Powered by Deep Web Technologies
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.


1

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

2

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

3

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

4

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

5

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

6

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

7

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

8

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

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

9

Rotary Firing in Ring-Shaped Protein Explains Unidirectionality  

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

backbone. The sixth subunit does not significantly contact the RNA and lies midway between the top and bottom steps of the staircase. The positional relationships...

10

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

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

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

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

Study of CMOS APS Responsivity Enhancement: Ring-Shaped Photodiode  

E-Print Network [OSTI]

Study of CMOS APS Responsivity Enhancement: Ring-Shaped Photodiode Tatiana Danov, Igor Shcherback obtained from various ring-shaped pixel photodiodes with different inner radius, implemented in a standard illumination. We show that the photodiodes with a small ring-opening exhibit better sensitivity in the blue

15

Ring-shaped luminescence pattern in biased quantum wells studied as a steady-state reaction front  

Science Journals Connector (OSTI)

Under certain conditions, focused laser excitation in semiconductor quantum well structures can lead to a charge separation and a circular reaction front, which is visible as a ring-shaped photoluminescence pattern. The diffusion-reaction equations governing the system are studied here with the aim of a detailed understanding of the steady state. The qualitative asymmetry in the sources for the two carriers is found to lead to unusual effects which dramatically affect the steady-state configuration. Analytic expressions are derived for carrier distributions and interface positions for a number of cases. These are compared with steady-state information obtained from simulations of the diffusion-reaction equations.

Masudul Haque

2006-06-07T23:59:59.000Z

16

Criteria of radio-frequency ring-shaped hollow cathode discharge using H{sub 2} and Ar gases for plasma processing  

SciTech Connect (OSTI)

In order to achieve high-density capacitively coupled plasma, a radio-frequency (RF) ring-shaped hollow cathode discharge has been developed as a candidate for processing plasma sources. The plasma density in the hollow cathode discharge reaches a high magnitude of 10{sup 10}-10{sup 11} cm{sup -3}. The RF ring-shaped hollow cathode discharge depends on the pressure and mass of the working gas. Criteria required for producing a RF ring-shaped hollow cathode discharge have been investigated for various gas pressures using H{sub 2} and Ar gases for high-density plasma production. The results reveal that the criteria for the occurrence of the hollow cathode effect are that the trench width should be approximately equal to the sum of the electron-neutral mean free paths and twice the sheath thickness of the RF powered electrode.

Ohtsu, Yasunori; Kawasaki, Yujiro [Department of Electrical and Electronic Engineering, Graduate School of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502 (Japan)

2013-01-21T23:59:59.000Z

17

Observation of radio frequency ring-shaped hollow cathode discharge plasma with MgO and Al electrodes for plasma processing  

SciTech Connect (OSTI)

Various high-density plasma sources have been proposed for plasma processing. Especially, the hollow cathode discharge is one of the powerful ones. In this work, radio-frequency (RF) driven ring-shaped hollow cathode discharges with high secondary-electron emission have been investigated, using an aluminum (Al) cathode, coated or not with magnesium oxide (MgO). The thickness of MgO thin film is approximately 200?nm. The RF discharge voltage for the coated cathode is almost the same as that for the uncoated one, in a wide range of Ar gas pressure, from 5.3 to 53.2?Pa. The results reveal that the plasma density has a peak at an Ar gas pressure of 10.6?Pa for both cathodes. The plasma density for the coated cathode is about 1.53 times higher than that for the uncoated one, at various gas pressures. To the contrary, the electron temperature for the coated cathode is lower than temperature obtained with the uncoated cathode, at various gas pressures. Radial profiles of electron saturation current, which is proportional to plasma flux, are also examined for a wide range of gas pressure. Radial profiles of electron temperature at various axial positions are almost uniform for both cathodes so that the diffusion process due to density gradient is dominant for plasma transport. The secondary electrons emitted from the coated cathode contribute to the improvement of the plasma flux radial profile obtained using the uncoated cathode.

Ohtsu, Yasunori, E-mail: ohtsuy@cc.saga-u.ac.jp; Matsumoto, Naoki [Department of Electrical and Electronic Engineering, Graduate School of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502 (Japan)

2014-05-15T23:59:59.000Z

18

Review: LAN Technologies Explained  

Science Journals Connector (OSTI)

...Book Review Review: LAN Technologies Explained Reviewed by Peter...Glamorgan University LAN Technologies Explained Philip Miller and...data to HTML, building an intranet, creating a single and multi-source...Networks Star rating ??? LAN Technologies Explained Philip Miller and......

Peter Hodson

2001-01-01T23:59:59.000Z

19

Protein Structure Suggests Role as Molecular Adapter  

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

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

20

Proteins  

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

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

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

Proteins  

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

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

22

Ocean currents help explain population genetic structure  

Science Journals Connector (OSTI)

...original work is properly cited. Ocean currents help explain population genetic...larval dispersal estimates based on ocean current observations, we demonstrate...Data-assimilated models of ocean currents for the study region were produced...

2010-01-01T23:59:59.000Z

23

The Subsumptive Constraints Account of why explaining "why?" helps learning  

E-Print Network [OSTI]

2010). Why does explaining help learning? Insight from anand development .. 8 1.3. Why does explaining why? helpof why explaining why? helps learning by Joseph Jay

Williams, Joseph Jay

2013-01-01T23:59:59.000Z

24

New Crystal Structures Lift Fog around Protein Folding  

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

New Crystal Structures Lift Fog around Protein Folding Print 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.

25

Grazing resistance allows bloom formation and may explain ...  

Science Journals Connector (OSTI)

Grazing resistance allows bloom formation and may explain invasion success of Gonyostomum semen. Karen Lebret, Mara Fernndez Fernndez, Camilla...

26

Power, policy and war : explaining the Iran-Iraq War.  

E-Print Network [OSTI]

??The failure of traditional analytical tools in successfully predicting the end of the Cold War has seen a series of competing methods seeking to explain (more)

Donovan, Jerome Denis

2008-01-01T23:59:59.000Z

27

Senescence Can Explain Microbial Persistence I. Klappera,b  

E-Print Network [OSTI]

@math.montana.edu. Running Title: Senescence Can Explain Microbial Persistence Contents Category: Theoretical Microbiology 1 been observed (Balaban et al., 2004; Bigger, 1944; Gilbert et al., 1990; Green- wood & O'Grady, 1970

Klapper, Isaac

28

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

29

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

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

30

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

31

Phosphor: Explaining Transitions in the User Interface Using Afterglow Effects  

E-Print Network [OSTI]

Phosphor: Explaining Transitions in the User Interface Using Afterglow Effects Patrick Baudisch, especially in situations where users did not need an explanation. We propose a different approach. Phosphor in retrospect. Manipulating a phosphor slider, for example, leaves an afterglow that illustrates how the knob

Hunt, Galen

32

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

33

Calorimetric glass transition explained by hierarchical dynamic facilitation  

E-Print Network [OSTI]

Calorimetric glass transition explained by hierarchical dynamic facilitation Aaron S. Keysa Contributed by David Chandler, February 11, 2013 (sent for review November 15, 2012) The glass transition different on cooling than on heating, and the response to melting a glass depends markedly on the cooling

Garrahan, Juan P.

34

Questions and Answers - How do you explain electrical resistance?  

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

35

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

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

36

Physics of Intrinsic Plasma Rotation Explained for the First Time  

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

37

Explaining investors' reaction to internet security breach using deterrence theory  

Science Journals Connector (OSTI)

This study uses the deterrence theory to explain investors' behaviour towards the announcement of internet security breaches in the public media. Using the event study methodology, we compute the abnormal returns over a three day window. We then use decision tree induction to investigate how firm type and time affect the likelihood that an attack would lead to abnormal returns. The results reveal that investors are more likely to react negatively to announcements involving internet firms. In addition, investors are more likely to react negatively to more recent attacks. We argue that managers, especially in Net firms, should develop effective mechanisms to address security breach since investors interpret a security breach as management's failure to deter computer abusers from violating organisational security policies and controls. From a theoretical perspective, we demonstrate that event study research can use theory to explain investor's behaviour towards announcement of events in the public media.

Francis Kofi Andoh-Baidoo

2013-01-01T23:59:59.000Z

38

Does the European Marriage Pattern Explain Economic Growth?  

E-Print Network [OSTI]

Does the European Marriage Pattern Explain Economic Growth? Tracy Dennison Sheilagh Ogilvie California Institute of Technology University of Cambridge Division of the Humanities and Social Sciences MC 101-40 Pasadena, CA... . Between the 1960s and the 1990s, scholars occasionally speculated about links between the EMP and economic growth (Landes 1969; Todd 1983; Laslett 1988; Solar 1995), but the vast bulk of research on the EMP was empirical, investigating its prevalence...

Dennison, Tracy; Ogilvie, Sheilagh

2014-08-29T23:59:59.000Z

39

Truth may not explain predictive success, but truthlikeness does  

Science Journals Connector (OSTI)

Abstract In a recent paper entitled Truth does not explain predictive success (Analysis, 2011), Carsten Held argues that the so-called No-Miracles Argument for scientific realism is easily refuted when the consequences of the underdetermination of theories by the evidence are taken into account. We contend that the No-Miracles Argument, when it is deployed within the context of sophisticated versions of realism, based on the notion of truthlikeness (or verisimilitude), survives Helds criticism unscathed.

Gustavo Cevolani; Luca Tambolo

2013-01-01T23:59:59.000Z

40

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

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

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

42

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

43

Mesoscale symmetries explain dynamical equivalence of food webs  

Science Journals Connector (OSTI)

A goal of complex system research is to identify the dynamical implications of network structure. While early results focused mainly on local or global structural properties, there is now growing interest in mesoscale structures that comprise more than one node but not the whole network. A central challenge is to discover under what conditions the occurrence of a specific mesoscale motif already allows conclusions on the dynamics of a network as a whole. In this paper, we investigate the dynamics of ecological food webs, complex heterogeneous networks of interacting populations. Generalizing the results of MacArthur and Snchez-Garca (2009 Phys. Rev. E 80 26117), we show that certain mesoscale symmetries imply the existence of localized dynamical modes. If these modes are unstable the occurrence of the corresponding mesoscale motif implies dynamical instability regardless of the structure of the embedding network. In contrast, if the mode is stable it means that the symmetry can be exploited to reduce the number of nodes in the model, without changing the dynamics of the system. This result explains a previously observed dynamical equivalence between food webs containing a different number of species.

Helge Aufderheide; Lars Rudolf; Thilo Gross

2012-01-01T23:59:59.000Z

44

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

45

Crystallography Explained  

Science Journals Connector (OSTI)

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

William Bassett

1993-06-25T23:59:59.000Z

46

GDI Explained  

Science Journals Connector (OSTI)

Some of you...may have previous experience programming in the graphics device interface (GDI) and want to know whats new...

Nick Symmonds

2002-01-01T23:59:59.000Z

47

From%laggard%to%leader:%% Explaining%offshore%wind%developments%in%  

E-Print Network [OSTI]

From%laggard%to%leader:%% Explaining%offshore%wind%developments%in% the%UK% Florian!laggard!to!leader:!Explaining! offshore!wind!developments!in!the!UK! Florian Kern1* , Adrian Smith1 , Chris Shaw1 , Rob Raven2 and Bram for publication in Energy Policy, 19 Feb 2014 Abstract Offshore wind technology has recently undergone rapid

Sussex, University of

48

EMSL - proteins  

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

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

49

Constraints on adaptation: explaining deviation from optimal sex ratio using artificial neural networks  

E-Print Network [OSTI]

Y Keywords: adaptation; artificial neural networks; evolutionary constraints; parasitoid; sex ratio by modelling information acquisition and processing using artificial neural networks (ANNs) evolving accordingConstraints on adaptation: explaining deviation from optimal sex ratio using artificial neural

West, Stuart

50

Company Summary Comment Example RPI NYS Walmart Rice 1 Line Pitch Explain your venture in 140  

E-Print Network [OSTI]

Company Summary Comment Example RPI NYS Walmart Rice 1 Line Pitch Explain your venture in 140 Members Advisors Previous Investors Elevator Pitch 60 second pitch. Do this at the end. Contact Name x x x

Linhardt, Robert J.

51

Three-dimensional space: locomotory style explains memory differences in rats and hummingbirds  

Science Journals Connector (OSTI)

...locomotory style explains memory differences in rats and hummingbirds I. Nuri Flores-Abreu 1 T. Andrew...In the cubic mazes in which we trained and tested rats and hummingbirds, rats moved more vertically than horizontally, whereas...

2014-01-01T23:59:59.000Z

52

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

53

Protein Structure  

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

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

54

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

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

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.

55

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

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

56

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

SciTech Connect (OSTI)

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

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

2011-12-31T23:59:59.000Z

57

Is the Donnan effect sufficient to explain swelling in brain tissue slices?  

Science Journals Connector (OSTI)

...effect sufficient to explain swelling in brain tissue slices? Georgina E. Lang 1 Peter...University of Glasgow, , Glasgow, UK Brain tissue swelling is a dangerous consequence...mechanical effects that drive swelling of brain tissue slices in an ionic solution bath...

2014-01-01T23:59:59.000Z

58

ULO Course Learning Outcome Assessment Method Pedagogy 08-Explain how an external change to a  

E-Print Network [OSTI]

as the addition of a solute to a material, or a phase change) affects the structure, proper- ties, processing and to a material (such as a change in tempera- ture, or an applied stress), and/or an internal change (suchENGR245 ULO Course Learning Outcome Assessment Method Pedagogy 08- Explain how an external change

Barrash, Warren

59

Tutorial Eight 1. Explain the addressing scheme used in Mobile IP?  

E-Print Network [OSTI]

COMP 347 Tutorial Eight Mobile IP 1. Explain the addressing scheme used in Mobile IP? 2. One simple method to implement mobility is to let the mobile host change its address as it goes to the new network with this approach? 3. What role does a mobile host, a home agent and a foreign agent play in mobile IP protocol? 4

Hamey, Len

60

ACARYOCHLORIS EXPLAINING THE RIDDLE OF CHLOROPHYLL D IN RED ALGAE AND EXPANDING PAR FOR OXYGENIC PHOTOSYNTHESIS  

E-Print Network [OSTI]

ACARYOCHLORIS ­ EXPLAINING THE RIDDLE OF CHLOROPHYLL D IN RED ALGAE AND EXPANDING PAR FOR OXYGENIC strain is shown to live epi- phytically on the red alga Gelidium caulacantheum, which itself is harvested by the red alga. Availability of far red light, however, is relatively unaffected by DOM or red

Oregon, University of

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

Climate and Soil Type Together Explain the Distribution of Microendemic Species in a Biodiversity Hotspot  

E-Print Network [OSTI]

Climate and Soil Type Together Explain the Distribution of Microendemic Species in a Biodiversity Biodiversite´ et d'Ecologie terrestre et marine, Aix-Marseille Universite´/ CNRS/IRD/UAPV, UMR 237 IRD, Centre in a Biodiversity Hotspot. PLoS ONE 8(12): e80811. doi:10.1371/journal.pone.0080811 Editor: Valerio Ketmaier

62

Total 100pts 1.Please use brief statements to explain the following terms in engineering  

E-Print Network [OSTI]

is loaded and supported as shown in the following.Determine a. The reactions at supports4 B, and C. (6%) bTotal 100pts 1.Please use brief statements to explain the following terms in engineering mechanics is simply supported and carries a uniformly distributed load of 5 kN/m over the fill length of the beam

Huang, Haimei

63

View a Grant This user guide will explain how to a Grant record in IRMA  

E-Print Network [OSTI]

View a Grant This user guide will explain how to a Grant record in IRMA LOGGING ON TO IRMA: 1. Open. Click "Login" to log into IRMA VIEW A GRANT RECORD: 1) After logging on, you should see something like;Printed: 16 November 2012 2/3 3) Click on the "List Existing Records" under the Contracts/ Grants icon

64

Application of the Second Law of Thermodynamics To Explain the Working of Toys  

Science Journals Connector (OSTI)

This teaching activity consists of challenging students to explain the working principle behind three scientific toys: a drinking bird, a radiometer, and a Stirling engine. ... The toys used for this purpose were a drinking bird, a radiometer, and a Stirling engine. ... Stirling Engine ...

Erick Castelln

2014-04-11T23:59:59.000Z

65

Features of glacial valley profiles simply explained Robert S. Anderson,1  

E-Print Network [OSTI]

. [1] Glacial occupation of alpine valleys results in a distinct signature in the long-valley profile quantitatively the long timescale pattern of valley erosion while acknowledg- ing both the variability of climateFeatures of glacial valley profiles simply explained Robert S. Anderson,1 Peter Molnar,2 and Mark A

Mojzsis, Stephen J.

66

Explaining Recent Connecticut Bank Failures: Did Managerial Inefficiency Play a Role  

E-Print Network [OSTI]

Explaining Recent Connecticut Bank Failures: Did Managerial Inefficiency Play a Role Stephen M. Miller The University of Connecticut and Athanasios G. Noulas* University of Macedonia August 1998 important questions about bank performance. We develop a failure-prediction model for Connecticut banks

Ahmad, Sajjad

67

Chapter 5 - The boundaries of instance-based learning theory for explaining decisions from experience  

Science Journals Connector (OSTI)

Abstract Most demonstrations of how people make decisions in risky situations rely on decisions from description, where outcomes and their probabilities are explicitly stated. But recently, more attention has been given to decisions from experience where people discover these outcomes and probabilities through exploration. More importantly, risky behavior depends on how decisions are made (from description or experience), and although prospect theory explains decisions from description, a comprehensive model of decisions from experience is yet to be found. Instance-based learning theory (IBLT) explains how decisions are made from experience through interactions with dynamic environments (Gonzalez et al., 2003). The theory has shown robust explanations of behavior across multiple tasks and contexts, but it is becoming unclear what the theory is able to explain and what it does not. The goal of this chapter is to start addressing this problem. I will introduce IBLT and a recent cognitive model based on this theory: the IBL model of repeated binary choice; then I will discuss the phenomena that the IBL model explains and those that the model does not. The argument is for the theory's robustness but also for clarity in terms of concrete effects that the theory can or cannot account for.

Cleotilde Gonzalez

2013-01-01T23:59:59.000Z

68

Structural parameters The analytical model proposed here can explain high fracture  

E-Print Network [OSTI]

Structural parameters · The analytical model proposed here can explain high fracture toughness, P.J., et al., Engineering Fracture Mechanics, 2007. 74: p. 19281941. 4. Ritchie, R.O., et al Tensile strength Fracture toughness Composite properties E max S )~( ~ aJ III. Fracture toughness

Barthelat, Francois

69

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.

70

Au#sm Explained: Synergis#c Poisoning from Aluminum and Glyphosate  

E-Print Network [OSTI]

Au#sm Explained: Synergis#c Poisoning from Aluminum and Glyphosate Stephanie #12;Outline · Glyphosate and AuOsm · Aluminum, glyphosate, sulfate and the pineal gland ­ Sunlight Deficiency ­ SynergisOc Effects of Glyphosate and Aluminum

Seneff, Stephanie

71

Can selection on nest size from nest predation explain the latitudinal gradient in clutch size?  

E-Print Network [OSTI]

Can selection on nest size from nest predation explain the latitudinal gradient in clutch size. 2. The nest size hypothesis posits that higher nest predation in the tropics favours selection for smaller nests and thereby constrains clutch size by shrinking available space for eggs and/or nestlings

Martin, Thomas E.

72

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

E-Print Network [OSTI]

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

J. C. Phillips

2010-11-18T23:59:59.000Z

73

Can Nutrition Explain the Pattern of International Epidemiology of Hormone-dependent Cancers?  

Science Journals Connector (OSTI)

...breast cancer and per capita consumption of total fat, animal protein...would obtain running a diesel engine on high-octane airplane fuel. The onset and frequency...Mortality Data and per capita Food Consumption. Brit. J. Cancer, 29...

John W. Berg

1975-11-01T23:59:59.000Z

74

Can Nutrition Explain the Pattern of International Epidemiology of Hormone-dependent Cancers?  

Science Journals Connector (OSTI)

...breast cancer and per capita consumption of total fat, animal protein...one would obtain running a diesel engine on high-octane airplane fuel. The onset and frequency...Data and per capita Food Consumption. Brit. J. Cancer, 29...

John W. Berg

1975-11-01T23:59:59.000Z

75

Manipulating and Visualizing Proteins  

E-Print Network [OSTI]

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

Simon, Horst D.

2003-01-01T23:59:59.000Z

76

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

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

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

77

Explaining the convenience yield in the WTI crude oil market using realized volatility and jumps  

Science Journals Connector (OSTI)

Abstract In this paper, we first provide an empirical evidence of the existence of intraday jumps in the crude oil price series. We then show that these jumps, in conjunction with realized volatility measures, are important in modeling the convenience yield over the 20012010 period. Our empirical results indicate that lagged jump mean only explains around 16% of the weekly convenience yield. Our best specification, including variation in inventories, 8-week realized variance and the 250-day jump mean is able to explain around 61% of the weekly convenience yield. Importantly, our results are not driven by the simultaneous determination of the various variables at work as we only use lagged variables in all regressions.

Benot Svi

2015-01-01T23:59:59.000Z

78

How radiation and its effect were explained?: Scientific communication after the Fukushima Daiichi nuclear disaster  

Science Journals Connector (OSTI)

In this paper we examine eight popular books published immediately after the Fukushima Daiichi nuclear disaster. Our aim is to clarify the characteristics, problems in the scientific communication related to the health effects of radiation. The eight books are compared from the aspects of: 1) how units such as Bq, Gy and Sv are defined; 2) how the dose limits are explained; 3) how deterministic and stochastic effects of radiation are differentiated; 4) how LNT model is explained and evaluated; 5) how the fact that we evolved in the midst of natural background radiation is treated. The main finding of our survey is that although the authors of the examined texts start from the same 'scientific facts', in trying to make these facts easily understandable, they adopt different rhetorical strategies and eventually they end up delivering quite different and conflicting messages to the people.

Kazuhisa Todayama; Kaori Karasawa

2013-01-01T23:59:59.000Z

79

Predicting protein folding pathways  

Science Journals Connector (OSTI)

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

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

2004-08-01T23:59:59.000Z

80

Discover protein sequence signatures from protein-protein interaction data  

E-Print Network [OSTI]

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

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

2005-11-23T23:59:59.000Z

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

Conformational Changes in the Hepatitis B Virus Core Protein Are Consistent with a Role for Allostery in Virus Assembly  

Science Journals Connector (OSTI)

...B virus (HBV) core protein dimer, which can spontaneously...differences between core protein dimer and capsid conformations...is more accurately an ensemble of conformations. Simulations...would explain how capsid proteins avoid packaging the...which appears to be disordered based on image reconstructions...

Charles Packianathan; Sarah P. Katen; Charles E. Dann III; Adam Zlotnick

2009-11-25T23:59:59.000Z

82

Shotgun protein sequencing.  

SciTech Connect (OSTI)

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

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

2009-06-01T23:59:59.000Z

83

Anticipation in the Rodent Head Direction System Can Be Explained by an Interaction of Head Movements and Vestibular Firing Properties  

E-Print Network [OSTI]

Anticipation in the Rodent Head Direction System Can Be Explained by an Interaction of Head Rossum MC. Anticipation in the rodent head direction system can be explained by an interaction of head, 2007; doi:10.1152/jn.00233.2007. The rodent head-direction (HD) system, which codes for the animal

van Rossum, Mark

84

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

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

85

Diatom Genome Helps Explain Their Great Diversity and Success in Trapping  

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

86

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

87

EXPLAINING THE Sr AND Ba SCATTER IN EXTREMELY METAL-POOR STARS  

SciTech Connect (OSTI)

Compilations of abundances of strontium and barium in extremely metal-poor stars show that an apparent cutoff is observed for [Sr/Ba] at [Fe/H] < -3.6 and large fluctuations for [Fe/H] > -3.6 with a clear upper bound depending on metallicity. We study the factors that place upper limits on the logarithmic ratio [Sr/Ba]. A model is developed in which the collapses of type II supernovae are found to reproduce many of the features seen in the data. This model is consistent with galactic chemical evolution constraints of light-element enrichment in metal-poor stars. Effects of turbulence in an explosive site have also been simulated, and are found to be important in explaining the large scatter observed in the [Sr/Ba] data.

Aoki, W.; Suda, T.; Boyd, R. N.; Kajino, T.; Famiano, M. A., E-mail: aoki.wako@nao.ac.jp, E-mail: takuma.suda@nao.ac.jp, E-mail: richard11boyde@comcast.net, E-mail: kajino@nao.ac.jp, E-mail: michael.famiano@wmich.edu [National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo 181-8588 (Japan)

2013-03-20T23:59:59.000Z

88

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

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

89

Natively Disordered Proteins  

Science Journals Connector (OSTI)

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

Dr Pedro Romero; Zoran Obradovic; A. Keith Dunker

2004-06-01T23:59:59.000Z

90

Function of proteins  

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

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

91

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

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

92

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

SciTech Connect (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

93

Approximate Mirror Symmetry in Heliospheric Plasma Flow Explains VOYAGER 2 Observations  

E-Print Network [OSTI]

The Sun and the undisturbed interstellar magnetic field and plasma velocity vectors (Bis,Vis) define a mirror symmetry plane of the flow at large heliospheric distances. We show that for the Bis direction defined by IBEX Ribbon center, the radial direction of Voyager 2 over the last decade, and the (thermal proton) plasma velocity measured by the spacecraft since 2010.5, are almost parallel to the (Bis,Vis)-plane, which coincides in practice with the Hydrogen Deflection Plane. These facts can be simply explained if approximate mirror symmetry is also maintained on the inner side of the heliopause. Such approximate symmetry is possible since the solar wind ram pressure is almost spherically symmetric and the plasma beta value in the inner heliosheath is high. In the proposed symmetry, the plasma flow speed measured by Voyager 2 in the inner heliosheath is expected to rotate more in the transverse than in the polar direction (explanation alternative to McComas & Schwadron (2014)), in evident agreement with ...

Grygorczuk, Jolanta; Grzedzielski, Stan

2015-01-01T23:59:59.000Z

94

Can photo-ionization explain the decreasing fraction of X-ray obscured AGN with luminosity?  

E-Print Network [OSTI]

Chandra and XMM surveys show that the fraction of obscured AGN decreases rapidly with increasing luminosity. Although this is usually explained by assuming that the covering factor of the central engine is much smaller at luminous QSOs, the exact origin of this effect remains unknown. We perform toy simulations to test whether photo-ionisation of the obscuring screen in the presence of a strong radiation field can reproduce this effect. In particular, we create X-ray spectral simulations using a warm absorber model assuming a range of input column densities and ionization parameters. We fit instead the simulated spectra with a simple cold absorption power-law model that is the standard practice in X-ray surveys. We find that the fraction of absorbed AGN should fall with luminosity as $L^{-0.16\\pm0.03}$ in rough agreement with the observations. Furthermore, this apparent decrease in the obscuring material is consistent with the dependence of the FeK$\\alpha$ narrow-line equivalent width on luminosity, ie. the X-ray Baldwin effect.

A. Akylas; I. Georgantopoulos

2008-01-29T23:59:59.000Z

95

CAN DRY MERGING EXPLAIN THE SIZE EVOLUTION OF EARLY-TYPE GALAXIES?  

SciTech Connect (OSTI)

The characteristic size of early-type galaxies (ETGs) of given stellar mass is observed to increase significantly with cosmic time, from redshift z approx> 2 to the present. A popular explanation for this size evolution is that ETGs grow through dissipationless ('dry') mergers, thus becoming less compact. Combining N-body simulations with up-to-date scaling relations of local ETGs, we show that such an explanation is problematic, because dry mergers do not decrease the galaxy stellar-mass surface density enough to explain the observed size evolution, and also introduce substantial scatter in the scaling relations. Based on our set of simulations, we estimate that major and minor dry mergers increase half-light radius and projected velocity dispersion with stellar mass as R{sub e} propor to M{sup 1.09+}-{sup 0.29}{sub *} and sigma{sub e2} propor to M{sup 0.07+}-{sup 0.11}{sub *}, respectively. This implies that: (1) if the high-z ETGs are indeed as dense as estimated, they cannot evolve into present-day ETGs via dry mergers; (2) present-day ETGs cannot have assembled more than approx45% of their stellar mass via dry mergers. Alternatively, dry mergers could be reconciled with the observations if there was extreme fine tuning between merger history and galaxy properties, at variance with our assumptions. Full cosmological simulations will be needed to evaluate whether this fine-tuned solution is acceptable.

Nipoti, C. [Dipartimento di Astronomia, Universita di Bologna, via Ranzani 1, I-40127 Bologna (Italy); Treu, T.; Auger, M. W. [Department of Physics, University of California, Santa Barbara, CA 93106-9530 (United States); Bolton, A. S., E-mail: carlo.nipoti@unibo.i [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Dr., Honolulu, HI 96822 (United States)

2009-11-20T23:59:59.000Z

96

The HPr Proteins from the Thermophile Bacillus stearothermophilus Can Form Domain-swapped Dimers  

SciTech Connect (OSTI)

The study of proteins from extremophilic organisms continues to generate interest in the field of protein folding because paradigms explaining the enhanced stability of these proteins still elude us and such studies have the potential to further our knowledge of the forces stabilizing proteins. We have undertaken such a study with our model protein HPr from a mesophile, Bacillus subtilis, and a thermophile, Bacillus stearothermophilus. We report here the high-resolution structures of the wild-type HPr protein from the thermophile and a variant, F29W. The variant proved to crystallize in two forms: a monomeric form with a structure very similar to the wild-type protein as well as a domain-swapped dimer. Interestingly, the structure of the domain-swapped dimer for HPr is very different from that observed for a homologous protein, Crh, from B. subtilis. The existence of a domain-swapped dimer has implications for amyloid formation and is consistent with recent results showing that the HPr proteins can form amyloid fibrils. We also characterized the conformational stability of the thermophilic HPr proteins using thermal and solvent denaturation methods and have used the high-resolution structures in an attempt to explain the differences in stability between the different HPr proteins. Finally, we present a detailed analysis of the solution properties of the HPr proteins using a variety of biochemical and biophysical methods.

Sridharan, Sudharsan; Razvi, Abbas; Scholtz, J. Martin; Sacchettini, James C. (TAM)

2010-07-20T23:59:59.000Z

97

Enriched Protein-Protein Interactions from Biomedical Text  

E-Print Network [OSTI]

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

Edinburgh, University of

98

Protein-protein interaction Functional Genomics  

E-Print Network [OSTI]

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

Spang, Rainer

99

Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

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

Vladimir N. Uversky

2014-01-01T23:59:59.000Z

100

Optimization Approaches to Protein Folding.  

E-Print Network [OSTI]

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

Yoon, Hyun-suk

2006-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "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

Electrostatics in intrinsically disordered proteins.  

E-Print Network [OSTI]

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

Wong, Eric Tsz Chung

2012-01-01T23:59:59.000Z

102

Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

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

V.N. Uversky

2013-01-01T23:59:59.000Z

103

Simulations of Protein Folding  

E-Print Network [OSTI]

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

Michael Cahill; Mark Fleharty; Kevin Cahill

1999-09-17T23:59:59.000Z

104

Using Superfolder Green Fluorescent Protein for Periplasmic Protein Localization Studies  

Science Journals Connector (OSTI)

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

Thuy Dinh; Thomas G. Bernhardt

2011-07-15T23:59:59.000Z

105

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

E-Print Network [OSTI]

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

Jager, M; Michalet, X; Weiss, Shimon

2005-01-01T23:59:59.000Z

106

Quantum Computing The fundamental goal of Science is to explain/predict natural phenomena using simple models. For example, a  

E-Print Network [OSTI]

Chapter 1 Quantum Computing The fundamental goal of Science is to explain/predict natural phenomena involve O(n) parameters, and not, say#5 n ). This requirement seems so natural and obvious that it is hardly discussed. On the other hand, the behaviour of nature at microscopic levels seems to defy

Ranade, Abhiram G.

107

Psychology is a science that seeks to understand and explain thoughts, emotions and behavior. There are many  

E-Print Network [OSTI]

Psychology is a science that seeks to understand and explain thoughts, emotions and behavior. There are many specialties within the field of psychology and there are two different general approaches. Some individuals in psychology do experiments and theorize, while others focus on applying theory to real

Saldin, Dilano

108

The unusual gamma-ray burst GRB 101225A explained as a minor body falling onto a neutron star  

Science Journals Connector (OSTI)

... onto neutron stars in our Galaxy. Here we report that the peculiarities of the Christmas gamma-ray burst (GRB 101225A) can be explained by a tidal disruption event ... long-lasting counterpart to the GRB. Strong variability is observed in the early X-ray light curve. The optical counterpart, which was detected in all of the UltravioletOptical Telescope ...

S. Campana; G. Lodato; P. DAvanzo; N. Panagia; E. M. Rossi; M. Della Valle; G. Tagliaferri; L. A. Antonelli; S. Covino; G. Ghirlanda; G. Ghisellini; A. Melandri; E. Pian; R. Salvaterra; G. Cusumano; V. DElia; D. Fugazza; E. Palazzi; B. Sbarufatti; S. D.Vergani

2011-11-30T23:59:59.000Z

109

A fluid approach to HIV A readable anthropological account of social networks in South Africa and Uganda explains differences in  

E-Print Network [OSTI]

and Uganda explains differences in the spread of sexually transmitted diseases in those countries, finds, but it was a "ritualistic act of cleansing and strengthening", says Thornton. Uganda's HIV story offers a more pleasant in its fight against the virus. Uganda reduced HIV prevalence by two- thirds during the 1990s. Causes

Cai, Long

110

Hydrogen Fuel Cell Problems 1) Explain why the hydrogen fuel cell vehicle is not as efficient as the reported "tank  

E-Print Network [OSTI]

Hydrogen Fuel Cell Problems 1) Explain why the hydrogen fuel cell vehicle is not as efficient as the reported "tank to wheel" efficiencies would suggest. Hydrogen must be produced, stored, and transported to heat and leaking of hydrogen in the atmosphere. Additionally it takes power to produce hydrogen

Bowen, James D.

111

Seafood proteins and preparation of protein concentrates  

Science Journals Connector (OSTI)

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

F. Shahidi

1994-01-01T23:59:59.000Z

112

Protein kinesis: The dynamics of protein trafficking and stability  

SciTech Connect (OSTI)

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

NONE

1995-12-31T23:59:59.000Z

113

Protein folding tames chaos  

E-Print Network [OSTI]

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

Xia, Kelin

2013-01-01T23:59:59.000Z

114

Inferring the Rate-Length Law of Protein Folding  

E-Print Network [OSTI]

We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. We demonstrate that chain length is a dominant factor determining folding times, and that the unambiguous determination of the way chain length corre- lates with folding times could provide key mechanistic insight into the folding process. Four specific proposed laws (power law, exponential, and two stretched exponentials) are tested against one an- other, and it is found that the power law best explains the data. At the same time, the fit power law results in rates that are very fast, nearly unreasonably so in a biological context. We show that any of the proposed forms are viable, conclude that more data is necessary to unequivocally infer the rate-length law, and that such data could be obtained through a small number of protein folding experiments on large protein domains.

Lane, Thomas J

2013-01-01T23:59:59.000Z

115

Protein folding and heteropolymers  

E-Print Network [OSTI]

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

T. Garel; H. Orland; E. Pitard

1997-06-12T23:59:59.000Z

116

White Means Never Having to Say You're Sorry The Racial Project in Explaining Mass Shootings  

E-Print Network [OSTI]

WHITE MEANS NEVER HAVING TO SAY YOURE SORRY THE RACIAL PROJECT IN EXPLAINING MASS SHOOTINGS WILLIAM MINGUS University of Illinois, Chicago BRADLEY ZOPF... later, on February 14, 2008, another man entered Cole Hall at Northern Illinois University (NIU) in 'H.DOE#15;#3;,OOLQRLV#17;#3;#3;$UPHG#3;ZLWK#3;D#3;VKRWJXQ#3;DQG#3;WKUHH#3;KDQGJXQV#15;#3;KH#3; walked onto a stage at the...

Mingus, William; Zopf, Bradley

2010-01-01T23:59:59.000Z

117

Proteins at interfaces.  

E-Print Network [OSTI]

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

Evers, Florian

2010-01-01T23:59:59.000Z

118

Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments  

E-Print Network [OSTI]

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

Haspel, Nurit

119

Biophysics of protein evolution and evolutionary protein biophysics  

Science Journals Connector (OSTI)

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

2014-01-01T23:59:59.000Z

120

Wavelength and Resolution Explained  

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

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

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

122

Millennium Bridge wobble explained  

Science Journals Connector (OSTI)

... opened in June 2000, but swiftly closed again because it started to wobble disconcertingly when pedestrians tried to cross it. The blame was initially placed on a human tendency to ... findings form the basis of a formula that Arup now uses to predict how many pedestrians should be allowed on a bridge. ...

Katharine Sanderson

2008-12-17T23:59:59.000Z

123

A hypothesis of inductive drive to explain the sawtooth measurements of tokamak experiment for technology oriented research (TEXTOR)  

SciTech Connect (OSTI)

A hypothesis, based on the current density profile determined from the principle of minimum dissipation of magnetic energy, is applied to explain the measurement of q(0) and current variation in a sawtooth cycle in tokomak experiment for technology oriented research (TEXTOR) [Plasma Physics and Controlled Nuclear Fusion Research (IAEA, Vienna, 1985), Vol. I, p. 193]. A sawtooth oscillation is triggered when the on-axis current density in a configuration with m=0 and n=0 symmetry is driven inductively to a limit.

Chu, T. K. [Plasma Physics Laboratory, Princeton University, P. O. Box 451, Princeton, New Jersey 08543 (United States)

2006-07-15T23:59:59.000Z

124

Power Law Size-Distributed Heterogeneity Explains Colloid Retention on Soda Lime Glass in the Presence of Energy Barriers  

Science Journals Connector (OSTI)

Power Law Size-Distributed Heterogeneity Explains Colloid Retention on Soda Lime Glass in the Presence of Energy Barriers ... This is shown in Figure 1 under the condition of 80 nm heterodomains and 6 mM IS, where the ZOIs and the corresponding colloidcollector interaction force profiles as a function of minimum separation distance (H) are shown for the three colloid sizes examined in this study (blue = 0.25 ?m, green = 1.1 ?m, red = 1.95 ?m). ... Such work will determine whether representing retention via discrete heterogeneity yields a distinct but logical set of heterodomain representations among mineral surfaces predominant in groundwater aquifers. ...

Eddy Pazmino; Jacob Trauscht; Brittany Dame; William P. Johnson

2014-04-28T23:59:59.000Z

125

Explaining the CMS eejj Excess With R?parity Violating Supersymmetry and Implications for Neutrinoless Double Beta Decay  

E-Print Network [OSTI]

IPPP/14/78, DCPT/14/156 Explaining the CMS eejj Excess With R?parity Violating Supersymmetry and Implications for Neutrinoless Double Beta Decay Ben Allanach,1 Sanjoy Biswas,2 Subhadeep Mondal,3 and Manimala Mitra4 1DAMTP, CMS, Wilberforce Road... production, followed by the three body decays of neutralino and chargino via R-parity violating coupling. These fit the excess for slepton and sneutrino masses around 2 TeV. This scenario can further be tested in neutrinoless double beta decay experiment (0...

Allanach, Ben; Biswas, Sanjoy; Mondal, Subhadeep; Mitra, Manimala

2015-01-01T23:59:59.000Z

126

Dark matter conversion as a source of boost factor for explaining the cosmic ray positron and electron excesses  

E-Print Network [OSTI]

In interacting multi-component dark matter (DM) models, if the DM components are nearly degenerate in mass and the interactions between them are strong enough, the relatively heavy DM components can be converted into lighter ones at late time after the thermal decoupling. Consequently, the relic density of the lightest DM component can be considerably enhanced at late time. This may contribute to an alternative source of boost factor required to explain the positron and electron excesses reported by the recent DM indirect search experiments such as PAMELA, Fermi-LAT and HESS etc..

Ze-Peng Liu; Yue-Liang Wu; Yu-Feng Zhou

2011-12-17T23:59:59.000Z

127

Structural Plasticity Underpins Promiscuous Binding of the Prosurvival Protein A1  

SciTech Connect (OSTI)

Apoptotic pathways are regulated by protein-protein interactions. Interaction of the BH3 domains of proapoptotic Bcl-2 family proteins with the hydrophobic groove of prosurvival proteins is critical. Whereas some BH3 domains bind in a promiscuous manner, others exhibit considerable selectivity and the sequence characteristics that distinguish these activities are unclear. In this study, crystal structures of complexes between the prosurvival protein A1 and the BH3 domains from Puma, Bmf, Bak, and Bid have been solved. The structure of A1 is similar to that of other prosurvival proteins, although features, such as an acidic patch in the binding groove, may allow specific therapeutic modulation of apoptosis. Significant conformational plasticity was observed in the intermolecular interactions and these differences explain some of the variation in affinity. This study, in combination with published data, suggests that interactions between conserved residues demarcate optimal binding.

Smits,C.; Czabotar, P.; Hinds, M.; Day, C.

2008-01-01T23:59:59.000Z

128

Roles of diet protein and temperature in the nutritional energetics of juvenile slider turtles, Trachemys scripta:  

SciTech Connect (OSTI)

Juvenile slider turtles (Trachemys scripta) were used in laboratory experiments to determine the effects of dietary protein and ambient temperature on growth rates, food consumption rates, digestion rates and digestive efficiencies, in order to better understand how the interactive roles these environmental factors may potentially influence body sizes and growth rates of individuals among wild slider turtle populations. Changes in plastron length, carapace length and body mass were significantly greater for Trachemys scripta eating 25% and 40% crude protein diets than for those eating 10% crude protein. Those consuming 10% crude protein showed significant decreases in all measurements of body size over a 13 wk period. These data suggest that dietary protein may be an important nutritional component to the growth of juvenile slider turtles, and that elevated thermal conditions, combined with a high dietary protein availability, may in part explain the exceedingly high growth rates of slider turtles attained in certain wild populations. 63 refs., 11 figs., 6 tabs.

Avery, H.W.

1988-08-01T23:59:59.000Z

129

DNA's Role with Proteins  

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

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

130

Protein Folding Simulation in CCP  

Science Journals Connector (OSTI)

A protein is a list of linked units called aminoacids. There are 20 different kinds of aminoacids and the typical length of a protein is 100500 units. The Protein Structure Prediction Problem (PSP) is the pro...

Alessandro Dal Pal; Agostino Dovier; Federico Fogolari

2004-01-01T23:59:59.000Z

131

Structural Characterization of Disordered States of Proteins.  

E-Print Network [OSTI]

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

Marsh, Joseph Arthur

2010-01-01T23:59:59.000Z

132

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 An alternative theory eliminates dark energy by placing Earth at the center of expansion Expanding Universe What;10/14/09 2:35 PMMathematicians' Alternate Model of the Universe Explains Away the Need For Dark Energy

Temple, Blake

133

Viruses and viral proteins  

Science Journals Connector (OSTI)

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

Verdaguer, N.

2014-10-14T23:59:59.000Z

134

Protein folding and cosmology  

E-Print Network [OSTI]

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

Gonzlez-Diz, P F

1997-01-01T23:59:59.000Z

135

Protein folding and cosmology  

E-Print Network [OSTI]

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

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

1997-06-04T23:59:59.000Z

136

Report on Ngai et al.: Change of Caged Dynamics at Tg in hydrated proteins found after suppressing the methyl group rotation contribution"  

E-Print Network [OSTI]

neutron scattering data of solvated proteins, the solvent is now restricted to hydration water: The authors belong to the elastic neutron scattering community, which intends to explain protein dynamics of dynamic information. The full dynamic information derivable from neutron scattering experiments

Doster, Wolfgang

137

Protein Folding and Assembly  

Science Journals Connector (OSTI)

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

D.P. Goldenberg

2013-01-01T23:59:59.000Z

138

Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction  

E-Print Network [OSTI]

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

Teichmann, Sarah

139

Explaining a CMS $eejj$ Excess With $\\mathcal{R}-$parity Violating Supersymmetry and Implications for Neutrinoless Double Beta Decay  

E-Print Network [OSTI]

A recent CMS search for the right handed gauge boson $W_R$ reports an interesting deviation from the Standard Model. The search has been conducted in the $eejj$ channel and has shown a 2.8$\\sigma$ excess around $m_{eejj} \\sim 2$ TeV. In this work, we explain the reported CMS excess with R-parity violating supersymmetry (SUSY). We consider resonant selectron and sneutrino production, followed by the three body decays of the neutralino and chargino via an $\\mathcal{R}-$parity violating coupling. We fit the excess for slepton masses around 2 TeV. The scenario can further be tested in neutrinoless double beta decay ($0\

Ben Allanach; Sanjoy Biswas; Subhadeep Mondal; Manimala Mitra

2014-12-01T23:59:59.000Z

140

Explaining the CMS $eejj$ and $e \\slashed {p}_T jj$ Excess and Leptogenesis in Superstring Inspired $E_6$ Models  

E-Print Network [OSTI]

We show that superstring inspired $E_6$ models can explain both the recently detected excess $eejj$ and $e \\slashed p_T jj$ signals at CMS, and also allow for leptogenesis. Working in a R-parity conserving low energy supersymmetric effective model, we show that the excess CMS events can be produced via the decay of exotic sleptons in alternative left-right symmetric models of $E_6$, which can also accommodate leptogenesis at a high scale. On the other hand, either the $eejj$ excess or the $e \\slashed p_T jj$ excess can be produced via the decays of right handed gauge bosons, but some of these scenarios may not accommodate letptogenesis as there will be strong $B-L$ violation at low energy, which, along with the anomalous fast electroweak $B+L$ violation, will wash out all baryon asymmetry. Baryogenesis below the electroweak scale may then need to be implemented in these models.

Dhuria, Mansi; Rangarajan, Raghavan; Sarkar, Utpal

2015-01-01T23:59:59.000Z

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.


141

Protein folding: concepts and perspectives  

Science Journals Connector (OSTI)

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

J. M. Yon

1997-07-01T23:59:59.000Z

142

INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION  

E-Print Network [OSTI]

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

Halligan, Daniel

143

Computer Simulations of Protein Folding  

E-Print Network [OSTI]

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

Sorin, Eric J.

144

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

E-Print Network [OSTI]

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

Raines, Ronald T.

145

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

E-Print Network [OSTI]

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

Honavar, Vasant

146

Predicting mostly disordered proteins by using structure-unknown protein data  

Science Journals Connector (OSTI)

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

Kana Shimizu; Yoichi Muraoka; Shuichi Hirose; Kentaro Tomii

2007-03-01T23:59:59.000Z

147

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

E-Print Network [OSTI]

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

Bigelow, Stephen

148

Identifying protein-protein interactions of a cell cycle regulator  

E-Print Network [OSTI]

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

Amos, Joseph Edward

2013-02-22T23:59:59.000Z

149

Thermodynamics of protein folding: a random matrix formulation  

E-Print Network [OSTI]

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows however that the evolution of the statistical measures e.g Gibbs free energy, heat capacity, entropy is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies.

Pragya Shukla

2010-10-16T23:59:59.000Z

150

Production-ecological modelling explains the difference between potential soil N mineralisation and actual herbage N uptake  

Science Journals Connector (OSTI)

Abstract We studied two different grassland fertiliser management regimes on sand and peat soils: above-ground application of a combination of organic N-rich slurry manure and solid cattle manure (SCM) vs. slit-injected, mineral N-rich slurry manure, whether or not supplemented with chemical fertiliser (non-SCM). Measurements of field N mineralisation as estimated from herbage N uptake in unfertilised plots were compared with (i) potential N mineralisation as determined from a standard laboratory soil incubation, (ii) the contribution of groups of soil organisms to N mineralisation based on production-ecological model calculations, and (iii) N mineralisation calculated according to the Dutch fertilisation recommendation for grasslands. Density and biomass of soil biota (bacteria, fungi, enchytraeids, microarthropods and earthworms) as well as net plant N-uptake were higher in the SCM input grasslands compared to the non-SCM input grasslands. The currently used method in Dutch fertilisation recommendations underestimated actual soil N supply capacity by, on average, 102kg Nha?1 (202 vs. 304kgha?1=34%). The summed production-ecological model estimate for N mineralisation by bacteria, fungi, protozoa, and enchytraeids was 87120% of the measured potential soil N mineralisation. Adding the modelled N mineralisation by earthworms to potential soil N mineralisation explained 98107% of the measured herbage N uptake from soil. For all grasslands and soil biota groups together, the model estimated 105% of the measured net herbage N uptake from soil. Soil biota production-ecological modelling is a powerful tool to understand and predict N uptake in grassland, reflecting the effects of previous manure management and soil type. The results show that combining production ecological modelling to predict N supply with existing soil N tests using aerobic incubation methods, can add to a scientifically based improvement of the N fertilisation recommendations for production grasslands.

Muhammad Imtiaz Rashid; Ron G.M. de Goede; Lijbert Brussaard; Jaap Bloem; Egbert A. Lantinga

2014-01-01T23:59:59.000Z

151

Neutron Diffraction Studies of Proteins  

Science Journals Connector (OSTI)

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

1980-01-01T23:59:59.000Z

152

Autoproteolysis in hedgehog protein biogenesis  

Science Journals Connector (OSTI)

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

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

1994-12-02T23:59:59.000Z

153

Simplified Models of Protein Folding  

Science Journals Connector (OSTI)

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

Hue Sun Chan

2005-01-01T23:59:59.000Z

154

Simulated annealing in protein folding  

Science Journals Connector (OSTI)

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

Avner Friedman

1992-01-01T23:59:59.000Z

155

A Novel Topology for Representing Protein Folds  

E-Print Network [OSTI]

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

Segal, Mark R

2009-01-01T23:59:59.000Z

156

Hydration dynamics near a model protein surface  

E-Print Network [OSTI]

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

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

2003-01-01T23:59:59.000Z

157

Protein synthesis in the dendrite  

Science Journals Connector (OSTI)

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

2002-01-01T23:59:59.000Z

158

Petaflop Computing for Protein Folding  

E-Print Network [OSTI]

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

Izaguirre, Jesús A.

159

Hydrophobic tint of knot proteins  

Science Journals Connector (OSTI)

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

P. Lissy Anto; S. Nair Achuthsankar

2010-02-01T23:59:59.000Z

160

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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

Thirumalai, Devarajan

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

Challenging Proteins Principles and Methods  

E-Print Network [OSTI]

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

Jacobsen, Steve

162

Protein domain organisation: adding order  

E-Print Network [OSTI]

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

Kummerfeld, Sarah K; Teichmann, Sarah A

2009-01-29T23:59:59.000Z

163

Mathematical methods for protein science  

SciTech Connect (OSTI)

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

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

1997-12-31T23:59:59.000Z

164

IMPROVING SEQUENCE ALIGNMENTS FOR INTRINSICALLY DISORDERED PROTEINS  

E-Print Network [OSTI]

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

Radivojac, Predrag

165

Ontological foundation for protein data models  

Science Journals Connector (OSTI)

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

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

2005-10-01T23:59:59.000Z

166

On the rough folding landscape of green fluorescent protein  

E-Print Network [OSTI]

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

Andrews, Benjamin Thomas

2008-01-01T23:59:59.000Z

167

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

168

Can 3-D models explain the observed fractions of fossil and non-fossil carbon in and near Mexico City?  

SciTech Connect (OSTI)

Abstract. A 3-D chemistry-transport model has been applied to the Mexico City metropolitan area to investigate the origin of elevated levels of non-fossil (NF) carbonaceous aerosols observed in this highly urbanized region. High time resolution measurements of the fine aerosol concentration and composition, and 12 or 24 h integrated 14C measurements of aerosol modern carbon have been performed in and near Mexico City during the March 2006 MILAGRO field experiment. The non-fossil carbon fraction (fNF), which is lower than the measured modern fraction (fM) due to the elevated 14C in the atmosphere caused by nuclear bomb testing, is estimated from the measured fM and the source-dependent information on modern carbon enrichment. The fNF contained in PM1 total carbon analyzed by a US team (f TC NF ) ranged from 0.37 to 0.67 at the downtown location, and from 0.50 to 0.86 at the suburban site. Substantially lower values (i.e. 0.240.49) were found for PM10 filters downtown by an independent set of measurements (Swiss team), which are inconsistent with the modeled and known differences between the size ranges, suggesting higher than expected uncertainties in the measurement techniques of 14C. An increase in the non-fossil organic carbon (OC) fraction (f OC NF ) by 0.100.15 was observed for both sets of filters during periods with enhanced wildfire activity in comparison to periods when fires were suppressed by rain, which is consistent with the wildfire impacts estimated with other methods. Model results show that the relatively high fraction of nonfossil carbon found in Mexico City seems to arise from the combination in about equal proportions of regional biogenic SOA, biomass burning POA and SOA, as well as non-fossil urban POA and SOA. Predicted spatial and temporal variations for f OC NF are similar to those in the measurements between the urban vs. suburban sites, and high-fire vs. low-fire periods. The absolute modeled values of f OC NF are consistent with the Swiss dataset but lower than the US dataset. Resolving the 14C measurement discrepancies is necessary for further progress in model evaluation. The model simulations that included secondary organic aerosol (SOA) formation from semi-volatile and intermediate volatility (S/IVOC) vapors showed improved closure for the total OA mass compared to simulations which only included SOA from VOCs, providing a more realistic basis to evaluate the fNF predictions. f OC NF urban sources of modern carbon are important in reducing or removing the difference in fNF between model and measurements, even though they are often neglected on the interpretation of 14C datasets. An underprediction of biomass burning POA by the model during some mornings also explains a part of the model-measurement differences. The fNF of urban POA and SOA precursors is an important parameter that needs to be better constrained by measurements. Performing faster ( 3 h) 14C measurements in future campaigns is critical to further progress in this area. To our knowledge this is the first time that radiocarbon measurements are used together with aerosol mass spectrometer (AMS) organic components to assess the performance of a regional model for organic aerosols.

Hodzic, Alma; Jimenez, Jose L.; Prevot, A. S. H.; Szidat, S.; Fast, Jerome D.; Madronich, Sasha

2010-11-25T23:59:59.000Z

169

Explaining the observed long coherence effects by 2D photon echo experiments in photosynthetic EET : Two-Component Phonon Spectrum model  

E-Print Network [OSTI]

We propose a simple stochastic model which successfully explains the long coherence effects observed in photosynthetic Excitation Energy Transport (EET) by 2D photon echo experiments of G. S. Engel et. al. (Nature, {\\bf 446} 782, (2007)). Our Two-Component Phonon Spectrum (TCPS) model is based upon the division of phonon degrees of freedom into a systematic component which is treated through polaron transformation and a stochastic component which is treated through dynamical disorder. This model successfully explains the observed long coherence upto $ \\sim 600 fsec$ in EET experiments.

Singh, Navinder; Amritkar, R E

2011-01-01T23:59:59.000Z

170

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

SciTech Connect (OSTI)

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

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

2006-01-01T23:59:59.000Z

171

A single wind-mediated mechanism explains high-altitude non-goal oriented headings and layering of nocturnally migrating insects  

Science Journals Connector (OSTI)

...research-article Research articles 1001 14 A single wind-mediated mechanism explains high-altitude...remained a mystery. Here we show how a wind-mediated mechanism accounts for the common...cue, thus adding their air speed to the wind speed and significantly increasing their...

2010-01-01T23:59:59.000Z

172

CSE 4153/6153 Assignment 1 Solutions Fall 2008 1. What are the seven network layer in the OSI model? Briefly (one or two lines) explain their functions  

E-Print Network [OSTI]

Presentation Layer: Syntax and semantics of data (handle differences between little-endian and big medium) Physical Layer: Convert data link frames into electrical electromagnetic signals to transmit them? Briefly (one or two lines) explain their functions Application Layer: Enable applications to exchange data

Ramkumar, Mahalingam

173

A Description of the Water-Works at London-Bridge, Explaining the Draught of T a b. I. By H. Beighton, F. R. S.  

Science Journals Connector (OSTI)

1731-1732 research-article A Description of the Water-Works at London-Bridge, Explaining the Draught of T a b. I. By H. Beighton, F. R. S. H. Beighton The Royal Society is collaborating with JSTOR to digitize, preserve, and...

1731-01-01T23:59:59.000Z

174

This factsheet explains what international students in the Netherlands must do to be properly insured. For some students, this means that they are obliged to take  

E-Print Network [OSTI]

This factsheet explains what international students in the Netherlands must do to be properly internship, your stay in the Netherlands is classified as not being solely for study purposes. As an employee is irrelevant. (2) People under the age of 30, who are in the Netherlands solely for study purposes do not need

van Suijlekom, Walter

175

Variations in the morphology of wood structure can explain why hardwood species of similar density have very different resistances to impact and compressive loading  

Science Journals Connector (OSTI)

...Smith Variations in the morphology of wood structure can explain why hardwood species...used. The disparate size of different wood cells in the hardwoods results in heterogeneous...energy-absorbing capabilities of the wood, despite the density being reduced. These...

2002-01-01T23:59:59.000Z

176

Hydrodynamic Description of Protein Folding  

Science Journals Connector (OSTI)

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

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

2008-01-11T23:59:59.000Z

177

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

178

Waterprotein interactions from highresolution protein crystallography  

Science Journals Connector (OSTI)

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

2004-01-01T23:59:59.000Z

179

Manipulating Protein Adsorption using a Patchy Protein-Resistant Brush  

Science Journals Connector (OSTI)

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

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

2010-06-17T23:59:59.000Z

180

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

E-Print Network [OSTI]

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

Hsu, Wei-Lun

2014-01-01T23:59:59.000Z

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

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

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

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

182

Convergent evolution of protein structure  

E-Print Network [OSTI]

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

Fischer, Daniel

183

Chloroplast ribosomes and protein synthesis.  

Science Journals Connector (OSTI)

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

E H Harris; J E Boynton; N W Gillham

1994-12-01T23:59:59.000Z

184

Introduction to Grid computing Protein folding  

E-Print Network [OSTI]

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

Boyar, Joan

185

Fusion Protein Products Screen Purify Detect Cleave  

E-Print Network [OSTI]

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

Lebendiker, Mario

186

Do viral proteins possess unique biophysical features?  

E-Print Network [OSTI]

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

Tawfik, Dan S.

187

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

E-Print Network [OSTI]

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

Zhu, L; Kaback, HR; Dalbey, RE

2013-01-01T23:59:59.000Z

188

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

Science Journals Connector (OSTI)

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

Zsuzsanna Dosztnyi; Blint Mszros; Istvn Simon

2009-10-15T23:59:59.000Z

189

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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

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

2010-07-18T23:59:59.000Z

190

Probing Single-Molecule Protein Conformational Dynamics. | EMSL  

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

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

191

Improvement of the Protein Quality of Corn With Soybean Protein  

Science Journals Connector (OSTI)

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

Ricardo Bressani; Luiz G. Elas

1978-01-01T23:59:59.000Z

192

Waterprotein interactions from highresolution protein crystallography  

Science Journals Connector (OSTI)

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

2004-01-01T23:59:59.000Z

193

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

194

Optimized Null Model for Protein Structure Networks  

E-Print Network [OSTI]

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

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

2009-01-01T23:59:59.000Z

195

A motion planning approach to protein folding  

E-Print Network [OSTI]

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

Song, Guang

2004-09-30T23:59:59.000Z

196

Mutagenic effects on protein folding and stability  

E-Print Network [OSTI]

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

Anderson, Thomas Anthony, 1973-

2002-01-01T23:59:59.000Z

197

Principles of Chaperone-Mediated Protein Folding  

Science Journals Connector (OSTI)

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

1995-01-01T23:59:59.000Z

198

Pathway and Stability of Protein Folding  

Science Journals Connector (OSTI)

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

1991-01-01T23:59:59.000Z

199

Models of Cooperativity in Protein Folding  

Science Journals Connector (OSTI)

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

1995-01-01T23:59:59.000Z

200

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

Science Journals Connector (OSTI)

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

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "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

Metal-directed protein self-assembly  

E-Print Network [OSTI]

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

Salgado. Eric N.

2010-01-01T23:59:59.000Z

202

Towards a Molecular Understanding of Protein Solubility  

E-Print Network [OSTI]

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

Kramer, Ryan 1984-

2011-05-31T23:59:59.000Z

203

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

204

Protein crystallography with spallation neutrons  

SciTech Connect (OSTI)

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

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

2003-01-01T23:59:59.000Z

205

Adhesives from modified soy protein  

DOE Patents [OSTI]

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

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

2008-08-26T23:59:59.000Z

206

Elastic energy of proteins and the stages of protein folding  

E-Print Network [OSTI]

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

Lei, Jinzhi

2010-01-01T23:59:59.000Z

207

Combining in vivo and in silico screening for protein stability  

E-Print Network [OSTI]

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

Barakat, Nora Hisham

2007-01-01T23:59:59.000Z

208

Extending the theoretical framework of protein folding dynamics  

E-Print Network [OSTI]

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

Yang, Sichun

2006-01-01T23:59:59.000Z

209

Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures  

SciTech Connect (OSTI)

Bin/amphipysin/Rvs (BAR)-domain proteins sculpt cellular membranes and have key roles in processes such as endocytosis, cell motility and morphogenesis. BAR domains are divided into three subfamilies: BAR- and F-BAR-domain proteins generate positive membrane curvature and stabilize cellular invaginations, whereas I-BAR-domain proteins induce negative curvature and stabilize protrusions. We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane tubulation but promotes the formation of planar membrane sheets. Structural and mutagenesis analyses reveal that the BAR domain of Pinkbar has a relatively flat lipid-binding interface and that it assembles into sheet-like oligomers in crystals and in solution, which may explain its unique membrane-deforming activity.

Pyklinen, Anette; Boczkowska, Malgorzata; Zhao, Hongxia; Saarikangas, Juha; Rebowski, Grzegorz; Jansen, Maurice; Hakanen, Janne; Koskela, Essi V.; Pernen, Johan; Vihinen, Helena; Jokitalo, Eija; Salminen, Marjo; Ikonen, Elina; Dominguez, Roberto; Lappalainen, Pekka (Helsinki); (Penn)

2013-05-29T23:59:59.000Z

210

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

Office of Scientific and Technical Information (OSTI)

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

211

Search for: "protein folding" | DOE PAGES  

Office of Scientific and Technical Information (OSTI)

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

212

Antimicrobial protein protects grapevines from pathogen  

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

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

213

Protein secretion in Bacillus species.  

Science Journals Connector (OSTI)

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

M Simonen; I Palva

1993-03-01T23:59:59.000Z

214

Protein Folding Sculpting Evolutionary Change  

E-Print Network [OSTI]

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

Lindquist, Susan

215

Turbulent phenomena in protein folding  

Science Journals Connector (OSTI)

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

Igor V. Kalgin and Sergei F. Chekmarev

2011-01-31T23:59:59.000Z

216

Protein Flips Lipids Across Membranes  

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

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

217

Fast events in protein folding  

SciTech Connect (OSTI)

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

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

1996-04-01T23:59:59.000Z

218

Physics of Caustics and Protein Folding: Mathematical Parallels  

E-Print Network [OSTI]

The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how energy from diverse small sources can drive a complex molecule to a unique state. We explore the possibility that the missing factor is in the geometry. A comparison of folding with other physical phenomena, together with analytic modeling of a molecule, led us to analyze the physics of optical caustic formation and of folding behavior side-by-side. The physics of folding and caustics is ostensibly very different but there are several strong parallels. This comparison emphasizes the mathematical similarity and also identifies differences. Since the 1970's, the physics of optical caustics has been developed to a very high degree of mathematical sophistication using catastrophe theory. That kind of quantitative application of catastrophe theory has not previously been applied ...

Simmons, Walter

2011-01-01T23:59:59.000Z

219

Can Neural Networks Explain Stuttering?  

Science Journals Connector (OSTI)

Recently, neural networks have received a great deal of attention from various disciplines. [1,2] In medicine neural network technology is considered helpful both as a new way of constructing systems for clini...

Maikl Braamhof

1990-01-01T23:59:59.000Z

220

France and US explain failures  

Science Journals Connector (OSTI)

... uncertain ignitions and failures early in the programme, to the small size of the "pyrotechnic" that lights the engine.

Robert Walgate; Joseph Palca

1986-07-10T23:59:59.000Z

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.


221

Laboratories to Explore, Explain VLBACHANDRA  

E-Print Network [OSTI]

Institute of Technology Idaho National Engineering Laboratory Lawrence Livermore National Laboratory, at least, be one that allows the scientific exploration of burning plasmas" and if Japan and Europe do

222

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

DOE Patents [OSTI]

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

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

2002-10-15T23:59:59.000Z

223

3.2 Energetics of Protein Folding  

Science Journals Connector (OSTI)

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

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

2012-01-01T23:59:59.000Z

224

Flavors of Protein Disorder Slobodan Vucetic,1  

E-Print Network [OSTI]

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

Vucetic, Slobodan

225

Advanced Review Ordered and disordered proteins  

E-Print Network [OSTI]

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

Kumar, Sanjay

226

Intrinsically Disordered Protein A. Keith Dunker1  

E-Print Network [OSTI]

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

Obradovic, Zoran

227

Thermodynamics of Protein Folding Erik Sandelin  

E-Print Network [OSTI]

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

Sandelin, Erik

228

272 Dispatch Protein folding: Chaperones get Hip  

E-Print Network [OSTI]

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

Craig, Elizabeth A

229

Systematic characterization of protein glycosylation of bacteria cell surface proteins  

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

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

230

Protein Flips Lipids Across Membranes  

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

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

231

Protein Flips Lipids Across Membranes  

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

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

232

Characterization of protein folding intermediates  

SciTech Connect (OSTI)

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

Kim, P.S.

1986-01-01T23:59:59.000Z

233

Denaturant-Induced Conformational Transitions in Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

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

Paolo Neyroz; Stefano Ciurli

2012-01-01T23:59:59.000Z

234

A phenomenological model of protein folding  

E-Print Network [OSTI]

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

Danielsson, Ulf H; Niemi, Antti J

2009-01-01T23:59:59.000Z

235

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

E-Print Network [OSTI]

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

Bigelow, Stephen

236

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

237

Protein folding in the ER.  

SciTech Connect (OSTI)

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

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

1999-10-01T23:59:59.000Z

238

Tailoring Peptidomimetics for Targeting ProteinProtein Interactions  

Science Journals Connector (OSTI)

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

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

2014-07-01T23:59:59.000Z

239

SINGLE CELL PROTEIN | The Algae  

Science Journals Connector (OSTI)

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

M. Garca-Garibay; L. Gmez-Ruiz; A.E. Cruz-Guerrero; E. Brzana

2014-01-01T23:59:59.000Z

240

First Knot Discovered in Ancient Bacterium Protein  

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

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

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

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

E-Print Network [OSTI]

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

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

2012-07-11T23:59:59.000Z

242

Building Biochips: A Protein Production Pipeline  

SciTech Connect (OSTI)

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

de Carvalho-Kavanagh, M; Albala, J S

2004-02-09T23:59:59.000Z

243

Laboratory-Directed Protein Evolution  

Science Journals Connector (OSTI)

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

Ling Yuan; Itzhak Kurek; James English; Robert Keenan

2005-09-01T23:59:59.000Z

244

3.9 Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

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

V.N. Uversky; A.K. Dunker

2012-01-01T23:59:59.000Z

245

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

246

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

E-Print Network [OSTI]

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

Phillips, Aaron Hale

2010-01-01T23:59:59.000Z

247

Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding  

SciTech Connect (OSTI)

The Lum-Chandler-Weeks theory of hydrophobicity [J. Phys. Chem. 103, 4570 (1999)] is applied to treat the temperature dependence of hydrophobic solvation in water. The application illustrates how the temperature dependence for hydrophobic surfaces extending less than 1nm differs significantly from that for surfaces extending more than 1nm. The latter is the result of water depletion, a collective effect, that appears at length scales of 1nm and larger. Due to the contrasting behaviors at small and large length scales, hydrophobicity by itself can explain the variable behavior of protein folding.

Huang, David M.; Chandler, David

2000-04-01T23:59:59.000Z

248

Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.  

SciTech Connect (OSTI)

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

2005-03-01T23:59:59.000Z

249

Protein structures by spallation neutron crystallography  

Science Journals Connector (OSTI)

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

Langan, P.

2008-04-18T23:59:59.000Z

250

Molecular Dynamics Simulations of Protein Folding  

Science Journals Connector (OSTI)

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

Angel E. Garcia

2008-01-01T23:59:59.000Z

251

Characterization of disordered proteins with ENSEMBLE  

Science Journals Connector (OSTI)

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

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

2013-02-01T23:59:59.000Z

252

Characterization of disordered proteins with ENSEMBLE  

Science Journals Connector (OSTI)

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

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

2013-02-01T23:59:59.000Z

253

Archaic chaos: intrinsically disordered proteins in Archaea  

Science Journals Connector (OSTI)

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

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

2010-05-01T23:59:59.000Z

254

Bioinformatics analysis of disordered proteins in prokaryotes  

Science Journals Connector (OSTI)

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

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

2011-03-01T23:59:59.000Z

255

Intrinsic Fluorescence of Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

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

Paolo Neyroz; Stefano Ciurli

2012-01-01T23:59:59.000Z

256

Nanomechanics of Proteins, Both Folded and Disordered  

Science Journals Connector (OSTI)

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

Rubn Hervs; Albert Galera-Prat

2013-01-01T23:59:59.000Z

257

Sensitivity and Selectivity in Protein Sequence Comparison  

Science Journals Connector (OSTI)

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

William R. Pearson

1987-01-01T23:59:59.000Z

258

Seafood Protein in Human and Animal Nutrition  

Science Journals Connector (OSTI)

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

Shi-Yen Shiau

1995-01-01T23:59:59.000Z

259

Topology to geometry in protein folding: -Lactoglobulin  

E-Print Network [OSTI]

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

Berry, R. Stephen

260

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

E-Print Network [OSTI]

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

Anderson, William David

2007-01-01T23:59:59.000Z

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

Struts, springs and crumple zones: protein structures under force  

E-Print Network [OSTI]

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

Dill, Jesse

2012-01-01T23:59:59.000Z

262

Computational Modeling of Protein Interactions at Multiple Lengthscales  

E-Print Network [OSTI]

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

Yap, Eng Hui

2010-01-01T23:59:59.000Z

263

Protein-Folding Landscapes in Multi-Chain Systems  

E-Print Network [OSTI]

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

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

2005-01-01T23:59:59.000Z

264

Protein-folding via divide-and-conquer optimization  

E-Print Network [OSTI]

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

Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

2004-01-01T23:59:59.000Z

265

The unfolded protein response during prostate cancer development  

E-Print Network [OSTI]

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

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

2009-01-01T23:59:59.000Z

266

Intermediates and the folding of proteins L and G  

E-Print Network [OSTI]

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

Brown, Scott; Head-Gordon, Teresa

2008-01-01T23:59:59.000Z

267

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

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

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

268

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

269

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

E-Print Network [OSTI]

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

Guo, Minghao

2014-01-01T23:59:59.000Z

270

Toy model for protein folding  

Science Journals Connector (OSTI)

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

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

1993-08-01T23:59:59.000Z

271

Protein folding using contact maps  

E-Print Network [OSTI]

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

Michele Vendruscolo; Eytan Domany

1999-01-21T23:59:59.000Z

272

Protein Structures Revealed at Record Pace  

ScienceCinema (OSTI)

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

Hura, Greg

2013-05-29T23:59:59.000Z

273

Protein Structures Revealed at Record Pace  

ScienceCinema (OSTI)

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

Greg Hura

2010-01-08T23:59:59.000Z

274

JBS Protein Transduction Kit Cell Penetration  

E-Print Network [OSTI]

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

Lebendiker, Mario

275

How Nature Fine Tunes Protein Stability  

E-Print Network [OSTI]

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

Wickstrom, Megan

2007-07-14T23:59:59.000Z

276

EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS  

E-Print Network [OSTI]

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

Guibas, Leonidas J.

277

Amphiphiles for protein solubilization and stabilization  

DOE Patents [OSTI]

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

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

2014-11-04T23:59:59.000Z

278

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

279

Synthetic mimetics of protein secondary structure domains  

Science Journals Connector (OSTI)

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

2010-01-01T23:59:59.000Z

280

GREEN FLUORESCENT PROTEIN The green revolution  

E-Print Network [OSTI]

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

Stearns, Tim

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

Protein folding: not just another optimization  

E-Print Network [OSTI]

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

Karplus, Kevin

282

UNCORRECTED 3 Protein folding: Then and now  

E-Print Network [OSTI]

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

Dokholyan, Nikolay V.

283

Atomistic Protein Folding Simulations on the  

E-Print Network [OSTI]

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

Snow, Christopher

284

Disulfide-Linked Protein Folding Pathways  

E-Print Network [OSTI]

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

Bardwell, James

285

STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS  

E-Print Network [OSTI]

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

Dinner, Aaron

286

Intracellular Signaling by the Unfolded Protein  

E-Print Network [OSTI]

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

Mullins, Dyche

287

Approximate Inference and Protein-Folding  

E-Print Network [OSTI]

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

Weiss, Yair

288

Extracellular secretion of recombinant proteins  

DOE Patents [OSTI]

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

Linger, Jeffrey G.; Darzins, Aldis

2014-07-22T23:59:59.000Z

289

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

E-Print Network [OSTI]

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

Chan, Hue Sun

290

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

E-Print Network [OSTI]

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

Walter, Peter

291

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

E-Print Network [OSTI]

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

Dinner, Aaron

292

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Studying submicrosecond protein folding  

E-Print Network [OSTI]

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

293

Chapter Eight - Intrinsically Disordered ProteinsRelation to General Model Expressing the Active Role of the Water Environment  

Science Journals Connector (OSTI)

Abstract This work discusses the role of unstructured polypeptide chain fragments in shaping the protein's hydrophobic core. Based on the fuzzy oil drop model, which assumes an idealized distribution of hydrophobicity density described by the 3D Gaussian, we can determine which fragments make up the core and pinpoint residues whose location conflicts with theoretical predictions. We show that the structural influence of the water environment determines the positions of disordered fragments, leading to the formation of a hydrophobic core overlaid by a hydrophilic mantle. This phenomenon is further described by studying selected proteins which are known to be unstable and contain intrinsically disordered fragments. Their properties are established quantitatively, explaining the causative relation between the protein's structure and function and facilitating further comparative analyses of various structural models.

Barbara Kalinowska; Mateusz Banach; Leszek Konieczny; Damian Marchewka; Irena Roterman

2014-01-01T23:59:59.000Z

294

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

295

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

Science Journals Connector (OSTI)

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

Yasuaki Kazuta; Tomoaki Matsuura; Norikazu Ichihashi; Tetsuya Yomo

2014-01-01T23:59:59.000Z

296

CONNNECT TO WiFi USING PROXY SETTINGS (MAC) This guide explains how to set up a modern Apple Mac (running OSX 10.3 or higher) to connect to the internet,  

E-Print Network [OSTI]

CONNNECT TO WiFi USING PROXY SETTINGS (MAC) This guide explains how to set up a modern Apple Mac Apple on the left of the menu bar. 2. Click on `System Preferences'. 3. Click on `Network'. 4. A window

Mottram, Nigel

297

Review Protein Folding and Misfolding on Surfaces  

E-Print Network [OSTI]

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

Massimo Stefani

2008-01-01T23:59:59.000Z

298

Computational and experimental investigations of forces in protein folding  

E-Print Network [OSTI]

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

Schell, David Andrew

2005-02-17T23:59:59.000Z

299

Protein folding using contact maps Michele Vendruscolo and Eytan Domany  

E-Print Network [OSTI]

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

Domany, Eytan

300

Neutron protein crystallography: beyond the folding structure of biological macromolecules  

Science Journals Connector (OSTI)

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

Niimura, N.

2007-12-21T23:59:59.000Z

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

Advancing theory and application of cognitive research in sport: Using representative tasks to explain and predict skilled anticipation, decision-making, and option-generation behavior  

Science Journals Connector (OSTI)

AbstractObjectives Three main goals were addressed in this research. First, we tested the claims of two cognitive mechanisms that have been proposed to explain expert performance. This was done during assessment and intervention phases of decision making. Second, we tested the validity of an online test of perceptual-cognitive skill in soccer: The Online Assessment of Strategic Skill In Soccer (OASSIS). Third, we compared the OASSIS to other predictors of skill in soccer. Design Over the course of a three-part experiment, participants completed an updated version of the option-generation paradigm employed by Ward, Ericsson, and Williams (2013), the OASSIS, and a battery of other cognitive tests. Performance on these tests was used to inform theory and validate the OASSIS as an applied tool for domain professionals. Methods NCAA Division 1 and recreational-level soccer players completed a battery of tests, both using paper/pencil (see Ward etal., 2013) and online. Results Support for Long Term Working Memory theory (LTWM; see Ericsson & Kintsch, 1995) was observed during both phases of decision making, though the prescriptions of the Take-The-First heuristic (see Johnson & Raab, 2003) tend to hold, particularly within intervention phase. When used to predict skill-group membership, the OASSIS accounted for more variance than domain-general tests of cognition. Furthermore, scores on the OASSIS correlated with other measures of perceptual-cognitive skill in soccer and the process-level predictions made by LTWM. Conclusions Updates to our theoretical understanding of expert performance are provided and the validity of the OASSIS is demonstrated.

Patrick K. Belling; Joel Suss; Paul Ward

2014-01-01T23:59:59.000Z

302

Glassy dynamics of protein folding  

Science Journals Connector (OSTI)

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

Erkan Tzel and Ay?e Erzan

2000-02-01T23:59:59.000Z

303

Energy barriers, cooperativity, and hidden intermediates in the folding of small proteins  

SciTech Connect (OSTI)

Current theoretical views of the folding process of small proteins (<{approx}100 amino acids) postulate that the landscape of potential mean force (PMF) for the formation of the native state has a funnel shape and that the free energy barrier to folding arises from the chain configurational entropy only. However, recent theoretical studies on the formation of hydrophobic clusters with explicit water suggest that a barrier should exist on the PMF of folding, consistent with the fact that protein folding generally involves a large positive activation enthalpy at room temperature. In addition, high-resolution structural studies of the hidden partially unfolded intermediates have revealed the existence of non-native interactions, suggesting that the correction of the non-native interactions during folding should also lead to barriers on PMF. To explore the effect of a PMF barrier on the folding behavior of proteins, we modified Zwanzig's model for protein folding with an uphill landscape of PMF for the formation of transition states. We found that the modified model for short peptide segments can satisfy the thermodynamic and kinetic criteria for an apparently two-state folding. Since the Levinthal paradox can be solved by a stepwise folding of short peptide segments, a landscape of PMF with a locally uphill search for the transition state and cooperative stabilization of folding intermediates/native state is able to explain the available experimental results for small proteins. We speculate that the existence of cooperative hidden folding intermediates in small proteins could be the consequence of the highly specific structures of the native state, which are selected by evolution to perform specific functions and fold in a biologically meaningful time scale.

Bai Yawen [Laboratory of Biochemistry, National Cancer Institute, NIH, Building 37, Room 6114E, Bethesda, MD 20892 (United States)]. E-mail: yawen@helix.nih.gov

2006-02-17T23:59:59.000Z

304

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

Science Journals Connector (OSTI)

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

O. V. Galzitskaya

2010-06-01T23:59:59.000Z

305

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

E-Print Network [OSTI]

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

Obradovic, Zoran

306

The Biochemical Investigation and Isolation of Small Molecule Inhibitors for Two Essential Proteins of Mycobacterium tuberculosis H37Rv: IspD and Wag31  

E-Print Network [OSTI]

residues that made it more flexible and may help explain the difference in the reaction kinetics between the two homologs. 1.3 Wag31 DivIVA family of proteins The DivIVA protein is highly conserved in gram positive bacteria. It is a cell division.... It is known that DivIVA localization at the poles is due to its recognition of the spherical inward curve of these cells near the poles compared to the remaining portion (which maintains a cylindrical curve which is less sharp). Furthermore, it has been...

Joseph, Sonia

2014-06-12T23:59:59.000Z

307

Dominant Pathways in Protein Folding  

E-Print Network [OSTI]

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

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

2006-07-27T23:59:59.000Z

308

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

Science Journals Connector (OSTI)

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

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

2009-01-01T23:59:59.000Z

309

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

Science Journals Connector (OSTI)

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

Benita Sjgren

2011-01-01T23:59:59.000Z

310

Brownian Dynamics Simulation of Protein Solutions: Structural...  

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

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

311

Year 2 Report: Protein Function Prediction Platform  

SciTech Connect (OSTI)

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

Zhou, C E

2012-04-27T23:59:59.000Z

312

Protein Folding: Generalized-Ensemble Algorithms  

Science Journals Connector (OSTI)

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

Ulrich H. E. Hansmann

2009-01-01T23:59:59.000Z

313

Simulating Temperature Jumps for Protein Folding Studies.  

E-Print Network [OSTI]

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

Kim, Seonah

2007-01-01T23:59:59.000Z

314

Protein Engineering of Bacillus thuringiensis ?-Endotoxins  

Science Journals Connector (OSTI)

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

Dr. Alvaro M. Florez; Dr. Cristina Osorio

2012-01-01T23:59:59.000Z

315

Controlling membrane protein folding using photoresponsive surfactant.  

E-Print Network [OSTI]

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

Chang, Chia Hao

2012-01-01T23:59:59.000Z

316

Knots and Swelling in Protein Folding  

E-Print Network [OSTI]

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

Martin Lundgren; Antti J. Niemi

2009-06-26T23:59:59.000Z

317

Collaboration drives achievement in protein structure research  

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

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

318

Physics of Caustics and Protein Folding: Mathematical Parallels  

E-Print Network [OSTI]

The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how energy from diverse small sources can drive a complex molecule to a unique state. We explore the possibility that the missing factor is in the geometry. A comparison of folding with other physical phenomena, together with analytic modeling of a molecule, led us to analyze the physics of optical caustic formation and of folding behavior side-by-side. The physics of folding and caustics is ostensibly very different but there are several strong parallels. This comparison emphasizes the mathematical similarity and also identifies differences. Since the 1970's, the physics of optical caustics has been developed to a very high degree of mathematical sophistication using catastrophe theory. That kind of quantitative application of catastrophe theory has not previously been applied to folding nor have the points of similarity with optics been identified or exploited. A putative underlying physical link between caustics and folding is a torsion wave of non-constant wave speed, propagating on the dihedral angles and $\\Psi$ found in an analytical model of the molecule. Regardless of whether we have correctly identified an underlying link, the analogy between caustic formation and folding is strong and the parallels (and differences) in the physics are useful.

Walter Simmons; Joel L. Weiner

2011-08-13T23:59:59.000Z

319

Dominant Pathways in Protein Folding  

Science Journals Connector (OSTI)

We present a method to investigate the kinetics of protein folding and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. By writing the solution of the Fokker-Planck equation in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is applied to the folding of the Villin headpiece subdomain simulated using a Go model. An initial collapsing phase driven by the initial configuration is followed by a rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This completely general method does not require the prior knowledge of any reaction coordinate and is an efficient tool to perform simulations of the entire folding process with available computers.

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

2006-09-06T23:59:59.000Z

320

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

E-Print Network [OSTI]

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

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

2009-04-29T23:59:59.000Z

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

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

Science Journals Connector (OSTI)

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

Kim Lan Sim; Tomoyuki Uchida; Satoru Miyano

2001-04-01T23:59:59.000Z

322

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

Science Journals Connector (OSTI)

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

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

2012-09-10T23:59:59.000Z

323

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

Science Journals Connector (OSTI)

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

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

2009-07-29T23:59:59.000Z

324

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

Science Journals Connector (OSTI)

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

Ana Cristina Sotomayor-Prez; Johanna C. Karst

2012-01-01T23:59:59.000Z

325

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

Science Journals Connector (OSTI)

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

U Jahnke; EH Fischer; EC Alvord Jr

1985-07-19T23:59:59.000Z

326

ALSNews Vol. 308  

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

327

ALSNews Vol. 308  

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

328

ALSNews Vol. 308  

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

329

ALSNews Vol. 308  

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

330

ALSNews Vol. 308  

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

331

ALSNews Vol. 308  

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

332

ALSNews Vol. 308  

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

333

ALSNews Vol. 308  

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

334

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

Science Journals Connector (OSTI)

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

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

2005-05-01T23:59:59.000Z

335

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

E-Print Network [OSTI]

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

Englander, S. Walter

336

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

E-Print Network [OSTI]

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

Walter, Peter

337

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

Science Journals Connector (OSTI)

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

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

2010-01-01T23:59:59.000Z

338

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

Science Journals Connector (OSTI)

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

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

2009-01-01T23:59:59.000Z

339

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

SciTech Connect (OSTI)

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

B Wallace; R Janes

2011-12-31T23:59:59.000Z

340

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

Science Journals Connector (OSTI)

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

2011-01-01T23:59:59.000Z

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

NASA's Protein Crystal Work Gets Mixed Reviews  

Science Journals Connector (OSTI)

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

LOIS EMBER

2000-03-13T23:59:59.000Z

342

Biophysical characterization of protein folding and misfolding.  

E-Print Network [OSTI]

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

Schmittschmitt, Jason Peter

2004-09-30T23:59:59.000Z

343

Trafficking of Proteins through Plastid Stromules  

Science Journals Connector (OSTI)

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

Maureen R. Hanson; Amirali Sattarzadeh

2013-08-27T23:59:59.000Z

344

Solvent-induced forces in protein folding  

SciTech Connect (OSTI)

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

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

1990-08-23T23:59:59.000Z

345

MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY  

E-Print Network [OSTI]

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

Quake, Stephen R.

346

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

347

Antimicrobial protein protects grapevines from pathogen  

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

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

348

Unusual biophysics of intrinsically disordered proteins  

Science Journals Connector (OSTI)

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

Vladimir N. Uversky

2013-01-01T23:59:59.000Z

349

Protein Folding Challenge and Theoretical Computer Science Somenath Biswas  

E-Print Network [OSTI]

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

Biswas, Somenath

350

A Visual Analytics Approach for Protein Disorder Prediction  

E-Print Network [OSTI]

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

Park, Haesun

351

Can Contact Potentials Reliably Predict Stability of Proteins?  

E-Print Network [OSTI]

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

Khatun, Jainab

352

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

SciTech Connect (OSTI)

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

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

2003-01-01T23:59:59.000Z

353

Cotranslational protein folding with L-systems  

E-Print Network [OSTI]

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

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

354

Plasma Protein Concentrations in Interstitial Fluid from Human Aortas  

Science Journals Connector (OSTI)

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

1982-01-01T23:59:59.000Z

355

Trends in template/fragment-free protein structure prediction  

E-Print Network [OSTI]

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

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

2011-01-01T23:59:59.000Z

356

Exploring zipping and assembly as a protein folding principle  

E-Print Network [OSTI]

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

Voelz, Vince A; Dill, Ken A

2007-01-01T23:59:59.000Z

357

Protein folding in the secretory pathway of animal cells  

Science Journals Connector (OSTI)

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

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

1995-01-01T23:59:59.000Z

358

PREDICTION OF BOUNDARIES BETWEEN INTRINSICALLY ORDERED AND DISORDERED PROTEIN REGIONS  

E-Print Network [OSTI]

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

Obradovic, Zoran

359

Comprehensive large-scale assessment of intrinsic protein disorder  

Science Journals Connector (OSTI)

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

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

2014-10-01T23:59:59.000Z

360

Intrinsic Disorder and Protein Function A. Keith Dunker,,  

E-Print Network [OSTI]

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

Obradovic, Zoran

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

DisProt: a database of protein disorder  

Science Journals Connector (OSTI)

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

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

2005-01-01T23:59:59.000Z

362

Exploiting Heterogeneous Sequence Properties Improves Prediction of Protein Disorder  

E-Print Network [OSTI]

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

Obradovic, Zoran

363

ESpritz: accurate and fast prediction of protein disorder  

Science Journals Connector (OSTI)

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

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

2012-02-15T23:59:59.000Z

364

Proteins without 3D structure: definition, detection and beyond  

Science Journals Connector (OSTI)

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

Ferenc Orosz; Judit Ovdi

2011-06-01T23:59:59.000Z

365

Measuring and comparing structural fluctuation patterns in large protein datasets  

Science Journals Connector (OSTI)

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

Edvin Fuglebakk; Julin Echave; Nathalie Reuter

2012-10-01T23:59:59.000Z

366

Methods for Improving Protein Disorder Prediction Slobodan Vucetic1  

E-Print Network [OSTI]

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

Vucetic, Slobodan

367

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS DISORDER: ASSESSMENT  

E-Print Network [OSTI]

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

Sussman, Joel L.

368

Disordered binding regions of Ewings sarcoma fusion proteins  

Science Journals Connector (OSTI)

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

R. Todorova

2014-01-01T23:59:59.000Z

369

Septin Self-Assembly: Plasticity and Protein Scaffolding  

E-Print Network [OSTI]

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

Garcia, III, Galo

2012-01-01T23:59:59.000Z

370

New Crystal Structures Lift Fog around Protein Folding  

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

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

371

THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES  

E-Print Network [OSTI]

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

Sosnick, Tobin R.

372

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding  

E-Print Network [OSTI]

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

373

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping  

E-Print Network [OSTI]

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

Baker, David

374

Introducing Protein Folding Using Simple Models  

E-Print Network [OSTI]

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

D. Thirumalai; D. K. Klimov

2001-01-04T23:59:59.000Z

375

Efficient inference of protein structural ensembles  

E-Print Network [OSTI]

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

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

2014-01-01T23:59:59.000Z

376

Constructing ensembles for intrinsically disordered proteins  

Science Journals Connector (OSTI)

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

Charles K Fisher; Collin M Stultz

2011-01-01T23:59:59.000Z

377

Nonlinear conformation of secondary protein folding  

E-Print Network [OSTI]

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

Januar, M; Handoko, L T

2012-01-01T23:59:59.000Z

378

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

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

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

379

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

Science Journals Connector (OSTI)

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

Christian Schaefer; Avner Schlessinger; Burkhard Rost

2010-03-01T23:59:59.000Z

380

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

Science Journals Connector (OSTI)

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

Rostislav Skrabana; Jozef Sevcik; Michal Novak

2006-11-01T23:59:59.000Z

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

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

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

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

382

Protein-Based Nanomedicine Platforms for Drug Delivery. | EMSL  

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

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

383

Stable Isotope, Site-Specific Mass Tagging For Protein Identification  

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

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

384

How many water molecules can be detected by protein crystallography?  

Science Journals Connector (OSTI)

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

Carugo, O.

1999-02-01T23:59:59.000Z

385

Protein Folding Pathways Implementing Dihedral Angle Variable Speed  

Science Journals Connector (OSTI)

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

Mikel Diez; Victor Petuya; Mnica Urizar

2012-01-01T23:59:59.000Z

386

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

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

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

387

Ensemble FRET Methods in Studies of Intrinsically Disordered Proteins  

Science Journals Connector (OSTI)

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

Elisha Haas

2012-01-01T23:59:59.000Z

388

DPROT: prediction of disordered proteins using evolutionary information  

Science Journals Connector (OSTI)

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

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

2008-10-01T23:59:59.000Z

389

Determining a substitution matrix for the alignment of disordered proteins.  

E-Print Network [OSTI]

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

Kim, Dong

2013-01-01T23:59:59.000Z

390

Amino acid treatment enhances protein recovery from sediment...  

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

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

391

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

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

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

392

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

E-Print Network [OSTI]

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

De Micheli, Giovanni

393

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

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

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

394

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

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

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

395

Versatile Apoferritin Nanoparticle Labels for Assay of Protein...  

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

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

396

Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios  

E-Print Network [OSTI]

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

Berry, R. Stephen

397

SciTech Connect: Manipulating and Visualizing Proteins  

Office of Scientific and Technical Information (OSTI)

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

398

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

Office of Scientific and Technical Information (OSTI)

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

399

New Crystal Structures Lift Fog around Protein Folding  

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

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

400

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

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

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

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

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

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

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

402

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

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

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

403

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

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

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

404

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

405

Telomere-associated proteins in Arabidopsis thaliana  

E-Print Network [OSTI]

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

Surovtseva, Yulia V.

2009-05-15T23:59:59.000Z

406

IR laser-induced protein crystal transformation  

Science Journals Connector (OSTI)

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

Kiefersauer, R.

2014-04-26T23:59:59.000Z

407

Prion protein in health and disease  

E-Print Network [OSTI]

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

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

2008-01-01T23:59:59.000Z

408

Structural and Energetic Heterogeneity in Protein Folding  

E-Print Network [OSTI]

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

Steven S. Plotkin; Jose N. Onuchic

2000-09-27T23:59:59.000Z

409

Proline peptide isomerization and protein folding  

Science Journals Connector (OSTI)

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

A. Salahuddin

1984-10-01T23:59:59.000Z

410

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

411

Enhanced sampling and applications in protein folding.  

E-Print Network [OSTI]

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

Zhang, Cheng

2013-01-01T23:59:59.000Z

412

Femtosecond X-ray protein nanocrystallography  

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

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

413

Energetics of protein charge transfer and photosynthesis  

E-Print Network [OSTI]

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

Matyushov, Dmitry

414

Genetic noise control via protein oligomerization  

SciTech Connect (OSTI)

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

Ghim, C; Almaas, E

2008-06-12T23:59:59.000Z

415

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

416

Rhoptry protein 6 from Toxoplasma gondii is an intrinsically disordered protein  

Science Journals Connector (OSTI)

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

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

2014-01-01T23:59:59.000Z

417

Protein Folding: A Perspective From Statistical Physics  

E-Print Network [OSTI]

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

Jinzhi Lei; Kerson Huang

2010-02-26T23:59:59.000Z

418

Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA  

E-Print Network [OSTI]

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

Simona Cocco; John F. Marko; Remi Monasson

2014-05-26T23:59:59.000Z

419

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

Science Journals Connector (OSTI)

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

Langan, P.

2004-03-17T23:59:59.000Z

420

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

Science Journals Connector (OSTI)

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

Arieh Ben-Naim

2013-01-01T23:59:59.000Z

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

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

SciTech Connect (OSTI)

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

Eliezer, D.

1994-06-01T23:59:59.000Z

422

Protein folding in crowded environments and living cells.  

E-Print Network [OSTI]

??Biomolecular dynamics and stability are predominantly investigated in vitro, and extrapolated to explain function in the living cell. In this thesis, we attempt to bridge (more)

Dhar, Apratim

2011-01-01T23:59:59.000Z

423

Distribution of Protein Folds in the Three Superkingdoms of Life  

E-Print Network [OSTI]

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

424

Guide to Red Fluorescent Proteins and Biosensors for Flow Cytometry  

E-Print Network [OSTI]

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

Verkhusha, Vladislav V.

425

ProDy: Protein Dynamics Inferred from Theory and Experiments  

Science Journals Connector (OSTI)

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

Ahmet Bakan; Lidio M. Meireles; Ivet Bahar

2011-06-01T23:59:59.000Z

426

Intrinsic Protein Disorder in Complete Genomes A. Keith Dunker1  

E-Print Network [OSTI]

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

Obradovic, Zoran

427

Sequence Complexity of Disordered Protein Pedro Romero,1#  

E-Print Network [OSTI]

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

Obradovic, Zoran

428

THOUSANDS OF PROTEINS LIKELY TO HAVE LONG DISORDERED REGIONS  

E-Print Network [OSTI]

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

Obradovic, Zoran

429

GlobPlot: exploring protein sequences for globularity and disorder  

E-Print Network [OSTI]

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

430

INTRODUCTION Proteins must mature to their native confor-  

E-Print Network [OSTI]

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

Hebert, Daniel N.

431

Introduction Protein secretion is an essential process in prokaryotes and  

E-Print Network [OSTI]

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

Cheng, Chi-Hing Christina

432

Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics  

E-Print Network [OSTI]

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

Santiago, Juan G.

433

DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS  

E-Print Network [OSTI]

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

Langmead, Christopher James

434

FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

435

Cellular mechanisms of membrane protein folding William R Skach  

E-Print Network [OSTI]

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

Cai, Long

436

Evolutionary Monte Carlo for protein folding simulations Faming Lianga)  

E-Print Network [OSTI]

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

Liang, Faming

437

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

E-Print Network [OSTI]

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

Smith, J. MacGregor

438

Adaptive dimensionality reduction of stochastic differential equations for protein dynamics  

E-Print Network [OSTI]

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

Izaguirre, Jesús A.

439

Folding simulations of small proteins Seung-Yeon Kima  

E-Print Network [OSTI]

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

Lee, Jooyoung

440

High-Yield Secretion of Multiple Client Proteins in Aspergillus  

SciTech Connect (OSTI)

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

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

2012-07-15T23:59:59.000Z

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

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

Science Journals Connector (OSTI)

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

Chengwei Lei; Jianhua Ruan

2013-02-01T23:59:59.000Z

442

ClusPro: a fully automated algorithm for protein protein docking  

E-Print Network [OSTI]

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

Vajda, Sandor

443

Replica exchange simulations of transient encounter complexes in proteinprotein association  

Science Journals Connector (OSTI)

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

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

2008-01-01T23:59:59.000Z

444

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS PROTS: A fragment based protein  

E-Print Network [OSTI]

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

Zhang, Yang

445

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

E-Print Network [OSTI]

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

Cox, Michael M.

446

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

E-Print Network [OSTI]

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

Unger, Ron

447

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

E-Print Network [OSTI]

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

Walter, Peter

448

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

E-Print Network [OSTI]

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

Lathrop, Richard H.

449

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

E-Print Network [OSTI]

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

Obradovic, Zoran

450

Dynamic interactions of proteins in complex networks  

SciTech Connect (OSTI)

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

Appella, E.; Anderson, C.

2009-10-01T23:59:59.000Z

451

The Colorful Journey of Green Fluorescent Protein  

Science Journals Connector (OSTI)

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

Jin Zhang

2009-02-20T23:59:59.000Z

452

ET Kinetics of Bifunctional Redox Protein Maquettes  

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

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

453

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

E-Print Network [OSTI]

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

Annunziata, Onofrio

454

Exploration of homodimer receptor: homodimer protein interactions  

Science Journals Connector (OSTI)

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

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

2009-01-01T23:59:59.000Z

455

Protein synthesis driven by dynamical stochastic transcription  

E-Print Network [OSTI]

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

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

2014-06-12T23:59:59.000Z

456

Protein Folding in Contact Map Space  

Science Journals Connector (OSTI)

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

M. Vendruscolo; R. Najmanovich; E. Domany

1999-01-18T23:59:59.000Z

457

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

458

Preparation of white sunflower protein isolates  

E-Print Network [OSTI]

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

Wen, Hwei-Mei

2012-06-07T23:59:59.000Z

459

Rigidity Analysis for Modeling Protein Motion  

E-Print Network [OSTI]

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

Thomas, Shawna L.

2010-07-14T23:59:59.000Z

460

Toward a Theory on the Stability of Protein Folding: Challenges for Folding Models  

E-Print Network [OSTI]

We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the progress from the random coil to the native state. In this paper we explore the stability of folding using established methods from physics and mathematics. Our result is a preliminary theory of the physics of folding. We suggest some tests of these ideas using folding simulations. We begin by supposing that folding events are related in some way to mechanical waves on the molecule. We adopt an analytical approach to the physics which was pioneered by M.V. Berry, (in another context), based upon mathematics developed mainly by R. Thom and V.I. Arnold. We find that the stability of the folding process can be understood in terms of structures known as caustics, which occur in many kinds of wave phenomena. The picture that emerges is that natural selection has given us a set of protein molecules which have mechanical waves that propagate according to several mathematically specific restrictions. Successful simulations of folding can be used to test and constrain these wave motions. With some additional assumptions the theory explains or is consistent with a number of experimental facts about folding. We emphasize that this wave-based approach is fundamentally different from energy-based approaches.

Walter Simmons; Joel L. Weiner

2011-12-28T23:59:59.000Z

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.


461

The Principle of Stationary Action in Biophysics: Stability in Protein Folding  

E-Print Network [OSTI]

Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action principle can be applied directly to study the stability of biological processes. The action principle in classical physics starts with the first variation of the action and leads immediately to the equations of motion. The second variation of the action leads in a natural way to powerful theorems that provide quantitative treatment of stability and focusing and also explain how some very complex processes can behave as though some seemingly important forces drop out. We first apply these ideas to the non-equilibrium states involved in two-state folding. We treat torsional waves and use the action principle to talk about critical points in the dynamics. For some proteins the theory resembles TST. We reach several quantitative and qualitative conclusions. Besides giving an e...

Simmons, Walter

2013-01-01T23:59:59.000Z

462

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

463

Explaining the Price of Voluntary Carbon Offsets  

E-Print Network [OSTI]

Greenhouse Gas Initiative (RGGI) of 10 Northeastern and Mid-32, partici- pants in the RGGI are allowed to offset up to

Conte, Marc N.; Kotchen, Matthew

2009-01-01T23:59:59.000Z

464

Argonne explains nuclear recycling in 4 minutes  

SciTech Connect (OSTI)

Currently, when using nuclear energy only about five percent of the uranium used in a fuel rod gets fissioned for energy; after that, the rods are taken out of the reactor and put into permanent storage. There is a way, however, to use almost all of the uranium in a fuel rod. Recycling used nuclear fuel could produce hundreds of years of energy from just the uranium we've already mined, all of it carbon-free. Problems with older technology put a halt to recycling used nuclear fuel in the United States, but new techniques developed by scientists at Argonne National Laboratory address many of those issues. For more information, visit http://www.anl.gov/energy/nuclear-energy.

None

2012-01-01T23:59:59.000Z

465

CARES Helps Explain Secondary Organic Aerosols  

ScienceCinema (OSTI)

What happens when urban man-made pollution mixes with what we think of as pristine forest air? To know more about what this interaction means for the climate, the Carbonaceous Aerosol and Radiative Effects Study, or CARES, field campaign was designed in 2010. The sampling strategy during CARES was coordinated with CalNex 2010, another major field campaign that was planned in California in 2010 by the California Air Resources Board (CARB), the National Oceanic and Atmospheric Administration (NOAA), and the California Energy Commission (CEC). "We found two things. When urban pollution mixes with forest pollutions we get more secondary organic aerosols," said Rahul Zaveri, FCSD scientist and project lead on CARES. "SOAs are thought to be formed primarily from forest emissions but only when they interact with urban emissions. The data is saying that there will be climate cooling over the central California valley because of these interactions." Knowledge gained from detailed analyses of data gathered during the CARES campaign, together with laboratory experiments, is being used to improve existing climate models.

Zaveri, Rahul

2014-06-02T23:59:59.000Z

466

Laboratories are Needed to Explore, Explain VLBACHANDRA  

E-Print Network [OSTI]

of Fusion Science #12;Outline · Objectives for a Next Step Experiment in Magnetic Fusion · Burning Plasma, D) RPE Waste PE Balance of Plant Plasma Confinement and External Heating Key Plasma Performance of Fusion Research · Burning Plasma Physics - strong nonlinear coupling inherent in a fusion dominated

467

Laboratories are Needed to Explore, Explain VLBACHANDRA  

E-Print Network [OSTI]

://fire.pppl.gov Exploring the Frontiers of Burning Plasma Science #12;Outline · Objectives for a Next Step Experiment in Magnetic Fusion · Burning Plasma Performance Considerations · Compact High Field Approach - General, and it produces negligible nuclear waste or pollutants." What should we do to be ready? #12;Activities to Assess

468

Explain cosmic acceleration? First, correct Einstein  

E-Print Network [OSTI]

In creating his gravitational field equations Einstein unjustifiedly assumed that inertial mass, and its energy equivalent, is a source of gravity. Denying this assumption allows modifying the field equations to a form in which a positive cosmological constant appears as a uniform density of gravitationally repulsive matter. This repulsive matter is identified as the back sides of the 'drainholes' (called by some 'traversable wormholes') introduced by the author in 1973, which attract on the high, front sides and repel more strongly on the low, back sides. The field equations with a scalar field added produce cosmological models that 'bounce' off a positive minimum of the scale factor and accelerate throughout history. The 'dark drainholes' that radiate nothing visible are hypothesized to constitute the 'dark matter' inferred from observation, their excess of negative active mass over positive active mass driving the accelerating expansion. For a universe with spatial curvature zero, and the ratio of scale fa...

Ellis, H G

2006-01-01T23:59:59.000Z

469

Predicting and Explaining Success and Task Duration  

E-Print Network [OSTI]

(National Wildlife Coordinating Group 1985). The spread of fires is influenced by wind and moisture National Park and a model of fire spread from the National Wildlife Coordinating Group Fireline Handbook

470

Explaining data-driven document classifications  

Science Journals Connector (OSTI)

Many document classification applications require human understanding of the reasons for data-driven classification decisions by managers, client-facing employees, and the technical team. Predictive models treat documents as data to be classified, and ... Keywords: comprehensibility, document classification, instance level explanation, text mining

David Martens, Foster Provost

2014-03-01T23:59:59.000Z

471

Drastic growth effect explains sympatric cannibalistic  

E-Print Network [OSTI]

: Energy conversion factor ( fitness to its carrier will increase (Darwinian theory of evolution). If animal behavior is determined

Wakano, Joe Yuichiro

472

Explaining the Price of Voluntary Carbon Offsets  

E-Print Network [OSTI]

on fuel efficiency, hydropower, fuel substitution, solarbiomass methane, wind, hydropower, solar, and other. 8 OECDtypes of biomass methane, hydropower, so- lar, and wind. All

Conte, Marc N.; Kotchen, Matthew

2009-01-01T23:59:59.000Z

473

Argonne explains nuclear recycling in 4 minutes  

ScienceCinema (OSTI)

Currently, when using nuclear energy only about five percent of the uranium used in a fuel rod gets fissioned for energy; after that, the rods are taken out of the reactor and put into permanent storage. There is a way, however, to use almost all of the uranium in a fuel rod. Recycling used nuclear fuel could produce hundreds of years of energy from just the uranium we've already mined, all of it carbon-free. Problems with older technology put a halt to recycling used nuclear fuel in the United States, but new techniques developed by scientists at Argonne National Laboratory address many of those issues. For more information, visit http://www.anl.gov/energy/nuclear-energy.

None

2013-04-19T23:59:59.000Z

474

Explaining species distribution patterns through hierarchical modeling  

E-Print Network [OSTI]

, and its lower right at 34?20.5 S, 19?16.5 E, with total area of 4,456 km2. It comprises a rectangular area including the Kogelberg Biosphere Reserve and beyond, extending 41m east and 107m north from Cape Hangklip. The region is shown in Figure 1.... The survey paper of Guisan and Zimmerman (2000) provides discussion and extensive referencing. Let log ( p(k)i 1 ? p(k)i ) = wi??k + ?k + ?i, (5) where wi is a vector of grid cell level characteristics, and the ?ks are species level coefficients associated...

Gelfand, Alan E.; Silander, John A., Jr.; Wu, Shanshan; Latimer, Andrew; Lewis, Paul O.; Rebelo, Anthony G.; Holder, Mark T.

2006-01-01T23:59:59.000Z

475

Fractal Networks Explain Regional Myocardial Flow Heterogeneity  

Science Journals Connector (OSTI)

Regional myocardial blood flow is very heterogeneous. This has been found by injection of radioactively labeled microspheres, or the molecular microsphere iododesmethylimipramine, and measuring the depositio...

Johannes H. G. M. van Beek; James B. Bassingthwaighte

1989-01-01T23:59:59.000Z

476

NDA Explained | National Nuclear Security Administration  

National Nuclear Security Administration (NNSA)

Twitter Youtube Flickr RSS People Mission Managing the Stockpile Preventing Proliferation Powering the Nuclear Navy Emergency Response Recapitalizing Our Infrastructure...

477

1.17 - Protein Folding in the Endoplasmic Reticulum  

Science Journals Connector (OSTI)

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

N. Naidoo

2011-01-01T23:59:59.000Z

478

Extracellular Proteins Promote Zinc Sulfide Aggregation  

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

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

479

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

Science Journals Connector (OSTI)

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

2012-01-01T23:59:59.000Z

480

Type IV Pilin Proteins: Versatile Molecular Modules  

Science Journals Connector (OSTI)

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

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

2012-12-01T23:59:59.000Z

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.


481

Collection of very low resolution protein data  

Science Journals Connector (OSTI)

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

Miller, S.T.

1999-12-01T23:59:59.000Z

482

Energy use by biological protein transport pathways  

E-Print Network [OSTI]

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

Economou, Tassos

483

CORN GERM: A VALUABLE PROTEIN FOOD  

Science Journals Connector (OSTI)

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

H. H. MITCHELL; JESSIE R. BEADLES

1944-02-11T23:59:59.000Z

484

Critical aspects of hierarchical protein folding  

E-Print Network [OSTI]

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

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

1998-01-13T23:59:59.000Z

485

PROTEIN INTERACTIONS AND DISEASE MARICEL KANN  

E-Print Network [OSTI]

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

Radivojac, Predrag

486

Introduction to protein folding for physicists  

E-Print Network [OSTI]

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

Pablo Echenique

2007-05-13T23:59:59.000Z

487

The Low Polarity of Many Membrane Proteins  

Science Journals Connector (OSTI)

...buried in the hydrophobic interior of the membrane. from their Thus, the polarity index appears to be a useful parameter for edia. the characterization of membrane proteins. 45.6 46.1 48.1 48.3 50.0 52.0 37 38 12 39 27 27 This work was supported...

Roderick A. Capaldi; Garret Vanderkooi

1972-01-01T23:59:59.000Z

488

Abstract 3411: Targeting of EWS-FLI1 with small molecule YK-4-279 reduces xenograft growth by disruption of disordered protein-protein interactions  

Science Journals Connector (OSTI)

...xenograft growth by disruption of disordered protein-protein interactions Jeffrey A...revealed its significant intrinsically disordered regions. The intrinsically disordered regions enhance protein-protein interactions while presenting...

Jeffrey A. Toretsky; Hayriye V. Erkizan; Yali Kong; Melinda Merchant; Julie S. Barber-Rotenberg; Milton L. Brown; and Aykut ren

2010-04-15T23:59:59.000Z

489

Molecular nonlinear dynamics and protein thermal uncertainty quantification  

SciTech Connect (OSTI)

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

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

2014-03-15T23:59:59.000Z

490

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

491

Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions  

Science Journals Connector (OSTI)

To demonstrate a new strategy for engineering crystal lattices through metal-mediated interactions, apo acyl carrier protein has been crystallized in the presence of zinc ions. The structure was solved with MAD phasing using zinc anomalous signals.

Qiu, X.

2004-08-26T23:59:59.000Z

492

HIV-1 Tat protein and endothelium: From protein/cell interaction to AIDS-associated pathologies  

Science Journals Connector (OSTI)

Tat protein, the transactivating factor of the human immunodeficiency virus type 1 (HIV-1), is a small cationic polypeptide that can be released from HIV-1 infected cells. Extracellular Tat elicits different biol...

Marco Rusnati; Marco Presta

2002-01-01T23:59:59.000Z

493

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

SciTech Connect (OSTI)

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

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

2007-01-01T23:59:59.000Z

494

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

E-Print Network [OSTI]

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

Shang, Yue

2007-09-17T23:59:59.000Z

495

Photon Sciences | About Photon Sciences | What About Proteins?  

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

496

2D Ising model for hydrated protein surfaces  

Science Journals Connector (OSTI)

To understand the nature of the glassy dielectric relaxation recently observed in hydrated protein powders, we model the protein surface as a 2D Ising square net, and identify frustration at the...

G. Careri

497

Production and Functional Analysis of Recombinant Bovine Morphogenic Protein 15  

E-Print Network [OSTI]

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

Burns, Gregory Willis

2013-11-21T23:59:59.000Z

498

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

499

PURIFICATION OF GST-TAGGED PROTEINS Materials/Solutions  

E-Print Network [OSTI]

PURIFICATION OF GST-TAGGED PROTEINS Materials/Solutions: Glutathione Agarose or Glutathione fraction + 90 ul water + 1 ml Bradford reagent; measure absorbance at 595 nm and calculate protein

Lamond, Angus I.

500

Protein quality control in the mammalian endoplasmic reticulum  

E-Print Network [OSTI]

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

Klemm, Elizabeth J. (Elizabeth Joanna)

2011-01-01T23:59:59.000Z