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1

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

2

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

3

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

4

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

5

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

6

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

7

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

8

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

9

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

10

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

11

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

12

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

13

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

14

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported...

15

Experimental generation of ring-shaped beams with random sources  

E-Print Network (OSTI)

We have experimentally reproduced ring shaped beams from the scattered Laguerre-Gaussian and Bessel- Gaussian beams. A rotating ground glass plate is used as a scattering medium and a plano convex lens collects the scattered light to generate ring shaped beams at the Fourier plane. The experimental results are in good agreement with the theoretical results of Mei and Korotkova (Opt. Lett. 38, 91{93 (2013)).

Reddy, Salla Gangi; Prabhakar, Shashi; Singh, R P

2013-01-01T23:59:59.000Z

16

Atomic-phase interference devices based on ring-shaped Bose-Einstein condensates: Two ring case  

E-Print Network (OSTI)

We theoretically investigate the ground-state properties and quantum dynamics of a pair of adjacent ring-shaped Bose-Einstein condensates that are coupled via tunneling. This device, which is the analogue of a symmetric superconducting quantum interference device, is the simplest version of what we term an Atomic-Phase Interference Device (APHID). The two-ring APHID is shown to be sensitive to rotation.

B. P. Anderson; K. Dholakia; E. M. Wright

2002-09-10T23:59:59.000Z

17

Dirac bound state solutions of spherically ring-shaped q-deformed Woods-Saxon potential for any L-state  

E-Print Network (OSTI)

Approximate bound state solutions of the Dirac equation with -deformed Woods-Saxon plus a new generalized ring-shaped potential are obtained for any arbitrary L-state. The energy eigenvalue equation and corresponding two-component wave function are calculated by solving the radial and angular wave equations within a shortcut of the Nikiforov-Uvarov method. The solutions of the radial and polar angular parts of the wave function are expressed in terms of the Jacobi polynomials. A new approximation being expressed in terms of the potential parameters is carried out to deal with the strong singular centrifugal potential term L(L+1)/r^2. Under some limitations, we can obtain solution for the ring-shaped Hulth\\'en potential and the standard usual spherical Woods-Saxon potential (q=1).

Sameer M. Ikhdair; Majid Hamzavi

2013-07-31T23:59:59.000Z

18

Exact solutions of the pseudo-Coulomb potential plus ring-shaped potential in the D-dimensional Schrodinger equation by the Nikiforov-Uvarov method  

E-Print Network (OSTI)

We present analytically the exact energy bound-states solutions of the Schrodinger equation in D-dimensions for an alternative (often used) pseudo-Coulomb potential-plus- ring-shaped potential of the form $V(r)=-% \\frac{a}{r}+\\frac{b}{r^{2}}+\\frac{\\beta \\cos ^{2}\\theta}{r^{2}\\sin ^{2}\\theta }+c$ by means of the conventional Nikiforov-Uvarov method. We give a clear recipe of how to obtain an explicit solution to the radial and angular parts of the wave functions in terms of orthogonal polynomials. The total energy of the system is different from the pseudo-Coulomb potential because of the contribution of the angular part. The general results obtained in this work can be reduced to the standard forms given in literature.

Sameer M. Ikhdair; Ramazan Sever

2007-03-06T23:59:59.000Z

19

Wedding ring shaped excitation coil  

DOE Patents (OSTI)

A high frequency inductively coupled electrodeless lamp includes an excitation coil with an effective electrical length which is less than one half wavelength of a driving frequency applied thereto, preferably much less. The driving frequency may be greater than 100 MHz and is preferably as high as 915 MHz. Preferably, the excitation coil is configured as a non-helical, semi-cylindrical conductive surface having less than one turn, in the general shape of a wedding ring. At high frequencies, the current in the coil forms two loops which are spaced apart and parallel to each other. Configured appropriately, the coil approximates a Helmholtz configuration. The lamp preferably utilizes an bulb encased in a reflective ceramic cup with a pre-formed aperture defined therethrough. The ceramic cup may include structural features to aid in alignment and/or a flanged face to aid in thermal management. The lamp head is preferably an integrated lamp head comprising a metal matrix composite surrounding an insulating ceramic with the excitation integrally formed on the ceramic. A novel solid-state oscillator preferably provides RF power to the lamp. The oscillator is a single active element device capable of providing over 70 watts of power at over 70% efficiency.

MacLennan, Donald A. (Gaithersburg, MD); Tsai, Peter (Olney, MD)

2001-01-01T23:59:59.000Z

20

Explain Spires Terms  

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

Spires terms Enter term below Example:   index :: Browse Examples Search Help :: About Explain SPIRES TopCites HEP Reviews SPIRES News Playground Preprint listings Resources...

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Protein Structure Suggests Role as Molecular Adapter  

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

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

22

Proteins  

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

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

23

Proteins  

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

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

24

Proteins  

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

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

25

Explaining Embedded Software Modelling Decisions Jelena Marincic  

E-Print Network (OSTI)

Explaining Embedded Software Modelling Decisions Jelena Marincic Faculty of Electrical Engineering's devices, gadgets and machines become more intelligent, the complexity of embedded software con- trolling Mader Faculty of Electrical Engineering, Mathematics and Computer Science University of Twente

Al Hanbali, Ahmad

26

Using arguments for making and explaining decisions  

Science Conference Proceedings (OSTI)

Arguments play two different roles in day life decisions, as well as in the discussion of more crucial issues. Namely, they help to select one or several alternatives, or to explain and justify an already adopted choice. This paper proposes the first ... Keywords: Argumentation, Decision making

Leila Amgoud; Henri Prade

2009-03-01T23:59:59.000Z

27

Mining and explaining relationships in wikipedia  

Science Conference Proceedings (OSTI)

Mining and explaining relationships between objects are challenging tasks in the field of knowledge search. We propose a new approach for the tasks using disjoint paths formed by links in Wikipedia. To realizing this approach, we propose a naive and ... Keywords: generalized max-flow, link analysis, relationship, wikipedia mining

Xinpeng Zhang; Yasuhito Asano; Masatoshi Yoshikawa

2010-08-01T23:59:59.000Z

28

Explaining ML type errors by data flows  

Science Conference Proceedings (OSTI)

We present a novel approach to explaining ML type errors: Since the type system inhibits data flows that would abort the program at run-time, our type checker identifies as explanations those data flows that violate the typing rules. It also detects ...

Holger Gast

2004-09-01T23:59:59.000Z

29

New Crystal Structures Lift Fog around Protein Folding  

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

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

30

NERSC Supercomputers Help Explain the Last Big Freeze  

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

NERSC Supercomputers Help Explain the Last Big Freeze NERSC Supercomputers Help Explain the Last Big Freeze January 31, 2013 | Tags: Biological and Environmental Research (BER),...

31

Can Bounded Rationality Explain Excess Capacity? ?  

E-Print Network (OSTI)

Excess capacity is observed in many markets especially those where a substantial initial investment is required. The theoretical literature often explains this feature by strategic attempts to deter entry or to limit new entrants market shares but the empirical evidence for such a rationale is mixed. Moreover, excess capacity has also been observed in experimental studies on capacityconstrained games where there is no entry (and therefore no entry-deterrence motive). This paper explores experimentally another rationale for excess capacity: rather than (in addition to) being a threat to (potential) entrants, excess capacity held by incumbents may constitute a valuable option to reap extra gains from competition with an inexperienced entrant, if he turns out to makes a mistake. In our experimental design we used the level of experience (the number of periods played) as a proxy for the level of rationality and matched subjects with different levels of experience. We find evidence of excess capacity decreasing with opponents experience. ? This paper is a sustantially revised version of a chapter of Le Coq and Sturlusons 2003 Stockholm School of Economics Ph.D. thesis. It was before circulated as "Does Opponents experience matter?". The authors would like to thank Tore Ellingsen for his insightful comments in the projects infancy, Urs Fischbacher for allowig us tousethez-TreesoftwareandHans-TheoNorman for technical help. We thank also seminar participants at the IIOC 2004 (Chicago), EARIE 2003 (Lausanne), SAET 2003 (Rhodos) for helpful comments. We gratefully acknowledge financial

Chlolecoq Jon; Thor Sturluson

2006-01-01T23:59:59.000Z

32

Interaction between motor domains can explain the complex dynamics of heterodimeric kinesins Rahul Kumar Das and Anatoly B. Kolomeisky  

E-Print Network (OSTI)

Interaction between motor domains can explain the complex dynamics of heterodimeric kinesins Rahul Received 12 March 2008; revised manuscript received 7 May 2008; published 17 June 2008 Motor proteins-molecule experiments indicate that motor proteins, consisting of two motor domains, move in a hand- over-hand mechanism

33

Coal - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Solar Thermal Power Plants; Solar Thermal Collectors; ... Lignite is mainly burned at power plants to generate electricity. Also on Energy Explained. Use of Coal;

34

Physics of Intrinsic Plasma Rotation Explained for the First...  

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

Explained for First Time Key understanding for modeling future fusion reactors such as ITER July 23, 2013 | Tags: Fusion Energy Sciences (FES), Hopper CHANG.JPG Flamelets or hot...

35

SLAC National Accelerator Laboratory - SLAC's Sandy Merola Explains...  

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

SLAC's Sandy Merola Explains Energy Science Network's Importance on YouTube By Mike Ross November 30, 2011 Sandy Merola, SLAC's Chief Operating Officer, has a prominent role in a...

36

Property:EstimatedTimeExplained | Open Energy Information  

Open Energy Info (EERE)

EstimatedTimeExplained EstimatedTimeExplained Jump to: navigation, search Property Name EstimatedTimeExplained Property Type Text Description An explanation of the accompanying time estimate, including any influential factors or variables. Subproperties This property has the following 40 subproperties: G GRR/Elements/14-CA-b.1 - NPDES Permit Application GRR/Elements/14-CA-b.10 - Did majority of RWQCB approve the permit GRR/Elements/14-CA-b.11 - EPA Review of Adopted Permit GRR/Elements/14-CA-b.12 - Were all EPA objections resolved GRR/Elements/14-CA-b.13 - NPDES Permit issued GRR/Elements/14-CA-b.2 - Review of application for completeness GRR/Elements/14-CA-b.3 - Is the application complete for the Regional Water Quality Control Board GRR/Elements/14-CA-b.4 - EPA review for completeness

37

Nuclear Power and the Environment - Energy Explained, Your Guide To  

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

Explained > Nonrenewable Sources > Nuclear > Nuclear Power & the Environment Explained > Nonrenewable Sources > Nuclear > Nuclear Power & the Environment Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Emissions Come From Outlook for Future Emissions Recycling and Energy Nonrenewable Sources Oil and Petroleum Products Refining Crude Oil Where Our Oil Comes From Imports and Exports Offshore Oil and Gas Use of Oil Prices and Outlook Oil and the Environment Gasoline Where Our Gasoline Comes From

38

Home - Energy Explained, Your Guide To Understanding Energy - Energy  

Gasoline and Diesel Fuel Update (EIA)

Explained Explained Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Emissions Come From Outlook for Future Emissions Recycling and Energy Nonrenewable Sources Oil and Petroleum Products Refining Crude Oil Where Our Oil Comes From Imports and Exports Offshore Oil and Gas Use of Oil Prices and Outlook Oil and the Environment Gasoline Where Our Gasoline Comes From Use of Gasoline Prices and Outlook Factors Affecting Gasoline Prices Regional Price Differences

39

Measuring and Explaining Electricity Price Changes in Restructured States  

Science Conference Proceedings (OSTI)

An effort to determine the effect of restructuring on prices finds that, on average, prices for industrial customers in restructured states were lower, relative to predicted prices, than prices for industrial customers in non-restructured states. This preliminary analysis also finds that these price changes are explained primarily by high pre-restructuring prices, not whether or not a state restructured. (author)

Fagan, Mark L.

2006-06-15T23:59:59.000Z

40

Continued on next page A letter explaining the 2005 HVAC  

E-Print Network (OSTI)

Continued on next page A letter explaining the 2005 HVAC Change-out to consumers is available this bulletin, or downloaded from the 2005 HVAC Change out Information website at: www.energy.ca.gov/title24 duct sealing requirements for HVAC change-outs in existing homes become effective October 1, 2005

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Percolation Explains How Earth's Iron Core Formed | Stanford Synchrotron  

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

Percolation Explains How Earth's Iron Core Formed Percolation Explains How Earth's Iron Core Formed Wednesday, November 27, 2013 The formation of Earth's metallic core, which makes up a third of our planet's mass, represents the most significant differentiation event in Earth's history. Earth's present layered structure with a metallic core and an overlying silicate mantle would have required mechanisms to separate iron alloy from a silicate phase. Percolation of liquid iron alloy moving through a solid silicate matrix (much as water percolates through porous rock, or even coffee grinds) has been proposed as a possible model for core formation (Figure 1). Many previous experimental results have ruled out percolation as a major core formation mechanism for Earth at the relatively lower pressure conditions in the upper mantle, but until now experimental

42

Physics of Intrinsic Plasma Rotation Explained for the First Time  

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

Physics of Intrinsic Physics of Intrinsic Plasma Rotation Explained for First Time Physics of Intrinsic Plasma Rotation Explained for First Time Key understanding for modeling future fusion reactors such as ITER July 23, 2013 | Tags: Fusion Energy Sciences (FES), Hopper CHANG.JPG Flamelets or hot spots along the plasma edge (a) drive turbulence intensity (b), temperature intensity (c), and intrinsic torque (d) inward, converting heat into toroidal rotation. (S. Ku et al.) If humans could harness nuclear fusion, the process that powers stars like our sun, the world could have an inexhaustible, clean energy source. Scientists have taken another step towards that goal with research that uncovers why the hot, gaseous stews used in fusion reactions sometimes spontaneously rotate in their donut-shaped containment "pots," called

43

Questions and Answers - How do you explain electrical resistance?  

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

is an electric current? is an electric current? Previous Question (What is an electric current?) Questions and Answers Main Index Next Question (Do you know what an electromagnet is?) Do you know whatan electromagnet is? How do you explain electrical resistance? I'm assuming you are asking for advice on "how to" explain resistance - perhaps to a school class. At any rate, here's a reasonably non-technical description you can consider. In a metal, the atoms are arranged in a crystal-like configuration. The type of metal will determine how the bonds are arranged, and how closely the atoms are grouped. Electrons can inhabit energy levels. Generally, only the "outer" electrons in an atom interact to form the bonds with other atoms. These outer electrons are held to the atom with a relatively small

44

Electricity in the United States - Energy Explained, Your Guide To  

Gasoline and Diesel Fuel Update (EIA)

Secondary Sources > Electricity > Electricity in the U.S. Secondary Sources > Electricity > Electricity in the U.S. Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Emissions Come From Outlook for Future Emissions Recycling and Energy Nonrenewable Sources Oil and Petroleum Products Refining Crude Oil Where Our Oil Comes From Imports and Exports Offshore Oil and Gas Use of Oil Prices and Outlook Oil and the Environment Gasoline Where Our Gasoline Comes From Use of Gasoline

45

Refining Crude Oil - Energy Explained, Your Guide To Understanding Energy -  

Gasoline and Diesel Fuel Update (EIA)

Oil and Petroleum Products > Refining Crude Oil Oil and Petroleum Products > Refining Crude Oil Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Emissions Come From Outlook for Future Emissions Recycling and Energy Nonrenewable Sources Oil and Petroleum Products Refining Crude Oil Where Our Oil Comes From Imports and Exports Offshore Oil and Gas Use of Oil Prices and Outlook Oil and the Environment Gasoline Where Our Gasoline Comes From Use of Gasoline Prices and Outlook

46

Galactic structure explained with dissipative mirror dark matter  

E-Print Network (OSTI)

Dissipative dark matter, such as mirror dark matter and related hidden sector dark matter candidates, requires an energy source to stabilize dark matter halos in spiral galaxies. It has been proposed previously that supernovae could be the source of this energy. Recently, it has been argued that this mechanism might explain two galactic scaling relations inferred from observations of spiral galaxies. One of which is that $\\rho_0 r_0$ is roughly constant, and another relates the galactic luminosity to $r_0$. [$\\rho_0$ is the dark matter central density and $r_0$ is the core radius.] Here we derive equations for the heating of the halo via supernova energy, and the cooling of the halo via thermal bremsstrahlung. These equations are numerically solved to obtain constraints on the $\\rho_0, \\ r_0$ parameters appropriate for spiral galaxies. These constraints are in remarkable agreement with the aforementioned scaling relations.

R. Foot

2013-04-17T23:59:59.000Z

47

Can the photosynthesis first step quantum mechanism be explained?  

E-Print Network (OSTI)

Photosynthesis first step mechanism concerns the sunlight absorption and both negative and positive charges separation. Recent and important photosynthesis literature claims that this mechanism is quantum mechanics controlled, however without presenting qualitative or quantitative scientifically based mechanism. The present accepted and old-fashioned photosynthesis mechanism model suffers from few drawbacks and an important issue is the absence of driving force for negative and positive charges separation. This article presents a new qualitative model for this first step mechanism in natural catalytic systems such as photosynthesis in green leaves. The model uses a concept of semiconductor band gap engineering, such as the staggered energy band gap line-up in semiconductors. To explain the primary mechanism in natural photosynthesis the proposal is the following: incident light is absorbed inside the leaves causing charges separation. The only energetic configuration that allows charges separation under illum...

Sacilotti, Marco; Mota, Claudia C B O; Nunes, Frederico Dias; Gomes, Anderson S L

2010-01-01T23:59:59.000Z

48

Explaining cross-country variation in cigarette consumption  

E-Print Network (OSTI)

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This short paper uses cross-country data on per capita cigarette consumption and selected socioeconomic variables to explain inter-country differentials in consumption. It is found that the proportion of the aged in the total population and higher literacy among women have relatively greater and positive impact on cigarette consumption. Even after controlling for the effect of the two variables, a country's industrialized status has a positive impact on consumption. It would thus seem that aging and economic, and social developments are pro-cigarette consumption. Background The US Surgeon General's initial report on smoking was nearly 40 years old. All these years, health warnings on cigarette packs have been in place. Despite the "warnings" and concerted efforts to dissuade potential smokers, cigarettes are here to stay. Global cigarette production and consumption have been rising steadily since cigarettes were introduced at the beginning of the 20 th century (see Table 1 for evidence on growth during 19602000). It is estimated that at present about 1.1 billion people close to a fifth of the global population are smokers and the number is expected to rise to more than 1.6 billion by

Kolluru Srinivas; Bhanoji Rao; Open Access

2009-01-01T23:59:59.000Z

49

doi:10.1093/nar/gkl864 Stimulation of MCM helicase activity by a Cdc6 protein in the archaeon Thermoplasma acidophilum  

E-Print Network (OSTI)

Replicative DNA helicases are ring-shaped hexamers that play an essential role in chromosomal DNA replication. They unwind the two strands of the duplex DNA and provide the single-stranded (ss) DNA substrate for the polymerase. The minichromosome maintenance (MCM) proteins are thought to function as the replicative helicases in eukarya and archaea. The proteins of only a few archaeal organisms have been studied and revealed that although all have similar amino acid sequences and overall structures they differ in their biochemical properties. In this report the biochemical properties of the MCM protein from the archaeon Thermoplasma acidophilum is described. The enzyme has weak helicase activity on a substrate containing only a 30-ssDNA overhang region and the protein requires a forked DNA structure for efficient helicase activity. It was also found that the helicase activity is stimulated by one of the two T.acidophilum Cdc6 homologues. This is an interesting observation as it is in sharp contrast to observations made with MCM and Cdc6 homologues from other archaea in which the helicase activity is inhibited when bound to Cdc6.

Gyri Teien Haugl; Jae-ho Shin; Zvi Kelman

2006-01-01T23:59:59.000Z

50

Mick Jagger Explains High Crude Oil Prices How can Mick Jagger of The Rolling Stones help explain the current high crude oil  

E-Print Network (OSTI)

Mick Jagger Explains High Crude Oil Prices How can Mick Jagger of The Rolling Stones help explain the current high crude oil price? It does not relate to Mick' short stint at the London School of Economics, the oil industry operates on the same principle, at least in the short run. The industry relies on proven

Ahmad, Sajjad

51

Explaining the light curves of Gamma-ray Bursts with precessing jets  

E-Print Network (OSTI)

A phenomenological model is presented to explain the light curves of gamma-ray bursts. Gamma-rays are produced in a narrow beam which sweeps through space due to the precession of a slaved accretion disc. The light curve expected from such a precessing luminosity cone can explain the complex temporal behavior of bright gamma-ray bursts.

Simon Portegies Zwart

1999-03-13T23:59:59.000Z

52

Materiomics: biological protein materials, from nano to macro  

E-Print Network (OSTI)

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

Cranford, Steven Wayne

53

Bankruptcy, guns or campaigns : explaining armed organizations' post-war trajectories  

E-Print Network (OSTI)

This project seeks to explain what happens to armed organizations after they sign peace accords. Why do they dissolve, return to war, or form non-violent socio-political entities (political parties or civic associations)? ...

Daly, Sarah Zukerman

2011-01-01T23:59:59.000Z

54

Explaining ethnic conflict in the South Caucasus : Mountainous Karabagh, Abkhazia, and South Ossetia  

E-Print Network (OSTI)

(cont.) the USSR and finds that a focus on opportunity provides the best explanation for the presence or absence of mass mobilization. Finally, the dissertation argues that conventional state security concerns best explain ...

Welt, Cory

2004-01-01T23:59:59.000Z

55

From hutong to hi-rise : explaining the transformation of Old Beijing, 1990-2002  

E-Print Network (OSTI)

This thesis attempts to explain the redevelopment of Old Beijing during the period 1990-2002. During this time, at least one third of the Old City was transformed from an urban fabric consisting principally of courtyard ...

Goldman, Jasper, 1978-

2003-01-01T23:59:59.000Z

56

U.S. Energy Facts - Energy Explained, Your Guide To Understanding Energy -  

U.S. Energy Information Administration (EIA) Indexed Site

Explained Explained Home > Energy Explained > U.S. Energy Facts Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Emissions Come From Outlook for Future Emissions Recycling and Energy Nonrenewable Sources Oil and Petroleum Products Refining Crude Oil Where Our Oil Comes From Imports and Exports Offshore Oil and Gas Use of Oil Prices and Outlook Oil and the Environment Gasoline Where Our Gasoline Comes From Use of Gasoline Prices and Outlook

57

Protein Structure  

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

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

58

Getting Ready for LEDs: LED Lighting Video Series Explains the Basics |  

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

for LEDs: LED Lighting Video Series Explains the for LEDs: LED Lighting Video Series Explains the Basics Getting Ready for LEDs: LED Lighting Video Series Explains the Basics November 26, 2012 - 3:09pm Addthis Part 1 of the ElectricTV.net video series. Part 2 of the ElectricTV.net video series. Roland Risser Roland Risser Program Director, Building Technologies Office How can I participate? Learn more about the advantages and accessiblity of LED lighting from this series of videos. If you haven't been down the lighting aisle of your favorite home improvement store lately, you may be surprised at how many LED lighting products have arrived. Solid-state lighting (LEDs are one type) will soon have a strong impact on how buildings and homes are lit, in part because of its potential to reduce U.S. lighting energy usage by nearly one half.

59

Questions and Answers - How can I explain the Quantum/Wave theory to my  

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

What is a meniscus? What is a meniscus? Previous Question (What is a meniscus?) Questions and Answers Main Index Next Question (What is the sun made from?) What is the sun made from? How can I explain the Quantum/Wave theory to my class? You can't! The folks who have postulated the quantum nature of matter and wave-particle duality, and other quantum theories have trouble explaining it in terms other than mathematical equations. When trying to explain it in conceptual terms, we're asked to accept things that don't make sense, and in some ways, physicists use this as justification that the theory is correct. Anyway, here are a couple ideas for discussing the quantum/wave properties of energy. Until around 1900, when Max Planck developed the idea of quanta, energy had been thought to be a phenomenon of continuous flow - basically waves.

60

Can precessing jets explain the light curves of Gamma-ray Bursts?  

E-Print Network (OSTI)

We present a phenomenological model to explain the light curves of gamma-ray bursts. In the model a black hole is orbited by a precessing accretion disc which is fed by a neutron star. Gamma-rays are produced in a highly collimated beam via the Blandford-Znajek mechanism. The gamma-ray beam sweeps through space due to the precession of the slaved accretion disc. The light curve expected from such a precessing luminosity cone can explain the complex temporal behavior of observed bright gamma-ray bursts.

Simon Portegies Zwart; Chang-Hwan Lee; Hyun Kyu Lee

1998-08-19T23:59:59.000Z

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

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

Science Conference Proceedings (OSTI)

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

62

Explaining Long-Run Changes in the Energy Intensity of the U.S. Economy  

E-Print Network (OSTI)

Recent events have revived interest in explaining the long-run changes in the energy intensity of the U.S. economy. We use a KLEM dataset for 35 industries over 39 years to decompose changes in the aggregate energy-GDP ...

Sue Wing, Ian.

63

Better Technologies Key to Addressing Climate Change Energy Department official explains U.S. initiatives  

E-Print Network (OSTI)

Better Technologies Key to Addressing Climate Change Energy Department official explains U.S emissions and addressing climate change, according to a U.S. Department of Energy (DOE) official speaking of the DOE statement follows: [U.S. Department of Energy] Intervention by the United States Panel

64

Explaining Sources of Discrepancy in SSM/I Water Vapor Algorithms  

Science Conference Proceedings (OSTI)

This study examines a mix of seven statistical and physical Special Sensor Microwave Imager (SSM/I) passive microwave algorithms that were designed for retrieval of over-ocean precipitable water (PW). The aim is to understand and explain why the ...

Byung-Ju Sohn; Eric A. Smith

2003-10-01T23:59:59.000Z

65

PERSPECTIVE---Explaining Influence Rents: The Case for an Institutions-Based View of Strategy  

Science Conference Proceedings (OSTI)

Research in strategy has identified and tried to explain four types of rents: monopolistic rents, efficiency rents, quasi rents, and Schumpeterian rents. Building on previous work on political and institutional strategies, we add a fifth type of rent: ... Keywords: generic strategies, influence rents, institutions

Gautam Ahuja; Sai Yayavaram

2011-11-01T23:59:59.000Z

66

Epigenetic modifications and chromatin loop organization explain the different expression profiles of the Tbrg4, WAP and Ramp3 genes  

Science Conference Proceedings (OSTI)

Whey Acidic Protein (WAP) gene expression is specific to the mammary gland and regulated by lactogenic hormones to peak during lactation. It differs markedly from the more constitutive expression of the two flanking genes, Ramp3 and Tbrg4. Our results show that the tight regulation of WAP gene expression parallels variations in the chromatin structure and DNA methylation profile throughout the Ramp3-WAP-Tbrg4 locus. Three Matrix Attachment Regions (MAR) have been predicted in this locus. Two of them are located between regions exhibiting open and closed chromatin structures in the liver. The third, located around the transcription start site of the Tbrg4 gene, interacts with topoisomerase II in HC11 mouse mammary cells, and in these cells anchors the chromatin loop to the nuclear matrix. Furthermore, if lactogenic hormones are present in these cells, the chromatin loop surrounding the WAP gene is more tightly attached to the nuclear structure, as observed after a high salt treatment of the nuclei and the formation of nuclear halos. Taken together, our results point to a combination of several epigenetic events that may explain the differential expression pattern of the WAP locus in relation to tissue and developmental stages.

Montazer-Torbati, Mohammad Bagher; Hue-Beauvais, Cathy; Droineau, Stephanie; Ballester, Maria; Coant, Nicolas; Aujean, Etienne; Petitbarat, Marie [UR1196, Unite de Genomique et Physiologie de la Lactation, INRA, F-78 352 Jouy en josas (France); Rijnkels, Monique [Children's Nutrition Research Center (CNRC)-Baylor College of Medicine, 1100 Bates Street, Houston TX (United States); Devinoy, Eve [UR1196, Unite de Genomique et Physiologie de la Lactation, INRA, F-78 352 Jouy en josas (France)], E-mail: eve.devinoy@jouy.inra.fr

2008-03-10T23:59:59.000Z

67

Smil, Vaclav, Does Energy Efficiency Explain Japan's Economic Success? , Current History, 90:555 (1991:Apr.) p.175  

E-Print Network (OSTI)

Smil, Vaclav, Does Energy Efficiency Explain Japan's Economic Success? , Current History, 90:555 (1991:Apr.) p.175 #12;Smil, Vaclav, Does Energy Efficiency Explain Japan's Economic Success? , Current History, 90:555 (1991:Apr.) p.175 #12;Smil, Vaclav, Does Energy Efficiency Explain Japan's Economic

Smil, Vaclav

68

8. EXPLAIN HOW YOU BELIEVE YOU WERE DISCRIMINATED AGAINST (TREATED DIFFERENTLY FROM OTHER EMPLOYEES OR  

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

8. EXPLAIN HOW YOU BELIEVE YOU WERE DISCRIMINATED AGAINST (TREATED DIFFERENTLY FROM OTHER EMPLOYEES OR 8. EXPLAIN HOW YOU BELIEVE YOU WERE DISCRIMINATED AGAINST (TREATED DIFFERENTLY FROM OTHER EMPLOYEES OR APPLICANTS) BECAUSE OF YOUR RACE, COLOR, RELIGION, SEX, AGE, NATIONAL ORIGIN, RETALIATION, OR PHYSICAL AND/OR MENTAL DISABILITY. (For each allegation, please state to the best of your knowledge, information and belief what incident occurred and when the incident occurred. You may continue your answer on another sheet of paper if you need more space.) FOR AGENCY USE DOE F 1600.1 (06-96) All Other Editions Are Obsolete U.S. DEPARTMENT OF ENERGY COMPLAINT OF DISCRIMINATION (Because of Race, Color, Religion, Sex, Age, National Origin, Retaliation, or Physical and/or Mental Disability) (See Reverse for Instructions) 1. COMPLAINANT'S FULL NAME

69

Can a Long Nanoflare Storm Explain the Observed Emission Measure Distributions in Active Region Cores?  

E-Print Network (OSTI)

All theories that attempt to explain the heating of the high temperature plasma observed in the solar corona are based on short bursts of energy. The intensities and velocities measured in the cores of quiescent active regions, however, can be steady over many hours of observation. One heating scenario that has been proposed to reconcile such observations with impulsive heating models is the "long nanoflare storm," where short duration heating events occur infrequently on many sub-resolutions strands; the emission of the strands is then averaged together to explain the observed steady structures. In this Letter, we examine the emission measure distribution predicted for such a long nanoflare storm by modeling an arcade of strands in an active region core. Comparisons of the computed emission measure distributions with recent observations indicate that that the long nanoflare storm scenario implies greater than 5 times more 1 MK emission than is actually observed for all plausible combinations of loop lengths,...

Mulu-Moore, Fana M; Warren, Harry P

2012-01-01T23:59:59.000Z

70

Explaining Angular Correlations Observed at RHIC with Flow and Local Charge Conservation  

E-Print Network (OSTI)

The observation of fluctuations of parity-odd angular observables at RHIC has been interpreted as a signal of a local parity violation. We show how the observed signal can be explained by local charge conservation at freeze-out combined with elliptic flow. Calculations from a blast wave model, which overlays thermal emission onto a collective flow profile, are shown to account for the experimentally observed signal.

Soeren Schlichting; Scott Pratt

2010-05-28T23:59:59.000Z

71

Letter to the Editor Explaining the mass-to-light ratios of globular clusters  

E-Print Network (OSTI)

Context. The majority of observed mass-to-light ratios of globular clusters are too low to be explained by canonical cluster models, in which dynamical effects are not accounted for. Moreover, these models do not reproduce a recently reported trend of increasing M/L with cluster mass, but instead predict mass-to-light ratios that are independent of cluster mass for a fixed age and metallicity. Aims. This study aims to explain the M/L of globular clusters in four galaxies by including stellar evolution, stellar remnants, and the preferential loss of low-mass stars due to energy equipartition. Methods. Analytical cluster models are applied that account for stellar evolution and dynamical cluster dissolution to samples of globular clusters in Cen A, the Milky Way, M31 and the LMC. The models include stellar remnants and cover metallicities in the range Z = 0.00040.05. Results. Both the low observed mass-to-light ratios and the trend of increasing M/L with cluster mass can be reproduced by including the preferential loss of low-mass stars, assuming reasonable values for the dissolution timescale. This leads to a mass-dependent M/L evolution and increases the explained percentage of the observations from 39 % to 92%. Conclusions. This study shows that the hitherto unexplained discrepancy between observations and models of the massto-light ratios of globular clusters can be explained by dynamical effects, provided that the globular clusters exhibiting low M/L have dissolution timescales within the ranges assumed in this Letter. Furthermore, it substantiates that M/L cannot be assumed to be constant with mass at fixed age and metallicity.

J. M. Diederik Kruijssen

2008-01-01T23:59:59.000Z

72

Interaction Between Motor Domains Can Explain the Complex Dynamics of Heterodimeric Kinesins  

E-Print Network (OSTI)

Abstract. Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule experiments suggest that motor proteins, consisting of two motor domains, move in a hand-over-hand mechanism when each subunit changes between trailing and leading positions in alternating steps, and these subunits do not interact with each other. However, recent experiments on heterodimeric kinesins suggest that the motion of motor domains is not independent, but rather strongly coupled and coordinated, although the mechanism of these interactions are not known. We propose a simple discrete stochastic model to describe the dynamics of homodimeric and heterodimeric two-headed motor proteins. It is argued that interactions between motor domains modify free energy landscapes of each motor subunit, and motor proteins still move via the hand-over-hand mechanism but with different transitions rates. Our calculations of biophysical properties agree with experimental observations. Several ways to test the theoretical model are proposed.

Rahul Kumar Das; Anatoly B. Kolomeisky

2007-01-01T23:59:59.000Z

73

Interaction Between Motor Domains Can Explain the Complex Dynamics of Heterodimeric Kinesins  

E-Print Network (OSTI)

Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule experiments suggest that motor proteins, consisting of two motor domains, move in a hand-over-hand mechanism when each subunit changes between trailing and leading positions in alternating steps, and these subunits do not interact with each other. However, recent experiments on heterodimeric kinesins suggest that the motion of motor domains is not independent, but rather strongly coupled and coordinated, although the mechanism of these interactions are not known. We propose a simple discrete stochastic model to describe the dynamics of homodimeric and heterodimeric two-headed motor proteins. It is argued that interactions between motor domains modify free energy landscapes of each motor subunit, and motor proteins still move via the hand-over-hand mechanism but with different transitions rates. Our calculations of biophysical properties agree with experimental observations. Several ways to test the theoretical model are proposed.

Rahul Kumar Das; Anatoly B. Kolomeisky

2007-03-22T23:59:59.000Z

74

Does Weather Explain the Cost and Quality? An Analysis of UK Electricity Distribution Companies  

E-Print Network (OSTI)

and business consumers are described in Yu et al. (2007). Energy loss (EL) is measured in GWh and valued at average industrial electricity price. The price of Opex and Totex is by convention set to 1. The weather data were obtained from the UK... www.electricitypolicy.org.uk E P R G W O R K IN G P A P E R Abstract Does Weather Explain the Cost and Quality Performance? An Analysis of UK Electricity Distribution Companies EPRG Working Paper 0827 Cambridge Working Paper...

Yu, William; Jamasb, Tooraj; Pollitt, Michael G.

75

CAN A LONG NANOFLARE STORM EXPLAIN THE OBSERVED EMISSION MEASURE DISTRIBUTIONS IN ACTIVE REGION CORES?  

Science Conference Proceedings (OSTI)

All theories that attempt to explain the heating of the high-temperature plasma observed in the solar corona are based on short bursts of energy. The intensities and velocities measured in the cores of quiescent active regions, however, can be steady over many hours of observation. One heating scenario that has been proposed to reconcile such observations with impulsive heating models is the 'long nanoflare storm', where short-duration heating events occur infrequently on many sub-resolution strands; the emission of the strands is then averaged together to explain the observed steady structures. In this Letter, we examine the emission measure distribution predicted for such a long nanoflare storm by modeling an arcade of strands in an active region core. Comparisons of the computed emission measure distributions with recent observations indicate that the long nanoflare storm scenario implies greater than five times more 1 MK emission than is actually observed for all plausible combinations of loop lengths, heating rates, and abundances. We conjecture that if the plasma had 'super coronal' abundances, the model may be able to match the observations at low temperatures.

Mulu-Moore, Fana M.; Winebarger, Amy R. [NASA Marshall Space Flight Center, VP 62, Huntsville, AL 35812 (United States); Warren, Harry P., E-mail: fanamariam.mulumoore@nasa.gov [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States)

2011-11-20T23:59:59.000Z

76

Shotgun protein sequencing.  

Science Conference Proceedings (OSTI)

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

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

2009-06-01T23:59:59.000Z

77

Essential proteins discovery from weighted protein interaction networks  

Science Conference Proceedings (OSTI)

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

Min Li; Jianxin Wang; Huan Wang; Yi Pan

2010-05-01T23:59:59.000Z

78

Diatom Genome Helps Explain Their Great Diversity and Success in Trapping  

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

5, 2008 5, 2008 Diatom Genome Helps Explain Their Great Diversity and Success in Trapping Excess Carbon in Oceans WALNUT CREEK, CA-Diatoms, mighty microscopic algae, have profound influence on climate, producing 20 percent of the oxygen we breathe by capturing atmospheric carbon and in so doing, countering the greenhouse effect. Since their evolutionary origins these photosynthetic wonders have come to acquire advantageous genes from bacterial, animal and plant ancestors enabling them to thrive in today's oceans. These findings, based on the analysis of the latest sequenced diatom genome, Phaeodactylum tricornutum, are published in 15 October edition of the journal Nature by an international team of researchers led by the U.S. Department of Energy Joint Genome Institute (DOE JGI) and the Ecole Normale Supérieure of

79

Where Our Natural Gas Comes From - Energy Explained, Your Guide To  

Gasoline and Diesel Fuel Update (EIA)

Natural Gas > Where Our Natural Gas Comes From Natural Gas > Where Our Natural Gas Comes From Energy Explained - Home What Is Energy? Forms of Energy Sources of Energy Laws of Energy Units and Calculators Energy Conversion Calculators British Thermal Units (Btu) Degree-Days U.S. Energy Facts State and U.S. Territory Data Use of Energy In Industry For Transportation In Homes In Commercial Buildings Efficiency and Conservation Energy and the Environment Greenhouse Gases Effect on the Climate Where Emissions Come From Outlook for Future Emissions Recycling and Energy Nonrenewable Sources Oil and Petroleum Products Refining Crude Oil Where Our Oil Comes From Imports and Exports Offshore Oil and Gas Use of Oil Prices and Outlook Oil and the Environment Gasoline Where Our Gasoline Comes From Use of Gasoline Prices and Outlook

80

Questions and Answers - Can you explain why the United States uses  

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

did Thomas Jeffersondo as a scientist? did Thomas Jefferson<br>do as a scientist? Previous Question (What did Thomas Jefferson do as a scientist?) Questions and Answers Main Index Next Question (How long would it take a person on a bicycle-type generator to create an atom?) How long would it take a person on abicycle-type generator to create an atom? Can you explain why the United States uses Fahrenheit instead of Celsius? Answer 1 The answer to the your question is in Sir Isaac Newton's first law of motion, which is more commonly known as inertia. That is, that when something gets going it is hard to stop it or change its direction. It would be a really good thing if we just bit the bullet and made the change to the metric system or, more properly, to International Units. Even NASA

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Can Rossby waves explain the cyclic magnetic activity of the Sun and solar-type stars?  

E-Print Network (OSTI)

Magnetic activity is a global property of the Sun; the complex processes of solar activity are connected with the solar magnetic fields. For solar-type stars and the Sun magnetic activity depends on the physical parameters of the star. In this article we study the relationships between the duration of activity cycle and effective temperature for solar-type stars and the Sun. We've tried to explain these relationships due to the existence of layer of laminar convection near the bottom of the convective zone of the star. In this layer the Rossby waves are formed. They generate the primary poloidal magnetic field, which is the source of energy of the complex phenomena of magnetic activity.

Bruevich, E A

2013-01-01T23:59:59.000Z

82

Adsorption of organic molecules may explain growth of newly nucleated clusters and new particle formation  

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

Adsorption Adsorption of organic molecules may explain growth of newly nucleated clusters and new particle formation Jian Wang 1 and Anthony S. Wexler 2 Received 21 February 2013; revised 4 April 2013; accepted 5 April 2013. [1] New particle formation consists of homogeneous nucleation of thermodynamically stable clusters followed by growth of these clusters to a detectable size. For new particle formation to take place, these clusters need to grow sufficiently fast to escape coagulation with preexisting particles. Previous studies indicated that condensation of low-volatility organic vapor may play an important role in the initial growth of the clusters. However, due to the relatively high vapor pressure and partial molar volume of even highly oxidized organic compounds, the strong Kelvin effect may prevent typical ambient organics from condensing on these small clusters. Here we show

83

Mining from proteinprotein interactions  

Science Conference Proceedings (OSTI)

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

Hiroshi Mamitsuka

2012-09-01T23:59:59.000Z

84

Function of proteins  

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

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

85

Questions and Answers - Could you please explain density? What is it? What  

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

wouldit take to create a ton? would<br>it take to create a ton? Previous Question (How many atoms would it take to create a ton?) Questions and Answers Main Index Next Question (How do I find the number of protons, electrons and neutrons in an atom?) How do I find the number of protons,electrons and neutrons in an atom? Could you please explain density? What is it? What is the concept of D = M over V? Density is how much mass a material has for a given volume. Think about a sponge. Most artificial sponges today are made of a foamed plastic. Assume you have a one pound sponge. If you melt it down to a plastic soup with all the bubbles gone, it will be much smaller, but it will still weigh one pound. It is now denser. We use water as sort of a standard for density. We say water has a density of 1. If something weighs twice as much as the same

86

Electrokinetic behavior of fluoride salts as explained from water structure considerations  

Science Conference Proceedings (OSTI)

Unlike the other silver halides, silver fluoride is positively charged in its saturated solution as determined by nonequilibrium electrophoresis measurements. In the absence of surface hydrolysis reactions, other fluoride salts (LiF, CaF{sub 2}, and MgF{sub 2}) also are positively charged in their saturation solutions. Furthermore, the electrokinetic behavior of these fluoride salts is rather insensitive to the fluoride ion activity in neutral or acidic solutions, and reversal of the sign of the surface charge by fluoride addition is not possible. Based on FTIR transmission spectra to describe the water structure of ionic solutions, in situ FTIR/internal reflection spectroscopy (FTIR/IRS) has been used to spectroscopically characterize interfacial water at fluoride salt surfaces. The experimental spectra were examined by consideration of the O-H stretching region (3,000--3,800 cm{sup {minus}1}) associated with the vibrational spectra of interfacial water. These results reveal a unique hydration state for fluorides and explain the anomalous electrokinetic behavior of fluoride salts such as LiF, CaF{sub 2}, and MgF{sub 2}, which show an unexpected insensitivity to the fluoride ion concentration in solution. It appears that this insensitivity is due to the formation of strong hydrogen bonding of the fluoride ions with water molecules. This hydration state prevents the accommodation of excess fluoride ions at surface lattice sites and accounts for the observed electrokinetic behavior.

Hu, Y.; Lu, Y.; Veeramasuneni, S.; Miller, J.D. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Metallurgical Engineering

1997-06-01T23:59:59.000Z

87

Petrology of the Devonian gas-bearing shale along Lake Erie helps explain gas shows  

DOE Green Energy (OSTI)

Comprehensive petrologic study of 136 thin sections of the Ohio Shale along Lake Erie, when combined with detailed stratigraphic study, helps explain the occurrence of its gas shows, most of which occur in the silty, greenish-gray, organic poor Chagrin Shale and Three Lick Bed. Both have thicker siltstone laminae and more siltstone beds than other members of the Ohio Shale and both units also contain more clayshales. The source of the gas in the Chagrin Shale and Three Lick Bed of the Ohio Shale is believed to be the bituminous-rich shales of the middle and lower parts of the underlying Huron Member of the Ohio Shale. Eleven petrographic types were recognized and extended descriptions are provided of the major ones - claystones, clayshales, mudshales, and bituminous shales plus laminated and unlaminated siltstones and very minor marlstones and sandstones. In addition three major types of lamination were identified and studied. Thirty-two shale samples were analyzed for organic carbon, whole rock hydrogen and whole rock nitrogen with a Perkin-Elmer 240 Elemental Analyzer and provided the data base for source rock evaluation of the Ohio Shale.

Broadhead, R.F.; Potter, P.E.

1980-11-01T23:59:59.000Z

88

Do two flavour oscillations explain both KamLAND data and the Solar Neutrino Spectrum?  

E-Print Network (OSTI)

The recent measurement of Delta_{sol} by the KamLAND experiment with very small errors, makes definitive predictions for the energy dependence of the solar neutrino survival probability P_{ee}. We fix Delta_{sol} to be the KamLAND best fit value of 8*10^{-5} eV^2 and study the energy dependence of P_{ee} for solar neutrinos in the framework of two flavour oscillations and also of three flavour oscillations. For the case of two flavour oscillations, P_{ee} has a measurable slope in the 5-8 MeV range but the solar spectrum measurements in this range find P_{ee} to be flat. The predicted values of P_{ee}, even for the best fit value of theta_{sol}, differ by 2 to 3 sigma from the Super-K measured values in each of the three energy bins of the 5-8 MeV range. If future measurements of solar neutrinos by Super-K and SNO find a flat spectrum with reduced error bars (by a factor of 2), it will imply that two flavour oscillations can no longer explain both KamLAND data and the solar spectrum. However a flat solar neutrino spectrum and the Delta_{sol} measured by KamLAND can be reconciled in a three flavour oscillation framework with a moderate value of theta_{13} approx 13 degrees.

Bipin Singh Koranga; Mohan Narayan; S. Uma Sankar

2005-03-10T23:59:59.000Z

89

Explaining the relationship between prehistoric agriculture and environment at Chaco Canyon, New Mexico  

E-Print Network (OSTI)

Chaco Canyon, the Pueblo settlement of New Mexico, represents one of the major cultural developments in the prehistoric Southwest. Between A.D. 900 and A.D. 1100 Chaco reached its peak of cultural florescence. This period was characterized by considerable building activities, appearance of Chaco outliers, and the construction of an extensive road system. After this period a dramatic decline in population and a cessation of building activity took place. Archaeologists call this phenomenon abandonment. In general, development and abandonment of Chaco Canyon coincided with changes in climatic conditions. Between A.D. 900 and A.D. 1100 there was a gradual increase in effective moisture and warmer temperature which proved favorable for agriculture there. With these optimal climatic conditions,development of Chaco Canyon witnessed a great increase in population. However, the Chaco Canyon region could not support a large population indefinitely because of its agricultural marginality. To solve this population-resource imbalance, Chacoan farmers of this period intensified their agricultural activities by constructing water control systems such as check dams, contour terraces, canals, and ditches. These measures worked for a while and the influence of Chaco Canyon was felt in the political, economic, and religious life of a broad geographic region. However, summer moisture began to decrease in the years between A.D. 1130 and A.D. 1180. This decrease became a full scale drought from A.D. 1157 to A.D. 1179 that seems to have severely affected agriculture and wild food resources available for the Chacoans. In addition, the Chacoan water control system designed to capture runoff probably proved to be inadequate as a buffering mechanism. Consequently, population at Chaco Canyon began to decrease and the region was abandoned after A.D. 1140. In an attempt at explaining the specific abandonment of Chaco Canyon, this thesis focuses on relationship between prehistoric agriculture and environment.

Gang, G-Young

1993-01-01T23:59:59.000Z

90

Can the standard model CP violation near the W bags explain the cosmological baryonic asymmetry?  

Science Conference Proceedings (OSTI)

In the scenario of cold electroweak baryogenesis, oscillations of the Higgs field lead to metastable domains of unbroken phase where the Higgs field nearly vanishes. Those domains have also been identified with the W-t-t bags, a nontopological solitons made of large number ({approx}1000) of gauge quanta and heavy (top and antitop) quarks. As real-time numerical studies had shown, sphalerons (topological transition events violating the baryon number) occur only inside those bags. In this work we estimate the amount of CP violation in this scenario coming from the standard model, via the Cabibbo-Kobayashi-Maskawa (CKM) quark mixing matrix, resulting in top-minus-antitop difference of the population in the bags. Since these tops/antitops are recycled by sphalerons, this population difference leads directly to the baryonic asymmetry of the Universe. We look at the effect appearing in the 4th order in weak W diagrams describing interference of different quark flavor contributions. We found that there are multiple cancellations of diagrams and clearly sign-definite effect appears only in the 6th-order expansion over flavor-dependent phases. We then estimate contributions to these diagrams in which weak interaction occurs (i) inside, (ii) near and (iii) far from the W-t-t b-bags, optimizing the contributions in each of them. We conclude that the second (near) scenario is the dominant one, producing CP violation of the order of 10{sup -10}, in our crude estimates. Together with the baryon violation rate of about 10{sup -2}, previously demonstrated for this scenario, it puts the resulting asymmetry close to what is needed to explain the observed baryonic asymmetry in the Universe. Our answer also has a definite sign, which apparently seems to be the correct one.

Burnier, Yannis; Shuryak, Edward [Department of Physics, State University of New York, Stony Brook, New York 11794 (United States)

2011-10-01T23:59:59.000Z

91

Mining and analysing scale-free protein protein interaction network  

Science Conference Proceedings (OSTI)

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

Xiaohua Hu

2005-04-01T23:59:59.000Z

92

Soy Protein Products  

Science Conference Proceedings (OSTI)

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

93

Highly thermostable fluorescent proteins  

DOE Patents (OSTI)

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

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

2011-03-22T23:59:59.000Z

94

vol. 179, no. 3 the american naturalist march 2012 Insects on Plants: Explaining the Paradox of Low Diversity  

E-Print Network (OSTI)

species pools. Herbivore diversity increases as a power function of plant diversity, and the rate specialized herbivores or pathogens have density-dependent effects on plant growth and fitness, put- tingvol. 179, no. 3 the american naturalist march 2012 Insects on Plants: Explaining the Paradox of Low

95

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

E-Print Network (OSTI)

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

Fernndez Surez, Marta

2008-01-01T23:59:59.000Z

96

Wavelength and Resolution Explained  

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

ªiªø©M¸ѪR«× ªiªø©M¸ѪR«× ¨㦳ªøªiªøªºªF¦è´N¦n¹³¬}¥ެG¨Ƥ¤ªºÄx²y¡A¨âª̬Ҥ£¯ണ¨ѤӦh¦³Ãö³Q¼²ª«ªº²Ӹ`¡C¨㦳µuªiªøªºªF¦è´N¹³¬G¨Ƥ¤ªº¤j²z¥ۡA¥i¥H´£¨ѧA³Q¼²ª«¬۷í¸ԲӪº°T®§¡C±´¤lªºªiªø·Uµu¡A§A¥i¥H±o¨ì·U¦h¦³Ãö³Q¼²ª«ªº°T®§¡C ´åªa¦À¬Oªiªø»P¸ѪR«תº¤@-Ӧn¨Ҥl¡C¦pªG§A¦³¤@-Ӵåªa¦À¡A¨䤤ªº¤ôªiªiªø¤@¤½¤تø¡AµM«á§â¤@-ӮãªK±À¨ì¤ô¸̡A´åªa¦Àªºªi¥u¬O³q¹L®ãªK¡C¦]¬°ªiªø¤@¤½¤طN¨ýµۦÀ¤¤ªº¤ôªi¤£·|³Q¦p¦¹¤pªºªF¦è¼vÅT¡C ©Ҧ³ªº²ɤl³£¨㦳ªi°ʯS©ʡC©ҥH¡A·í§ڭ̨ϥβɤl§@¬°±´¤l¡A§ڭ̻ݭn§Q¥Ψ㦳µuªiªøªº²ɤl¡A¤~¯à±o¨ì¤pªF¦誺¸ԲӰT®§¡C¤@-ӹê¥Ϊº²ʲ¤-ì«h¡G²ɤl³̦h¥u¯౴´ú¨ì»P¨äªiªøµ¥ªøªº¶ZÂ÷¡C-n±´´ú§ó¤pªº¤ثסA±´¤lªºªiªø ´N¥²¶·§óµu¡C

97

Fundamentals Explain High Prices  

Gasoline and Diesel Fuel Update (EIA)

9 9 Notes: One can use a simple model to deal with price/fundamental relationships. This one predicts monthly average WTI price as a function of OECD total petroleum stock deviations from the normal levels . The graph shows the model as it begins predicting prices in 1992. It shows how well the model has predicted not only the direction, but the magnitude of prices over this 8+ year period. While the model is simple and not perfect, it does predict the overall trends and, in particular, the recent rise in prices. It also shows that prices may have over-shot the fundamental balance for a while -- at least partially due to speculative concerns over Mideast tensions, winter supply adequacy, and Iraq's export policies. Prices now seem to be correcting, and may even undershoot briefly

98

Explaining Soft Law  

E-Print Network (OSTI)

by the Nuclear Nonproliferation Treaty. 37 For each of thesecontained in the Nuclear Nonproliferation Treaty (NPT) notoutside of the nuclear nonproliferation regime threatened

Guzman, Andrew T.; Meyer, Timothy L.

2009-01-01T23:59:59.000Z

99

Explaining Soft Law  

E-Print Network (OSTI)

by the Nuclear Nonproliferation Treaty. 38 For each of thesecontained in the Nuclear Nonproliferation Treaty (NPT) notoutside of the nuclear nonproliferation regime threatened

Guzman, Andrew; Meyer, Timothy L.

2010-01-01T23:59:59.000Z

100

Explaining Soft Law  

E-Print Network (OSTI)

the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996their stockpiles of nuclear weapons. If Russia subsequently

Guzman, Andrew T.; Meyer, Timothy L.

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Explaining Soft Law  

E-Print Network (OSTI)

the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996the Threat or Use of Nuclear Weapons, Advisory Opinion, 1996their stockpiles of nuclear weapons. If Russia subsequently

Guzman, Andrew; Meyer, Timothy L.

2010-01-01T23:59:59.000Z

102

Explaining Collaborative Filtering Recommendations  

E-Print Network (OSTI)

Automated collaborative filtering (ACF) systems predict a person's affinity for items or information by connecting that person's recorded interests with the recorded interests of a community of people and sharing ratings between likeminded persons. However, current recommender systems are black boxes, providing no transparency into the working of the recommendation. Explanations provide that transparency, exposing the reasoning and data behind a recommendation. In this paper, we address explanation interfaces for ACF systems -- how they should be implemented and why they should be implemented. To explore how, we present a model for explanations based on the user's conceptual model of the recommendation process. We then present experimental results demonstrating what components of an explanation are the most compelling. To address why, we present experimental evidence that shows that providing explanations can improve the acceptance of ACF systems. We also describe some initial explor...

Jonathan Herlocker Joseph; Joseph A. Konstan; John Riedl

2000-01-01T23:59:59.000Z

103

Research Types Explained  

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

NONPROPRIETARY RESEARCH Access to the User Facility is based on a peer-reviewed proposal process. User may access the User Facility with or without collaboration of Argonne...

104

Presenting and Explaining Mizar  

Science Conference Proceedings (OSTI)

The Mizar proof language has both many human-friendly presentation features, and also firm semantical level allowing rigorous proof checking. Both the presentation features and the semantics are important for users, and an ideal Mizar presentation should ... Keywords: ATP, MML Query, MPTP, Mizar, proof objects, proof presentation

Josef Urban; Grzegorz Bancerek

2007-05-01T23:59:59.000Z

105

DNA's Role with Proteins  

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

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

106

Protein from algae  

SciTech Connect

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

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

1978-01-01T23:59:59.000Z

107

A Case Study of NGO-Government Collaboration in Vietnam: Partnership Dynamics Explained through Contexts, Incentives, and Barriers  

E-Print Network (OSTI)

Collaboration between international NGOs (INGOs) and governmental organizations (GOs) have contributed significantly to the goals of poverty alleviation and agricultural development in developing countries. Much of the literatures on NGO-GO partnerships have explored theoretically or empirically what motivate and hinder cross-sector collaboration. But not many have studied cross-sector collaboration from both analytical and descriptive perspectives. This study filled in this gap by drawing from previous studies a conceptual framework through which contexts, incentives, and barriers that influence INGO-GO partnerships were described and explained. The researcher adopted a qualitative case-study method with emergent design. Personal interviews were conducted with 20 key informants, including eight Vietnamese staff from one INGO and 12 government officials from six GOs who partnered with the INGO. All participating organizations were institutions serving agricultural and rural development in the south of Vietnam. The data were collected in 2010 and analyzed using the software package ATLAS.ti. The results showed four categories that interact to form a framework of a dynamic continuum of partnership development. The four categories included conditioning factors, incentives, barriers, and feedback loop. The categories held the following themes: 1) socio-political contexts and organizational natures for conditioning factors, 2) shared missions, resource mobilization, capacity building, and networking for incentives, 3) ideological conflicts, structural constraints, and operational hurdles for barriers, and 4) reflections and recommendations for feedback loop. The study contributed a theoretical- and empirical-based perspective on INGO-GO partnerships in post-reform countries. It provided a framework that comprehensively describes and explains partnership dynamics. The study also shared knowledge of the intricacies of INGO-GO partnerships in rural Vietnam. For institutions serving agricultural and rural development, the study could assist in strategic management to minimize constraints and maximize opportunities in collaborative environments.

Nguyen, Anh Thuc

2011-08-01T23:59:59.000Z

108

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

109

Cost Avoidance vs. Utility Bill Accounting - Explaining theDiscrepancy Between Guaranteed Savings in ESPC Projects and UtilityBills  

SciTech Connect

Federal agencies often ask if Energy Savings PerformanceContracts (ESPCs) result in the energy and cost savings projected duringthe project development phase. After investing in ESPCs, federal agenciesexpect a reduction in the total energy use and energy cost at the agencylevel. Such questions about the program are common when implementing anESPC project. But is this a fair or accurate perception? Moreimportantly, should the federal agencies evaluate the success or failureof ESPCs by comparing the utility costs before and after projectimplementation?In fact, ESPC contracts employ measurement andverification (M&V) protocols to measure and ensure kilowatt-hour orBTU savings at the project level. In most cases, the translation toenergy cost savings is not based on actual utility rate structure, but acontracted utility rate that takes the existing utility rate at the timethe contract is signed with a clause to escalate the utility rate by afixed percentage for the duration of the contract. Reporting mechanisms,which advertise these savings in dollars, may imply an impact to budgetsat a much higher level depending on actual utility rate structure. FEMPhas prepared the following analysis to explain why the utility billreduction may not materialize, demonstrate its larger implication onagency s energy reduction goals, and advocate setting the rightexpectations at the outset to preempt the often asked question why I amnot seeing the savings in my utility bill?

Kumar, S.; Sartor, D.

2005-08-15T23:59:59.000Z

110

Stabilized polyacrylic saccharide protein conjugates  

DOE Patents (OSTI)

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

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

1996-01-01T23:59:59.000Z

111

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

112

Infrared Protein Crystallography  

DOE Green Energy (OSTI)

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

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

2011-12-31T23:59:59.000Z

113

Visualizing the protein sequence universe  

Science Conference Proceedings (OSTI)

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

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

2012-06-01T23:59:59.000Z

114

Computational Studies of Protein Folding  

Science Conference Proceedings (OSTI)

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

2001-01-01T23:59:59.000Z

115

NMR Spectroscopy Protein-NMR  

E-Print Network (OSTI)

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

Schüler, Axel

116

The Most Severe Test for Hydrophobicity Scales: Two Proteins with 88% Sequence Identity but Different Structure and Function  

E-Print Network (OSTI)

Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD) concluded that the "simplicity and graphic nature of hydrophobicity scales make them very useful tools for the evaluation of protein structures". In practice, however, attempts to develop hydrophobicity scales (for example, compatible with classical force fields (CFF) in calculating the energetics of protein folding) have encountered many difficulties. Here we suggest an entirely different approach, based on the idea that proteins are self-organized networks, subject to finite-scale criticality (like some network glasses). We test this proposal against two small proteins that are delicately balanced between alpha and alpha/beta structures, with different functions encoded with only 12% of their amino acids. This example explains why protein structure prediction is so challenging, and it provides a severe test for the accuracy and content of hydrophobicity scales. The new method confirms KD's evaluation, and at the same time suggests that protein structure, dynamics and function can be best discussed without using CFF.

Alexander E. Kister; James C. Phillips

2008-03-18T23:59:59.000Z

117

10/14/09 2:35 PMMathematicians' Alternate Model of the Universe Explains Away the Need For Dark Energy | Popular Science Page 1 of 13http://www.popsci.com/military-aviation-amp-space/article/2009-09/mathematicians-seek-explain-away-dark-energy-universe  

E-Print Network (OSTI)

-09/mathematicians-seek-explain-away-dark-energy-universe Mathematicians' Alternate Model of the Universe Explains Away the Need For Dark Energy By Jeremy Hsu Posted 09.25.2009 at 2:15 pm RELATED ARTICLES Most Convincing Sign of Dark Energy's Presence Yet? Dark Energy Hits Tenth Birthday, Still a Mystery Dark Energy

Temple, Blake

118

A randomized global optimization method for protein-protein docking  

E-Print Network (OSTI)

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

119

Explaining EIA Crude Oil and Petroleum Product Price Data and Comparing with Other U.S. Government Data Sources, 2001 to 2010  

Gasoline and Diesel Fuel Update (EIA)

Explaining EIA Crude Oil and Explaining EIA Crude Oil and Petroleum Product Price Data and Comparing with Other U.S. Government Data Sources, 2001 to 2010 December 2012 (February 2013-Revised Tables 5, 6 and 15 and associated links) Independent Statistics & Analysis www.eia.gov U.S. Department of Energy Washington, DC 20585 U.S. Energy Information Administration | Explaining EIA Crude Oil and Petroleum Product Price Data and Comparing with Other U.S. Government Data Sources, 2001 to 2010 ii This report was prepared by the U.S. Energy Information Administration (EIA), the statistical and analytical agency within the U.S. Department of Energy. By law, EIA's data, analyses, and forecasts are independent of approval by any other officer or employee of the United States Government. The views

120

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

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

122

Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription  

Science Conference Proceedings (OSTI)

Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.

Vaidya, Anand T.; Chen, Chen-Hui; Dunlap, Jay C.; Loros, Jennifer J.; Crane, Brian R. (Dartmouth-MED); (Cornell)

2012-10-25T23:59:59.000Z

123

Connecting Windows 7 to the Riverpoint Wireless Network This document explains how to connect Windows 7 to the wireless network at the WSU-Spokane campus.  

E-Print Network (OSTI)

Connecting Windows 7 to the Riverpoint Wireless Network This document explains how to connect Windows 7 to the wireless network at the WSU-Spokane campus. 1. Click the wireless icon on your desktop name and password in the Windows Security dialog box that appears. You are now connected

Collins, Gary S.

124

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

E-Print Network (OSTI)

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

de Meyer, Frdrick Jean-Marie

2010-01-01T23:59:59.000Z

125

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

126

Protein structure classification by structural transformatio  

Science Conference Proceedings (OSTI)

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

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

1996-11-01T23:59:59.000Z

127

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

128

Optimal contact map alignment of proteinprotein interfaces  

E-Print Network (OSTI)

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

Pulim, Vinay

129

Molecular characterization and evolutionary plasticity of protein-protein interfaces  

E-Print Network (OSTI)

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

Bickerton, George Richard James

130

Protein and Co-Products Division  

Science Conference Proceedings (OSTI)

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

131

Methods and applications in computational protein design  

E-Print Network (OSTI)

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

Biddle, Jason Charles

2010-01-01T23:59:59.000Z

132

Soy Protein Products - Electronic Version  

Science Conference Proceedings (OSTI)

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

133

Predicting Continuous Epitopes in Proteins  

Science Conference Proceedings (OSTI)

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

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

2005-08-01T23:59:59.000Z

134

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

135

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

E-Print Network (OSTI)

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

Stowers, R Steven; Isacoff, Ehud Y

2007-01-01T23:59:59.000Z

136

Lesquerella fendleri Protein Fractionation and Characterization  

Science Conference Proceedings (OSTI)

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

137

Decomposition of overlapping protein complexes: A graph ...  

E-Print Network (OSTI)

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

138

Protein Flips Lipids Across Membranes  

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

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

139

Prediction and integration of regulatory and protein-protein interactions  

Science Conference Proceedings (OSTI)

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

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

2009-04-20T23:59:59.000Z

140

Explaining Harvard's Greenhouse Gas Inventory  

E-Print Network (OSTI)

No data available Factors from EPA's eGRID database, MA-specific Factors from ISO NE's emission reports

Paulsson, Johan

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Systematic characterization of protein glycosylation of bacteria cell surface proteins  

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

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

142

Protein Flips Lipids Across Membranes  

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

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

143

SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION  

SciTech Connect

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

JOHN C WALKER

2011-11-01T23:59:59.000Z

144

Protein Flips Lipids Across Membranes  

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

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

145

Recombinant fluorescent protein microsphere calibration standard  

SciTech Connect

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

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

2001-01-01T23:59:59.000Z

146

Protein Puzzles and Scientific Solutions  

Office of Science (SC) Website

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

147

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

Science Conference Proceedings (OSTI)

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

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

2007-07-01T23:59:59.000Z

148

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

Science Conference Proceedings (OSTI)

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

Guillaume Blin; Florian Sikora; Stephane Vialette

2010-10-01T23:59:59.000Z

149

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

150

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

151

First Knot Discovered in Ancient Bacterium Protein  

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

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

152

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

E-Print Network (OSTI)

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

Chen, Tsan-Chou Scott

2012-01-01T23:59:59.000Z

153

Proteins  

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

can lead to a multitude of possibilities, such as enhancing cellulose degradation for biofuels based on understanding the enzymes that naturally degrade it (cellulases) or...

154

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

155

PERSPECTIVE Directed Evolution of Novel Protein Functions  

E-Print Network (OSTI)

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

Zhao, Huimin

156

Erythropoietin binding protein from mammalian serum  

DOE Patents (OSTI)

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

Clemons, Gisela K. (Berkeley, CA)

1997-01-01T23:59:59.000Z

157

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

158

Erythropoietin binding protein from mammalian serum  

DOE Patents (OSTI)

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

Clemons, G.K.

1997-04-29T23:59:59.000Z

159

Active Sites by Computational Protein Design  

Science Conference Proceedings (OSTI)

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

Pablo Tortosa; Alfonso Jaramillo

2006-01-01T23:59:59.000Z

160

Binding of Proteins to Copolymers of Varying  

E-Print Network (OSTI)

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

Dubin, Paul D.

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Evaluation of physicochemical properties of modified algae protein adhesives.  

E-Print Network (OSTI)

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

Borgen, Kelly

2012-01-01T23:59:59.000Z

162

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

163

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

Science Conference Proceedings (OSTI)

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

Hiroshi Mamitsuka

2005-04-01T23:59:59.000Z

164

An improved oxygen diffusion model to explain the effect of low-temperature baking on high field losses in niobium superconducting cavities  

SciTech Connect

Radio-frequency (RF) superconducting cavities made of high purity niobium are widely used to accelerate charged particle beams in particle accelerators. The major limitation to achieve RF field values approaching the theoretical limit for niobium is represented by ''anomalous'' losses which degrade the quality factor of the cavities starting at peak surface magnetic fields of about 100 mT, in absence of field emission. These high field losses are often referred to as ''Q-drop''. It has been observed that the Q-drop is drastically reduced by baking the cavities at 120 C for about 48 h under ultrahigh vacuum. An improved oxygen diffusion model for the niobium-oxide system is proposed to explain the benefit of the low-temperature baking on the Q-drop in niobium superconducting rf cavities. The model shows that baking at 120 C for 48 h allows oxygen to diffuse away from the surface, and therefore increasing the lower critical field towards the value for pure niobium.

Gianluigi Ciovati

2005-09-15T23:59:59.000Z

165

Bath and Shower Effects in the Rat Parotid Gland Explain Increased Relative Risk of Parotid Gland Dysfunction After Intensity-Modulated Radiotherapy  

Science Conference Proceedings (OSTI)

Purpose: To assess in a rat model whether adding a subtolerance dose in a region adjacent to a high-dose irradiated subvolume of the parotid gland influences its response (bath-and-shower effect). Methods and Materials: Irradiation of the whole, cranial 50%, and/or the caudal 50% of the parotid glands of Wistar rats was performed using 150-MeV protons. To determine suitable (i.e., subtolerance) dose levels for a bath-dose, both whole parotid glands were irradiated with 5 to 25 Gy. Subsequently groups of Wistar rats received 30 Gy to the caudal 50% (shower) and 0 to 10 Gy to the cranial 50% (bath) of both parotid glands. Stimulated saliva flow rate (function) was measured before and up to 240 days after irradiation. Results: Irradiation of both glands up to a dose of 10 Gy did not result in late loss of function and is thus regarded subtolerance. Addition of a dose bath of 1 to 10 Gy to a high-dose in the caudal 50% of the glands resulted in enhanced function loss. Conclusion: Similar to the spinal cord, the parotid gland demonstrates a bath and shower effect, which may explain the less-than-expected sparing of function after IMRT.

Luijk, Peter van [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands)], E-mail: p.van.luijk@rt.umcg.nl; Faber, Hette [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Schippers, Jacobus M. [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Accelerator Department, Paul Scherrer Institut, Villigen (Switzerland); Brandenburg, Sytze [Kernfysisch Versneller Instituut, University of Groningen, Groningen (Netherlands); Langendijk, Johannes A.; Meertens, Harm [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Coppes, Robert P. [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Department of Cell Biology, Section Radiation and Stress Cell Biology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands)

2009-07-15T23:59:59.000Z

166

Tubulin and microtubule associated proteins  

SciTech Connect

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

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

1989-01-01T23:59:59.000Z

167

The Plexus Model for the Inference of Ancestral Multidomain Proteins  

Science Conference Proceedings (OSTI)

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

John Wiedenhoeft; Roland Krause; Oliver Eulenstein

2011-07-01T23:59:59.000Z

168

Bacteria Modified to Secrete Biologically Active Protein for ...  

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

169

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

Science Conference Proceedings (OSTI)

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

2013-03-13T23:59:59.000Z

170

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

Science Conference Proceedings (OSTI)

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

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

2010-10-01T23:59:59.000Z

171

Statistical Mechanics Model for Protein Folding  

E-Print Network (OSTI)

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

Yakubovich, A V; Greiner, W

2010-01-01T23:59:59.000Z

172

Year 2 Report: Protein Function Prediction Platform  

SciTech Connect

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

Zhou, C E

2012-04-27T23:59:59.000Z

173

DIP: The Database of Interacting Proteins  

DOE Data Explorer (OSTI)

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

International Molecular Interaction Exchange (IMEx) Consortium

174

Computational Method for Detecting and Enhancing Protein ...  

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

175

Understanding Protein Solution Phase Behavior via Coarse ...  

Science Conference Proceedings (OSTI)

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

2013-02-14T23:59:59.000Z

176

Synthesizing Membrane Proteins Using In Vitro Methodology ...  

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

177

Fast Dynamics in Stabilization of Proteins  

Science Conference Proceedings (OSTI)

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

178

Soy Protein ProductsChapter 3 Protein Quality and Human Nutrition  

Science Conference Proceedings (OSTI)

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

179

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

E-Print Network (OSTI)

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

Shang, Yue

2003-05-01T23:59:59.000Z

180

Coupling between motor proteins determines dynamic behaviors of motor protein assemblies  

E-Print Network (OSTI)

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Identifying the nature of the interface in protein-protein complexes  

Science Conference Proceedings (OSTI)

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

Pralay Mitra

2010-02-01T23:59:59.000Z

182

Mechanisms ?of? change ?in ?protein ?architecture  

E-Print Network (OSTI)

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

Buljan, Marija

2011-01-11T23:59:59.000Z

183

Bayesian Nonparametric Methods for Protein Structure Prediction  

E-Print Network (OSTI)

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

Lennox, Kristin Patricia

2010-08-01T23:59:59.000Z

184

Antimicrobial protein protects grapevines from pathogen  

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

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

185

Dynamic Phase Transitions in Coupled Motor Proteins  

E-Print Network (OSTI)

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

Evgeny B. Stukalin; Anatoly B. Kolomeisky

2005-09-16T23:59:59.000Z

186

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

187

Research Article: Bacterial protein structures reveal phylum dependent divergence  

Science Conference Proceedings (OSTI)

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

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

2011-02-01T23:59:59.000Z

188

On the optimal contact potential of proteins  

E-Print Network (OSTI)

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

Kinjo, Akira R

2008-01-01T23:59:59.000Z

189

ALSNews Vol. 308  

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

8 Print 8 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

190

ALSNews Vol. 308  

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

8 Print 8 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

191

ALSNews Vol. 308  

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

8 Print 8 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

192

ALSNews Vol. 308  

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

08 Print 08 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

193

ALSNews Vol. 308  

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

8 Print 8 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

194

ALSNews Vol. 308  

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

8 Print 8 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

195

ALSNews Vol. 308  

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

8 Print 8 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

196

ALSNews Vol. 308  

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

8 Print 8 Print In This Issue Rotary Firing in Ring-Shaped Protein Explains Unidirectionality Biomimetic Dye Molecules for Solar Cells Photon Science for Renewable Energy: A News ALS Brochure Everything You Wanted To Know About ALS Proposals, Beam Time Allocations ALS Science Cafés Successful, Continue VUVX 2010 Conference Update Ring Leaders: Scientific Support Group Announcements: Vogue Shines Light on the ALS, ALS Facebook Flourishing, Guest House Special Extended Who's in the News Operations Update News Links RingLeaders Ring Leaders Scientific Support Division Deputy for Scientific Support Zahid Hussein introduces the Scientific Support Group's duties, goals, and achievements. Read the Article announcements Announcements Vogue Shines Light on the ALS The April issue of Vogue magazine features "Great American Women," including Facebook COO Sheryl Sandberg, whose photo was taken in front of the microARPES endstation of the MAESTRO beamline (Sector 7). The computers all show Facebook, but the high-tech background of the endstation stands out behind Sandberg. Read the Vogue story

197

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

198

Protein structure alignment using elastic shape analysis  

Science Conference Proceedings (OSTI)

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

Wei Liu; Anuj Srivastava; Jinfeng Zhang

2010-08-01T23:59:59.000Z

199

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

200

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Green fluorescent protein as a mechanical sensor  

E-Print Network (OSTI)

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

Muso, Taro M. (Taro Michael)

2007-01-01T23:59:59.000Z

202

Protein Structure Suggests Role as Molecular Adapter  

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

Berkeley, recently determined the structure of the ATPase region of DnaC, a bacterial helicase loader. The structure revealed that DnaC is a close cousin of DnaA, the protein...

203

Inferring evolutionary scenarios for protein domain compositions  

Science Conference Proceedings (OSTI)

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

John Wiedenhoeft; Roland Krause; Oliver Eulenstein

2010-05-01T23:59:59.000Z

204

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

205

Computer Simulations of Protein Dynamics and Thermodynamics  

Science Conference Proceedings (OSTI)

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

David Case

1993-10-01T23:59:59.000Z

206

IAPSAP, International Association for Protein Structure Analysis  

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

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

207

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

E-Print Network (OSTI)

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

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

2010-01-01T23:59:59.000Z

208

Exo-endo cellulase fusion protein  

DOE Patents (OSTI)

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

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

2012-01-17T23:59:59.000Z

209

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

210

Genetic noise control via protein oligomerization  

Science Conference Proceedings (OSTI)

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

Ghim, C; Almaas, E

2008-06-12T23:59:59.000Z

211

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

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

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

212

The Molecular Structure of a Key Viral Protein  

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

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

213

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

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

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

214

Free energy functions in protein structural stability and folding kinetics.  

E-Print Network (OSTI)

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

Morozov, Alexandre V., 1973-

2009-01-01T23:59:59.000Z

215

New Crystal Structures Lift Fog around Protein Folding  

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

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

216

Statistical Thermodynamics of Membrane Bending-Mediated ProteinProtein Attractions  

E-Print Network (OSTI)

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

Tom Chou; Ken S. Kim; George Oster

2001-01-01T23:59:59.000Z

217

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

E-Print Network (OSTI)

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

Huang, Ying

2012-05-01T23:59:59.000Z

218

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

SciTech Connect

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

Eliezer, D.

1994-06-01T23:59:59.000Z

219

An analysis pipeline for the inferenceof protein-protein interaction networks  

Science Conference Proceedings (OSTI)

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

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

2009-09-01T23:59:59.000Z

220

A Novel Shape Complementarity Scoring Function for Protein-Protein Docking  

E-Print Network (OSTI)

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

Weng, Zhiping

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Modeling sequence and function similarity between proteins for protein functional annotation  

Science Conference Proceedings (OSTI)

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

Roger Higdon; Brenton Louie; Eugene Kolker

2010-06-01T23:59:59.000Z

222

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

Science Conference Proceedings (OSTI)

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

Thanh-Phuong Nguyen; Tu-Bao Ho

2012-01-01T23:59:59.000Z

223

Protein and Co-Products Division Newsletter 10/12  

Science Conference Proceedings (OSTI)

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

224

Annual Meeting 2010 Hot Topic on High-Protein Diets  

Science Conference Proceedings (OSTI)

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

225

NIST Quantifies Low Levels of 'Heart Attack Risk' Protein  

Science Conference Proceedings (OSTI)

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

2012-10-02T23:59:59.000Z

226

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

227

ET Kinetics of Bifunctional Redox Protein Maquettes  

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

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

228

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

229

Protein Synthesis Initiation Factors: Phosphorylation and Regulation  

SciTech Connect

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

Karen S. Browning

2009-06-15T23:59:59.000Z

230

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

231

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

232

Facilitated diffusion of proteins on chromatin  

E-Print Network (OSTI)

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

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

2010-06-24T23:59:59.000Z

233

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

Science Conference Proceedings (OSTI)

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

Zhihao Yang; Hongfei Lin; Yanpeng Li

2010-02-01T23:59:59.000Z

234

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

E-Print Network (OSTI)

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

Apgar, James R. (James Reasoner)

2008-01-01T23:59:59.000Z

235

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

E-Print Network (OSTI)

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

Zeng, Bin

2009-01-01T23:59:59.000Z

236

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

E-Print Network (OSTI)

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

Fu, Hailong

2009-05-01T23:59:59.000Z

237

Fundamentals Explain High Crude Oil Prices  

Gasoline and Diesel Fuel Update (EIA)

6 6 Notes: One can use a simple model to deal with price/fundamental relationships. This one predicts monthly average WTI price as a function of OECD total petroleum stock deviations from the normal levels. The graph shows the model as it begins predicting prices in 1992. It shows how well the model has predicted not only the direction, but the magnitude of prices over this 8+ year period. While the model is simple and not perfect, it does predict the overall trends and, in particular, the recent rise in prices. It also shows that prices may have over-shot the fundamental balance for a while -- at least partially due to speculative concerns over Mideast tensions, winter supply adequacy, and Iraq's export policies. Prices moved lower in December, and even undershot briefly the

238

Is Quantum Mechanics needed to explain consciousness ?  

E-Print Network (OSTI)

In this short comment to a recent contribution by E. Manousakis [1] it is argued that the reported agreement between the measured time evolution of conscious states during binocular rivalry and predictions derived from quantum mechanical formalisms does not require any direct effect of QM. The recursive consumption analysis process in the Ouroboros Model can yield the same behavior.

Knud Thomsen

2007-11-13T23:59:59.000Z

239

Explaining the International Spread of Casino Gambling  

Science Conference Proceedings (OSTI)

Dec 13, 2009 ... were also legalization events in such diverse places as St. Lucia, Peru, and Vietnam during the 1990s. The next section provides a review of...

240

Factors Affecting Electricity Prices - Energy Explained, Your ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Explaining Activities as Consistent Groups of Events  

Science Conference Proceedings (OSTI)

We propose a method for disambiguating uncertain detections of events by seeking global explanations for activities. Given a noisy visual input, and exploiting our knowledge of the activity and its constraints, one can provide a consistent set of events ... Keywords: Activity analysis, Event recognition, Global explanations

Dima Damen; David Hogg

2012-05-01T23:59:59.000Z

242

Lederman Science Center: Physicists Explain Exhibits  

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

Science Adventures Teacher Resource Center video video video video video Welcome Accelerators Detectors Methods Ideas Leon Lederman Welcome These streams are being brought to...

243

Explaining the Price of Voluntary Carbon Offsets  

E-Print Network (OSTI)

prices. In both specifications, statisti- cally significant coefficients are those on the project types of biomass

Conte, Marc N.; Kotchen, Matthew

2009-01-01T23:59:59.000Z

244

Gasoline - Energy Explained, Your Guide To Understanding ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & ...

245

Do Disaster Expectations Explain Household Portfolios?  

E-Print Network (OSTI)

use the American Consumer Expenditure Survey (CEX) for consumption ex- penditure information. The data covers the period between 1983 and 2004. The expenditure information is recorded quarterly with approximately 5000 households in each wave. Every...

Alan, Sule

246

Bayesian Segmentation of Protein Secondary Structure  

E-Print Network (OSTI)

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

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

2000-01-01T23:59:59.000Z

247

Protein and Co-Products Division List  

Science Conference Proceedings (OSTI)

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

248

Molecular Nanosprings for Protein-Based Nanorobotics  

E-Print Network (OSTI)

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

Mavroidis, Constantinos

249

Extracellular Proteins Promote Zinc Sulfide Aggregation  

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

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

250

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

251

Study of structure-function relationships in proteins: Techniques and applications ot cytochrome c: Final report January 15, 1988--January 14, 1989  

SciTech Connect

During the initial period of this work we explored the differential geometry results which had been used to explain the structure-function relationships in the set of yeast iso-1-cytochrome c mutants studied under the initial contract. In addition we continued the development of techniques which would permit the structural characterization and comparison of proteins in a very efficient manner. We have expanded the studies based on the characterization of the structural preferences of various residues in a sample of twenty six globular proteins. It has been demonstrated that the overall structural preferences and the amino acid specific preferences seen in the analysis carried out at the five alpha carbon level can not be explained by the results of the analysis carried out at the four alpha carbon level. Thus the structural preferences seen must be described by considering groups of five or more residues. We do no yet have enough data to extend the analysis to the six alpha carbon unit level. We have also verified that the yeast/tuna structural analogy which we used before was justified, and have performed a conformational energy minimization of the reduced yeast cytochrome c crystal data in order to have a baseline for the study of mutant proteins. 6 refs.

Goldstein, D.A.; Rackovsky, S.R.

1989-08-01T23:59:59.000Z

252

Photon Sciences | About Photon Sciences | What About Proteins?  

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

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

253

Engineering Mammalian Cells for Improved Recombinant Protein Production  

E-Print Network (OSTI)

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

Wong, Niki S.C.

254

Protein and Co-Products Division Student Poster Competition  

Science Conference Proceedings (OSTI)

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

255

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

256

Protein structure prediction by a data-level parallel algorithm  

Science Conference Proceedings (OSTI)

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

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

1989-08-01T23:59:59.000Z

257

BIOINFORMATICS APPLICATIONS NOTE PIVOT: Protein Interactions VisualizatiOn Tool  

E-Print Network (OSTI)

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

Shamir, Ron

258

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

259

Extracellular Proteins Promote Zinc Sulfide Aggregation  

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

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

260

Extracellular Proteins Promote Zinc Sulfide Aggregation  

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

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Recombinant Proteins in Milk A Bioreactor That Eats Hay  

Science Conference Proceedings (OSTI)

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

2011-10-25T23:59:59.000Z

262

Cellulosic Fiber Composites Using Protein Hydrolysates and Methods ...  

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

263

Sequence space and the ongoing expansion of the protein universe  

E-Print Network (OSTI)

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

Dean, Matthew D.

264

Photoswitchable method for the ordered attachment of proteins to surfaces  

DOE Patents (OSTI)

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

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

2011-07-05T23:59:59.000Z

265

A Study of Hierarchical and Flat Classification of Proteins  

Science Conference Proceedings (OSTI)

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

Arthur Zimek; Fabian Buchwald; Eibe Frank; Stefan Kramer

2010-07-01T23:59:59.000Z

266

An overview of protein-folding techniques: issues and perspectives  

Science Conference Proceedings (OSTI)

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

Abdur Rahman; Albert Y. Zomaya

2005-04-01T23:59:59.000Z

267

The Dynamic Transition of Protein Hydration Water  

E-Print Network (OSTI)

Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic neutron scattering can be explained by a hidden critical point of bulk water. Based on more sensitive measurements of water on perdeuterated phycocyanin, using the new neutron backscattering spectrometer SPHERES, and an improved data analysis, we present results that show no sign of such a fragile-to-strong transition. The inflection of the elastic intensity at 220 K has a dynamic origin that is compatible with a calorimetric glass transition at 170 K. The temperature dependence of the relaxation times is highly sensitive to data evaluation; it can be brought into perfect agreement with the results of other techniques, without any anomaly.

W. Doster; S. Busch; A. M. Gaspar; M. -S. Appavou; J. Wuttke; H. Scheer

2009-11-26T23:59:59.000Z

268

E-Science and Protein Crystallography  

SciTech Connect

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

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

2012-08-09T23:59:59.000Z

269

E-Science and Protein Crystallography  

Science Conference Proceedings (OSTI)

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

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

2012-08-09T23:59:59.000Z

270

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

E-Print Network (OSTI)

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

Titus, Mitchell

2007-01-01T23:59:59.000Z

271

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

DOE Green Energy (OSTI)

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

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

2005-06-17T23:59:59.000Z

272

ProMAT: protein microarray analysis tool  

SciTech Connect

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

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

2006-04-04T23:59:59.000Z

273

TIGRFAMS: The TIGRFAMs database of protein families  

DOE Data Explorer (OSTI)

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

274

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

275

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

Science Conference Proceedings (OSTI)

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

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

2006-04-01T23:59:59.000Z

276

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

277

Protein Solubility, Digestibility and Fractionation after Germination of Sorghum Varieties  

E-Print Network (OSTI)

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

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

2011-01-01T23:59:59.000Z

278

Comment on Yu et al., "High Quality Binary Protein Interaction Map of the Yeast Interactome Network." Science 322, 104 (2008)  

E-Print Network (OSTI)

We test the claim by Yu et al. -- presented in Science 322, 104 (2008) -- that the degree distribution of the yeast (Saccharomyces cerevisiae) protein-interaction network is best approximated by a power law. Yu et al. consider three versions of this network. In all three cases, however, we find the most likely power-law model of the data is distinct from and incompatible with the one given by Yu et al. Only one network admits good statistical support for any power law, and in that case, the power law explains only the distribution of the upper 10% of node degrees. These results imply that there is considerably more structure present in the yeast interactome than suggested by Yu et al., and that these networks should probably not be called "scale free."

Clauset, Aaron

2009-01-01T23:59:59.000Z

279

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

Science Conference Proceedings (OSTI)

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

Jeremy A. Horst; Ram Samudrala

2010-10-01T23:59:59.000Z

280

Stable Isotope, Site-Specific Mass Tagging For Protein Identification  

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

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Cornell researchers take step in deciphering what proteins look like  

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

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

282

New Crystal Structures Lift Fog around Protein Folding  

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

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

283

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

E-Print Network (OSTI)

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

Stowers, R Steven; Isacoff, Ehud Y

2007-01-01T23:59:59.000Z

284

BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Fusion  

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

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

285

DAPS: Database of Aligned Protein Structures  

DOE Data Explorer (OSTI)

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

Mallick, Parag; Rice, Danny; Eisenberg, David

286

Structure and Function of Microbial Metal-Reduction Proteins  

SciTech Connect

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

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

2009-09-02T23:59:59.000Z

287

Recombinant HT{sub m4} gene, protein and assays  

DOE Patents (OSTI)

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

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

1996-09-03T23:59:59.000Z

288

Heat capacity and compactness of denatured proteins  

E-Print Network (OSTI)

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

Themis Lazaridis; Martin Karplus

1999-01-01T23:59:59.000Z

289

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

Science Conference Proceedings (OSTI)

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

Jae-Hyung Lee

2007-12-01T23:59:59.000Z

290

Lateral Transfer of a Lectin-Like Antifreeze Protein Gene in Fishes  

E-Print Network (OSTI)

Fishes living in icy seawater are usually protected from freezing by endogenous antifreeze proteins (AFPs) that bind to ice crystals and stop them from growing. The scattered distribution of five highly diverse AFP types across phylogenetically disparate fish species is puzzling. The appearance of radically different AFPs in closely related species has been attributed to the rapid, independent evolution of these proteins in response to natural selection caused by sea level glaciations within the last 20 million years. In at least one instance the same type of simple repetitive AFP has independently originated in two distant species by convergent evolution. But, the isolated occurrence of three very similar type II AFPs in three distantly related species (herring, smelt and sea raven) cannot be explained by this mechanism. These globular, lectin-like AFPs have a unique disulfide-bonding pattern, and share up to 85 % identity in their amino acid sequences, with regions of even higher identity in their genes. A thorough search of current databases failed to find a homolog in any other species with greater than 40 % amino acid sequence identity. Consistent with this result, genomic Southern blots showed the lectin-like AFP gene was absent from all other fish species tested. The remarkable conservation of both intron and exon sequences, the lack of correlation between evolutionary distance and mutation rate, and the pattern of silent vs non-silent codon changes make it unlikely that the gene for this AFP pre-existed but was lost from most branches of the teleost radiation. We propose instead that lateral gene transfer has resulted in the occurrence of the type II AFPs in herring, smelt and sea raven and

Laurie A. Graham; Stephen C. Lougheed; K. Vanya Ewart; Peter L. Davies

2008-01-01T23:59:59.000Z

291

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

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

292

A bacterial factory for the production of MEMBRANE PROTEINS  

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

293

Three Frontiers in the Thermodynamics of Protein Solutions  

E-Print Network (OSTI)

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

Prausnitz, John M; Foose, Loddie

2007-01-01T23:59:59.000Z

294

Three Frontiers in the Thermodynamics of Protein Solutions  

E-Print Network (OSTI)

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

Prausnitz, John; Hagar, Loddie

2008-01-01T23:59:59.000Z

295

Phenylpropanoid related regulatory protein-regulatory region associations  

SciTech Connect

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

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

2012-01-03T23:59:59.000Z

296

Soy Protein ProductsChapter 1 Historical Aspects  

Science Conference Proceedings (OSTI)

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

297

Improved Processes for the Production of Proteins and ...  

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

298

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

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

299

MTBreg: The Database of Conditionally Regulated Proteins in Mycobacterium Tuberculosis  

DOE Data Explorer (OSTI)

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

Kaufman, Markus; Pal, Debnath; Eisenberg, David

300

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

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

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

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

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

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

302

Structures for Three Membrane Transport Proteins Yield Functional...  

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

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

303

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

E-Print Network (OSTI)

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

Ahn, Jin Ho

304

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

E-Print Network (OSTI)

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

Wirmer, Julia

2005-01-01T23:59:59.000Z

305

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

E-Print Network (OSTI)

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

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

2011-07-29T23:59:59.000Z

306

Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (VSP1) of Borrelia Turicatae  

Science Conference Proceedings (OSTI)

Vsp surface lipoproteins are serotype-defining antigens of relapsing fever spirochetes that undergo multiphasic antigenic variation to allow bacterial persistence in spite of an immune response. Two isogenic serotypes of Borrelia turicatae strain Oz1 differ in their Vsp sequences and in disease manifestations in infected mice: Vsp1 is associated with the selection of a neurological niche, while Vsp2 is associated with blood and skin infection. We report here crystal structures of the Vsp1 dimer at 2.7 and 2.2 Angstroms. The structures confirm that relapsing fever Vsp proteins share a common helical fold with OspCs of Lyme disease-causing Borrelia. The fold features an inner stem formed by highly conserved N and C termini and an outer 'dome' formed by the variable central residues. Both Vsp1 and OspC structures possess small water-filled cavities, or pockets, that are lined largely by variable residues and are thus highly variable in shape. These features appear to signify tolerance of the Vsp-OspC fold for imperfect packing of residues at its antigenic surface. Structural comparison of Vsp1 with a homology model for Vsp2 suggests that observed differences in disease manifestation may arise in part from distinct differences in electrostatic surface properties; additional predicted positively charged surface patches on Vsp2 compared to Vsp1 may be sufficient to explain the relative propensity of Vsp2 to bind to acidic glycosaminoglycans.

Lawson,C.; Yung, B.; Barbour, A.; Zuckert, W.

2006-01-01T23:59:59.000Z

307

Protein and Energy Supplementation to Beef Cows Grazing  

E-Print Network (OSTI)

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

Castillo, Steven P.

308

Review: Protein knots and fold complexity: Some new twists  

Science Conference Proceedings (OSTI)

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

William R. Taylor

2007-06-01T23:59:59.000Z

309

Cold shock and regulation of surface protein trafficking convey sensitization  

E-Print Network (OSTI)

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

Arnold, Jonathan

310

Facilitating protein solubility by use of peptide extensions  

DOE Patents (OSTI)

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

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

2013-09-17T23:59:59.000Z

311

An expert system to predict protein thermostability using decision tree  

Science Conference Proceedings (OSTI)

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

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

2009-07-01T23:59:59.000Z

312

PERSPECTIVE Automated protein structure calculation from NMR data  

E-Print Network (OSTI)

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

Craven, Jeremy

313

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

Science Conference Proceedings (OSTI)

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

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

2003-01-01T23:59:59.000Z

314

The requirement of the DEAD-box protein DDX24 for the packaging of human immunodeficiency virus type 1 RNA  

Science Conference Proceedings (OSTI)

RNA helicases play important roles in RNA metabolism. Human immunodeficiency virus type 1 (HIV-1) does not carry its own RNA helicase, the virus thus needs to exploit cellular RNA helicases to promote the replication of its RNA at various steps such as transcription, folding and transport. In this study, we report that knockdown of a DEAD-box protein named DDX24 inhibits the packaging of HIV-1 RNA and thus diminishes viral infectivity. The decreased viral RNA packaging as a result of DDX24-knockdown is observed only in the context of the Rev/RRE (Rev response element)-dependent but not the CTE (constitutive transport element)-mediated nuclear export of viral RNA, which is explained by the specific interaction of DDX24 with the Rev protein. We propose that DDX24 acts at the early phase of HIV-1 RNA metabolism prior to nuclear export and the consequence of this action extends to the viral RNA packaging stage during virus assembly.

Ma Jing; Rong Liwei; Zhou Yongdong; Roy, Bibhuti Bushan; Lu, Jennifer; Abrahamyan, Levon; Mouland, Andrew J.; Pan Qinghua; Chen Liang, E-mail: chen.liang@mcgill.ca

2008-05-25T23:59:59.000Z

315

Zoomable map of poplar proteins | ornl.gov  

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

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

316

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

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

317

Proteins' Amazing Origami Powers: Insight for Potential Disease Treatments  

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

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

318

The functions of tryptophan residues in membrane proteins  

SciTech Connect

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

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

1994-08-01T23:59:59.000Z

319

A novel family of small proteins that affect plant development  

Science Conference Proceedings (OSTI)

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

John Charles Walker

2011-04-29T23:59:59.000Z

320

Temperature dependence of the radiation inactivation of proteins  

Science Conference Proceedings (OSTI)

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

Beauregard, G.; Potier, M.

1985-10-01T23:59:59.000Z

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Promoters and proteins from Clostridium thermocellum and uses thereof  

DOE Patents (OSTI)

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

Wu, J. H. David; Newcomb, Michael

2012-11-13T23:59:59.000Z

322

Automating the determination of 3D protein structure  

SciTech Connect

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

Rayl, K.D.

1993-12-31T23:59:59.000Z

323

A thermodynamic model for agglomeration of DNA-looping proteins  

E-Print Network (OSTI)

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

Sumedha; Martin Weigt

2008-01-09T23:59:59.000Z

324

Shedding Light on Protein Drug Interactions | Advanced Photon Source  

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

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

325

Electrorheological crystallization of proteins and other molecules  

DOE Patents (OSTI)

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

Craig, G.D.; Rupp, B.

1996-06-11T23:59:59.000Z

326

Electrorheological crystallization of proteins and other molecules  

DOE Patents (OSTI)

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

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

1996-01-01T23:59:59.000Z

327

Construction of artificial pigment-protein antennae  

DOE Green Energy (OSTI)

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

Sibbald, J.

1997-01-10T23:59:59.000Z

328

High-Resolution Design of a Protein Loop  

DOE Green Energy (OSTI)

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

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

2007-01-01T23:59:59.000Z

329

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

E-Print Network (OSTI)

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

Nicolas Meilhac; Nicolas Destainville

2011-06-07T23:59:59.000Z

330

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

E-Print Network (OSTI)

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

Schuler, Ben

331

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

Science Conference Proceedings (OSTI)

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

Andrs Maldonado; Francisco Vara; Antonio Sillero

2008-01-01T23:59:59.000Z

332

The determination of protonation states in proteins  

Science Conference Proceedings (OSTI)

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

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

2008-09-17T23:59:59.000Z

333

Lipid ion channels and the role of proteins  

E-Print Network (OSTI)

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

Lars D. Mosgaard; Thomas Heimburg

2013-07-11T23:59:59.000Z

334

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

E-Print Network (OSTI)

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

Aubin-Tam, Marie-Eve

2008-01-01T23:59:59.000Z

335

Methods and constructs for expression of foreign proteins in photosynthetic organisms  

DOE Patents (OSTI)

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

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

2002-01-01T23:59:59.000Z

336

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

E-Print Network (OSTI)

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

Huang, Austin V., 1980-

2009-01-01T23:59:59.000Z

337

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

Science Conference Proceedings (OSTI)

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

338

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

Science Conference Proceedings (OSTI)

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

339

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

E-Print Network (OSTI)

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

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

2013-02-11T23:59:59.000Z

340

Protein Puzzles and Scientific Solutions | Department of Energy  

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

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

How the Membrane Protein AmtB Transports Ammonia  

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

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

342

Robust, High-Throughput Analysis of Protein Structures  

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

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

343

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

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

344

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

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

345

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

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

346

Synthetic scaffolds and protein assemblies for engineering applications  

E-Print Network (OSTI)

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

Norville, Julie Erin, 1980-

2004-01-01T23:59:59.000Z

347

20 petaflops simulation of proteins suspensions in crowding conditions  

Science Conference Proceedings (OSTI)

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

Massimo Bernaschi, Mauro Bisson, Massimiliano Fatica, Simone Melchionna

2013-11-01T23:59:59.000Z

348

Protein Thermostability Calculations Using Alchemical Free Energy Simulations  

E-Print Network (OSTI)

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

de Groot, Bert

349

Insights into protein function from evolutionary and conformational dynamics  

E-Print Network (OSTI)

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

Bransford, Philip W

2011-01-01T23:59:59.000Z

350

Nanofluidic devices for rapid analysis of DNA and proteins  

E-Print Network (OSTI)

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

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

2007-01-01T23:59:59.000Z

351

Soy Protein ProductsChapter 7 Regulations Regarding Usage  

Science Conference Proceedings (OSTI)

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

352

Molecular Computations for the Stabilization of Therapeutic Proteins  

E-Print Network (OSTI)

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

Trout, Bernhardt L.

353

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

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

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

354

NMR structure of hypothetical protein MG354 from Mycoplasma genitalium  

E-Print Network (OSTI)

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

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

2005-01-01T23:59:59.000Z

355

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

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

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

356

Theoretical Study on Catalysis by Protein Enzymes and Ribozyme  

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

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

357

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

E-Print Network (OSTI)

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

Ko, Eunhwa

2012-05-01T23:59:59.000Z

358

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

E-Print Network (OSTI)

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

Hagopian, Jonathan Charles

2008-01-01T23:59:59.000Z

359

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

E-Print Network (OSTI)

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

Lucas, Craig

2007-01-01T23:59:59.000Z

360

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

E-Print Network (OSTI)

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

Grosvenor, Anita J.

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

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

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

362

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

E-Print Network (OSTI)

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

Giaquinto, Laura

2006-01-01T23:59:59.000Z

363

Structures for Three Membrane Transport Proteins Yield Functional Insights  

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

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

364

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

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

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

365

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

SciTech Connect

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

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

2013-10-01T23:59:59.000Z

366

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

E-Print Network (OSTI)

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

Hosur, Raghavendra

367

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

SciTech Connect

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

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

2010-01-01T23:59:59.000Z

368

Digestion of protein in the equine small and large intestines  

E-Print Network (OSTI)

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

Farley, Eleanor Baker

1995-01-01T23:59:59.000Z

369

From Protein Structure to Function: Ring Cycle for Dilating and  

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

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

370

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-Print Network (OSTI)

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

Michael Bachmann; Wolfhard Janke

2007-10-25T23:59:59.000Z

371

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

Science Conference Proceedings (OSTI)

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

Alena Shmygelska

2007-07-01T23:59:59.000Z

372

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

DOE Patents (OSTI)

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

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

2011-06-07T23:59:59.000Z

373

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

Science Conference Proceedings (OSTI)

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

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

2005-09-01T23:59:59.000Z

374

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

E-Print Network (OSTI)

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

Bissonnette, Sarah Ayano

2010-01-01T23:59:59.000Z

375

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

SciTech Connect

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

Agarwal, Pratul Kumar (Knoxville, TN)

2011-07-19T23:59:59.000Z

376

Crystal Structure of a Protein Kinase A Complex  

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

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

377

Translationally Controlled Tumor Protein Protects against DNA Damage in Low  

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

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

378

Scientists ratchet up understanding of cellular protein factory  

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

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

379

Crystal Structure of a Protein Kinase A Complex  

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

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

380

Large Scale Quantum-mechanical Calculations of Proteins, Nanomaterials and  

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

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

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Direct detection of x-rays for protein crystallography  

DOE Patents (OSTI)

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

Atac, Muzaffer; McKay, Timothy

1997-12-01T23:59:59.000Z

382

Order parameter prediction from molecular dynamics simulations in proteins  

E-Print Network (OSTI)

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

Perilla, Juan R

2011-01-01T23:59:59.000Z

383

Crystal Structure of a Protein Kinase A Complex  

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

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

384

Past MPSA Meetings, IAPSAP, International Association for Protein Structure  

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

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

385

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

E-Print Network (OSTI)

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

Liu, Yilin

2005-12-01T23:59:59.000Z

386

Directed transport as a mechanism for protein folding in vivo  

E-Print Network (OSTI)

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

Gonzalez-Candela, Ernesto

2009-01-01T23:59:59.000Z

387

Directed transport as a mechanism for protein folding in vivo  

E-Print Network (OSTI)

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

Ernesto Gonzalez-Candela; Victor Romero-Rochin

2009-09-23T23:59:59.000Z

388

Photoconversion of organic materials into single-cell protein  

DOE Patents (OSTI)

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

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

2001-01-01T23:59:59.000Z

389

Photoconversion of organic materials into single-cell protein  

DOE Patents (OSTI)

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

Weaver, P.F.

1991-12-31T23:59:59.000Z

390

High-Resolution Differential Ion Mobility Spectrometry of a Protein  

SciTech Connect

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

Shvartsburg, Alexandre A.; Smith, Richard D.

2013-01-17T23:59:59.000Z

391

Divinyl ether synthase gene and protein, and uses thereof  

DOE Patents (OSTI)

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

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

2011-09-13T23:59:59.000Z

392

From Protein Structure to Function: Ring Cycle for Dilating and  

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

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

393

From Protein Structure to Function: Ring Cycle for Dilating and  

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

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

394

Length control of microtubules by depolymerizing motor proteins  

E-Print Network (OSTI)

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

Bindu S. Govindan; Manoj Gopalakrishnan; Debashish Chowdhury

2007-09-24T23:59:59.000Z

395

Go-ing for the prediction of protein folding mechanisms  

E-Print Network (OSTI)

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

Takada, Shoji

396

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters  

E-Print Network (OSTI)

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

397

Probabilistic annotation of protein sequences based on functional classifications  

E-Print Network (OSTI)

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

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

2005-12-14T23:59:59.000Z

398

Soy Protein ProductsChapter 6 Uses in Food Systems  

Science Conference Proceedings (OSTI)

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

399

Protein structure prediction enhanced with evolutionary diversity : SPEED.  

SciTech Connect

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

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

2010-03-01T23:59:59.000Z

400

Contrasting HIV phylogenetic relationships and V3 loop protein similarities  

Science Conference Proceedings (OSTI)

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

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

1992-12-31T23:59:59.000Z

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Contrasting HIV phylogenetic relationships and V3 loop protein similarities  

Science Conference Proceedings (OSTI)

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

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

1992-01-01T23:59:59.000Z

402

Electrostatics Controls the Formation of Amyloid Superstructures in Protein Aggregation  

E-Print Network (OSTI)

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

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

2013-09-05T23:59:59.000Z

403

Preserving Genome Integrity: The DdrA Protein  

E-Print Network (OSTI)

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

Raines, Ronald T.

404

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops  

Science Conference Proceedings (OSTI)

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

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

2008-10-01T23:59:59.000Z

405

Methods of use of cellulose binding domain proteins  

DOE Patents (OSTI)

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

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

1997-09-23T23:59:59.000Z

406

Prolinks: A Database of Protein Functional Linkages Derived from Coevolution  

DOE Data Explorer (OSTI)

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

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

407

Protein kinase and phosphatase activities of thylakoid membranes  

DOE Green Energy (OSTI)

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

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

1987-01-01T23:59:59.000Z

408

Methods of use of cellulose binding domain proteins  

SciTech Connect

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

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

1997-01-01T23:59:59.000Z

409

RESEARCH ARTICLES Effective Energy Function for Proteins in Solution  

E-Print Network (OSTI)

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

Lazaridis, Themis

410

Structural alignment of largesize proteins via lagrangian relaxation  

Science Conference Proceedings (OSTI)

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

Alberto Caprara; Giuseppe Lancia

2002-04-01T23:59:59.000Z

411

A model for the self-organization of vesicular flux and protein distributions in the Golgi apparatus  

E-Print Network (OSTI)

The generation of two non-identical membrane compartments via exchange of vesicles is considered to require two types of vesicles specified by distinct cytosolic coats that selectively recruit cargo and two membrane-bound SNARE pairs that specify fusion and differ in their affinities for each type of vesicles. The mammalian Golgi complex is composed of 6-8 non-identical cisternae that undergo gradual maturation and replacement yet features only two SNARE pairs. We present a model that explains how the distinct composition of Golgi cisternae can be generated with two and even a single SNARE pair and one vesicle coat. A decay of active SNARE concentration in aging cisternae provides the seed for a cis > trans SNARE gradient that generates the predominantly retrograde vesicle flux which further enhances the gradient. This flux in turn yields the observed inhomogeneous steady-state distribution of Golgi enzymes, which compete with each other and with the SNAREs for incorporation into transport vesicles. We show analytically that the steady state SNARE concentration decays exponentially with the cisterna number. Numerical solutions of rate equations reproduce the experimentally observed SNARE gradients, overlapping enzyme peaks in cis, medial and trans and the reported change in vesicle nature across Golgi: Vesicles originating from younger cisternae mostly contain Golgi enzymes and SNAREs enriched in these cisternae and extensively recycle through the Endoplasmic Reticulum (ER), while the other subpopulation of vesicles contains Golgi proteins prevalent in older cisternae and hardly reaches the ER.

Iaroslav Ispolatov; Anne Muesch

2013-09-06T23:59:59.000Z

412

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

E-Print Network (OSTI)

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

Raychaudhuri, Soumya

413

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

E-Print Network (OSTI)

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

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

2004-01-01T23:59:59.000Z

414

The Collagen Protein Viewed at Unprecedented Detail | Advanced Photon  

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

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

415

Toluene 4-Monooxygenase and its Complex with Effector Protein T4moD  

Science Conference Proceedings (OSTI)

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

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

2012-10-16T23:59:59.000Z

416

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

E-Print Network (OSTI)

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

Ganim, Ziad

2010-01-01T23:59:59.000Z

417

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

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

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

418

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

E-Print Network (OSTI)

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

Schneider, Curtiss P. (Curtiss Paul)

2011-01-01T23:59:59.000Z

419

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

E-Print Network (OSTI)

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

Smith, Peter Thomas

2009-01-01T23:59:59.000Z

420

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

E-Print Network (OSTI)

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

Lin, Michael F.

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

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

E-Print Network (OSTI)

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

Zou, Peng, 1985-

2013-01-01T23:59:59.000Z

422

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

E-Print Network (OSTI)

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

Baaske, Philipp

423

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

E-Print Network (OSTI)

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

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

2012-01-01T23:59:59.000Z

424

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

E-Print Network (OSTI)

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

Chen, Mark M

2009-01-01T23:59:59.000Z

425

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

DOE Patents (OSTI)

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

Schabacker, Daniel S. (Naperville, IL)

2010-09-21T23:59:59.000Z

426

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

E-Print Network (OSTI)

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

Jones, Kevin C. (Kevin Chapman)

2012-01-01T23:59:59.000Z

427

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

E-Print Network (OSTI)

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

Richardson, David

428

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

E-Print Network (OSTI)

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

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

2011-01-01T23:59:59.000Z

429

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

E-Print Network (OSTI)

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

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

2013-01-01T23:59:59.000Z

430

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

E-Print Network (OSTI)

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

Keten, Sinan

2010-01-01T23:59:59.000Z

431

Cross-linking proteins with bimetallic tetracarboxylate compounds of transition metals  

DOE Patents (OSTI)

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

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

1991-03-05T23:59:59.000Z

432

Regulation of Nuclear Localization of Signaling Proteins by Cytokinin  

SciTech Connect

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

Kieber, J.J.

2010-05-01T23:59:59.000Z

433

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

Science Conference Proceedings (OSTI)

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

434

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

DOE Patents (OSTI)

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

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

1997-01-01T23:59:59.000Z

435

Cellulosic Fiber Composites Using Protein Hydrolysates and Methods of Making Same  

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

436

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

DOE Patents (OSTI)

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

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

1997-01-28T23:59:59.000Z

437

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

DOE Patents (OSTI)

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

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

1990-02-02T23:59:59.000Z

438

p38 mitogen-activated protein kinase plays a key role in regulating MAPKAPK2 expression  

Science Conference Proceedings (OSTI)

One of three major families of the mitogen-activated kinases (MAPK), p38 as well as JNK, has been shown to transduce extracellular stress stimuli into cellular responses by phospho-relay cascades. Among p38 families, p38{alpha} is a widely characterized isoform and the biological phenomena are explained by its kinase activity regulating functions of its downstream substrates. However, its specific contributions to each phenomenon are yet not fully elucidated. For better understanding of the role of MAPKs, especially p38{alpha}, we utilized newly established mouse fibroblast cell lines originated from a p38{alpha} null mouse, namely, a parental cell line without p38{alpha} gene locus, knockout of p38{alpha} (KOP), Zeosin-resistant (ZKOP), revertant of p38{alpha} (RKOP), and Exip revertant (EKOP). EKOP is smaller in size but grows faster than the others. Although comparable amounts of ERK and JNK are expressed in each cell line, ERK is highly phosphorylated in EKOP even in normal culture conditions. Serum stimulation after serum starvation led to ERK phosphorylation in RKOP and ZKOP, but not in EKOP as much. On the contrary, relative phosphorylation level of JNK to total JNK in response to UV was low in RKOP. And its phosphorylation as well as total JNK is slightly lower in EKOP. RKOP is less sensitive to UV irradiation as judged by the survival rate. Stress response upon UV or sorbitol stimuli, leading to mitogen activate protein kinase activated kinase 2 (MAPKAPK2) phosphorylation, was only observed in RKOP. Further experiments reveal that MAPKAPK2 expression is largely suppressed in ZKOP and EKOP. Its expression was recovered by re-introduction of p38{alpha}. The loss of MAPKAPK2 expression accompanied by the defect of p38{alpha} is confirmed in an embryonic extract prepared from p38{alpha} null mice. These data demonstrate that p38 signal pathway is regulated not only by phosphorylation but also by modulation of the expression of its component. Together, we have established cell lines that can be used in analyzing the functions of MAPKs, especially p38{alpha}, and show that p38 is indispensable for MAPKAPK2 expression.

Sudo, Tatsuhiko [Antibiotics Laboratory and Bioarchitect Research Group, DRI, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)]. E-mail: sudo@riken.jp; Kawai, Kayoko [Antibiotics Laboratory and Bioarchitect Research Group, DRI, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama, Saitama 338-8570 (Japan); Matsuzaki, Hiroshi [Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama, Saitama 338-8570 (Japan); Osada, Hiroyuki [Antibiotics Laboratory and Bioarchitect Research Group, DRI, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama, Saitama 338-8570 (Japan)

2005-11-18T23:59:59.000Z

439

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

E-Print Network (OSTI)

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

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

2006-05-31T23:59:59.000Z

440

Secrecy, deception and intelligence failure : explaining operational surprise in war  

E-Print Network (OSTI)

Operational surprise attacks are large-scale, theater-level intrawar attacks, which result from a country misestimating the capabilities and intentions of its enemies. This thesis analyzes how these massive surprise attacks ...

Waters, Lonn Augustine

2005-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Snow Crystal Habit Changes Explained by Layer Nucleation  

Science Conference Proceedings (OSTI)

Critical supersaturations have been measured for the vapor growth of ice crystals on both the basal and prism faces between ?16 and ?0.4C. The values are low: approximately constant at 0.4% for the prism face, less for the basal face between ?3...

Jon Nelson; Charles Knight

1998-04-01T23:59:59.000Z

442

Degree-Days - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

443

How much in the Universe can be explained by geometry?  

E-Print Network (OSTI)

The paper uses geometrical arguments to derive equations with relevance for cosmology; 5-dimensional spacetime is assumed because it has been shown in other works to provide a setting for significant unification of different areas of physics. Monogenic functions, which zero the vector derivative are shown to effectively model electrodynamics and relativistic dynamics if one allows for space curvature. Applying monogenic functions to flat space, the Hubble relation can be derived straightforwardly as a purely geometrical effect. Consideration of space curvature induced by mass density allows the derivation of flat rotation curves for galaxies without appealing for dark matter. Similarly, a small overall mass density in the Universe is shown to provide a possible explanation for recent supernovae observations, without the need for a cosmological constant.

Almeida, Jose B

2008-01-01T23:59:59.000Z

444

Explaining the causes and consequences of internationally monitored elections  

E-Print Network (OSTI)

to negotiate with Azerbaijan over the territorial conflictThe conflict with Azerbaijan over the Nagorno-Karabakhthe region, which is part of Azerbaijan but is composed of

Hyde, Susan Dayton

2006-01-01T23:59:59.000Z

445

Electricity in the United States - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Solar Thermal Power Plants; Solar Thermal Collectors; Solar Energy ... Run-of-river power plants are more dependent on river flows than hydro plants with reservoirs ...

446

Heating Oil - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Solar Thermal Power Plants; Solar Thermal Collectors; Solar Energy & the Environment. Secondary Sources. Electricity. The Science of Electricity. Magnets and Electricity;

447

Natural Gas Prices - Energy Explained, Your Guide To Understanding ...  

U.S. Energy Information Administration (EIA)

Solar Thermal Power Plants; Solar Thermal Collectors; Solar Energy & the Environment. Secondary Sources. Electricity. The Science of Electricity. Magnets and Electricity;

448

Home - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Most of the energy consumed in the United States comes from fossil fuels petroleum, coal, and natural gas, with crude oil-based petroleum products as the dominant ...

449

Forms of Energy - Energy Explained, Your Guide To Understanding ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

450

Ocean Thermal Energy Conversion - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

451

Secondary Energy Sources - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

452

Regional Gasoline Price Differences - Energy Explained, Your Guide ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

453

Physical Model Explaining the Periodic Pattern of the Chemical Elements  

E-Print Network (OSTI)

The fundamental organizing principle resulting in the periodic table is the nuclear charge. Arranging the chemical elements in an increasing atomic number order, a symmetry pattern known as the Periodic Table is detectable. The correlation between nuclear charge and the Periodic System of the Chemical Elements (PSCE) indicates that the symmetry emerges from the nucleus. Nuclear symmetry can only be developed if the positions of the nucleons are preserved. Thus the phase of the nucleus must be solid where the positions of the nucleons are preserved in a lattice. A lattice model, representing the protons and the neutrons by equal spheres and arranging them alternately in a face centered cubic structure forming a double tetrahedron, is able to reproduce all of the properties of the nucleus including the quantum numbers and the periodicity of the elements. Using this nuclear structure model, an attempt is made here to give a physical explanation for the periodicity of the chemical elements.

Jozsef Garai

2011-01-24T23:59:59.000Z

454

Home - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

455

Can the Podkletnov effect be explained by quantised inertia?  

E-Print Network (OSTI)

The Podkletnov effect is an unexplained loss of weight of between 0.05% and 0.07% detected in test masses suspended above supercooled levitating superconducting discs exposed to AC magnetic fields. A larger weight loss of up to 0.5% was seen over a disc spun at 5000 rpm. The effect has so far been observed in only one laboratory. Here, a new model for inertia that assumes that inertial mass is caused by Unruh radiation which is subject to a Hubble-scale Casimir effect (called MiHsC or quantised inertia) is applied to this anomaly. When the disc is exposed to the AC magnetic field it vibrates (accelerates), and MiHsC then predicts that the inertial mass of the nearby test mass increases, so that to conserve momentum it must accelerate upwards against freefall by 0.0029 m/s^2 or 0.03% of g, about half of the weight loss observed. With disc rotation, MiHsC predicts an additional weight loss, but 28 times smaller than the rotational effect observed. MiHsC suggests that the effect should increase with disc radius and rotation rate, the AC magnetic field strength (as observed), and also with increasing latitude and for lighter discs.

M. E. McCulloch

2011-08-15T23:59:59.000Z

456

Learned Factorization Models to Explain Variability in Natural Image Sequences  

E-Print Network (OSTI)

Recognition, pages 416422, 1999. [Fukushima, 1980] K.Fukushima. Neocognitron: A self-organizing neural networkwhich cortex achieves it. Fukushimas neocognitron, in which

Culpepper, Benjamin Jackson

2011-01-01T23:59:59.000Z

457

Explaining cohesion, fragmentation, and control in insurgent groups  

E-Print Network (OSTI)

The internal unity and discipline of insurgent groups helps us understand the military effectiveness of armed groups, patterns of violence against civilians, and the ability of insurgent organizations to negotiate and ...

Staniland, Paul Stephen

2010-01-01T23:59:59.000Z

458

The Golden Lariat : explaining American aid to Israel  

E-Print Network (OSTI)

An observational study was conducted to determine the most likely explanation of American support for Israel. Several extant hypotheses were considered, most particularly, and at greatest length, that of a pro-Israel ...

Kraus, Richard (Richard A.)

2009-01-01T23:59:59.000Z

459

Heating Oil Prices and Outlook - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

460

British Thermal Units (Btu) - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

Note: This page contains sample records for the topic "ring-shaped protein explains" 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

Oil Imports and Exports - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

462

Hydropower and the Environment - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

463

History of Gasoline - Energy Explained, Your Guide To ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

464

Delivery and Storage of Natural Gas - Energy Explained, Your Guide ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

465

Nuclear - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & the Environment; Biodiesel;

466

Fluid Mechanics Explains Cosmology, Dark Matter, Dark Energy, and Life  

E-Print Network (OSTI)

Observations of the interstellar medium by the Herschel, Planck etc. infrared satellites throw doubt on standard {\\Lambda}CDMHC cosmological processes to form gravitational structures. According to the Hydro-Gravitational-Dynamics (HGD) cosmology of Gibson (1996), and the quasar microlensing observations of Schild (1996), the dark matter of galaxies consists of Proto-Globular-star-Cluster (PGC) clumps of Earth-mass primordial gas planets in metastable equilibrium since PGCs began star production at 0.3 Myr by planet mergers. Dark energy and the accelerating expansion of the universe inferred from SuperNovae Ia are systematic dimming errors produced as frozen gas dark matter planets evaporate to form stars. Collisionless cold dark matter that clumps and hierarchically clusters does not exist. Clumps of PGCs began diffusion from the Milky Way Proto-Galaxy upon freezing at 14 Myr to give the Magellanic Clouds and the faint dwarf galaxies of the 10^22 m diameter baryonic dark matter Galaxy halo. The first stars persist as old globular star clusters (OGCs). Water oceans and the biological big bang occurred at 2-8 Myr. Life inevitably formed and evolved in the cosmological primordial organic soup provided by 10^80 big bang planets and their hot oceans as they gently merged to form larger binary planets and small binary stars.

Carl H. Gibson

2012-11-02T23:59:59.000Z

467

Explaining the International Environmental Cooperation of Democratic Countries  

E-Print Network (OSTI)

1996. Directory of International Organizations. Washington,by the Directory of International Organizations (Schraepler

Recchia, Steven

2001-01-01T23:59:59.000Z

468

Property:If Yes, Please Explain | Open Energy Information  

Open Energy Info (EERE)

M MHK TechnologiesOyster + Oyster 1 delivered in excess of 6000 operational hours offshore, as well as survival through winter seasons in line with its two-year design life....

469

Explaining Extreme Events of 2011 from a Climate Perspective  

Science Conference Proceedings (OSTI)

Attribution of extreme events shortly after their occurrence stretches the current state-of-theart of climate change assessment. To help foster the growth of this science, this article illustrates some approaches to answering questions about the role of ...

Thomas C. Peterson; Peter A. Stott; Stephanie Herring

2012-07-01T23:59:59.000Z

470

NIST Telescope Calibration May Help Explain Mystery of ...  

Science Conference Proceedings (OSTI)

... They will use this information to calibrate a much larger telescopethe Large Synoptic Survey Telescope, planned for construction in Chile. ...

2011-01-05T23:59:59.000Z

471

Can Fireball or Firecone Models Explain Gamma Ray Bursts?  

E-Print Network (OSTI)

The observed afterglows of gamma ray bursts, in particular that of GRB 970228 six months later, seem to rule out relativistic fireballs and relativistic firecones driven by merger or accretion induced collapse of compact stellar objects in galaxies as the origin of GRBs. GRBs can be produced by superluminal jets from such events.

Arnon Dar

1997-09-24T23:59:59.000Z

472

Explaining Corporate Environmental Performance: How Does Regulation Matter?  

E-Print Network (OSTI)

for example, we release chlorine every Tuesday. The statecation, and (4) the percent chlorine dioxide substitutionfor unbleached or totally chlorine-free paper, none of the

Kagan, Robert A.; Gunningham, Neil; Thornton, Dorothy

2005-01-01T23:59:59.000Z

473

Explaining the Great Strength and Extensibility of Spider Silk  

Science Conference Proceedings (OSTI)

Fabrication of a Cellulosic Nanocomposite Scaffold with Improved Supermolecular Structure as a Potential Cardiovascular Tissue-Engineered Graft .

474

The Failure of Black Holes to Explain Quasars  

E-Print Network (OSTI)

Abstract: The scientific consensus, (religious dogma), that quasars are powered by supermassive black holes or black holes of any size is mathematically and observationally false. The consensus that quasars are powered by super-massive black holes is wrong because black holes do not exist as proven mathematically by Mr. Stephen Crothers. [1][2] Since black holes do not exist they can never power anything. This means that an actual explanation of the real mechanisms that power quasars is wide open, and that discovery as to the actual nature of these objects is open to amateurs and scientists who have not been brainwashed to believe in black holes. The author agrees with Mr. Halton Arp concerning them, as they probably eject from the location of active galaxies to become galaxies themselves. [3] It also should be mentioned that redshift as a determinate of quasar distance has also been falsified observationally by Mr. Halton Arp, as quasars are vastly closer than what the Big Bang Religion allows for. [4][5] References

Jeffrey J Wolynski

2013-01-01T23:59:59.000Z

475

Home - Energy Explained, Your Guide To Understanding Energy ...  

Annual Energy Outlook 2012 (EIA)

Surcharges Diesel & the Environment Heating Oil Where Our Heating Oil Comes From Use of Heating Oil Prices and Outlook Factors Affecting Heating Oil Prices Propane Delivery and...

476

Home - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Offshore Oil and Gas; Use of Oil; Prices and Outlook; Oil and the Environment. ... wind, geothermal, and solar Secondary Energy Sources electricity and hydrogen

477

Magnetic Ties May Explain High-Temp Superconductors  

Science Conference Proceedings (OSTI)

... storing and distributing electric energy, superconducting digital routers for high-speed communications, and more efficient generators and motors. ...

2013-08-13T23:59:59.000Z

478

HOW FAR CAN MINIMAL MODELS EXPLAIN THE SOLAR CYCLE?  

Science Conference Proceedings (OSTI)

A physically consistent model of magnetic field generation by convection in a rotating spherical shell with a minimum of parameters is applied to the Sun. Despite its unrealistic features the model exhibits a number of properties resembling those observed on the Sun. The model suggests the importance of the non-axisymmetric m = 1 or m = 2 component of the magnetic field for the large-scale solar dynamo.

Simitev, R. D. [School of Mathematics and Statistics, University of Glasgow, Glasgow, G12 8QW (United Kingdom); Busse, F. H. [Institute of Physics, University of Bayreuth, 95440 Bayreuth (Germany)

2012-04-10T23:59:59.000Z

479

Explaining Corporate Environmental Performance: How Does Regulation Matter?  

E-Print Network (OSTI)

Environmental Performance: How Does Regulation Matter?How and to what extent does regulation matter in shapingof social control, and how does it interact with those

Kagan, Robert A.; Gunningham, Neil; Thornton, Dorothy

2005-01-01T23:59:59.000Z

480

Explaining civil-military relations in Southeast Asia  

E-Print Network (OSTI)

Civil-military relations describe the interactions and balance of power between the civilians and the military in a nation state. Due to the organizational apparatus and capacity for forcible coercion that the military ...

Kwok, Jia-Chuan

2010-01-01T23:59:59.000Z

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481

Refining Crude Oil - Energy Explained, Your Guide To Understanding ...  

U.S. Energy Information Administration (EIA)

The resulting liquids and vapors are discharged into distillation towers. ... horizontal vessels and tall, skinny towers that loom above other ...

482

Home - Energy Explained, Your Guide To Understanding Energy ...  

U.S. Energy Information Administration (EIA)

Landfill Gas and Biogas; Biomass & the Environment See also: Biofuels. Biofuels: Ethanol & Biodiesel. Ethanol; Use of Ethanol; Ethanol & ...

483

Spirits of Capitalism: Explaining Industrial Variation in South Asia  

E-Print Network (OSTI)

of Industrial Policy in Pakistan, 1947-1971. Workingand the Development of Pakistan, 1913-1948. Journal of2008). Crossed Swords: Pakistan, its Army and the Wars

Naseemullah, Adnan

2010-01-01T23:59:59.000Z

484

Factors Affecting Natural Gas Prices - Energy Explained, Your ...  

U.S. Energy Information Administration (EIA)

Nuclear Power Plants; The Nuclear Fuel Cycle; Where Our Uranium Comes From; ... as both a plant fuel and as a feedstock for many products such as ...

485

Two paths to nationhood : explaining the goals of ethnic rebellions  

E-Print Network (OSTI)

Contrary to widely held assumptions in the ethnic conflict literature, ethnic rebellions do not have to be separatist. Indeed, roughly one third of the largest ethnic rebellions since World War II have been attempts to ...

Metz, Daniel M., 1972-

2005-01-01T23:59:59.000Z

486

Diesel Fuel - Energy Explained, Your Guide To Understanding ...  

U.S. Energy Information Administration (EIA)

... and electric utilities have diesel generators for backup and emergency power supply. Most remote villages in Alaska use diesel generators for ...

487

What Explains Manhattan's Declining Share of Residential Construction?  

E-Print Network (OSTI)

permits issued in Manhattan, with project level detail:public housing projects permitted in Manhattan and on year.multitous projects the analogous Manhattan share plotted in

DAVIDOFF, THOMAS

2007-01-01T23:59:59.000Z

488

High-Order Membrane Complexes from Activated G-Protein Subunits  

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

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

489

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

E-Print Network (OSTI)

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

Brand, Paul H.

490

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

Science Conference Proceedings (OSTI)

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

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

2009-11-01T23:59:59.000Z

491

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

DOE Patents (OSTI)

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

Waldo, Geoffrey S. (Santa Fe, NM)

2007-09-18T23:59:59.000Z

492

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

E-Print Network (OSTI)

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

Dreyfuss, Gideon

493

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

E-Print Network (OSTI)

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

494

High-Order Membrane Complexes from Activated G-Protein Subunits  

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

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

495

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

E-Print Network (OSTI)

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

Pandey, Shree P.

496

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

SciTech Connect

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

Garrison, W. M.

1981-12-01T23:59:59.000Z

497

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

E-Print Network (OSTI)

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

McDonald, Karin Rainey

2012-01-01T23:59:59.000Z

498

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

SciTech Connect

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

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

2012-10-24T23:59:59.000Z

499

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

Science Conference Proceedings (OSTI)

Plasma levels of the acute-phase reactant, C-reactive protein (CRP), increase up to one thousand-fold as a result of trauma or inflammation. CRP binds to phosphorylcholine (PC) in a calcium-ion dependent manner. The structural homology between PC and the major phospholipid component of surfactant, dipalmitoyl phosphatidylcholine (DPPC), led to the present study in which we examined if CRP levels might be increased in patients with adult respiratory distress syndrome (ARDS), and subsequently interfere with surfactant function. Our results showed that CRP levels in the bronchoalveolar fluid (BALF) was increased in patients with ARDS (97.8 +/- 84.2 micrograms/mg total protei