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

150

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

151

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

152

Introduction to Grid computing Protein folding  

E-Print Network [OSTI]

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

Boyar, Joan

153

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

E-Print Network [OSTI]

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

Zhu, L; Kaback, HR; Dalbey, RE

2013-01-01T23:59:59.000Z

154

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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

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

2010-07-18T23:59:59.000Z

155

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

156

EVA: evaluation of protein structure prediction servers  

E-Print Network [OSTI]

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

Sali, Andrej

157

Optimized Null Model for Protein Structure Networks  

E-Print Network [OSTI]

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

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

2009-01-01T23:59:59.000Z

158

GWIDD: Genome-wide protein docking database  

E-Print Network [OSTI]

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

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

2009-11-09T23:59:59.000Z

159

Metal-directed protein self-assembly  

E-Print Network [OSTI]

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

Salgado. Eric N.

2010-01-01T23:59:59.000Z

160

MODELING PROTEIN INTERACTIONS THROUGH STRUCTURE ALIGNMENT  

E-Print Network [OSTI]

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

Sinha, Rohita

2011-08-31T23:59:59.000Z

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

A motion planning approach to protein folding  

E-Print Network [OSTI]

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

Song, Guang

2004-09-30T23:59:59.000Z

162

Mutagenic effects on protein folding and stability  

E-Print Network [OSTI]

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

Anderson, Thomas Anthony, 1973-

2002-01-01T23:59:59.000Z

163

CrystalPlan: an Experiment Planning Tool for Crystallography  

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

164

Notes X-ray Crystallography Joseph H. Reibenspies  

E-Print Network [OSTI]

Solid, Liquid, Gas : Must contain a heavy atom (at least S). The more Heavy atoms the more complicated, What and how Many atoms are coordinated to Heavy atom. Range from heavy atom ~ 6·. #12;5 Crystals Key solute slowly Solvents: water/ acetone MeOH/ water CH2Cl2/ hydrocarbon MeOH/ benzene THF/ MeOH #12;7 4

Meagher, Mary

165

Crystallography of TWIP Steel Graduate Institute of Ferrous Technology  

E-Print Network [OSTI]

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

Cambridge, University of

166

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

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

It is also a great time to interact with other scientists, potential colleagues, and vendors of light source related products and services. For more information, please visit...

167

The role of crystallography and nanostructures on metallic friction.  

SciTech Connect (OSTI)

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

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

2010-06-01T23:59:59.000Z

168

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

169

SciTech Connect: Goniometer-based femtosecond crystallography...  

Office of Scientific and Technical Information (OSTI)

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

170

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

E-Print Network [OSTI]

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

Sherrill, David

171

Genentech Uses ALS Crystallography for Therapeutic Antibody Research  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-SeriesFlickr Flickr Editor'sshort version) Thelong

172

Media invited to join students in crystallography experiment  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fund LasDubey MathematicaMeasuring andSecurityMarch 16,

173

Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankCombustion | Department ofT ib l L d F S i DOEToward aInnovationHydrogenNRGA C U.S. DepartmentMaterials

174

Adhesives from modified soy protein  

DOE Patents [OSTI]

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

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

2008-08-26T23:59:59.000Z

175

Protein Flips Lipids Across Membranes  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProteinProteinProtein

176

Elastic energy of proteins and the stages of protein folding  

E-Print Network [OSTI]

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

Lei, Jinzhi

2010-01-01T23:59:59.000Z

177

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

178

Combining in vivo and in silico screening for protein stability  

E-Print Network [OSTI]

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

Barakat, Nora Hisham

2007-01-01T23:59:59.000Z

179

Extending the theoretical framework of protein folding dynamics  

E-Print Network [OSTI]

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

Yang, Sichun

2006-01-01T23:59:59.000Z

180

Quantitative proteomics analysis of adsorbed plasma proteins...  

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

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

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

Computational prediction and analysis of protein structure  

E-Print Network [OSTI]

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

Meruelo, Alejandro Daniel

2012-01-01T23:59:59.000Z

182

Automated Purification of Recombinant Proteins: Combining High...  

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

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

183

Protein Folding Sculpting Evolutionary Change  

E-Print Network [OSTI]

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

Lindquist, Susan

184

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

E-Print Network [OSTI]

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

Zharkova, Valentina V.

185

Fast events in protein folding  

SciTech Connect (OSTI)

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

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

1996-04-01T23:59:59.000Z

186

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

E-Print Network [OSTI]

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

Stevenson, Calum

2012-11-30T23:59:59.000Z

187

How Hydrogen Bond Redundancy Affects Protein Flexibility  

E-Print Network [OSTI]

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

Naomi Fox; Filip Jagodzinski; Jeanne Hardy; Ileana Streinu

188

272 Dispatch Protein folding: Chaperones get Hip  

E-Print Network [OSTI]

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

Craig, Elizabeth A

189

Thermodynamics of Protein Folding Erik Sandelin  

E-Print Network [OSTI]

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

Sandelin, Erik

190

SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION  

SciTech Connect (OSTI)

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

191

Characterization of protein folding intermediates  

SciTech Connect (OSTI)

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

Kim, P.S.

1986-01-01T23:59:59.000Z

192

A phenomenological model of protein folding  

E-Print Network [OSTI]

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

Danielsson, Ulf H; Niemi, Antti J

2009-01-01T23:59:59.000Z

193

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

E-Print Network [OSTI]

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

Weston, Ken

194

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

E-Print Network [OSTI]

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

Bigelow, Stephen

195

Protein folding in the ER.  

SciTech Connect (OSTI)

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

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

1999-10-01T23:59:59.000Z

196

Method for protein structure alignment  

DOE Patents [OSTI]

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

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

2005-02-22T23:59:59.000Z

197

Protein phase feeding of poultry  

E-Print Network [OSTI]

PROTEIN PHASE FEEDING OF POULTRY A Thesis By Larry Rufus Vest Submitted to the Graduate College of the Texas AM University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE January 1966 Major Subject Poultry... Science PROTEIN PHASE FEEDING OF POULTRY A Thesis Larry Rufus Vest Approved as to style and content by: man o o x tee par e em e e er January 1966 ACKNOWLEDGE MENTS Tbe author wishes to express his sincere gratitude and deep appreciation to Dr...

Vest, Larry Rufus

1966-01-01T23:59:59.000Z

198

Protein Flips Lipids Across Membranes  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProteinProtein Flips

199

Protein Flips Lipids Across Membranes  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProteinProtein

200

Method for voltage-gated protein fractionation  

DOE Patents [OSTI]

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

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

2012-04-24T23:59:59.000Z

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

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

E-Print Network [OSTI]

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

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

2012-07-11T23:59:59.000Z

202

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

203

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

204

protein structure communications 1. Introduction  

E-Print Network [OSTI]

protein structure communications 1. Introduction Phospholipases A2 (PLA2s) are widely distributed metabolism, signal transduction and eicosanoid production (Dennis, 1997 ). PLA2 enzymes are characterized PLA2s (80-110 kDa) are present in many cell types and are involved in phospholipid metabolism

Tsai, Ming-Daw

205

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

206

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

E-Print Network [OSTI]

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

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

2013-01-01T23:59:59.000Z

207

Identifying protein-protein interactions of a cell cycle regulator  

E-Print Network [OSTI]

of a Cell Cycle Regulator. (April 2001) Joseph Edward Amos Department of Biochemistry Texas A&M University Fellows Advisor: Dr. Sumana Datta Department of Biochemistry and Biophysics The role of anachronism (ana) protein in stem cell division...-157. 29 Vita Name: Joseph Edward Amos Permanent Address: 114 Stephanie Dr. Palestine, TX 75801 Educational Background: Texas A & M University Bachelor of Science Biochemistry, May 2001 Fall 1998-Spring 2001 Kilgore College Summer 1997-Fall 1998...

Amos, Joseph Edward

2013-02-22T23:59:59.000Z

208

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

209

Protein Thioester Synthesis Enabled by Sortase  

E-Print Network [OSTI]

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

Ling, Jingjing

210

Topology to geometry in protein folding: -Lactoglobulin  

E-Print Network [OSTI]

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

Berry, R. Stephen

211

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

E-Print Network [OSTI]

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

Allen, Peter K.

212

Streak Seeding Automation Using Silicon Tools CUCS-015-06  

E-Print Network [OSTI]

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

Georgiev, Atanas

213

Protein folding using contact maps  

E-Print Network [OSTI]

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

Michele Vendruscolo; Eytan Domany

1999-01-21T23:59:59.000Z

214

agouti related protein: Topics by E-print Network  

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

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

215

Structural and biological studies of bone morphogenetic protein-15  

E-Print Network [OSTI]

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

McMahon, Heather Eileen

2007-01-01T23:59:59.000Z

216

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

E-Print Network [OSTI]

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

Anderson, William David

2007-01-01T23:59:59.000Z

217

Struts, springs and crumple zones: protein structures under force  

E-Print Network [OSTI]

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

Dill, Jesse

2012-01-01T23:59:59.000Z

218

Computational Modeling of Protein Interactions at Multiple Lengthscales  

E-Print Network [OSTI]

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

Yap, Eng Hui

2010-01-01T23:59:59.000Z

219

Protein-Folding Landscapes in Multi-Chain Systems  

E-Print Network [OSTI]

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

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

2005-01-01T23:59:59.000Z

220

Protein-folding via divide-and-conquer optimization  

E-Print Network [OSTI]

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

Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

2004-01-01T23:59:59.000Z

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

The unfolded protein response during prostate cancer development  

E-Print Network [OSTI]

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

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

2009-01-01T23:59:59.000Z

222

Intermediates and the folding of proteins L and G  

E-Print Network [OSTI]

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

Brown, Scott; Head-Gordon, Teresa

2008-01-01T23:59:59.000Z

223

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

E-Print Network [OSTI]

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

Guo, Minghao

2014-01-01T23:59:59.000Z

224

Extracellular secretion of recombinant proteins  

DOE Patents [OSTI]

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

Linger, Jeffrey G.; Darzins, Aldis

2014-07-22T23:59:59.000Z

225

On the Complexity of Protein Folding  

E-Print Network [OSTI]

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

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

226

GREEN FLUORESCENT PROTEIN The green revolution  

E-Print Network [OSTI]

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

Stearns, Tim

227

Solvent dramatically affects protein structure refinement  

E-Print Network [OSTI]

Solvent dramatically affects protein structure refinement Gaurav Chopraa , Christopher M. Summab structure), also known as the protein structure refinement problem. It has been shown that improve- ment in protein structure refinement. Molecular dynamics in explicit sol- vent and energy minimization in both

Summa, Christopher M.

228

EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS  

E-Print Network [OSTI]

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

Guibas, Leonidas J.

229

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

230

Amphiphiles for protein solubilization and stabilization  

DOE Patents [OSTI]

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

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

2014-11-04T23:59:59.000Z

231

Iterative Information Model Development Protein sequence  

E-Print Network [OSTI]

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

232

UNCORRECTED 3 Protein folding: Then and now  

E-Print Network [OSTI]

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

Dokholyan, Nikolay V.

233

STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS  

E-Print Network [OSTI]

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

Dinner, Aaron

234

Protein Structures Revealed at Record Pace  

ScienceCinema (OSTI)

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

Hura, Greg

2013-05-29T23:59:59.000Z

235

Protein Structures Revealed at Record Pace  

ScienceCinema (OSTI)

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

Greg Hura

2010-01-08T23:59:59.000Z

236

Protein folding: not just another optimization  

E-Print Network [OSTI]

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

Karplus, Kevin

237

Disulfide-Linked Protein Folding Pathways  

E-Print Network [OSTI]

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

Bardwell, James

238

Atomistic Protein Folding Simulations on the  

E-Print Network [OSTI]

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

Snow, Christopher

239

How Nature Fine Tunes Protein Stability  

E-Print Network [OSTI]

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

Wickstrom, Megan

2007-07-14T23:59:59.000Z

240

Intracellular Signaling by the Unfolded Protein  

E-Print Network [OSTI]

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

Mullins, Dyche

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

Approximate Inference and Protein-Folding  

E-Print Network [OSTI]

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

Weiss, Yair

242

Proteins  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassive Solar HomePromising Science for PlutoniumAbout Us / OurBioscience: Bioenergy,

243

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

E-Print Network [OSTI]

of various genomics efforts has been a vast growth in putative protein sequences that lack any experimental there are numerous examples of proteins with similar folds that lack any significant sequence homology.8Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design

Powers, Robert

244

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

Langmead, Christopher James

245

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

E-Print Network [OSTI]

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

246

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

E-Print Network [OSTI]

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

247

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

E-Print Network [OSTI]

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

Dinner, Aaron

248

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Studying submicrosecond protein folding  

E-Print Network [OSTI]

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

249

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

250

Review Protein Folding and Misfolding on Surfaces  

E-Print Network [OSTI]

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

Massimo Stefani

2008-01-01T23:59:59.000Z

251

Protein folding using contact maps Michele Vendruscolo and Eytan Domany  

E-Print Network [OSTI]

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

Domany, Eytan

252

Computational and experimental investigations of forces in protein folding  

E-Print Network [OSTI]

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

Schell, David Andrew

2005-02-17T23:59:59.000Z

253

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

DOE Patents [OSTI]

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

Laible, Philip D; Hanson, Deborah K

2013-06-04T23:59:59.000Z

254

Dominant Pathways in Protein Folding  

E-Print Network [OSTI]

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

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

2006-07-27T23:59:59.000Z

255

Studies involving low protein broiler diets  

E-Print Network [OSTI]

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

Parkin, David Palmer

1971-01-01T23:59:59.000Z

256

Class II virus membrane fusion proteins  

SciTech Connect (OSTI)

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

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

2006-01-05T23:59:59.000Z

257

DIP: The Database of Interacting Proteins  

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

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

258

Simulating Temperature Jumps for Protein Folding Studies.  

E-Print Network [OSTI]

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

Kim, Seonah

2007-01-01T23:59:59.000Z

259

Controlling membrane protein folding using photoresponsive surfactant.  

E-Print Network [OSTI]

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

Chang, Chia Hao

2012-01-01T23:59:59.000Z

260

Knots and Swelling in Protein Folding  

E-Print Network [OSTI]

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

Martin Lundgren; Antti J. Niemi

2009-06-26T23:59:59.000Z

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

Brownian Dynamics Simulation of Protein Solutions: Structural...  

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

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

262

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

E-Print Network [OSTI]

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

Pace, Norman

263

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

E-Print Network [OSTI]

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

Mukherjee, Srayanta

2011-12-31T23:59:59.000Z

264

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

SciTech Connect (OSTI)

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

B Wallace; R Janes

2011-12-31T23:59:59.000Z

265

MP 33200 EZQ Protein Quantitation Kit  

E-Print Network [OSTI]

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

Lebendiker, Mario

266

Multiscale Approach to Protein Engineering in Bioluminescence  

E-Print Network [OSTI]

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

Maryland at College Park, University of

267

Solvent-induced forces in protein folding  

SciTech Connect (OSTI)

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

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

1990-08-23T23:59:59.000Z

268

Production of Therapeutic Proteins in Plants  

E-Print Network [OSTI]

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

Bradford, Kent

269

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

270

The chemical properties and biological significance of gossypol protein complexes  

E-Print Network [OSTI]

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

Baliga, Bantval Prabhakara

1956-01-01T23:59:59.000Z

271

Protein Folding Challenge and Theoretical Computer Science Somenath Biswas  

E-Print Network [OSTI]

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

Biswas, Somenath

272

A newly discovered protein export machine in malaria parasites  

E-Print Network [OSTI]

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

Arnold, Jonathan

273

Can Contact Potentials Reliably Predict Stability of Proteins?  

E-Print Network [OSTI]

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

Khatun, Jainab

274

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

SciTech Connect (OSTI)

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

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

2003-01-01T23:59:59.000Z

275

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

E-Print Network [OSTI]

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

Wensel, Theodore G.

276

Cotranslational protein folding with L-systems  

E-Print Network [OSTI]

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

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

277

Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation  

E-Print Network [OSTI]

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

Baer, Christina Elizabeth

2010-01-01T23:59:59.000Z

278

RACK1, A Multifaceted Scaffolding Protein: Structure and Function  

E-Print Network [OSTI]

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

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

2011-01-01T23:59:59.000Z

279

Trends in template/fragment-free protein structure prediction  

E-Print Network [OSTI]

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

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

2011-01-01T23:59:59.000Z

280

Septin Self-Assembly: Plasticity and Protein Scaffolding  

E-Print Network [OSTI]

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

Garcia, III, Galo

2012-01-01T23:59:59.000Z

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

THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES  

E-Print Network [OSTI]

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

Sosnick, Tobin R.

282

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding  

E-Print Network [OSTI]

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

283

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping  

E-Print Network [OSTI]

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

Baker, David

284

New Crystal Structures Lift Fog around Protein Folding  

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

New Crystal Structures Lift Fog around Protein Folding New Crystal Structures Lift Fog around Protein Folding Print Wednesday, 25 July 2012 00:00 Nature's proteins set a high bar...

285

Exploring zipping and assembly as a protein folding principle  

E-Print Network [OSTI]

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

Voelz, Vince A; Dill, Ken A

2007-01-01T23:59:59.000Z

286

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

287

Preparation of white sunflower protein isolates  

E-Print Network [OSTI]

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

Wen, Hwei-Mei

1982-01-01T23:59:59.000Z

288

Nonlinear conformation of secondary protein folding  

E-Print Network [OSTI]

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

Januar, M; Handoko, L T

2012-01-01T23:59:59.000Z

289

Introducing Protein Folding Using Simple Models  

E-Print Network [OSTI]

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

D. Thirumalai; D. K. Klimov

2001-01-04T23:59:59.000Z

290

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

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

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

291

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

292

Identification of a putative protein profile associating with...  

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

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

293

adhesion plaque protein: Topics by E-print Network  

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

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

294

adhesive protein inspired: Topics by E-print Network  

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

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

295

adhesion modification protein: Topics by E-print Network  

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

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

296

adhesion protein neuroligin: Topics by E-print Network  

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

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

297

astrovirus coat protein: Topics by E-print Network  

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

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

298

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

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

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

299

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

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

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

300

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

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

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

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

Amino acid treatment enhances protein recovery from sediment...  

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

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

302

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

E-Print Network [OSTI]

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

De Micheli, Giovanni

303

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

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

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

304

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

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

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

305

Shotgun Proteomics Identifies Proteins Specific for Acute Renal...  

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

was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have...

306

accurate protein identification: Topics by E-print Network  

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

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

307

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

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

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

308

Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios  

E-Print Network [OSTI]

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

Berry, R. Stephen

309

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

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

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

310

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

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

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

311

New Crystal Structures Lift Fog around Protein Folding  

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

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

312

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

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

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

313

Improving NMR Protein Structure Quality by Rosetta Refinement...  

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

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

314

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

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

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

315

Diamond X-ray photodiode for white and monochromatic SR beams  

SciTech Connect (OSTI)

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

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

2011-09-01T23:59:59.000Z

316

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

E-Print Network [OSTI]

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

Enrico Montanari; Pierluigi Fortini

1998-08-26T23:59:59.000Z

317

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

E-Print Network [OSTI]

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

Wanstrath, John Joseph

1971-01-01T23:59:59.000Z

318

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

SciTech Connect (OSTI)

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

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

2014-04-15T23:59:59.000Z

319

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

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLasDelivered energy consumption byAbout SRNL Home SRNL main campusMore thanX-RayX-ray ImagePhase

320

The Effects of Wave Energy Converters on a Monochromatic Wave Climate  

E-Print Network [OSTI]

available from the National Oceanic and Atmospheric Administration (NOAA). Wave energy converters were converters as well as the availability of energy in the ocean. This study will examine the effects of a wave and mean wave period of wave energy fields. There is tremendous energy potential in the ocean. Solar energy

Fox-Kemper, Baylor

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

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

322

Enhanced sampling and applications in protein folding.  

E-Print Network [OSTI]

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

Zhang, Cheng

2013-01-01T23:59:59.000Z

323

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

324

Orpinomyces xylanase proteins and coding sequences  

DOE Patents [OSTI]

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

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

1998-10-20T23:59:59.000Z

325

Energetics of protein charge transfer and photosynthesis  

E-Print Network [OSTI]

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

Matyushov, Dmitry

326

Validating Computer-Designed Proteins for Vaccines  

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

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

327

Biomimetic materials for protein storage and transport  

DOE Patents [OSTI]

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

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

2012-05-01T23:59:59.000Z

328

Prion protein in health and disease  

E-Print Network [OSTI]

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

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

2008-01-01T23:59:59.000Z

329

Structural and Energetic Heterogeneity in Protein Folding  

E-Print Network [OSTI]

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

Steven S. Plotkin; Jose N. Onuchic

2000-09-27T23:59:59.000Z

330

Telomere-associated proteins in Arabidopsis thaliana  

E-Print Network [OSTI]

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

Surovtseva, Yulia V.

2009-05-15T23:59:59.000Z

331

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

332

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

333

MEDIA ADVISORY  

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

skills to the test Monday in the Protein Crystallography Station at the Los Alamos Research Park. The students will learn about the history and theory of X-ray...

334

Protein Folding: A Perspective From Statistical Physics  

E-Print Network [OSTI]

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

Jinzhi Lei; Kerson Huang

2010-02-26T23:59:59.000Z

335

Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA  

E-Print Network [OSTI]

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

Simona Cocco; John F. Marko; Remi Monasson

2014-05-26T23:59:59.000Z

336

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

SciTech Connect (OSTI)

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

Eliezer, D.

1994-06-01T23:59:59.000Z

337

Membrane Proteins DOI: 10.1002/anie.201107343  

E-Print Network [OSTI]

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

Wallace, Mark

338

INTRODUCTION Proteins must mature to their native confor-  

E-Print Network [OSTI]

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

Hebert, Daniel N.

339

Guide to Red Fluorescent Proteins and Biosensors for Flow Cytometry  

E-Print Network [OSTI]

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

Verkhusha, Vladislav V.

340

Optik Giriim Grntleme -Molekler konformasyon ve protein dizin lmlerine uygulamalar  

E-Print Network [OSTI]

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

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

Distribution of Protein Folds in the Three Superkingdoms of Life  

E-Print Network [OSTI]

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

342

Introduction Protein secretion is an essential process in prokaryotes and  

E-Print Network [OSTI]

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

Cheng, Chi-Hing Christina

343

Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics  

E-Print Network [OSTI]

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

Santiago, Juan G.

344

FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

345

Cellular mechanisms of membrane protein folding William R Skach  

E-Print Network [OSTI]

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

Cai, Long

346

Evolutionary Monte Carlo for protein folding simulations Faming Lianga)  

E-Print Network [OSTI]

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

Liang, Faming

347

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

E-Print Network [OSTI]

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

Smith, J. MacGregor

348

DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS  

E-Print Network [OSTI]

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

Langmead, Christopher James

349

Adaptive dimensionality reduction of stochastic differential equations for protein dynamics  

E-Print Network [OSTI]

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

Izaguirre, Jesús A.

350

Folding simulations of small proteins Seung-Yeon Kima  

E-Print Network [OSTI]

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

Lee, Jooyoung

351

Evaluation of enzymatic modification of peanut protein isolate  

E-Print Network [OSTI]

of peanut protein ingredients . . . 2 Amino acid compositions of peanut protein isolate and casein . 3 Protein solubility of trypsin-hyd?olyzed peanut protein isolate 4 Protein solubility of chymotrypsin-hydrolyzed peanut protein isolate . 5 Protein... Acids Al anine Aspartic acid Cystine Glutamic acid Glycine Proline Serine Tyrosine 13. 1 3. 4 3. 4 6. 6 2. 9 0. 9 5. 5 2. 3 4. 3 3. 9 12. 5 22. 7 4. 0 4. 7 4. 9 4. 4 3. 8 2. 3 6. 1 10. 8 6. 8 2. 9 5. 5 4. 4 1. 2 6. 6 2...

Hostetler, Marsha Kay

1979-01-01T23:59:59.000Z

352

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

353

Structure and expression of a novel compact myelin protein – Small VCP-interacting protein (SVIP)  

SciTech Connect (OSTI)

Highlights: •SVIP (small p97/VCP-interacting protein) co-localizes with myelin basic protein (MBP) in compact myelin. •We determined that SVIP is an intrinsically disordered protein (IDP). •The helical content of SVIP increases dramatically during its interaction with negatively charged lipid membrane. •This study provides structural insight into interactions between SVIP and myelin membranes. -- Abstract: SVIP (small p97/VCP-interacting protein) was initially identified as one of many cofactors regulating the valosin containing protein (VCP), an AAA+ ATPase involved in endoplasmic-reticulum-associated protein degradation (ERAD). Our previous study showed that SVIP is expressed exclusively in the nervous system. In the present study, SVIP and VCP were seen to be co-localized in neuronal cell bodies. Interestingly, we also observed that SVIP co-localizes with myelin basic protein (MBP) in compact myelin, where VCP was absent. Furthermore, using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopic measurements, we determined that SVIP is an intrinsically disordered protein (IDP). However, upon binding to the surface of membranes containing a net negative charge, the helical content of SVIP increases dramatically. These findings provide structural insight into interactions between SVIP and myelin membranes.

Wu, Jiawen [Department of Neurology, Vanderbilt University School of Medicine (United States)] [Department of Neurology, Vanderbilt University School of Medicine (United States); Peng, Dungeng [Department of Biochemistry, Vanderbilt University School of Medicine (United States)] [Department of Biochemistry, Vanderbilt University School of Medicine (United States); Voehler, Markus [Center for Structural Biology, Vanderbilt University (United States)] [Center for Structural Biology, Vanderbilt University (United States); Sanders, Charles R. [Department of Biochemistry, Vanderbilt University School of Medicine (United States) [Department of Biochemistry, Vanderbilt University School of Medicine (United States); Center for Structural Biology, Vanderbilt University (United States); Li, Jun, E-mail: jun.li.2@vanderbilt.edu [Department of Neurology, Vanderbilt University School of Medicine (United States) [Department of Neurology, Vanderbilt University School of Medicine (United States); Tennessee Valley Healthcare System (TVHS) – Nashville VA (United States)

2013-10-11T23:59:59.000Z

354

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

E-Print Network [OSTI]

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

Vajda, Sandor

355

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS PROTS: A fragment based protein  

E-Print Network [OSTI]

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

Zhang, Yang

356

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

357

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

E-Print Network [OSTI]

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

Baker, David

358

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

E-Print Network [OSTI]

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

Cox, Michael M.

359

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

E-Print Network [OSTI]

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

Lathrop, Richard H.

360

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

E-Print Network [OSTI]

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

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

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

E-Print Network [OSTI]

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

Annunziata, Onofrio

362

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

363

Proteotronics: Electronic devices based on proteins  

E-Print Network [OSTI]

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

E. Alfinito; L. Reggiani; J. Pousset

2014-05-15T23:59:59.000Z

364

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

365

Protein Instability and Lou Gehrig's Disease  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassive Solar HomePromising Science for PlutoniumAbout Us / Our ProgramsProteinProtein

366

Protein Dynamics Hit the Big Screen  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedles for4-16HamadaBaO/Al2O3Protecting LabProtein BridgesProtein

367

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

E-Print Network [OSTI]

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

Slavoff, Sarah Ann

2010-01-01T23:59:59.000Z

368

Response of Penaeus vannamei to dietary protein level, protein source and polyculture  

E-Print Network [OSTI]

experiments. Growth and survival were evaluated over 30- day experiments; and, apparent protein, lipid and total d 1et digestibilit1es were measured over a 3-day period immediately following each growth experiment. In monoculture, feeds containing var 1ed... related to handling stress. Apparent protein (78. 7-85. 8 %%d), lipid (45. 1-64. 8 4) and total diet digestibilities (43. 9-58. 4X) were similar among the three sizes of P. vannamei and were unrelated to protein-source ratio. In polyculture, either 6...

Smith, Linda Louise

1988-01-01T23:59:59.000Z

369

Energy use by biological protein transport pathways  

E-Print Network [OSTI]

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

Economou, Tassos

370

Elucidating Amyloid -Protein Folding and Assembly: A  

E-Print Network [OSTI]

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

Stanley, H. Eugene

371

Supplemental Data Degradation-Mediated Protein  

E-Print Network [OSTI]

Supplemental Data Degradation-Mediated Protein Quality Control in the Nucleus Richard G. Gardner:FITC) and DAPI (UV-2E/C) were from Chroma Technology Corp (Brattleboro, Vermont). Images were captured were assayed on YEPD plates containing 0.01­0.3% MMS or EMS. UV sensitivity was assayed by plating 400

Gardner, Rich

372

PROTEIN INTERACTIONS AND DISEASE MARICEL KANN  

E-Print Network [OSTI]

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

Radivojac, Predrag

373

Materials and Methods Protein expression and purification  

E-Print Network [OSTI]

Materials and Methods Protein expression and purification The Full length Argonaute gene from protease system was a generous gift from Dr. Chris Lima. PfAgo was further purified with a heating step with #12;the program CNS (S7) against the SHARP amplitudes. Water molecules were added conservatively (for

Joshua-Tor, Leemor

374

Protein Data Bank Project at Rutgers University  

SciTech Connect (OSTI)

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

Berman, Helen

2002-07-18T23:59:59.000Z

375

Critical aspects of hierarchical protein folding  

E-Print Network [OSTI]

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

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

1998-01-13T23:59:59.000Z

376

Introduction to protein folding for physicists  

E-Print Network [OSTI]

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

Pablo Echenique

2007-05-13T23:59:59.000Z

377

Histone H1 proteins in Chlamydomonas reinhardtii  

E-Print Network [OSTI]

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

Salinger, Andrew Paul

1994-01-01T23:59:59.000Z

378

Neurofilament Proteins in Avian Auditory Hair Cells  

E-Print Network [OSTI]

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

Rubel, Edwin

379

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

E-Print Network [OSTI]

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

Alibes, Andreu

380

Molecular nonlinear dynamics and protein thermal uncertainty quantification  

SciTech Connect (OSTI)

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

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

2014-03-15T23:59:59.000Z

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

Corn Storage Protein - A Molecular Genetic Model  

SciTech Connect (OSTI)

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

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

2013-05-31T23:59:59.000Z

382

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

SciTech Connect (OSTI)

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

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

2009-03-01T23:59:59.000Z

383

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

384

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Role of partial protein unfolding in  

E-Print Network [OSTI]

Cl, guanidinium chloride; HX, hydrogen exchange; NMR, nuclear magnetic resonance; SEC, size exclusion- tein formulations,11 as an anesthetic,12 as a membrane fluidizer,13 as a heat shock protein inducer,14

Mallela, Krishna M. G.

385

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

SciTech Connect (OSTI)

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

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

2007-01-01T23:59:59.000Z

386

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

E-Print Network [OSTI]

Page 1 Ribbon diagram showing the structure of VHP and VlsE ......................... 12 2 Far-UV CD spectra for VHP and VlsE ...................................................... 13 3 Energy diagrams for protein folding reaction... interactions, hydrogen bonding and hydrophobic effect. The stabilizing effects of these interactions are largely opposed by the major destabilizing force, which is the conformational entropy loss upon protein folding. Other forces, such as electrostatic...

Fu, Hailong

2010-07-14T23:59:59.000Z

387

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

E-Print Network [OSTI]

Herman B. Scholthof Wayne K. Versaw Head of Department, Dennis C. Gross May 2007 Major Subject: Plant Pathology ABSTRACT Analysis of Secreted Proteins of Magnaporthe grisea and the Search for Protein Efectors... parents, Ying Ma and Delong Shang, who supported me through the chalenges of graduate life. v ACKNOWLEDGMENTS I would like to thank my commite chair, Dr. Daniel Ebbole, who has been an outstanding both mentor and advisor. He taught me a lot...

Shang, Yue

2007-09-17T23:59:59.000Z

388

Function of the anterior gradient protein family in cancer   

E-Print Network [OSTI]

Proteomic technologies verified Anterior Gradient 2, AGR-2, as a protein over-expressed in human cancers, including breast, prostate and oesophagus cancers, with the ability to inhibit the tumour suppressor protein p53. AGR-2 gene is a hormone...

Fourtouna, Argyro

2009-01-01T23:59:59.000Z

389

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases  

E-Print Network [OSTI]

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present ...

Dixit, Anshuman; Verkhivker, Gennady M.

2011-10-06T23:59:59.000Z

390

Rapid and Efficient Protein Digestion using Trypsin Coated Magnetic...  

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

were carried out on a single model protein, a five protein mixture, and a whole mouse brain proteome, and also compared for digestion at atmospheric pressure and 37 ºC for...

391

Self-assembly of globular protein-polymer diblock copolymers  

E-Print Network [OSTI]

Self-assembly of protein-polymer block copolymers provides a simple bottom-up approach towards protein nanopatteming for the fabrication of more effective and efficient bioelectronic and biocatalytic devices. Changes in ...

Thomas, Carla S. (Carla Stephanie)

2014-01-01T23:59:59.000Z

392

Protein quality control in the mammalian endoplasmic reticulum  

E-Print Network [OSTI]

Quality control is an important part of protein biogenesis. Aberrant proteins must be destroyed before they aggregate and cause deleterious effects. Failure to do so can result in cell death or malfunction and, ultimately, ...

Klemm, Elizabeth J. (Elizabeth Joanna)

2011-01-01T23:59:59.000Z

393

activation protein expression: Topics by E-print Network  

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

the relative rates of protein synthesis 98 Reduced 293T cell susceptibility to acrolein due to aldose reductase-like-1 protein expression CiteSeer Summary: Acrolein is a...

394

The effects of shared peptides on protein quantitation in label...  

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

The effects of shared peptides on protein quantitation in label-free proteomics by LCMSMS . The effects of shared peptides on protein quantitation in label-free proteomics by LC...

395

acid binding proteins: Topics by E-print Network  

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

The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

396

acidbinding protein concentration: Topics by E-print Network  

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

The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

397

Lipid-dependent regulation of the unfolded protein response  

E-Print Network [OSTI]

Protein folding homeostasis in the lumen of the endoplasmic reticulum is defended by signal transduction pathways that are activated by an imbalance between unfolded proteins and chaperones (so called ER stress). Collectively referred...

Volmer, Romain; Ron, David

2014-12-25T23:59:59.000Z

398

Small-Molecule Control of Protein Degradation Using Split Adaptors  

E-Print Network [OSTI]

Targeted intracellular degradation provides a method to study the biological function of proteins and has numerous applications in biotechnology. One promising approach uses adaptor proteins to target substrates with ...

Davis, Joseph H.

399

Why are MD simulated protein folding times wrong? Dmitry Nerukh  

E-Print Network [OSTI]

Why are MD simulated protein folding times wrong? Dmitry Nerukh Unilever Centre for Molecular.ac.uk The question of significant deviations of protein folding times simulated using molecular dynamics from

Nerukh, Dmitry

400

Protein Folding Simulation in CCP Luca Bortolussi1  

E-Print Network [OSTI]

Protein Folding Simulation in CCP Luca Bortolussi1 , Alessandro Dal Pal`u1 , Agostino Dovier1 as the protein folding. This problem is fundamental for biological and pharmaceutical research. Currently

Bortolussi, Luca

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

Structure and function of Pseudomonas aeruginosa protein PA1324 (21170)  

E-Print Network [OSTI]

Northwest National Laboratory, Biological Sciences Division, Northeast Structural Genomics Consortium and Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056 Received 12 June 2008 aeruginosa PA1324; NMR; functional genomics; NMR high-throughput screens; protein-ligand binding; protein

Powers, Robert

402

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

403

Consistent blind protein structure generation from NMR chemical shift data  

E-Print Network [OSTI]

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

Baker, David

404

Quantitative analysis of cell surface membrane proteins using...  

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

the quantification of membrane proteome changes, enriched membrane protein samples from wild-type and mutant cells (generated from deletion of a type II secretion protein, GspD)...

405

Thermal unfolding dynamics of proteins probed by nonlinear infrared spectroscopy  

E-Print Network [OSTI]

This thesis presents spectroscopic approaches to study the thermal unfolding dynamics of proteins. The spectroscopic tool is nonlinear infrared (IR) spectroscopy of the protein amide I band. Among various nonlinear IR ...

Chung, Hoi Sung

2007-01-01T23:59:59.000Z

406

Production and Functional Analysis of Recombinant Bovine Morphogenic Protein 15  

E-Print Network [OSTI]

dorsomorphin, a selective bone morphogenic protein receptor I inhibitor, demonstrated the purified proteins served as BMP15-like agonists. To examine the impact of our purified, bovine-specific peptides on oocyte maturation, cumulus oocyte complexes were...

Burns, Gregory Willis

2013-11-21T23:59:59.000Z

407

Experimental and Computational Studies on Protein Folding, Misfolding and Stability  

E-Print Network [OSTI]

Proteins need fold to perform their biological function. Thus, understanding how proteins fold could be the key to understanding life. In the first study, the stability and structure of several !-hairpin peptide variants derived from the C...

Wei, Yun

2010-07-14T23:59:59.000Z

408

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

409

DB-PABP: a database of polyanion-binding proteins  

E-Print Network [OSTI]

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many...

Fang, Jianwen; Dong, Yinghua; Slamat-Miller, Nazila; Middaugh, C. Russell

2007-10-04T23:59:59.000Z

410

autoinducer-2 processing protein: Topics by E-print Network  

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

of two fatty acids and a hydrophilic group provided by a phosphoric acid ester... Perez Hernandez, Gabriela 2005-08-29 82 Winter 2011 Evaluating Protein-Protein Docking Web...

411

Activity-based protein profiling of secreted cellulolytic enzyme...  

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

based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30 Activity-based protein profiling of secreted cellulolytic...

412

A comparative study of HPr proteins from extremophilic organisms  

E-Print Network [OSTI]

of the proteins were derived from moderate thermophiles (Streptococcus thermophilus and Bacillus staerothermophilus) and two from haloalkaliphilic organisms (Bacillus halodurans and Oceanobacillus iheyensis); these proteins were compared with HPr from...

Syed Ali, Abbas Razvi

2006-04-12T23:59:59.000Z

413

Protein Helical Topology Prediction Using Mixed-Integer Linear Programming  

E-Print Network [OSTI]

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

Singh, Jaswinder Pal

414

Framework for a Protein Ontology Darren A. Natale1  

E-Print Network [OSTI]

development of PRO, illustrated using human proteins from the TGF-beta signaling pathway (http://pir

415

RACK1, A Multifaceted Scaffolding Protein: Structure and Function  

E-Print Network [OSTI]

protein interacts with Helicobacter pylori VacA cytotoxin:16 (HPV 16) [213] and Helicobacter pylori [214]. There are

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

2011-01-01T23:59:59.000Z

416

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

E-Print Network [OSTI]

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

Vekich, John Alan

2013-01-01T23:59:59.000Z

417

Protein Vivisection Reveals Elusive Intermediates in Folding  

SciTech Connect (OSTI)

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

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

2010-05-25T23:59:59.000Z

418

Single proteins that serve linked functions in intracellular and extracellular microenvironments  

E-Print Network [OSTI]

listed above, these proteins lack exocytosis-targetingthe cell. These proteins often lack defined secretory signalthe lack of an exocytosis signal sequence in proteins with

Radisky, Derek C.

2009-01-01T23:59:59.000Z

419

E-Print Network 3.0 - active core protein Sample Search Results  

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

protein with extension pc0741 conserved hypothetical protein pc0743... the Evolutionary History of Chlamydiae" (Horn et al.) Supporting Online Material 2 protein sequence...

420

ATP Competitive Protein Kinase C Inhibitors Demonstrate Distinct State-Dependent Inhibition  

E-Print Network [OSTI]

ATP Competitive Protein Kinase C Inhibitors Demonstratepreviously reported that some ATP competitive protein kinaseSmith IM, Hoshi N (2011) ATP Competitive Protein Kinase C

Smith, Ida M.; Hoshi, Naoto

2011-01-01T23:59:59.000Z

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

E-Print Network 3.0 - abnormal protein bands Sample Search Results  

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

protein bands Search Powered by Explorit Topic List Advanced Search Sample search results for: abnormal protein bands Page: << < 1 2 3 4 5 > >> 1 An Introduction to Protein...

422

Redox Characterization of Proteins Involved in the Mitochondrial Intermembrane Space Pathway  

E-Print Network [OSTI]

Bardwell. 1999. Oxidative protein folding is driven by thecatalyzes oxidative protein folding in mitochondria. Naturecarriers in oxidative protein folding. International journal

Neal, Sonya Elina

2013-01-01T23:59:59.000Z

423

MORPH-PRO: a novel algorithm and web server for protein morphing  

E-Print Network [OSTI]

PA: Pathways to a protein folding intermediate observed in amotion planning to study protein folding pathways. J ComputGo N: Studies on protein folding, unfolding and fluctuations

2013-01-01T23:59:59.000Z

424

Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins  

E-Print Network [OSTI]

polyelec- trolytes and protein folding in particular, standsdynamics ? protein folding ? single-molecule ?uorescencestructure and dynamics. Protein folding is the most spec-

Laurence, T A; Kong, X X; Jager, M; Weiss, S

2005-01-01T23:59:59.000Z

425

The unfolded protein response : integrating stress signals from the endoplasmic reticulum to the nucleolus  

E-Print Network [OSTI]

for monitoring the protein-folding environment of the ER andconditions that disrupted protein folding in the ER, andinterfering with ER protein folding induces the expression

DuRose, Jenny Bratlien

2008-01-01T23:59:59.000Z

426

Carbon-deuterium bonds as an infrared probe of protein dynamics, local electrostatics and folding  

E-Print Network [OSTI]

and Englander, W. S. , Protein Folding: A Stepwise AssemblyEnglander, S. W. , Protein Folding Intermediates – NativeR. L. , How Does Protein Folding Get Started? Trends

Sagle, Laura B.

2006-01-01T23:59:59.000Z

427

Facilitation of protein 3-D structure determination using enhanced peptide amide deuterium exchange mass spectrometry (DXMS)  

E-Print Network [OSTI]

hydrophobic interaction in protein folding. Proc Natl Acad1999;28:1-27. 15. Protein Folding, Dynamics, and StructuralHydrogen exchange and protein folding. Curr. Opin. Struct.

Pantazatos, Dennis Peter

2006-01-01T23:59:59.000Z

428

Beyond the native state: Exploring the role of partially folded conformations on the protein energy landscape  

E-Print Network [OSTI]

L. & Englander, S. W. (1995). Protein folding intermediates:Unifying features in protein- folding mechanisms. Proc Natlintermediate state in protein folding by a hydrophobic

Connell, Katelyn Blair

2010-01-01T23:59:59.000Z

429

Effect of single-point sequence alterations on the aggregation propensity of a model protein  

E-Print Network [OSTI]

effect on both protein folding and its aggregationstudied sequences, improves protein folding rates, foldingmechanisms implicated in protein folding as opposed to

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

2005-01-01T23:59:59.000Z

430

E-Print Network 3.0 - ankyrin-repeat membrane protein Sample...  

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

10 Stabilizing IB by "Consensus" Design Diego U. Ferreiro1,3 Summary: Keywords: protein folding; ankyrin repeat protein; NF-B; transcription factor; repeat protein...

431

E-Print Network 3.0 - a-binding protein acbp6 Sample Search Results  

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

Biology and Medicine 3 Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding Summary: kinetics using FRET with acyl-CoA binding protein. In protein folding,...

432

E-Print Network 3.0 - ankyrin protein networks Sample Search...  

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

>> 21 Stabilizing IB by "Consensus" Design Diego U. Ferreiro1,3 Summary: Keywords: protein folding; ankyrin repeat protein; NF-B; transcription factor; repeat protein...

433

E-Print Network 3.0 - a-3 proteins weakly Sample Search Results  

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

structures of proteins are the support... focuses to understand the mechanisms of protein folding and stability. Furthermore, protein ... Source: Ecole Polytechnique, Centre de...

434

E-Print Network 3.0 - age-induced protein modifications Sample...  

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

organisms Lack of post- translational modifications Endotoxins... eukaryotic protein folding and modification machinery Protein ExpressionProtein Expression 12;2 Rapid...

435

E-Print Network 3.0 - accelerates protein gain Sample Search...  

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

state of the protein leading... of Protein Engineering Techniques to Elucidate Protein Folding Pathways. In P. Michael Conn, editor: Progress... : 978-0-12-374595-8 ...

436

E-Print Network 3.0 - auxilin-like j-domain protein Sample Search...  

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

conserved family of ubiquitous molecular chaperones that play essential roles in protein folding... Bcl-2 BAP : BiP-Associated Proteins ; proteins associes BiP CFTR : Cystic...

437

Signatures of the protein folding pathway in two-dimensional ultraviolet spectroscopy  

E-Print Network [OSTI]

2) Dobson, C. M. Protein Folding and Misfolding. Naturethe Complexity of Protein Folding. Curr. Opin. Struct. Biol.Signatures of the Protein Folding Pathway in Two-Dimensional

Jiang, J; Lai, Z; Wang, J; Mukamel, S

2014-01-01T23:59:59.000Z

438

Microfluidic advantage : novel techniques for protein folding and oxygen control in cell cultures  

E-Print Network [OSTI]

Novel Techniques for Protein Folding and Oxygen Control inTemperature Jump System to Study Fast Protein FoldingNovel Techniques for Protein Folding and Oxygen Control in

Polinkovsky, Mark E.; Polinkovsky, Mark E.

2012-01-01T23:59:59.000Z

439

Energy landscapes for protein folding, binding, and aggregation : simple funnels and beyond  

E-Print Network [OSTI]

coordinates capture protein folding on smooth landscapes.in the Prediction of Protein Folding Kinetics. Proc. Natl.Landscapes for Protein Folding, Binding, and Aggregation:

Cho, Samuel Sung-Il

2007-01-01T23:59:59.000Z

440

A Proteomic Study of Protein Tyrosine Nitration  

E-Print Network [OSTI]

chromatography mass spectrometry 2.2 Introduction Creatine kinase (CK) is a 37 kDa protein expressed in high energy demanding tissues such as heart, skeletal muscle and brain. CK plays an important role in energy metabolism by effectively catalyzing...: Reactive oxygen species - RNS: Reactive nitrogen species - CK: Creatine Kinase - HPLC-ESI-MS/MS: High performance liquid chromatography-electrospray ionization tandem mass spectrometry. - 3-NY: 3-nitrotyrosine - NO: nitrogen monoxide - ONOO...

Hong, Sung Jung

2008-08-28T23:59:59.000Z

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


441

Rigidity Analysis for Modeling Protein Motion  

E-Print Network [OSTI]

. ............................... 128 XIII Comparison of average relative exchange rate for both EX RS and EX CS between the entire protein and the experimentally defined folding core. ................................ 154 xii TABLE Page XIV Comparison between rigidityscores, cluster... exchange rates from rigidity scores and cluster scores to experimental data. ................... 131 50 Visual comparison of simulated exchange rates to experimental data. 149 51 Minimal variance thresholds (dashed lines) to cluster EX RS for Tendamistat...

Thomas, Shawna L.

2010-07-14T23:59:59.000Z

442

Rapid Protein Structure Detection and Assignment using Residual Dipolar Couplings  

E-Print Network [OSTI]

Rapid Protein Structure Detection and Assignment using Residual Dipolar Couplings Michael A substructures by exploiting the orientational constraint of residual dipolar coupling (RDC). PEPMORPH reverses: We have tested PEPMORPH on a variety of real proteins deposited in the Protein Data Base (PDB), using

443

Refolding of recombinant proteins Eliana De Bernardez Clark  

E-Print Network [OSTI]

in in vitro protein folding. New additives to prevent aggregation have been added to a growing list. A wealth of literature on the role of chaperones and foldases in in vivo protein folding has triggered the development the formation of inclusion bodies was first observed almost two decades ago, existing protein folding protocols

Lebendiker, Mario

444

Phosphorylation in Synechocystis 1 PHOSPHORYLATION OF PHYCOBILISOME LINKER PROTEINS  

E-Print Network [OSTI]

-NADPH reductase and the linker proteins of the phycobilisome antenna. Using mutants that lack specific setPhosphorylation in Synechocystis 1 JBC PHOSPHORYLATION OF PHYCOBILISOME LINKER PROTEINS@botanik.biologie.uni-muenchen.de The controversial issue of protein phosphorylation from the photosynthetic apparatus of Synechocystis sp. PCC 6803

Paris-Sud XI, Université de

445

The variable and conserved interfaces of modeled olfactory receptor proteins  

E-Print Network [OSTI]

of the odorants' contact residues in OR proteins remained unavailable. Due to the lack of X-ray crystallographicThe variable and conserved interfaces of modeled olfactory receptor proteins YITZHAK PILPEL models of other G-protein-coupled receptors, allows us to analyze the OR amino acid variability patterns

Church, George M.

446

Combinatorial Problems on Strings with Applications to Protein Folding  

E-Print Network [OSTI]

Combinatorial Problems on Strings with Applications to Protein Folding Alantha Newman MIT San Jose, CA 95120, USA ruhl@almaden.ibm.com Abstract We consider the problem of protein folding in linear time. 1 Introduction We consider the problem of protein folding in the HP model on the three

Newman, Alantha

447

Protein Folding Simulation by Two-Stage Optimization  

E-Print Network [OSTI]

Protein Folding Simulation by Two-Stage Optimization A. Dayem Ullah1 , L. Kapsokalivas1 , M. Mann2 propose a two-stage optimization approach for protein folding simulation in the FCC lattice, inspired from procedure based on simulated annealing alone. 1 Introduction The question of how proteins fold and whether

Will, Sebastian

448

Protein folding with stochastic L-systems Gemma Danks1  

E-Print Network [OSTI]

Protein folding with stochastic L-systems Gemma Danks1 , Susan Stepney1 and Leo Caves1 1 University-like structures. Models of protein folding vary in complexity and the amount of prior knowledge they contain). The energy landscape theory of protein folding (Onuchic et al., 1997) predicts a rugged funnel-like energy

Stepney, Susan

449

Site specific incorporation of keto amino acids into proteins  

DOE Patents [OSTI]

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

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

2009-04-28T23:59:59.000Z

450

Self-assembled lipid and membrane protein polyhedral nanoparticles  

E-Print Network [OSTI]

Self-assembled lipid and membrane protein polyhedral nanoparticles Tamara Bastaa,1 , Hsin-Jui Wub,1 for review January 28, 2012) We demonstrate that membrane proteins and phospholipids can self-assemble for the self-assembly of lipids and membrane proteins into closed polyhedral structures that can potentially

Stowell, Michael

451

Fra superledere over polymerer til proteiner: Hvis man vil fremstille  

E-Print Network [OSTI]

Fra superledere over polymerer til proteiner: Hvis man vil fremstille tyndfilm af komplicerede tyndfilm af organiske materialer, som består af store og komplicerede molekyler: Polymerer, proteiner, antistoffer og DNA. Tyndfilm af polymerer er interessante i sensorer, fordi bestemte polymerer eller proteiner

452

Comprehensive Superfamily and Function Classification of Protein Sequences  

E-Print Network [OSTI]

on the basis of end-to-end similarity and domain architecture. The protein superfamily organization of the PIR-International Protein Sequence Database (PIR-PSD) is the only comprehensive protein classification system that is based are facilitated by the PIR Annotation and Similarity Database, which includes a pre- computed FASTA Database

453

Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding  

E-Print Network [OSTI]

Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding David E. Hertzog,, Xavier a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 µs and sample) measurements of single-stranded DNA. We also demon- strate the feasibility of measuring fast protein folding

Michalet, Xavier

454

Polymer Collapse, Protein Folding, and the Percolation Threshold  

E-Print Network [OSTI]

Polymer Collapse, Protein Folding, and the Percolation Threshold HAGAI MEIROVITCH University (Macromolecules 1989, 22, 3986­3997) to study protein folding, where H and P are the hydrophobic and polar amino; computer simulation; collapse transition; protein folding Introduction The behavior of dilute polymer

Meirovitch, Hagai

455

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-Print Network [OSTI]

8 Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives Michael Bachmann applications. In this lecture, we focus on the anal- ysis of mesoscopic models for protein folding, aggregation for a more universal description of the notoriously difficult problem of protein fold- ing. In this approach

Janke, Wolfhard

456

Author's personal copy Protein folding in confined and crowded environments  

E-Print Network [OSTI]

Author's personal copy Review Protein folding in confined and crowded environments Huan-Xiang Zhou protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize

Weston, Ken

457

COMMUNICATION First Principles Prediction of Protein Folding Rates  

E-Print Network [OSTI]

COMMUNICATION First Principles Prediction of Protein Folding Rates Derek A. Debe and William A studies have demonstrated that many small, single-domain proteins fold via simple two-state kinetics. We. # 1999 Academic Press Keywords: protein folding; kinetics; diffusion; fold topology; nucleation

Goddard III, William A.

458

John von Neumann Institute for Computing Monte Carlo Protein Folding  

E-Print Network [OSTI]

John von Neumann Institute for Computing Monte Carlo Protein Folding: Simulations of Met://www.fz-juelich.de/nic-series/volume20 #12;#12;Monte Carlo Protein Folding: Simulations of Met-Enkephalin with Solvent-Accessible Area difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular

Hsu, Hsiao-Ping

459

Predicting Protein Folding Mohammed J. Zaki, Vinay Nadimpally, Deb  

E-Print Network [OSTI]

Predicting Protein Folding Pathways Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff 1. Predicting Protein Folding Pathways Summary. A structured folding pathway, which is a time ordered sequence of folding events, plays an important role in the protein folding process and hence

Zaki, Mohammed Javeed

460

Nonlinear dynamics of secondary protein folding Natalia G. Berloff  

E-Print Network [OSTI]

Nonlinear dynamics of secondary protein folding Natalia G. Berloff Department of Applied field varies. Pacs: 87.15.-v, 87.15By, 05.45.-a, 41.20Jb Keywords: Folding pathway, protein folding interaction and hydrophobic effects. The most common shapes of the protein folding are alpha () and beta

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

Protein folding: Then and now Yiwen Chen 1  

E-Print Network [OSTI]

Review Protein folding: Then and now Yiwen Chen 1 , Feng Ding 1 , Huifen Nie 1 , Adrian W decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally

Dokholyan, Nikolay V.

462

Protein folding by zipping and assembly S. Banu Ozkan*  

E-Print Network [OSTI]

Protein folding by zipping and assembly S. Banu Ozkan* , G. Albert Wu* , John D. Chodera, CA, May 2, 2007 (received for review April 13, 2006) How do proteins fold so quickly? Some denatured proteins fold to their native structures in only microseconds, on average, implying that there is a folding

Southern California, University of

463

Author's personal copy Protein folding: Then and now  

E-Print Network [OSTI]

Author's personal copy Review Protein folding: Then and now Yiwen Chen 1 , Feng Ding 1 , Huifen Nie Available online 8 June 2007 Abstract Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital

Dokholyan, Nikolay V.

464

Multi-Agent Simulation of Protein Folding Luca Bortolussi1  

E-Print Network [OSTI]

Multi-Agent Simulation of Protein Folding Luca Bortolussi1 , Agostino Dovier1 , and Federico residues) is known. The process for reaching this state is known as the protein fold- ing. This problem the feasibility and the power of the method. Keywords: Computational Biology, Agent-Based Technologies, Protein

Bortolussi, Luca

465

COMMUNICATION Are Residues in a Protein Folding Nucleus  

E-Print Network [OSTI]

COMMUNICATION Are Residues in a Protein Folding Nucleus Evolutionarily Conserved? Yan Yuan Tseng is the hallmark of life. It is important to understand how protein folding and evolution influence each other in protein folding nucleus as measured by experi- mental f-value and selection pressure as measured by v

Dai, Yang

466

MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix  

E-Print Network [OSTI]

MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix Department of Mathematics University of South Carolina Abstract. We present an elementary introduction to the protein folding problem directed toward, and biological problem, protein folding can also be precisely formulated as a set of mathematics problems. We

Dix, Daniel B.

467

Polypeptide chain collapse and protein folding Jayant B. Udgaonkar  

E-Print Network [OSTI]

Review Polypeptide chain collapse and protein folding Jayant B. Udgaonkar National Centre is an integral component of a protein folding reaction. In this review, exper- imental characterization solvent [2]. A distinctive physical feature of any protein folding reaction is the greater than 3-fold

468

MICROFLUIDIC DEVICE FOR SUPER-FAST EVALUATION OF MEMBRANE PROTEIN  

E-Print Network [OSTI]

MICROFLUIDIC DEVICE FOR SUPER-FAST EVALUATION OF MEMBRANE PROTEIN CRYSTALLIZATION Hsin-Jui Wu1- throughput membraneless microfluidic device to fast produce the reconstitution of membrane protein in microfluidic channel can be completed in seconds to form protein/lipid particles under multiple conditions

Stowell, Michael

469

Serodiagnosis of avian infectious bronchitis virus using recombinant nucleocapsid protein  

E-Print Network [OSTI]

A diagnostic immunoaassay using recombinant nucleocapsid protein to detect antibodies to I13V was designed. The nucleocapsid protein was expressed from an expression plasmid, Qiagen pQE8, in E. coli as a fusion protein that was purified on NI...

Ndifuna, Abdul-El-Nuru

1996-01-01T23:59:59.000Z

470

Early Events in Protein Folding Explored by Rapid Mixing Methods  

E-Print Network [OSTI]

15 Early Events in Protein Folding Explored by Rapid Mixing Methods Heinrich Roder, Kosuke Maki for Understanding Protein Folding As with any complex reaction, time-resolved data are essential for elucidating the mechanism of protein folding. Even in cases where the whole process of folding occurs in a single step

Roder, Heinrich

471

Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao  

E-Print Network [OSTI]

Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao Dept of Biology Rensselaer Polytechnic Institute, Troy, NY. e-mail:{bystrc, shaoy}@rpi.edu Summary Proteins fold through a series of intermediate states called a pathway. Protein folding pathways have been modeled using either simulations

Bystroff, Chris

472

www.activemotif.comwww.activemotif.com Protein Purification  

E-Print Network [OSTI]

, mammalian cells, yeast, and bacteria. For fast, small-scale purification of 6xHis-tagged proteins Binding, medium-scale purification of 6xHis-tagged proteins Binding capacity: 900 µg/column (45 nmol @ ~20 kwww.activemotif.comwww.activemotif.com Ni-TEDTM Protein Purification Active Motif 5431-C Avenida

Lebendiker, Mario

473

MICROPROTEOMICS: ANALYSIS OF PROTEIN DIVERSITY IN SMALL SAMPLES  

E-Print Network [OSTI]

MICROPROTEOMICS: ANALYSIS OF PROTEIN DIVERSITY IN SMALL SAMPLES Howard B. Gutstein,1 * Jeffrey S.interscience.wiley.com) DOI 10.1002/mas.20161 Proteomics, the large-scale study of protein expression in organisms, offers be expressed by the genetic material of an organism. Advancements in protein extraction, purification

474

Mini review Practical considerations in refolding proteins from inclusion bodies  

E-Print Network [OSTI]

, removal of the denaturant, and assistance of refolding by small molecule additives. We will review key concentration, and (3) the effect of small molecule additives on refolding and aggregation of the proteins. Ã?- nomic sequence database, on a rapid, large-scale pro- duction of recombinant proteins. The proteins thus

Lebendiker, Mario

475

Overview of facility usage Protein Technology Core Facility  

E-Print Network [OSTI]

performedFig9: Projects delivered Protein technology core has been successful as a small scale player expression and optimal purification is imperative for protein biology research groups in academia as well and technical guidance at all steps to optimize expression and purification to generate the protein of interest

Udgaonkar, Jayant B.

476

Automated Discovery of Structural Signatures of Protein Fold and Function  

E-Print Network [OSTI]

Automated Discovery of Structural Signatures of Protein Fold and Function Marcel Turcotte1 sys- tematically for protein fold signatures, we have explored the use of Inductive Logic Programming fold. The work showed that signatures of protein folds exist, about half of rules discov- ered

Muggleton, Stephen H.

477

Diffusion of a protein in configuration space  

SciTech Connect (OSTI)

Simulations of biomolecular dynamics are commonly interpreted in terms of harmonic or quasi-harmonic models for the dynamics of the system. These models assume that biomolecules exhibit oscillations around a single energy minimum. However, spectroscopic data on myoglobin suggest that proteins sample multiple minima. Transitions between minima reveal a broad distribution of energy barriers. This behavior has been observed in other biomolecular systems. To elucidate the nature of protein dynamics the authors have studied a 1.2ns molecular dynamics trajectory of crambin in aqueous solution. This trajectory samples multiple local energy minima. Transitions between minima involve collective motions of amino acids over long distances. The authors show that nonlinear motions are responsible for most of the atomic fluctuations of the protein. These atomic fluctuations are not well described by large motions of individual atoms or a small group of atoms, but rather by concerted motions of many atoms. These nonlinear motions describe transitions between different basins of attraction. The signature of these motions manifests in local and global structural variables. A method for extracting Molecule Optimal Dynamic Coordinates (MODC) is presented.

Garcia, A.E.; Blumenfeld, R.; Hummer, G.; Sobehart, J.

1995-09-01T23:59:59.000Z

478

Nucleic acids encoding human trithorax protein  

DOE Patents [OSTI]

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

Evans, Glen A. (Encinitas, CA); Djabali, Malek (Marseilles, FR); Selleri, Licia (Del Mar, CA); Parry, Pauline (San Diego, CA)

2001-01-01T23:59:59.000Z

479

Simple Models of the Protein Folding Problem  

E-Print Network [OSTI]

The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I will give an introduction to the problem, and then focus on some recent work concerning the so-called ``designability principle''. The designability of a structure is measured by the number of sequences that have that structure as their unique ground state. Structures differ drastically in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures 1) possess ``proteinlike'' secondary structures and motifs, 2) are thermodynamically more stable, and 3) fold faster than other structures. These results suggest that protein structures are selected in nature because they are readily designed and stable against mutations, and that such selection simultaneously leads to thermodynamic stability and foldability. According to this picture, a key to the protein folding problem is to understand the emergence and the properties of the highly designable structures.

Chao Tang

1999-12-26T23:59:59.000Z

480

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking  

E-Print Network [OSTI]

Background: Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve ...

Liu, Shiyong; Vakser, Ilya A.

2011-07-11T23:59:59.000Z

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.


481

Effect of dietary protein quality on fractional rates of muscle protein synthesis and catabolism in the rat  

E-Print Network [OSTI]

EFFECT OF DIETARY PROTEIN QUALITY ON FRACTIONAL RATES OF MUSCLE PROTEIN SYNTHESIS AND CATABOLISM IN THE RAT A Thesis by RICHARD ANTHONY ROEDER Submitted to the Graduate College of Texas A8cM University in partial fulfillment... of the requirement for the degree of MASTER OF SCIENCE August 1979 Major Subject: Animal Nutrition EFFECT OF DIETARY PROTEIN QUALITY ON FRACTIONAL RATES OF MUSCLE PROTEIN SYNTHESIS AND CATABOLISM IN THE RAT A Thesis by RICHARD ANTHONY ROEDER Approved...

Roeder, Richard Anthony

1979-01-01T23:59:59.000Z

482

A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants  

E-Print Network [OSTI]

. Clearly, a key step in such approaches is the development of reliable methods for estimating the relative stability of possible mutants to identify favorable mutations. Such methods may also help better understand the protein- folding problem since... the ultimate outcome of protein folding is a native structure with the lowest free energy among many possible structures of a protein. A common approach to study the thermostability of proteins is to perform comparative studies of the sequences and...

Li, Yunqi; Middaugh, C. Russell; Fang, Jianwen

2010-01-28T23:59:59.000Z

483

Protein Science (2000), 9: 197-200. Cambridge University Press. Printed in the USA. Copyright 2000 The Protein Society  

E-Print Network [OSTI]

on the history of proteins classified in the SCOP structure database, we expect that only about a quarter this question. The SCOP database (Murzin et al., 1995) organizes proteins according to their structural on a protein sequence identical or nearly identical to one already in the database, perhaps with some mutations

Levitt, Michael

484

Energy Landscape and Transition State of Protein-Protein Association Ramzi Alsallaq and Huan-Xiang Zhou  

E-Print Network [OSTI]

Energy Landscape and Transition State of Protein-Protein Association Ramzi Alsallaq and Huan as well as the transition state for association. The energy landscape is funnel-like, with the deep well and rotational freedom. Echoing the protein folding process, we have previously proposed a transition state

Weston, Ken

485

PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear  

E-Print Network [OSTI]

accuracy with a lower false positive rate. All materials are freely available to the scientific community and protein identification and can help reduce the number of false positive resulPILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass

Shorter, James

486

Abstract The Tat protein-export system serves to trans-locate folded proteins, often containing redox cofactors,  

E-Print Network [OSTI]

- location by the Sec system proceeds by a `threading' mechanism in which the essentially unfolded substrate-bound respiratory complexes by the Tat protein-transport system Received: 27 February 2002 / Revised: 16 April 2002Abstract The Tat protein-export system serves to trans- locate folded proteins, often containing

Palmer, Tracy

487

Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins  

E-Print Network [OSTI]

We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real proteins. We show that larger values of $\\Omega_{c}$ resembling those seen in proteins are obtained in lattice models with side chains (LMSC). The enhanced cooperativity in LMSC is due to the possibility of denser packing of side chains in the interior of the model protein. We also establish that $\\Omega_{c}$ correlates extremely well with (\\sigma = (T_{\\theta} -T_{f} )/T_{\\theta}), where (T_{\\theta}) and (T_{f}) are collapse and folding transition temperatures, respectively. These theoretical ideas are used to analyze folding transitions in various real proteins. The values of $\\Omega _{c}$ extracted from experiments show a correlation with $\\sigma $. We conclude that the degree of cooperativity can be expressed in terms of the single parameter $\\sigma $, which can be estimated from experimental data.

D. K. Klimov; D. Thirumalai

1998-04-22T23:59:59.000Z

488

RESEARCH ARTICLE Open Access Comparison of membrane proteins of Mycobacterium  

E-Print Network [OSTI]

Background: The potential causes for variation in virulence between distinct M. tuberculosis strains are still not fully known. However, differences in protein expression are probably an important factor. In this study we used a labelfree quantitative proteomic approach to estimate differences in protein abundance between two closely related M. tuberculosis strains; the virulent H37Rv strain and its attenuated counterpart H37Ra. Results: We were able to identify more than 1700 proteins from both strains. As expected, the majority of the identified proteins had similar relative abundance in the two strains. However, 29 membrane-associated proteins were observed with a 5 or more fold difference in their relative abundance in one strain compared to the other. Of note, 19 membrane- and lipo-proteins had higher abundance in H37Rv, while another 10 proteins had a higher abundance in H37Ra. Interestingly, the possible protein-export membrane protein SecF (Rv2586c), and three ABCtransporter proteins (Rv0933, Rv1273c and Rv1819c) were among the more abundant proteins in M. tuberculosis H37Rv. Conclusion: Our data suggests that the bacterial secretion system and the transmembrane transport system may be important determinants of the ability of distinct M. tuberculosis strains to cause disease. Background

Tuberculosis Hrv; Hra Strains; Hiwa Målen; Gustavo A De Souza; Sharad Pathak; Tina Søftel; Harald G Wiker

489

Controlled Activation of Protein Rotational Dynamics Using Smart Hydrogel Tethering  

SciTech Connect (OSTI)

Stimulus-responsive hydrogel materials that stabilize and control protein dynamics have the potential to enable a range of applications to take advantage of the inherent specificity and catalytic efficiencies of proteins. Here we describe the modular construction of a hydrogel using an engineered calmodulin (CaM) within a polyethylene glycol (PEG) matrix that involves the reversible tethering of proteins through an engineered CaM-binding sequence. For these measurements, maltose binding protein (MBP) was isotopically labeled with [13C] and [15N], permitting dynamic structural measurements using TROSY-HSQC NMR spectroscopy. Upon initial formation of hydrogels protein dynamics are suppressed, with concomitant increases in protein stability. Relaxation of the hydrogel matrix following transient heating results in the activation of protein dynamics and restoration of substrate-induced large-amplitude domain motions necessary for substrate binding.

Beech, Brenda M.; Xiong, Yijia; Boschek, Curt B.; Baird, Cheryl L.; Bigelow, Diana J.; Mcateer, Kathleen; Squier, Thomas C.

2014-09-05T23:59:59.000Z

490

Structure based alignment and clustering of proteins (STRALCP)  

DOE Patents [OSTI]

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

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

2013-06-18T23:59:59.000Z

491

Correlation analysis of the side-chains conformational distribution in bound and unbound proteins  

E-Print Network [OSTI]

Background: Protein interactions play a key role in life processes. Characterization of conformational properties of protein-protein interactions is important for understanding the mechanisms of protein association. The ...

Kirys, Tatsiana; Ruvinsky, Anatoly M.; Tuzikov, Alexander V.; Vakser, Ilya A.

2012-09-17T23:59:59.000Z

492

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

493

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?  

E-Print Network [OSTI]

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote ...

Sinha, Rohita; Kundrotas, Petras J.; Vakser, Ilya A.

2012-02-13T23:59:59.000Z

494

Comparative host protein interactions with HTLV-1 p30 and HTLV-2 p28: insights into difference in pathobiology of human retroviruses  

E-Print Network [OSTI]

Heat shock protein 90 beta Protein folding Heat shockprotein 90 alpha Protein folding Methylosome subunit pIClncis-trans isomerase Protein folding 60 S ribosomal protein

Doueiri, Rami; Anupam, Rajaneesh; Kvaratskhelia, Mamuka; Green, Kari B; Lairmore, Michael D; Green, Patrick L

2012-01-01T23:59:59.000Z

495

Effective protein-protein interaction from structure factor data of a lysozyme solution  

SciTech Connect (OSTI)

We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated.

Abramo, M. C.; Caccamo, C.; Costa, D.; Ruberto, R.; Wanderlingh, U. [Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina and CNISM (Consorzio Nazionale Interuniversitario di Struttura della Materia) Viale F. Stagno d'Alcontres 31, 98166 Messina (Italy)] [Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina and CNISM (Consorzio Nazionale Interuniversitario di Struttura della Materia) Viale F. Stagno d'Alcontres 31, 98166 Messina (Italy); Cavero, M. [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa)] [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa); Pellicane, G. [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa) [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa); National Institute for Theoretical Physics (NITheP), KZN node, Pietermaritzburg (South Africa)

2013-08-07T23:59:59.000Z

496

E-Print Network 3.0 - antifreeze protein nmr Sample Search Results  

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

) functioning as antifreezes or cryoprotectants, antifreeze proteins (AFPs; Duman, 2001), ice nucleators (Duman... ). In addition, both populations produce antifreeze proteins....

497

TIGRFAMS: The TIGRFAMs database of protein families  

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

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

498

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

499

Brain protein deciphered at Advanced Light Source  

SciTech Connect (OSTI)

This computer-generated model of a rat glutamate receptor is the first complete portrait of this important link in the nervous system. At the top of the Y-shaped protein, a pair of molecules splay outward like diverging prongs. The bottom section, which is embedded in a neuronal membrane, houses the ion channel. The resolution of this image is 3.6 angstroms per pixel, or just under four ten-billionths of a meter per image unit. http://newscenter.lbl.gov/feature-stories/2010/01/21/glutamate-receptor/

None

2010-01-01T23:59:59.000Z

500

Protein viscoelastic dynamics: a model system  

E-Print Network [OSTI]

A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the model is a strongly over-damped oscillator described by a harmonic restoring force for small displacements that reversibly yields to stress under sufficiently large displacement. This simple dynamical system also reveals unexpectedly rich behavior, exhibiting a series of dynamical transitions and analogies with equilibrium thermodynamic phase transitions. The effects of noise and of inertia are briefly considered and described.

Craig Fogle; Joseph Rudnick; David Jasnow

2015-02-02T23:59:59.000Z