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1

Horst and Graben | Open Energy Information  

Open Energy Info (EERE)

Horst and Graben Horst and Graben Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Print PDF Horst and Graben Dictionary.png Horst and Graben: Topographic features found in a normal fault zone forming ridges and valleys. A graben represents a block of land that has dropped down relative to the landscape and a horst represents a block of land remaining higher than the general landscape. Other definitions:Wikipedia Reegle Topographic Features List of topographic features commonly encountered in geothermal resource areas: Mountainous Horst and Graben Shield Volcano Flat Lava Dome Stratovolcano Cinder Cone Caldera Depression Resurgent Dome Complex A "horst and graben" is a crustal-extension structure, composed of a series of normal faults, typical of the Basin & Range region of the US and

2

John Horst  

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

John Horst is aPublic Affairs Specialist with the Office of Energy Efficiency and Renewable Energy.

3

Tectonic and flexural significance of Middle Devonian graben-fill sequence in new Albany shale, central Kentucky  

SciTech Connect

The third tectonic phase of the Acadian orogeny began in the late Middle Devonian, and the sedimentary record of that event is largely restricted to the deeper, more proximal portions of the Appalachian foreland and Illinois intercratonic basins. Much of the intervening area, on and near the Cincinnati arch, was uplifted and subjected to erosion by movement on the peripheral bulge accompanying the initiation of the third tectonic phase. However, bulge movement also reactivated basement fault systems in Kentucky and created a series of grabens that were filled with eroded sediments and debris flows from adjacent horsts. Although rarely preserved, a buried Devonian graben along Carpenter Fork in Boyle County, central Kentucky, reveals such a sequence. The graben is bounded by upthrown blocks of Middle Devonian Boyle Dolomite, which also floors the graben. Within the graben a black-shale unit, apparently absent elsewhere, conformably overlies the Boyle and grades upward into debris-flow deposits represented by the Duffin breccia facies of the New Albany Shale. The Duffin contains clasts of the shale, as well as of chert, silicified fossils, and fine to boulder-size dolostone clasts eroded from the Boyle high on the flanks of the graben. The underlying shale also exhibits evidence of penecontemporaneous soft-sediment deformation related to the debris-flow emplacement of Boyle residue in the graben and due to later loading by the Duffin.

Barnett, S.F.; Ettensohn, F.R.; Mellon, C. (Univ. of Kentucky, Lexington (USA))

1989-08-01T23:59:59.000Z

4

SOME CLASSES OF COMPLETELY MONOTONIC FUNCTIONS HORST ALZER AND CHRISTIAN BERG  

E-Print Network (OSTI)

SOME CLASSES OF COMPLETELY MONOTONIC FUNCTIONS HORST ALZER AND CHRISTIAN BERG Morsbacher Str. 10, D of Copenhagen, Universitetsparken 5, DK-2100, Denmark; berg@math.ku.dk Abstract. We prove: (i) Let Fn(x) = Pn of the most important 1 #12;2 HORST ALZER AND CHRISTIAN BERG properties of completely monotonic functions can

Berg, Christian

5

Folding@HomeFolding@Home Vijay Pande  

E-Print Network (OSTI)

Folding@HomeFolding@Home Vijay Pande #12;http://folding.stanford.edu © Vijay S. Pande 1999,000,000 PCs on the internet Folding@Home People donate their idle computer time They visit our website://folding.stanford.edu © Vijay S. Pande 1999-2003 Folding@HomeFolding@Home:: VeryVery powerful & cost effectivepowerful & cost

Dally, William J.

6

Tectonic evolution of the Thakkahola Graben and Dhaulagiri Himalaya, Central Nepal  

E-Print Network (OSTI)

Three extensional fault systems intersect in the central Nepal Himalaya: the South Tibetan fault system (STFS); the Thakkhola graben; and structures bounding the Upper Mustang Massif (UMM). Interactions between these systems ...

Hurtado, Jos Miguel, 1974-

2002-01-01T23:59:59.000Z

7

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

8

Simultaneous Inversion for 3-D Crustal Structure and Hypocentres Including Direct, Refracted and Reflected PhasesIII. Application to the Southern Rhine Graben Seismic Region, Germany  

Science Journals Connector (OSTI)

......model of the southern Wine Graben and phase notations...Graben is of much better quality than that of the northern...Using the same minimal quality criteria as in part I1...see Table 1). To increase the vertical resolution...the study is that an increase of the number of blocks......

Manfred Koch

1993-03-01T23:59:59.000Z

9

On the origin of graben and ridges within and near volcanically buried craters and basins in Mercury's northern plains  

E-Print Network (OSTI)

in Mercury's northern plains Andrew M. Freed,1 David M. Blair,1 Thomas R. Watters,2 Christian Klimczak,3 Paul volcanic plains taken by the MESSENGER spacecraft reveal a large number of buried impact craters and basins pooled lavas were thickest, and no graben are predicted within generally thinner plains outside of major

Zuber, Maria

10

Multiply folded graphene  

Science Journals Connector (OSTI)

The folding of paper, hide, and woven fabric has been used for millennia to achieve enhanced articulation, curvature, and visual appeal for intrinsically flat, two-dimensional materials. For graphene, an ideal two-dimensional material, folding may transform it to complex shapes with new and distinct properties. Here, we present experimental results that folded structures in graphene, termed grafold, exist, and their formations can be controlled by introducing anisotropic surface curvature during graphene synthesis or transfer processes. Using pseudopotential-density-functional-theory calculations, we also show that double folding modifies the electronic band structure of graphene. Furthermore, we demonstrate the intercalation of C60 into the grafolds. Intercalation or functionalization of the chemically reactive folds further expands grafold's mechanical, chemical, optical, and electronic diversity.

Kwanpyo Kim; Zonghoon Lee; Brad D. Malone; Kevin T. Chan; Benjamn Alemn; William Regan; Will Gannett; M. F. Crommie; Marvin L. Cohen; A. Zettl

2011-06-27T23:59:59.000Z

11

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

12

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

13

Predicting protein folding pathways  

Science Journals Connector (OSTI)

......residues is a good measure of the amount of water displaced by the residue- residue contact...twodomain ?/? enzyme that maintains pools of tetrahydrofolate used in nucleotide...H.J. and Wright,P.E. (2000) Conservation of folding pathways in evolutionary distant......

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

2004-08-01T23:59:59.000Z

14

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

15

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

16

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

17

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

18

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

19

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

20

Folded waveguide coupler  

DOE Patents (OSTI)

A resonant cavity waveguide coupler for ICRH of a magnetically confined plasma. The coupler consists of a series of inter-leaved metallic vanes disposed withn an enclosure analogous to a very wide, simple rectangular waveguide that has been "folded" several times. At the mouth of the coupler, a polarizing plate is provided which has coupling apertures aligned with selected folds of the waveguide through which rf waves are launched with magnetic fields of the waves aligned in parallel with the magnetic fields confining the plasma being heated to provide coupling to the fast magnetosonic wave within the plasma in the frequency usage of from about 50-200 mHz. A shorting plate terminates the back of the cavity at a distance approximately equal to one-half the guide wavelength from the mouth of the coupler to ensure that the electric field of the waves launched through the polarizing plate apertures are small while the magnetic field is near a maximum. Power is fed into the coupler folded cavity by means of an input coaxial line feed arrangement at a point which provides an impedance match between the cavity and the coaxial input line.

Owens, Thomas L. (Kingston, TN)

1988-03-01T23:59:59.000Z

Note: This page contains sample records for the topic "folds grabens horst" 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

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

22

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.

23

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.

24

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

25

Folding and binding Editorial overview  

E-Print Network (OSTI)

is on the study of how protein folding, unfolding and aggregation reactions commence, and on the study of California, Berkeley. Her lab focuses on studies of protein folding and dynamics. Currently she­based kinetics. Much of the progress that has been made in the past fifty years in the study of protein folding

26

Protein folding in the ER.  

SciTech Connect

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

27

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

28

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

29

Uncovering Allostery in a Uniquely Folded Metalloprotein /  

E-Print Network (OSTI)

M (2005) Downhill protein folding: evolution meets physics.based models for protein folding and function. Proteins:48-51). This is because protein folding and protein function

Baxter, Elizabeth Leigh

2013-01-01T23:59:59.000Z

30

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

31

Protein Folding Rates Correlate with Heterogeneity of Folding Mechanism  

Science Journals Connector (OSTI)

By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse-grained, C? model G? proteins, we show that folding rates correlate with the degree of heterogeneity in the formation of native contacts. Statistically significant correlations are observed between folding rates and measures of heterogeneity inherent in the native topology, as well as between rates and the variance in the distribution of either experimentally measured or simulated ? values.

B. ztop; M. R. Ejtehadi; S. S. Plotkin

2004-11-12T23:59:59.000Z

32

Fast events in protein folding  

SciTech Connect

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

33

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

34

PERSPECTIVES Photo:HorstWagner  

E-Print Network (OSTI)

of the population. Enormous po- tential is still lying fallow here, and Eu- rope needs to utilize it if it is to hold its own in the international context," em- phasized Gruss. This is the aim of the EU's new Teaming model: South Korea's government has explicitly named the prototype to be used in founding its Institute

35

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

36

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

37

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

38

Characterization of protein folding intermediates  

SciTech Connect

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

39

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

40

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

Note: This page contains sample records for the topic "folds grabens horst" 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

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

42

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

43

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

44

Investigating Protein Folding and Function by Manipulating Rare and Partially-Folded Conformations  

E-Print Network (OSTI)

and G.D. Rose, The protein-folding problem: the native foldZ. Zhou, and Y. Bai, A protein folding pathway with multipleintermediate state in protein folding by a hydrophobic

Horner, Geoffrey Ashworth

2010-01-01T23:59:59.000Z

45

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...

46

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...

47

Folding for binding or binding for folding? Amedeo Caflisch  

E-Print Network (OSTI)

that there exist soluble proteins which lack a well-defined folded structure or contain disordered segments [1, 2]. A computational approach trained on known proteins with intrinsic disorder has pre- dicted unstructured regions-425, 2003. It is posted with permission from Elsevier. November 20, 2003 Abstract A number of proteins

Caflisch, Amedeo

48

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

49

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

50

Folding in regions of extension  

Science Journals Connector (OSTI)

......isostatically compensated and why the Moho remains flat in such regions. Finally, the model accounts...extensional folds from examples in the Rocky Mountain Basin and Range province, U...the Basin and Range-Colorado Plateau-Rocky Mountain transition from coherence analysis......

F. Lvy; C. Jaupart

2011-06-01T23:59:59.000Z

51

Folding in regions of extension  

Science Journals Connector (OSTI)

......For the large crustal temperatures that are implied by the small...interesting feature is the Snake River Plain at the northern...implications for fold and rock fabric development, central Mojave metamorphic...Evans B., 1979. Stress and temperature in the bending lithosphere......

F. Lvy; C. Jaupart

2011-06-01T23:59:59.000Z

52

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

53

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

54

Seismic Techniques | Open Energy Information  

Open Energy Info (EERE)

Seismic Techniques Seismic Techniques Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Seismic Techniques Details Activities (0) Areas (0) Regions (0) NEPA(10) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Seismic Techniques Parent Exploration Technique: Geophysical Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation. Thermal: High temperatures and pressure impact the compressional and shear wave velocities.

55

Reflection Survey | Open Energy Information  

Open Energy Info (EERE)

Page Page Edit with form History Facebook icon Twitter icon » Reflection Survey Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Reflection Survey Details Activities (35) Areas (22) Regions (2) NEPA(3) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Seismic Techniques Parent Exploration Technique: Active Seismic Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation. Thermal: High temperatures and pressure impact the compressional and shear wave velocities.

56

Active Seismic Techniques | Open Energy Information  

Open Energy Info (EERE)

Active Seismic Techniques Active Seismic Techniques Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Active Seismic Techniques Details Activities (0) Areas (0) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Seismic Techniques Parent Exploration Technique: Seismic Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation. Thermal: High temperatures and pressure impact the compressional and shear wave velocities.

57

Teleseismic-Seismic Monitoring | Open Energy Information  

Open Energy Info (EERE)

Teleseismic-Seismic Monitoring Teleseismic-Seismic Monitoring Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Teleseismic-Seismic Monitoring Details Activities (33) Areas (18) Regions (5) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Seismic Techniques Parent Exploration Technique: Passive Seismic Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Map geothermal reservoir geometry. Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation.

58

Vertical Seismic Profiling | Open Energy Information  

Open Energy Info (EERE)

Vertical Seismic Profiling Vertical Seismic Profiling Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Vertical Seismic Profiling Details Activities (4) Areas (3) Regions (1) NEPA(0) Exploration Technique Information Exploration Group: Downhole Techniques Exploration Sub Group: Borehole Seismic Techniques Parent Exploration Technique: Borehole Seismic Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation. Thermal: High temperatures and pressure impact the compressional and shear wave velocities.

59

Borehole Seismic Techniques | Open Energy Information  

Open Energy Info (EERE)

Borehole Seismic Techniques Borehole Seismic Techniques Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Borehole Seismic Techniques Details Activities (0) Areas (0) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Downhole Techniques Exploration Sub Group: Borehole Seismic Techniques Parent Exploration Technique: Downhole Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation Thermal: High temperatures and pressure impact the compressional and shear wave velocities

60

Passive Seismic Techniques | Open Energy Information  

Open Energy Info (EERE)

Passive Seismic Techniques Passive Seismic Techniques Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Passive Seismic Techniques Details Activities (0) Areas (0) Regions (0) NEPA(4) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Seismic Techniques Parent Exploration Technique: Seismic Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation. Thermal: High temperatures and pressure impact the compressional and shear wave velocities.

Note: This page contains sample records for the topic "folds grabens horst" 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

Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways  

E-Print Network (OSTI)

Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways Ali induce dominant pathway mechanisms in protein folding. Citation: Mohazab AR, Plotkin SS (2013) Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways. PLoS ONE 8(1): e53642

Plotkin, Steven S.

62

Folding pathway of a lattice model for protein folding Vijay S. Pande1  

E-Print Network (OSTI)

Folding pathway of a lattice model for protein folding Vijay S. Pande1 and Daniel S. Rokhsar1 principles that describe protein folding, then one might expect them to apply to simplified models

Croquette, Vincent

63

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

64

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

65

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.

66

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

67

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.

68

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

69

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

70

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

71

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

72

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

73

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

74

Protein Folding Trajectories Analysis: Summarization, Event Detection and Consensus Partial Folding Pathway  

E-Print Network (OSTI)

Protein Folding Trajectories Analysis: Summarization, Event Detection and Consensus Partial Folding in protein folding trajectories. We pro- pose an approach that employs the simplicity of contact maps and po- tentially cure diseases caused by misfolding. The protein folding problem is therefore one

Yang, Hui

75

Computational investigations of folded self-avoiding walks related to protein folding  

E-Print Network (OSTI)

Computational investigations of folded self-avoiding walks related to protein folding Jacques M, protein folding, protein structure prediction 1. Introduction Self-avoiding walks (SAWs) have been studied, 9], authors of this manuscript have investigated some dynamic protein folding models. They have

Paris-Sud XI, Université de

76

A review of recent advances in ab initio protein folding by the Folding@home project  

E-Print Network (OSTI)

A review of recent advances in ab initio protein folding by the Folding@home project William Ito molecular simulations of protein folding. Thanks to engineering innovations like a Graphical Processing Unit power, allowing it to simulate longer and more complex protein folding mechanisms than ever before

77

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

78

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

79

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

80

Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity  

E-Print Network (OSTI)

C. (1999). Membrane protein folding and stability: PhysicalA. S. & Hristova, K. (1998). Protein folding in membranes:Mutational analysis of protein folding and stability. In

Fernndez-Vidal, Mnica; Jayasinghe, Sajith; Ladokhin, Alexey S; White, Stephen H

2007-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "folds grabens horst" 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

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

82

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

83

Protein Vivisection Reveals Elusive Intermediates in Folding  

SciTech Connect

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

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

2010-05-25T23:59:59.000Z

84

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

85

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

86

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

87

Microsoft Word - RNA_folding_Herschlag.doc  

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

March 2003 Exploring the Folding Landscape of a Structured RNA by SAXS Rick Russell, Ian S. Millett, Sebastian Doniach and Daniel Herschlag Stanford University One goal of genome...

88

Structural Insight into RNA Hairpin Folding Intermediates Gregory R. Bowman,  

E-Print Network (OSTI)

on the Folding@home infrastructure to obtain better sampling and, therefore, greater insight into RNA folding

Guibas, Leonidas J.

89

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

90

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

91

Fan-fold shielded electrical leads  

DOE Patents (OSTI)

Disclosed are fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate. 3 figs.

Rohatgi, R.R.; Cowan, T.E.

1996-06-11T23:59:59.000Z

92

Single-molecule studies of riboswitch folding  

Science Journals Connector (OSTI)

Abstract The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.

Andrew Savinov; Christian F. Perez; Steven M. Block

2014-01-01T23:59:59.000Z

93

Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and  

E-Print Network (OSTI)

Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics for studying protein folding kinetics. It uses the recently intro- duced Stochastic Roadmap Simulation (SRS validate the SRS method and indicate its potential as a general tool for studying protein folding kinetics

Pratt, Vaughan

94

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

95

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

96

Cooperativity and Contact Order in Protein Folding  

E-Print Network (OSTI)

The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as in the absence of cooperativity. For a fixed native geometry, small changes in the effective contact map may affect the folding times in a chance way and to the extent that is comparable to the shift in the folding times due to cooperativity. The contact order controlls folding scenarios: the average times necessary to bring pairs of amino acids into their near native separations depend on the sequential distances within the pairs. This dependence is largely monotonic, regardless of the cooperativity, and the dominant trend could be described by a single parameter like the average contact order. However, it is the deviations from the trend which are usually found to set the net folding times.

Marek Cieplak

2004-01-11T23:59:59.000Z

97

Cooperativity and contact order in protein folding  

Science Journals Connector (OSTI)

The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as in the absence of cooperativity. For a fixed native geometry, small changes in the effective contact map may affect the folding times in a chance way, and, to an extent that is comparable to the shift in the folding times due to cooperativity. The contact order controls folding scenarios: the average times necessary to bring pairs of amino acids into their near native separations depend on the sequential distances within the pairs. This dependence is largely monotonic, regardless of the cooperativity, and the dominant trend could be described by a single parameter like the average contact order. However, it is the deviations from the trend which are usually found to set the net folding times.

Marek Cieplak

2004-03-23T23:59:59.000Z

98

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

99

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

100

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 "folds grabens horst" 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

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

102

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

103

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

104

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

105

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

106

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

E-Print Network (OSTI)

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

Zaki, Mohammed Javeed

107

Data Analysis of Villin Headpiece Subdomain Folding Simulations.  

E-Print Network (OSTI)

seeks to understand the process of protein folding by analyzing the vast amount of data generated while simulating the folding of the villin headpiece. Introduction Protein folding has been called one proteins unlike homology or threading based approaches. Protein folding studies the folding trajectory

108

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

109

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

110

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

111

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.

112

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

113

Protein Folding: A New Geometric Analysis  

E-Print Network (OSTI)

A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it is possible that so many initial configurations proceed to fold to a unique final configuration. We put energy and dynamical considerations temporarily aside and focus upon the geometry alone. We parameterize the structure of an idealized protein using the concept of a ribbon from differential geometry. The deformation of the ribbon is described by introducing a generic twisting Ansatz. The folding process in this picture entails a change in shape guided by the local amino acid geometry. The theory is reparamaterization invariant from the start, so the final shape is independent of folding time. We develop differential equations for the changing shape. For some parameter ranges, a sine-Gordon torsion soliton is found. This purely geometric waveform has properties similar to dynamical solitons. Namely: A threshold distortion of the molecule is required to initiate the soliton, after which, small additional distortions do not change the waveform. In this analysis, the soliton twists the molecule until bonds form. The analysis reveals a quantitative relationship between the geometry of the amino acids and the folded form.

Walter A. Simmons; Joel L. Weiner

2008-09-11T23:59:59.000Z

114

Isolation, folding and structural investigations of the amino...  

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

folding and structural investigations of the amino acid transporter OEP16. Isolation, folding and structural investigations of the amino acid transporter OEP16. Abstract: Membrane...

115

Single-Molecule Dynamics Reveals Cooperative Binding-Folding...  

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

Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Abstract: The...

116

Journal Article: Folding and association of a homotetrameric...  

Office of Scientific and Technical Information (OSTI)

Folding and association of a homotetrameric protein complex in an all-atom Go model Citation Details Title: Folding and association of a homotetrameric protein complex in an...

117

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

118

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

119

Coarse grained description of protein folding  

Science Journals Connector (OSTI)

We consider two- and three-dimensional lattice models of proteins that were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of the effective states. The first method is based on the steepest descent mapping of states to underlying local energy minima and the other involves an additional projection to maximally compact conformations. Both methods generate connectivity patterns that allow one to distinguish between the good and bad folders. Connectivity graphs corresponding to the folding funnel have few loops and are thus treelike. The Arrhenius law for the median folding time of a 16-monomer sequence is established and the corresponding barrier is related to easily identifiable kinetic trap states.

Marek Cieplak and Trinh Xuan Hoang

1998-09-01T23:59:59.000Z

120

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

Note: This page contains sample records for the topic "folds grabens horst" 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

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 prot...

Simmons, Walter

2011-01-01T23:59:59.000Z

122

Energetic Components of Cooperative Protein Folding  

E-Print Network (OSTI)

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.

Huseyin Kaya; Hue Sun Chan

2000-10-11T23:59:59.000Z

123

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

124

Energetic Components of Cooperative Protein Folding  

Science Journals Connector (OSTI)

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptidelike local conformational restrictions and environment-dependent hydrogen-bondinglike interactions.

Hseyin Kaya and Hue Sun Chan

2000-11-27T23:59:59.000Z

125

Circular permutant GFP insertion folding reporters  

SciTech Connect

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

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

2011-06-14T23:59:59.000Z

126

Circular permutant GFP insertion folding reporters  

SciTech Connect

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

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

2008-06-24T23:59:59.000Z

127

Circular permutant GFP insertion folding reporters  

DOE Patents (OSTI)

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Waldo, Geoffrey S.; Cabantous, Stephanie

2013-04-16T23:59:59.000Z

128

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

129

CSAW: a dynamical model of protein folding  

E-Print Network (OSTI)

CSAW (conditioned self-avoiding walk) is a model of protein folding that combines SAW (self-avoiding walk) with Monte-Carlo. It simulates the Brownian motion of a chain molecule in the presence of interactions, both among chain residues, and with the environment. In a first model that includes the hydrophobic effect and hydrogen bonding, a chain of 30 residues folds into a native state with stable secondary and tertiary structures. The process starts with a rapid collapse into an intermediate "molten globule", which slowly decays into the native state afer a relatively long quiescent period. The behavior of the radius of gyration mimics experimental data.

Kerson Huang

2006-01-12T23:59:59.000Z

130

Circular permutant GFP insertion folding reporters  

SciTech Connect

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Waldo, Geoffrey S; Cabantous, Stephanie

2013-02-12T23:59:59.000Z

131

Algorithmic design of self-folding polyhedra  

Science Journals Connector (OSTI)

...chosen according to an algorithm described below. Fifty samples of each net were self-folded in the experiments. We used Autodesk AutoCAD to draw nets and then printed them on transparent sheets to make photomasks. Sides of a panel measured 300 {mu...

Shivendra Pandey; Margaret Ewing; Andrew Kunas; Nghi Nguyen; David H. Gracias; Govind Menon

2011-01-01T23:59:59.000Z

132

Simultaneous Alignment and Folding of Protein Sequences  

E-Print Network (OSTI)

is to predict for every input sequence the minimum free-energy non-crossing structure (in O(n3 ) time function. Since the structure of RNA is evolu- tionarily more conserved than its sequence, predicting a folding with minimal free energy [5, 6, 7, 8, 9]. Albeit this so-named thermodynamic approach is a success

Gifford, David K.

133

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

134

Solvent-induced forces in protein folding  

SciTech Connect

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

135

Folded-path optical analysis gas cell  

DOE Patents (OSTI)

A folded-path gas cell employs an elliptical concave mirror in confronting relationship to two substantially spherical concave mirrors. At least one of the spherical mirrors, and usually both, are formed with an added cylindrical component to increase orthogonal focii coincidence and thereby to increase the radiation energy throughput characteristic of the cell.

Carangelo, Robert M. (Glastonbury, CT); Wright, David D. (Vershire, VT)

1995-01-01T23:59:59.000Z

136

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.

137

Early Events in Protein Folding Explored by Rapid Mixing Methods  

E-Print Network (OSTI)

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

Roder, Heinrich

138

COMMUNICATION First Principles Prediction of Protein Folding Rates  

E-Print Network (OSTI)

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

Goddard III, William A.

139

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

140

Nonlinear dynamics of secondary protein folding Natalia G. Berloff  

E-Print Network (OSTI)

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

Note: This page contains sample records for the topic "folds grabens horst" 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 by zipping and assembly S. Banu Ozkan*  

E-Print Network (OSTI)

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

Southern California, University of

142

Polypeptide chain collapse and protein folding Jayant B. Udgaonkar  

E-Print Network (OSTI)

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

143

Automated Discovery of Structural Signatures of Protein Fold and Function  

E-Print Network (OSTI)

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

Muggleton, Stephen H.

144

Heteropolymer Folding 9 1. C. Gh'elis and J. Yon, Protein Folding (Academic, New York, 1982).  

E-Print Network (OSTI)

Heteropolymer Folding 9 References 1. C. Gh'elis and J. Yon, Protein Folding (Academic, New York, editor, The Protein Folding Problem (Westview, Boulder, 1984).. 5. N. G??o, Annu. Rev. Biophys. Bioeng. 12 for Protein Folding, Europhys. Lett. 6, 307 (1988). 14. G. Iori, E. Marinari, G. Parisi and M. V. Struglia

Roma "La Sapienza", Università di

145

Planning to fold multiple objects from a single self-folding sheet  

E-Print Network (OSTI)

This paper considers planning and control algorithms that enable a programmable sheet to realize different shapes by autonomous folding. Prior work on self-reconfiguring machines has considered modular systems in which ...

An, Byoung Kwon

146

New Monte Carlo Algorithm for Protein Folding  

Science Journals Connector (OSTI)

We demonstrate that the recently introduced pruned-enriched Rosenbluth method leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare the results to published Monte Carlo studies. In all cases our algorithms are faster than previous ones, and in several cases we find new minimal energy states. In addition, our algorithms give estimates for the partition sum at finite temperatures.

Helge Frauenkron; Ugo Bastolla; Erwin Gerstner; Peter Grassberger; Walter Nadler

1998-04-06T23:59:59.000Z

147

Simple Models of the Protein Folding Problem  

E-Print Network (OSTI)

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

Chao Tang

1999-12-26T23:59:59.000Z

148

Structure of a Folding Intermediate Reveals the Interplay Between Core and Peripheral Elements in RNA Folding  

SciTech Connect

Though the molecular architecture of many native RNA structures has been characterized, the structures of folding intermediates are poorly defined. Here, we present a nucleotide-level model of a highly structured equilibrium folding intermediate of the specificity domain of the Bacillus subtilis RNase P RNA, obtained using chemical and nuclease mapping, circular dichroism spectroscopy, small-angle X-ray scattering and molecular modeling. The crystal structure indicates that the 154 nucleotide specificity domain is composed of several secondary and tertiary structural modules. The structure of the intermediate contains modules composed of secondary structures and short-range tertiary interactions, implying a sequential order of tertiary structure formation during folding. The intermediate lacks the native core and several long-range interactions among peripheral regions, such as a GAAA tetraloop and its receptor. Folding to the native structure requires the local rearrangement of a T-loop in the core in concert with the formation of the GAAA tetraloop-receptor interaction. The interplay of core and peripheral structure formation rationalizes the high degree of cooperativity observed in the folding transition leading to the native structure.

Baird, Nathan J.; Westhof, Eric; Qin, Hong; Pan, Tao; Sosnick, Tobin R. (UC); (CNFRS)

2010-07-13T23:59:59.000Z

149

Solvent-Mediated Folding of a Doubly Charged Anion. | EMSL  

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

Solvent-Mediated Folding of a Doubly Charged Anion. Solvent-Mediated Folding of a Doubly Charged Anion. Abstract: The microsolvation of suberate dianion, -O2C(CH2)6CO2-, with two...

150

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

151

Why are MD simulated protein folding times wrong? Dmitry Nerukh  

E-Print Network (OSTI)

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

Nerukh, Dmitry

152

New Crystal Structures Lift Fog around Protein Folding  

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

153

Experimental and Computational Studies on Protein Folding, Misfolding and Stability  

E-Print Network (OSTI)

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

Wei, Yun

2010-07-14T23:59:59.000Z

154

Protein Folding Simulation in CCP Luca Bortolussi1  

E-Print Network (OSTI)

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

Bortolussi, Luca

155

Protein Folding Simulation by Two-Stage Optimization  

Science Journals Connector (OSTI)

This paper proposes a two-stage optimization approach for protein folding simulation in the FCC lattice, inspired from...

A. Dayem Ullah; L. Kapsokalivas; M. Mann

2009-01-01T23:59:59.000Z

156

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

157

Combinatorial Problems on Strings with Applications to Protein Folding  

E-Print Network (OSTI)

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

Newman, Alantha

158

Protein Folding Simulation by Two-Stage Optimization  

E-Print Network (OSTI)

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

Will, Sebastian

159

Protein folding with stochastic L-systems Gemma Danks1  

E-Print Network (OSTI)

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

Stepney, Susan

160

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

Note: This page contains sample records for the topic "folds grabens horst" 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

Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding  

E-Print Network (OSTI)

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

Michalet, Xavier

162

Polymer Collapse, Protein Folding, and the Percolation Threshold  

E-Print Network (OSTI)

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

Meirovitch, Hagai

163

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-Print Network (OSTI)

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

Janke, Wolfhard

164

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

E-Print Network (OSTI)

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

Weston, Ken

165

John von Neumann Institute for Computing Monte Carlo Protein Folding  

E-Print Network (OSTI)

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

Hsu, Hsiao-Ping

166

Protein folding: Then and now Yiwen Chen 1  

E-Print Network (OSTI)

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

Dokholyan, Nikolay V.

167

Author's personal copy Protein folding: Then and now  

E-Print Network (OSTI)

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

Dokholyan, Nikolay V.

168

Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao  

E-Print Network (OSTI)

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

Bystroff, Chris

169

COMMUNICATION Are Residues in a Protein Folding Nucleus  

E-Print Network (OSTI)

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

Dai, Yang

170

MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix  

E-Print Network (OSTI)

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

Dix, Daniel B.

171

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

172

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

173

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

174

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

175

Folding Kinetics of the Cooperatively Folded Subdomain of the IB Ankyrin Repeat Domain  

E-Print Network (OSTI)

Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina 3 Consejo Nacional de Investigaciones Cientificas y Tecnicas de Argentina, C1428EGA Buenos Aires, Argentina Received 17 December 2010 complex folding kinetics, with two sequential on-pathway high-energy intermedi- ates. The effect

Komives, Elizabeth A.

176

Protein-Folding Landscapes in Multi-Chain Systems  

SciTech Connect

Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the thermodynamics of folding for a Miyazawa-Jernigan model 64-mer in isolation to results obtained in the presence of additional chains. The melting temperature falls as the chain concentration increases. In multi-chain systems, free-energy landscapes for folding show an increased preference for misfolded states. Misfolding is accompanied by an increase in inter-protein interactions; however, near the folding temperature, the transition from folded chains to misfolded and associated chains isentropically driven. A majority of the most probable inter-protein contacts are also native contacts, suggesting that native topology plays a role in early stages of aggregation.

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

2005-06-20T23:59:59.000Z

177

The Quirky Collider Signals of Folded Supersymmetry  

SciTech Connect

We investigate the collider signals associated with scalar quirks ('squirks') in folded supersymmetric models. As opposed to regular superpartners in supersymmetric models these particles are uncolored, but are instead charged under a new confining group, leading to radically different collider signals. Due to the new strong dynamics, squirks that are pair produced do not hadronize separately, but rather form a highly excited bound state. The excited 'squirkonium' loses energy to radiation before annihilating back into Standard Model particles. We calculate the branching fractions into various channels for this process, which is prompt on collider time-scales. The most promising annihilation channel for discovery is W+photon which dominates for squirkonium near its ground state. We demonstrate the feasibility of the LHC search, showing that the mass peak is visible above the SM continuum background and estimate the discovery reach.

Burdman, Gustavo; Chacko, Z.; Goh, Hock-Seng; Harnik, Roni; Krenke, Christopher A.

2008-08-01T23:59:59.000Z

178

Single-Well And Cross-Well Seismic Imaging | Open Energy Information  

Open Energy Info (EERE)

Single-Well And Cross-Well Seismic Imaging Single-Well And Cross-Well Seismic Imaging (Redirected from Single-Well And Cross-Well Seismic) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Single-Well And Cross-Well Seismic Imaging Details Activities (2) Areas (2) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Downhole Techniques Exploration Sub Group: Borehole Seismic Techniques Parent Exploration Technique: Borehole Seismic Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation.

179

Single-Well And Cross-Well Seismic Imaging | Open Energy Information  

Open Energy Info (EERE)

Single-Well And Cross-Well Seismic Imaging Single-Well And Cross-Well Seismic Imaging Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Single-Well And Cross-Well Seismic Imaging Details Activities (2) Areas (2) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Downhole Techniques Exploration Sub Group: Borehole Seismic Techniques Parent Exploration Technique: Borehole Seismic Techniques Information Provided by Technique Lithology: Rock unit density influences elastic wave velocities. Stratigraphic/Structural: Structural geology- faults, folds, grabens, horst blocks, sedimentary layering, discontinuities, etc. Hydrological: Combining compressional and shear wave results can indicate the presence of fluid saturation in the formation. Thermal: High temperatures and pressure impact the compressional and shear wave velocities.

180

The folding energy landscape of Cytochrome c : theoretical and experimental investigations  

E-Print Network (OSTI)

Chemical Frustration in the Protein Folding Landscape: GrandChemical Frustration in the Protein Folding Landscape: GrandEnzyme Catalysis and Protein Folding (Freeman, New York). [

Weinkam, Patrick

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "folds grabens horst" 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

Topology, frustration, folding and function of the inflammatory cytokine Interleukin-1[beta  

E-Print Network (OSTI)

the features of protein folding, where proteins with manychain connectivity on protein folding (53). Application ofhave gone beyond protein folding and have characterized

Capraro, Dominique T.

2008-01-01T23:59:59.000Z

182

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

E-Print Network (OSTI)

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

Sagle, Laura B.

2006-01-01T23:59:59.000Z

183

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

E-Print Network (OSTI)

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

Connell, Katelyn Blair

2010-01-01T23:59:59.000Z

184

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

E-Print Network (OSTI)

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

Cho, Samuel Sung-Il

2007-01-01T23:59:59.000Z

185

Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications  

E-Print Network (OSTI)

e A) Variation in fold usage between organisms, in differentB) Variation in fold usage between minimal organisms onlyConservation of protein fold usage and evolutionary

Chandonia, John-Marc; Kim, Sung-Hou

2006-01-01T23:59:59.000Z

186

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

E-Print Network (OSTI)

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

Polinkovsky, Mark E.; Polinkovsky, Mark E.

2012-01-01T23:59:59.000Z

187

Accordian-folded boot shield for flexible swivel connection  

SciTech Connect

This patent describes an apparatus for connecting a first boot section to a second boot section, the first and second boots having openings therethrough, the second boot having at least two adjacent accordion folds at the end having the opening. The second boot is positioned through the opening of the first boot such that a first of the accordion folds is within the first boot and a second of the accordion folds is outside of the first boot comprising: first and second annular discs, the first disc being positioned within and across the first accordion fold, the second disc being positioned within and across the second accordion fold such that the first boot is moveably and rigidly connected between the first and second accordion folds.

Hoh, J.C.

1986-08-26T23:59:59.000Z

188

An energy landscape theory for cotranslational protein folding  

E-Print Network (OSTI)

Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome, there have been few attempts to modify energy landscape theory by accounting for cotranslational folding. This paper introduces a model for cotranslational folding that leads to a natural definition of a nested energy landscapes. By applying concepts drawn from submanifold differential geometry, the dynamics of protein folding on the ribosome can be explored in a quantitative manner and conditions on the nested potential energy landscapes for a good cotranslational folder are obtained. A generalisation of diffusion rate theory using van Kampen's technique of composite stochastic processes is then used to account for entropic contributions and the effects of variable translation rates on cotranslational folding. This stochastic approach agrees well with experimental results...

Tourigny, David S

2013-01-01T23:59:59.000Z

189

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

190

A dynamical approach to protein folding  

E-Print Network (OSTI)

In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the native configuration. The results reported in this paper have been obtained for a two-dimensional toy-model of amino acid sequences, whose native configurations were previously determined by Monte Carlo techniques. The somewhat controversial scenario emerging from the comparison among various thermodynamical indicators is definitely better resolved relying upon a truly dynamical description, that points out the crucial role played by long-range interactions in determining the characteristic step-wise evolution of ``good'' folders to their native state. It is worth stressing that this dynamical scenario is consistent with the information obtained by exploring the energy landscapes of different sequences. This suggests that even the identification of more efficient ``static'' indicators should take into account the peculiar features associated with the complex ``orography'' of the landscape.

Alessandro Torcini; Roberto Livi; Antonio Politi

2001-03-13T23:59:59.000Z

191

Energy landscapes, folding mechanisms and kinetics of RNA tetraloop hairpins  

Science Journals Connector (OSTI)

Energy landscapes, folding mechanisms and kinetics of RNA tetraloop hairpins ... In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. ... Our results show that the potential energy landscapes have a distinct funnel-like bias towards the folded hairpin state, consistent with efficient structure-seeking properties. ...

Debayan Chakraborty; Rosana Collepardo-Guevara; David J. Wales

2014-12-02T23:59:59.000Z

192

A Computational Genome-wide Study of Protein Folding Rate.  

E-Print Network (OSTI)

??Proteins should be able to fold to a native three-dimensional structure in a biologically relevant time to be functional. In our current study, we tried (more)

Gorla, Sandeep C.

2012-01-01T23:59:59.000Z

193

THE GEODESIC X-RAY TRANSFORM WITH FOLD CAUSTICS The ...  

E-Print Network (OSTI)

Aug 28, 2012 ... THE GEODESIC X-RAY TRANSFORM WITH FOLD CAUSTICS. PLAMEN STEFANOV AND GUNTHER UHLMANN. ABSTRACT. We give a...

2012-08-28T23:59:59.000Z

194

Application of optical tweezers in protein folding studies.  

E-Print Network (OSTI)

??Force spectroscopy has proven to be a very promising tool in the protein folding field. With multiple setups and methods to exert force it has (more)

Kooijman, L.

2014-01-01T23:59:59.000Z

195

Topological complexity, contact order and protein folding rates  

E-Print Network (OSTI)

Monte Carlo simulations of protein folding show the emergence of a strong correlation between the relative contact order parameter, CO, and the folding time, t, of two-state folding proteins for longer chains with number of amino acids, N>=54, and higher contact order, CO > 0.17. The correlation is particularly strong for N=80 corresponding to slow and more complex folding kinetics. These results are qualitatively compatible with experimental data where a general trend towards increasing t with CO is indeed observed in a set of proteins with chain length ranging from 41 to 154 amino acids.

P. F. N. Faisca; R. C. Ball

2002-05-29T23:59:59.000Z

196

Variational theory for site resolved protein folding free energy surfaces  

E-Print Network (OSTI)

We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to lambda-repressor and compare with site directed mutagenesis experiments. The formation of native structure and the free energy profile along the folding route are shown to be well described by the capillarity approximation but with some fine structure due to local folding topology.

John J. Portman; Shoji Takada; Peter G. Wolynes

1999-01-18T23:59:59.000Z

197

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

198

Biophysical Studies of Protein Folding and Binding Stability.  

E-Print Network (OSTI)

?? Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent (more)

Batra, Jyotica

2009-01-01T23:59:59.000Z

199

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

200

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...

Note: This page contains sample records for the topic "folds grabens horst" 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

New Crystal Structures Lift Fog around Protein Folding  

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

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

202

Protein folding: A complex potential for the driving force  

E-Print Network (OSTI)

Using the Helmholtz decomposition of the vector field of folding fluxes in a reduced space of collective variables, a potential of the driving force for protein folding is determined. The potential has two components and can be written as a complex function. One component is responsible for the source and sink of the folding flows (representing, respectively, the unfolded states and the native state of the protein), and the other accounts for the vorticity of the flow that is produced at the boundaries of the main flow by the contact of the moving folding "fluid" with the quiescent surroundings. The theoretical consideration is illustrated by calculations for a model $\\beta$-hairpin protein.

Chekmarev, Sergei F

2013-01-01T23:59:59.000Z

203

Thermodynamic control and dynamical regimes in protein folding  

E-Print Network (OSTI)

Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be single exponential in nature, while the second regime is typical of sequences longer than 80 amino acids and the folding performance achievable is sensitive to target conformation. The extent to which stability, as measured by the energy of a sequence in the target, is an essential requirement and affects the folding dynamics of protein molecules in the first regime is investigated. The folding dynamics of sequences whose design stage was restricted to a certain fraction of randomly selected amino acids shows that while some degree of stability is a necessary and sufficient condition for successful folding, designing sequences that provide the lowest energy in the target seems to be a superfluous constraint. By studying the dynamics of under annealed but otherwise freely designed sequences we explore the relation between stability and kinetic accessibility. We find that there is no one-to-one correspondence between having low energy and folding quickly to the target, as only a small fraction of the most stable sequences were also found to fold relatively quickly.

P. F. N. Faisca; R. C. Ball

2001-10-07T23:59:59.000Z

204

Statistical Analysis of Protein Folding Kinetics Aaron R. Dinner  

E-Print Network (OSTI)

Statistical Analysis of Protein Folding Kinetics Aaron R. Dinner , Sung-Sau So ¡ , and Martin and theoretical studies over several years have led to the emergence of a unified general mechanism for protein folding that serves as a framework for the design and interpretation of research in this area [1

Dinner, Aaron

205

Multi-Agent Simulation of Protein Folding Luca Bortolussi1  

E-Print Network (OSTI)

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

Bortolussi, Luca

206

A Single-Molecule Study of RNA Catalysis and Folding  

E-Print Network (OSTI)

A Single-Molecule Study of RNA Catalysis and Folding Xiaowei Zhuang,1 * Laura E. Bartley,2 * Hazen and undocks from the ribozyme core was observed directly in single-molecule time trajectories, allowing. These results establish single-molecule fluorescence as a pow- erful tool for examining RNA folding. Virtually

Herschlag, Dan

207

New Crystal Structures Lift Fog around Protein Folding  

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

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

208

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

209

Protein Folding Dynamics via Quantification of Kinematic Energy Landscape  

Science Journals Connector (OSTI)

We study folding dynamics of proteinlike sequences on a square lattice using a physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802?075 conformations of 16mers over 7orders of time span. We find that (i)folding rates of these proteinlike sequences of the same length can differ by 4orders of magnitude, (ii)folding rates of sequences of the same conformation can differ by a factor of190, and (iii)parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates; rather, a basin analysis of the kinematic energy landscape defined by the moves can provide an excellent account of the observed folding rates.

Sma Kachalo; Hsiao-Mei Lu; Jie Liang

2006-02-08T23:59:59.000Z

210

Glottal opening in patients with vocal fold tissue changes  

Science Journals Connector (OSTI)

Summary Synchronized videostroboscopy and electroglottography were applied to the measurement of anterior-to-posterior open glottal length in four groups of patients; two with no clinically significant voice disorder, one with vocal fold polyps, and one with vocal fold nodules. The data showed that the groups did not differ significantly when open glottal length was measured at the time of minimum glottal opening. The pathological groups had significantly lower open glottal length measurements, however, when measurements were obtained at the time that vocal fold contact was initiated during the glottal cycle. The findings are preliminary evidence that vocal fold neoplasms may not have the effect of reducing glottal closure, as previously suggested in the literature. The data also highlight the importance of examining differential effects of vocal fold neoplasms at various points throughout the glottal cycle.

Michael P. Karnell; Ligang Li; William R. Panje

1991-01-01T23:59:59.000Z

211

Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways  

E-Print Network (OSTI)

We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold $\\alpha$, $\\beta$, $\\alpha/\\beta$, and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-do...

Mohazab, Ali R

2012-01-01T23:59:59.000Z

212

New Crystal Structures Lift Fog around Protein Folding  

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

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

213

Criterion based Two Dimensional Protein Folding Using Extended GA  

E-Print Network (OSTI)

Abstract In the dynamite field of biological and protein research, the protein fold recognition for long pattern protein sequences is a great confrontation for many years. With that consideration, this paper contributes to the protein folding research field and presents a novel procedure for mapping appropriate protein structure to its correct 2D fold by a concrete model using swarm intelligence. Moreover, the model incorporates Extended Genetic Algorithm (EGA) with concealed Markov model (CMM) for effectively folding the protein sequences that are having long chain lengths. The protein sequences are preprocessed, classified and then, analyzed with some parameters (criterion) such as fitness, similarity and sequence gaps for optimal formation of protein structures. Fitness correlation is evaluated for the determination of bonding strength of molecules, thereby involves in efficient fold recognition task. Experimental results have shown that the proposed method is more adept in 2D protein folding and outperforms the existing algorithms. Index Terms classification, CMM, criterion analysis, EGA, protein folding, sequence gaps I.

T. Kalai Chelvi; P. Rangarajan

214

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

215

Modeling two-state cooperativity in protein folding  

E-Print Network (OSTI)

A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G\\={o} model, where the interaction energies are independent of the local conformations, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.

K. Fan; J. Wang; W. Wang

2001-03-19T23:59:59.000Z

216

Protein folding bottlenecks: A lattice Monte Carlo simulation  

Science Journals Connector (OSTI)

Results of Monte Carlo simulations of folding of a model protein, which is a freely joined 27-monomer chain on a simple cubic lattice with nearest-neighbor interactions, are reported. All compact self-avoiding conformations on this chain have been enumerated, and the conformation (native) corresponding to the global minimum of energy is known for each sequence. Only one out of thirty sequences folds and finds the global minimum. For this sequence, the folding process has a two-stage character, with a rapid noncooperative compactization followed by a slower transition over a free-energy barrier to the global minimum. The evolutionary implications of the results are discussed.

E. Shakhnovich; G. Farztdinov; A. M. Gutin; M. Karplus

1991-09-16T23:59:59.000Z

217

Modeling two-state cooperativity in protein folding  

Science Journals Connector (OSTI)

A protein model with the pairwise interaction energies varying as the local environment changes, i.e., including some kind of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G? model, where the interaction energies are independent of the local conformation, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.

Ke Fan; Jun Wang; Wei Wang

2001-09-21T23:59:59.000Z

218

Water dynamics clue to key residues in protein folding  

SciTech Connect

A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

Gao, Meng [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Zhu, Huaiqiu, E-mail: hqzhu@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Yao, Xin-Qiu [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China) [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Department of Biophysics, Kyoto University, Sakyo Kyoto 606-8502 (Japan); She, Zhen-Su, E-mail: she@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)

2010-01-29T23:59:59.000Z

219

Computational investigations of folded self-avoiding walks related to protein folding  

E-Print Network (OSTI)

Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are studied computationally in this article. We show that these two sets are equal and correspond to the whole $n$-step self-avoiding walks for $n\\leqslant 14$, but that they are different for numerous $n \\geqslant 108$, which are common protein lengths. Concrete counterexamples are provided and the computational methods used to discover them are completely detailed. A tool for studying these subsets of walks related to both pivot moves and proteins conformations is finally presented.

Bahi, Jacques M; Mazouzi, Kamel; Philippe, Laurent

2013-01-01T23:59:59.000Z

220

Investigation of Peptide Folding by Nuclear Magnetic Resonance Spectroscopy  

E-Print Network (OSTI)

. Solution-state nuclear magnetic resonance (NMR) is a powerful technique to investigate protein structure, dynamics, and folding mechanisms, since it provides residue-specific information. One of the major contributions that govern protein structure appears...

Hwang, SoYoun

2012-07-16T23:59:59.000Z

Note: This page contains sample records for the topic "folds grabens horst" 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.
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221

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

222

Office of Small and Disadvantaged Business Utilization Tri-Fold  

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

OSDBU has created a downloadable, print-on-demand tri-fold PDF that introduces the office, its role in the Department of Energy and its goals for supporting small business nationwide.

223

Determining the role of hydration forces in protein folding  

SciTech Connect

One of the primary issues in protein folding is determining what forces drive folding and eventually stabilize the native state. A delicate balance exists between electrostatic forces such as hydrogen bonding and salt bridges, and the hydrophobic effect, which are present for both intramolecular protein interactions and intermolecular contributions with the surrounding aqueous environment. This article describes a combined experimental, theoretical, and computational effort to show how the complexity of aqueous hydration can influence the structure, folding and aggregation, and stability of model protein systems. The unification of the theoretical and experimental work is the development or discovery of effective amino acid interactions that implicitly include the effects of aqueous solvent. The authors show that consideration of the full range of complexity of aqueous hydration forces such as many-body effects, long-ranged character of aqueous solvation, and the assumptions made about the degree of protein hydrophobicity can directly impact the observed structure, folding, and stability of model protein systems.

Sorenson, J.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry] [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Hura, G. [Univ. of California, Berkeley, CA (United States)] [Univ. of California, Berkeley, CA (United States); [Lawrence Berkeley National Lab., CA (United States). Life Sciences Div.; Soper, A.K. [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility] [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility; Pertsemlidis, A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry] [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Head-Gordon, T. [Lawrence Berkeley National Lab., CA (United States)] [Lawrence Berkeley National Lab., CA (United States)

1999-07-01T23:59:59.000Z

224

Low energy pathways for reproducible in vivo protein folding  

E-Print Network (OSTI)

Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for those two proteins, starting from two well defined initial conformations: a fully extended and a alpha-helical conformation. The results show that for both proteins the alpha-helical initial conformation provides overall lower energy pathways to the native state. For the alpha/beta protein, 30 % (40%) of the pathways from an initial alpha-helix (fully extended) structure lead to unentangled native folds, a success rate that can be increased to 85 % by the introduction of a well-defined intermediate structure. These results open up a new direction in which to look for a solution to the protein folding problem, as detailed at the end.

Leonor Cruzeiro

2011-01-03T23:59:59.000Z

225

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

226

Mechanisms of protein-folding diseases at a glance  

E-Print Network (OSTI)

For a protein to function appropriately, it must first achieve its proper conformation and location within the crowded environment inside the cell. Multiple chaperone systems are required to fold proteins correctly. In ...

Valastyan, Julie Suzanne

227

INTRODUCTION Lateral propagation of folds is a process in  

E-Print Network (OSTI)

; (2) decrease in elevation of wind gaps; (3) decrease in relief of the topographic profile along in rotation and inclination of the forelimb. As a result of style of folding and variable geomorphic response

Keller, Ed

228

Master equation approach to protein folding and kinetic traps  

E-Print Network (OSTI)

The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is governed by the longest relaxation time. For good folders, significant kinetic traps appear in the folding funnel whereas for bad folders, the traps also occur in non-native energy valleys.

Marek Cieplak; Malte Henkel; Jan Karbowski; Jayanth R. Banavar

1998-04-21T23:59:59.000Z

229

Unfolded protein ensembles, folding trajectories, and refolding rate prediction  

Science Journals Connector (OSTI)

Computer simulations can provide critical information on the unfolded ensemble of proteins under physiological conditions by explicitly characterizing the geometrical properties of the diverse conformations that are sampled in the unfolded state. A general computational analysis across many proteins has not been implemented however. Here we develop a method for generating a diverse conformational ensemble to characterize properties of the unfolded states of intrinsically disordered or intrinsically folded proteins. The method allows unfolded proteins to retain disulfide bonds. We examined physical properties of the unfolded ensembles of several proteins including chemical shifts clustering properties and scaling exponents for the radius of gyration with polymer length. A problem relating simulated and experimental residual dipolar couplings is discussed. We apply our generated ensembles to the problem of folding kinetics by examining whether the ensembles of some proteins are closer geometrically to their folded structures than others. We find that for a randomly selected dataset of 15 non-homologous 2- and 3-state proteins quantities such as the average root mean squared deviation between the folded structure and unfolded ensemble correlate with folding rates as strongly as absolute contact order. We introduce a new order parameter that measures the distance travelled per residue which naturally partitions into a smooth laminar and subsequent turbulent part of the trajectory. This latter conceptually simple measure with no fitting parameters predicts folding rates in 0 M denaturant with remarkable accuracy (r = ?0.95 p = 1 10?7). The high correlation between folding times and sterically modulated reconfigurational motion supports the rapid collapse of proteins prior to the transition state as a generic feature in the folding of both two-state and multi-state proteins. This method for generating unfolded ensembles provides a powerful approach to address various questions in protein evolution misfolding and aggregation transient structures and molten globule and disordered protein phases.

2013-01-01T23:59:59.000Z

230

Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude  

E-Print Network (OSTI)

Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds. Introduction When a protein folds, the backbone and sidechain atoms organize from the extensive number protein folding usually occurs on the order of milliseconds to seconds, it is gener- ally accepted

Mochrie, Simon

231

Using Bit-Vector Decision Procedures for Analysis of Protein Folding Pathways  

E-Print Network (OSTI)

Using Bit-Vector Decision Procedures for Analysis of Protein Folding Pathways Christopher James-vector decision procedures for the analysis of protein folding pathways. We argue that the protein fold- ing by the different nature of the protein folding problem, we present a translation of the protein folding pathways

Langmead, Christopher James

232

DOI: 10.1002/ijch.201300141 Exploring the Protein Folding Dynamics of Beta3s with  

E-Print Network (OSTI)

DOI: 10.1002/ijch.201300141 Exploring the Protein Folding Dynamics of Beta3s with Two folding process. Howev- er, monitoring protein folding dynamics is still challeng- ing. Experiments of protein folding. However, most folding processes of interest occur on timescales (microsecond to second

Mukamel, Shaul

233

RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki  

E-Print Network (OSTI)

RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki Abstract--Protein folding, and get a coarse view of the energy landscape. Keywords: protein folding, folding kinetics, roadmap methods, conformation sampling techniques, energy landscape. 1 Introduction Protein folding refers

Kavraki, Lydia E.

234

Protein Quaternary Fold Recognition Using Conditional Graphical Models Yan Liu Jaime Carbonell  

E-Print Network (OSTI)

02139 pweigele@mit.edu Abstract Protein fold recognition is a crucial step in infer- ring biological- acid sequences is protein fold recognition and alignment. Given a target protein fold 1 , the task-to-topology alignment against the fold. There are different kinds of protein folds based on their structural properties

Carbonell, Jaime

235

Kinetic Studies of the Folding of Heterodimeric Monellin: Evidence for Switching between Alternative  

E-Print Network (OSTI)

Keywords: monellin; heterodimeric protein; folding kinetics; parallel pathways Determining whether or not a protein uses multiple pathways to fold is an important goal in protein folding studies. When multiple to the protein folding reaction, and the utilization of more than one pathway would speed protein folding.2

236

Detection and characterization of partially folded forms on the protein energy landscape  

E-Print Network (OSTI)

can accelerate protein folding. Proc Natl Acad Sci U S A 96(coupling between protein folding and prolyl isomerization.The speed limit for protein folding measured by triplet-

Bernstein, Rachel Simma

2011-01-01T23:59:59.000Z

237

On the Complexity of Protein Folding Pierluigi Crescenzi, Deborah Goldman, Christos Papadimitriou  

E-Print Network (OSTI)

On the Complexity of Protein Folding Pierluigi Crescenzi, Deborah Goldman, Christos Papadimitriou Antonio Piccolboni, Mihalis Yannakakis Abstract We show that the protein folding problem in the two protein folding are the interactions between their monomers; recently, the view that non

California at Irvine, University of

238

Long-time protein folding dynamics from short-time molecular dynamics simulations  

E-Print Network (OSTI)

On the simulation of protein folding by short time scaleand W. A. Eaton, The protein folding speed limit, Curr.and T. Head-Gordon, Protein folding by distributed computing

Chodera, J D; Swope, W C; Pitera, J W; Dill, Ken A

2006-01-01T23:59:59.000Z

239

Crucial stages of protein folding through a solvable model: Predicting target sites  

E-Print Network (OSTI)

Crucial stages of protein folding through a solvable model: Predicting target sites for enzyme. Keywords: Protein-folding modeling; prediction of key folding sites; HIV-1 protease; drug resistance One

Cecconi, Fabio

240

Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding  

E-Print Network (OSTI)

Parallel Continuation­Based Global Optimization for Molecular Conformation and Protein Folding protein folding. Global minimization problems are difficult to solve when the objective functions have energy functions for molecular conformation and protein folding. Mathematical theory for the method

Neumaier, Arnold

Note: This page contains sample records for the topic "folds grabens horst" 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.
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to obtain the most current and comprehensive results.


241

Intermediates and the folding of proteins L and G  

SciTech Connect

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

Brown, Scott; Head-Gordon, Teresa

2003-07-01T23:59:59.000Z

242

Folding of a DNA Hairpin Loop Structure in Explicit SolventUsingRepli...  

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

Folding of a DNA Hairpin Loop Structure in Explicit Solvent UsingReplica-Exchange Molecular Dynamics Simulations. Folding of a DNA Hairpin Loop Structure in Explicit Solvent...

243

Directed Evolution Designed to Optimize the in vivo Protein Folding Environment.  

E-Print Network (OSTI)

??Protein folding is assisted by molecular chaperones and folding catalysts in vivo. Understanding how chaperones are regulated and how they function in vivo may provide (more)

Quan, Shu

2010-01-01T23:59:59.000Z

244

E-Print Network 3.0 - assisted protein folding Sample Search...  

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

protein folding Search Powered by Explorit Topic List Advanced Search Sample search results for: assisted protein folding Page: << < 1 2 3 4 5 > >> 1 BIOLOGICAL FRAMEWORKS FOR...

245

E-Print Network 3.0 - ab initio folding Sample Search Results  

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

fold recogniion Ab initio Methods... Methods Ab initio methods: solution of a protein folding problem search in conformational space Energy... Protein Structure Analysis...

246

E-Print Network 3.0 - acids detection folding Sample Search Results  

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

Medicine 4 International Scientific Conference Computer Science'2008 Near-Native Protein Folding Summary: folded proteins generally have polar amino acids on the outside of their...

247

SciTech Connect: Protein-folding via divide-and-conquer optimization  

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

Protein-folding via divide-and-conquer optimization Citation Details In-Document Search Title: Protein-folding via divide-and-conquer optimization Authors: Oliva, Ricardo;...

248

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

249

E-Print Network 3.0 - affecting protein folding Sample Search...  

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

protein folding Search Powered by Explorit Topic List Advanced Search Sample search results for: affecting protein folding Page: << < 1 2 3 4 5 > >> 1 Current status of membrane...

250

Protein Folding Kinetics and Thermodynamics from Atomistic Simulations  

Science Journals Connector (OSTI)

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.00.3 and 2.60.4???s, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.

David van der Spoel and M. Marvin Seibert

2006-06-15T23:59:59.000Z

251

Collective aspects of protein folding illustrated by a toy model  

SciTech Connect

A simple toy model for polypeptides serves as a testbed to illuminate some nonlocal, or collective, aspects of protein folding phenomena. The model is two dimensional and has only two amino acids, but involves a continuous range of backbone bend angles. Global potential energy minima and their folding structures have been determined for leading members of two special and contrasting polypeptide sequences, center doped and Fibonacci, named descriptively for their primary structures. The results display the presence of spontaneous symmetry breaking, elastic strain, and substantial conformational variation for specific embedded amino acid strings. We conclude that collective variables generated by the primary amino acid structure may be required for fully effective protein folding predictors, including those based on neural networks.

Stillinger, F.H. [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States)] [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States); Head-Gordon, T. [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)] [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)

1995-09-01T23:59:59.000Z

252

Heteropolymer freezing and design: Towards physical models of protein folding  

SciTech Connect

Protein folding has become one of the most actively studied problems in modern molecular biophysics. Approaches to the problem combine ideas from the physics of disordered systems, polymer physics, and molecular biology. Much can be learned from the statistical properties of model heteropolymers, the chain molecules having different monomers in irregular sequences. Even in highly evolved proteins, there is a strong random element in the sequences, which gives rise to a statistical ensemble of sequences for a given folded shape. Simple analytic models give rise to phase transitions between random, glassy, and folded states, depending on the temperature T and the design temperature T{sup des} of the ensemble of sequences. Besides considering the analytic results obtainable in a random-energy model and in the Flory mean-field model of polymers, the article reports on confirming numerical simulations. (c) 2000 The American Physical Society.

Pande, Vijay S. [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States)] [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States); Grosberg, Alexander Yu. [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States)] [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Tanaka, Toyoichi [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

2000-01-01T23:59:59.000Z

253

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

254

The effect of consensus mutation on the folding and binding kinetics of I(kappa)B(alpha)  

E-Print Network (OSTI)

in the transition state of protein folding: alternativeet al. (2008). "Protein folding and stability usingto enzyme catalysis and protein folding. New York, W.H.

DeVries, Ingrid L.

2011-01-01T23:59:59.000Z

255

The role of the energy gap in protein folding dynamics  

E-Print Network (OSTI)

The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The influence of the gap on the folding dynamics is studied, for various models of the transition probabilities between the different states of the protein. We show that for certain models, the relaxation to the native state is accelerated by increasing the gap, whereas for others it is slowed down .

Estelle Pitard; Henri Orland

1998-11-17T23:59:59.000Z

256

Characterization of Protein Folding by Dominant Reaction Pathways  

E-Print Network (OSTI)

We assess the reliability of the recently developed approach denominated Dominant Reaction Pathways (DRP) by studying the folding of a 16-residue beta-hairpin, within a coarse-grained Go-type model. We show that the DRP predictions are in quantitative agreement with the results of Molecular Dynamics simulations, performed in the same model. On the other hand, in the DRP approach, the computational difficulties associated to the decoupling of time scales are rigorously bypassed. The analysis of the important transition pathways supports a picture of the beta-hairpin folding in which the reaction is initiated by the collapse of the hydrophobic cluster.

Pietro Faccioli

2008-06-23T23:59:59.000Z

257

CFE resistivity studies at Cerro Prieto  

SciTech Connect

The electrical study and its correlation with data collected using other geophysical methods and from several deep wells show that regional anomalies of high and low resistivity are associated with horst, graben and en echelon faults. It should be noted, however, that the boundaries of the area which could potentially be developed cannot be defined, since no sharp resistivity contrasts were interpreted. 3 refs.

Razo, A.M.; Arellano, F.G.; Fonseca, H.L.

1980-01-01T23:59:59.000Z

258

Origin of the Native Driving Force for Protein Folding  

Science Journals Connector (OSTI)

We derive an expression with four adjustable parameters that reproduces well the 2020 Miyazawa-Jernigan potential matrix extracted from known protein structures. The numerical values of the parameters can be approximately computed from the surface tension of water, water-screened dipole interactions between residues and water and among residues, and average exposures of residues in folded proteins.

Zi-Hao Wang and H. C. Lee

2000-01-17T23:59:59.000Z

259

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-Print Network (OSTI)

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

Michael Bachmann; Wolfhard Janke

2007-10-25T23:59:59.000Z

260

Folded-Light-Path Colloidal Quantum Dot Solar Cells  

E-Print Network (OSTI)

Folded-Light-Path Colloidal Quantum Dot Solar Cells Ghada I. Koleilat*, Illan J. Kramer*, Chris T, Canada. Colloidal quantum dot photovoltaics combine low-cost solution processing with quantum size-effect tuning to match absorption to the solar spectrum. Rapid advances have led to certified solar power

Note: This page contains sample records for the topic "folds grabens horst" 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

Ultraviolet resonance Raman spectroscopy of the integral membrane protein OmpA : elucidating structure and tryptophan microenvironment of folded and unfolded states  

E-Print Network (OSTI)

Intermediates in Membrane Protein Folding, Biochemistry (Intermediates in Membrane Protein Folding, Biochemistry (Engelman. Membrane-Protein Folding and Oligomerization -

Neary, Tiffany Jonean

2008-01-01T23:59:59.000Z

262

International Scientific Conference Computer Science'2008 Near-Native Protein Folding  

E-Print Network (OSTI)

International Scientific Conference Computer Science'2008 61 Near-Native Protein Folding Stefka: The protein folding problem is a fundamental problem in computational molecular biology. The high resolution 3. After that the folding problem is de- fined like optimization problem. Keywords: Protein folding

Fidanova, Stefka

263

Estimates of the Loss of Main-Chain Conformational Entropy of Different Residues on Protein Folding  

E-Print Network (OSTI)

Estimates of the Loss of Main-Chain Conformational Entropy of Different Residues on Protein Folding energy of protein folding is not well understood. We have developed empirical scales for the loss; protein folding; pro- tein engineering INTRODUCTION When a protein folds into a compact globule, the resi

Pal, Debnath

264

Genetic Algorithm for Predicting Protein Folding in the 2D HP Model  

E-Print Network (OSTI)

Genetic Algorithm for Predicting Protein Folding in the 2D HP Model A Parameter Tuning Case Study of a protein, predicting its tertiary structure is known as the protein folding problem. This problem has been. The protein folding problem in the HP model is to find a conformation (a folded sequence) with the lowest

Emmerich, Michael

265

A New Algorithm for Protein Folding in the HP Model Alantha Newman *  

E-Print Network (OSTI)

876 A New Algorithm for Protein Folding in the HP Model Alantha Newman * Abstract We consider the problem of protein folding in the HP model ozt the two-dimensional square lattice. This problem.e.pairsof H's that are adjacent in the folding but not in the string) are present. The protein folding problem

Istrail, Sorin

266

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

DOE Patents (OSTI)

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

Waldo, Geoffrey S. (Santa Fe, NM)

2007-09-18T23:59:59.000Z

267

Internal friction in the ultrafast folding of the tryptophan cage q Linlin Qiu 1  

E-Print Network (OSTI)

Internal friction in the ultrafast folding of the tryptophan cage q Linlin Qiu 1 , Stephen J. Hagen is a diffusional process, and the speed of folding is controlled by the frictional forces that act important source of friction in folding reactions. By contrast, our studies of the folding dynamics

Hagen, Stephen J.

268

Identifying the importance of amino acids for protein folding from crystal structures  

E-Print Network (OSTI)

Identifying the importance of amino acids for protein folding from crystal structures Nikolay V and characterizing protein folding kinetics from crystal structures using computational techniques. We also describe as the protein folding prob- lem [1­25], is of great importance because understanding protein folding mechanisms

Stanley, H. Eugene

269

The energy landscape for protein folding and possible connections to function  

E-Print Network (OSTI)

The energy landscape for protein folding and possible connections to function Margaret S. Cheunga to study protein folding. As good agreement between computational/theoretical studies and experimental-state proteins and larger proteins with more complex folding kinetics. How proteins fold from one

Onuchic, José

270

A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate  

E-Print Network (OSTI)

A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate of determining and evaluating protein folding conditions, we have designed a new fractional factorial protein folding screen. The screen includes 12 factors shown by previous experiments to enhance protein folding

Lebendiker, Mario

271

J. Mol. Biol. (1996) 264, 11641179 How to Derive a Protein Folding Potential? A New  

E-Print Network (OSTI)

J. Mol. Biol. (1996) 264, 1164­1179 How to Derive a Protein Folding Potential? A New Approach of deriving a pairwise potentialHarvard University Department of Chemistry for protein folding. The potential of accuracy. 7 1996 Academic Press Limited *Corresponding author Keywords: protein folding; protein folding

Mirny, Leonid

272

Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding  

E-Print Network (OSTI)

Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al40 to study TSE to understand how proteins fold to its native state8,29,37 . Protein folding is a complex process that involves

Dai, Yang

273

BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum  

E-Print Network (OSTI)

BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum Marc Griesemer1. *, Carissa (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness

Petzold, Linda R.

274

Pairwise contact potentials are unsuitable for protein folding Michele Vendruscolo and Eytan Domany  

E-Print Network (OSTI)

Pairwise contact potentials are unsuitable for protein folding Michele Vendruscolo and Eytan Domany: protein folding; protein folding potential; contact map; neural networks; per­ ceptron. I. INTRODUCTION of protein folding [1] is to predict proteins' native structures from their amino acid sequences; solution

Domany, Eytan

275

Identification of characteristic protein folding channels in a coarse-grained hydrophobic-polar peptide model  

E-Print Network (OSTI)

Identification of characteristic protein folding channels in a coarse-grained hydrophobic of protein folding is one of the major challenges of modern interdisciplinary science. Proteins are linear simulations of protein folding are difficult, mainly for two reasons. Firstly, the folding process is so slow

Bachmann, Michael

276

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

277

In and Out of the ER: Protein Folding, Quality Control, Degradation, and Related Human Diseases  

E-Print Network (OSTI)

In and Out of the ER: Protein Folding, Quality Control, Degradation, and Related Human Diseases 1377 C. Protein folding 1378 II. Protein Translocation, Folding, and Quality Control in the Endoplasmic Reticulum 1379 A. Protein targeting to the ER 1379 B. Chaperone-assisted protein folding in the ER 1379 C

Hebert, Daniel N.

278

John von Neumann Institute for Computing Different Types of Protein Folding Identified with  

E-Print Network (OSTI)

John von Neumann Institute for Computing Different Types of Protein Folding Identified://www.fz-juelich.de/nic-series/volume40 #12;Different Types of Protein Folding Identified with a Coarse-Grained Heteropolymer Model Stefan The identification of folding channels is one of the key tasks of protein folding studies. While secondary structures

Janke, Wolfhard

279

Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation  

E-Print Network (OSTI)

Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation the transition state ensemble (TSE) and predict the rates and -values for protein folding. The new method as a gen- eral tool for studying protein folding kinetics. 1 Introduction Protein folding is a crucial

Pratt, Vaughan

280

A New Method for Modeling and Solving the Protein Fold Recognition Problem  

E-Print Network (OSTI)

Idstract A New Method for Modeling and Solving the Protein Fold Recognition Problem (Extended}@ornl.gov Computational recognition of native-like folds from a protein fold database is considered to be a promising recog- nition through optimally aligning (threading) an amino acid sequence and a protein fold (template

Istrail, Sorin

Note: This page contains sample records for the topic "folds grabens horst" 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

A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model  

E-Print Network (OSTI)

Article A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model Mao tool for the protein folding problem. Key words: protein folding, HP model, branch and bound, lattice Introduction The protein folding problem, or the protein struc- ture prediction problem, is one of the most

Istrail, Sorin

282

Autotransporters: The Cellular Environment Reshapes a Folding Mechanism to Promote Protein Transport  

E-Print Network (OSTI)

the cellular environment affects protein folding mechanisms. Here, we focus on one unique aspect affect protein folding kinetics and the conformations of folding intermediates? We focus on recent have been made to understand the mechanisms by which proteins fold to their native conformations.3

Clark, Patricia L.

283

Low-Dimensional Free Energy Landscapes of Protein Folding Reactions by Nonlinear Dimensionality Reduction  

E-Print Network (OSTI)

Low-Dimensional Free Energy Landscapes of Protein Folding Reactions by Nonlinear Dimensionality(26):9885-9890, 2006 #12;Abstract The definition of reaction coordinates for the characterization of a protein folding along the main folding route. These results clearly show that a complex process such as protein folding

Kavraki, Lydia E.

284

* Corresponding author. : Primary student contributor. Folding-aware and Structure-conscious 3D Substructures in Folding Data: Identification and Applications  

E-Print Network (OSTI)

employed by biologists to study the protein folding problem. Such simulations have resulted in a large number of protein folding trajectories, each of which consists of a sequence of three, and cross-trajectory comparison. Key Words: protein folding trajectories, 3D substructure identification

Yang, Hui

285

The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom  

E-Print Network (OSTI)

structures of proteins, has been extensively investigated to examine its role in protein folding. However the important role of sidechain packing in determining the specific pathway of protein folding. Additional 96 of Physics. DOI: 10.1063/1.1514574 I. INTRODUCTION Theoretical/computational studies of protein folding

Zhou, Yaoqi

286

Different Kinds of Protein Folding Identified with a Coarse-Grained Heteropolymer Model  

E-Print Network (OSTI)

Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing the equilibrium conformations with the folded state in terms of an angular overlap parameter. Although all investigated heteropolymer sequences contain the same content of hydrophobic and polar monomers, our analysis of the folding channels reveals a variety of characteristic folding behaviors known from realistic peptides.

Stefan Schnabel; Michael Bachmann; Wolfhard Janke

2009-02-16T23:59:59.000Z

287

Viscosity Dependence of the Folding Rates of Proteins  

Science Journals Connector (OSTI)

The viscosity (?) dependence of the folding rates for four sequences (the native state of three sequences is a ? sheet, while the fourth forms an ? helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is given by the Langevin equation, we show that the folding rates increase linearly at low viscosities ?, decrease as 1/? at large ?, and have a maximum at intermediate values. The Kramers' theory of barrier crossing provides a quantitative fit of the numerical results. By mapping the simulation results to real proteins we estimate that for optimized sequences the time scale for forming a four turn ?-helix topology is about 500 ns, whereas for ? sheet it is about 10 ?s.

D. K. Klimov and D. Thirumalai

1997-07-14T23:59:59.000Z

288

Strong Nernst-Ettingshausen effect in folded graphene  

E-Print Network (OSTI)

We study electronic transport in graphene under the influence of a transversal magnetic field $\\f{B}(\\f{r})=B(x)\\f{e}_z$ with the asymptotics $B(x\\to\\pm\\infty)=\\pm B_0$, which could be realized via a folded graphene sheet in a constant magnetic field, for example. By solving the effective Dirac equation, we find robust modes with a finite energy gap which propagate along the fold -- where particles and holes move in opposite directions. Exciting these particle-hole pairs with incident photons would then generate a nearly perfect charge separation and thus a strong magneto-thermoelectric (Nernst-Ettingshausen) or magneto-photoelectric effect -- even at room temperature.

Friedemann Queisser; Ralf Schtzhold

2013-01-17T23:59:59.000Z

289

A coarse-grained, ``realistic'' model for Protein Folding  

E-Print Network (OSTI)

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the number of secondary structure elements rather than with the number of residues. The hamiltonian presents both local (i.e. single helix, accounting for the stiffness of the chain) and non local (interactions between hydrophobically-charged helices) terms, and is expected to provide a first tool for studying the folding of real proteins. The partition function for a simplified, but by no means trivial, version of the model is calculated almost completely in an analytical way. The latter simplified model is also applied to the study of a synthetic protein, and some preliminary results are shown.

Pierpaolo Bruscolini

1997-07-24T23:59:59.000Z

290

Invariant patterns in crystal lattices: Implications for protein folding algorithms  

SciTech Connect

Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist invariants across lattices related to fundamental properties of the protein folding process. This paper considers whether performance-guaranteed approximability is such an invariant for HP lattice models. The authors define a master approximation algorithm that has provable performance guarantees provided that a specific sublattice exists within a given lattice. They describe a broad class of crystal lattices that are approximable, which further suggests that approximability is a general property of HP lattice models.

HART,WILLIAM E.; ISTRAIL,SORIN

2000-06-01T23:59:59.000Z

291

When pigs fly: a study of computer generated paper folding  

E-Print Network (OSTI)

&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved by: Chair of Committee, Carol LaFayette Committee Members, Frederic I. Parke Michael Greenwald Head of Department, Tim McLaughlin December 2008... Major Subject: Visualization Sciences iii ABSTRACT When Pigs Fly: A Study of Computer Generated Paper Folding. (December 2008) Elizabeth Jeanette Nitsch, B.E.D., Texas A&M University Chair of Advisory Committee: Prof. Carol LaFayette...

Nitsch, Elizabeth Jeanette

2009-05-15T23:59:59.000Z

292

Invariant patterns in crystal lattices: Implications for protein folding algorithms  

SciTech Connect

Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist ``invariants`` across lattices that define fundamental properties of protein folding process; an invariant defines a property that transcends particular lattice formulations. This paper identifies two classes of invariants, defined in terms of sublattices that are related to the design of algorithms for the structure prediction problem. The first class of invariants is, used to define a master approximation algorithm for which provable performance guarantees exist. This algorithm can be applied to generalizations of the hydrophobic-hydrophilic model that have lattices other than the cubic lattice, including most of the crystal lattices commonly used in protein folding lattice models. The second class of invariants applies to a related lattice model. Using these invariants, we show that for this model the structure prediction problem is intractable across a variety of three-dimensional lattices. It`` turns out that these two classes of invariants are respectively sublattices of the two- and three-dimensional square lattice. As the square lattices are the standard lattices used in empirical protein folding` studies, our results provide a rigorous confirmation of the ability of these lattices to provide insight into biological phenomenon. Our results are the first in the literature that identify algorithmic paradigms for the protein structure prediction problem which transcend particular lattice formulations.

Hart, W.E.; Istrail, S.

1995-12-11T23:59:59.000Z

293

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

294

Combined approach to the inverse protein folding problem. Final report  

SciTech Connect

The main scientific contribution of the project ''Combined approach to the inverse protein folding problem'' submitted in 1996 and funded by the Department of Energy in 1997 is the formulation and development of the idea of the multilink recognition method for identification of functional and structural homologues of newly discovered genes. This idea became very popular after they first announced it and used it in prediction of the threading targets for the CASP2 competition (Critical Assessment of Structure Prediction).

Ruben A. Abagyan

2000-06-01T23:59:59.000Z

295

Review Protein folding: Then and now www.elsevier.com/locate/yabbi  

E-Print Network (OSTI)

Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases.

Yiwen Chen; Feng Ding; Huifen Nie; Adrian W. Serohijos; Shantanu Sharma; Kyle C. Wilcox; Shuangye Yin; Nikolay V. Dokholyan

2007-01-01T23:59:59.000Z

296

Folded reflective tandem polymer solar cell doubles efficiency  

Science Journals Connector (OSTI)

Conjugated polymers are promising materials for the production of inexpensive and flexible photovoltaic cells. Organic materials display tunable optical absorption within a large spectral range. This enables the construction of organic tandem photovoltaic cells. The authors here demonstrate a reflective tandem cell where single cells are reflecting the nonabsorbed light upon another adjacent cell. By folding two planar but spectrally different cells toward each other spectral broadening and light trapping are combined to give an enhancement of power conversion efficiency of a factor of 1.8 0.3 .

Kristofer Tvingstedt; Viktor Andersson; Fengling Zhang; Olle Ingans

2007-01-01T23:59:59.000Z

297

Directed transport as a mechanism for protein folding in vivo  

E-Print Network (OSTI)

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

Ernesto Gonzalez-Candela; Victor Romero-Rochin

2009-09-23T23:59:59.000Z

298

Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics  

SciTech Connect

We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first demonstrated by Knight et al.[1]. Features of the mixer include 1 {micro}s mixing times, sample consumptions of order 1 nl/s, loading sample volumes on the order of microliters, and the ability to manufacture in fused silica for compatibility with most spectroscopic methods.

Hertzog, D E; Santiago, J G; Bakajin, O

2005-02-10T23:59:59.000Z

299

Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics  

SciTech Connect

We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first demonstrated by Knight et al.[1]. Features of the mixer include 1 {micro}s mixing times, sample consumptions of order 1 nl/s, loading sample volumes on the order of microliters, and the ability to manufacture in fused silica for compatibility with most spectroscopic methods.

Hertzog, D E; Santiago, J G; Bakajin, O

2003-06-25T23:59:59.000Z

300

Conformation changes and protein folding induced by \\phi^4 interaction  

E-Print Network (OSTI)

A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected non-linear sources are represented by the bosonic lagrangian with an additional \\phi^4 interaction for the sources. In the model the spring tension of protein representing the internal hydrogen bonds is realized as the interactions between individual amino acids and nonlinear sources. The folding pathway is determined by the strength of nonlinear sources that propagate through the protein backbone. It is also shown that the model reproduces the results in some previous works.

Januar, M; Handoko, L T

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "folds grabens horst" 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

Renaissance of paper models and folded plate structures in glass  

Science Journals Connector (OSTI)

This paper presents the development of glass folded plate structures. Glass will not only be used as a transparent covering but as a load-bearing element for the whole structure. A complete outline ranging from the architectural approach including simple paper models to structural analysis will be presented. The structural concept and its functional characteristics will be confirmed by finite element analysis. Moreover, this paper will also put into focus the geometrical diversity and individuality and will present mathematical algorithms as definitions of the geometrical freeform.

Stefan Trometer; Mathias Krupna

2010-01-01T23:59:59.000Z

302

A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples  

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

A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Authors: Zhao, Z., Yan, H., and Liu, Y. Title: A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples...

303

E-Print Network 3.0 - abakaliki fold belt Sample Search Results  

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

, British Columbia, Canada V8W 3P6 ABSTRACT--Two enigmas concerning the Cape Fold Belt (CFB), part... , and by convergence and the development of a foreland-verging fold and...

304

Protein folding and macromolecular dynamics : fundamental limits of length and time scales.  

E-Print Network (OSTI)

??In this thesis, physics-based models of protein folding at the secondary and tertiary level are developed to resolve long-standing issues of protein folding kinetics. As (more)

Lin, Milo M.

2012-01-01T23:59:59.000Z

305

SciTech Connect: Protein-folding via divide-and-conquer optimization  

Office of Scientific and Technical Information (OSTI)

Protein-folding via divide-and-conquer optimization Citation Details In-Document Search Title: Protein-folding via divide-and-conquer optimization You are accessing a document...

306

Protein folding and phylogenetic tree reconstruction using stochastic approximation Monte Carlo  

E-Print Network (OSTI)

folding problems. The numerical results indicate that it outperforms simulated annealing and conventional Monte Carlo algorithms as a stochastic optimization algorithm. We also propose one method for the use of secondary structures in protein folding...

Cheon, Sooyoung

2007-09-17T23:59:59.000Z

307

Self-organization and mismatch tolerance in protein folding: General theory and an application  

E-Print Network (OSTI)

Self-organization and mismatch tolerance in protein folding: General theory and an application approaches to the so-called protein folding problem, mainly because the microscopic models have no explicit

Berry, R. Stephen

308

SciTech Connect: Protein-Folding Landscapes in Multi-Chain Systems  

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

Protein-Folding Landscapes in Multi-Chain Systems Citation Details In-Document Search Title: Protein-Folding Landscapes in Multi-Chain Systems Computational studies of proteins...

309

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models  

E-Print Network (OSTI)

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models SOLOMON SHENKER,1 introduce a complete methodology to

Gifford, David K.

310

The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations  

E-Print Network (OSTI)

, ) 91 ps-1). The Folding@Home distributed computing project was used to generate an aggregate simulation

Snow, Christopher

311

Controlling protein molecular dynamics: How to accelerate folding while preserving the native state  

E-Print Network (OSTI)

pioneered, in particular, in the Folding@Home project and taken to the extent where hundred of thousands

Nerukh, Dmitry

312

Identification of Characteristic Protein Folding Channels in a Coarse-Grained Hydrophobic-Polar Peptide Model  

E-Print Network (OSTI)

Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a heteropolymer sequence lead to completely different folding behaviors. Studying three exemplified sequences with the same content of hydrophobic and polar residues, we can reproduce within this simple model two-state folding, folding through intermediates, as well as metastability.

Stefan Schnabel; Michael Bachmann; Wolfhard Janke

2007-10-25T23:59:59.000Z

313

Sticker controller and sticker programming for smart sheets (self-folding sheets)  

E-Print Network (OSTI)

This thesis describes a self-folding sheet that is capable of origami-style autonomous folding. We describe the hardware device we designed and fabricated. This device, called a self-folding sheet, is a sheet with a box-pleat ...

An, Byoungkwon

2011-01-01T23:59:59.000Z

314

How the diffusivity profile reduces the arbitrariness of protein folding free energies  

E-Print Network (OSTI)

How the diffusivity profile reduces the arbitrariness of protein folding free energies M 2010 The concept of a protein diffusing in its free-energy folding landscape has been fruitful for both as it stochastically folds and unfolds. The free-energy profiles for different RCs exhibit significant variations, some

Thirumalai, Devarajan

315

PROTEIN FOLD RECOGNITION USING RESIDUE-BASED ALIGNMENTS OF SEQUENCE AND SECONDARY STRUCTURE  

E-Print Network (OSTI)

PROTEIN FOLD RECOGNITION USING RESIDUE-BASED ALIGNMENTS OF SEQUENCE AND SECONDARY STRUCTURE Zafer methods [3,4]. Index Terms- protein fold recognition, secondary structure alignment, amino acid alignment &sabanciuniv.edu culated for each sequence-structure alignment. Protein fold recog- nition problem can

Erdogan, Hakan

316

A New Algorithm for Protein Folding in the HP Model Alantha Newman  

E-Print Network (OSTI)

A New Algorithm for Protein Folding in the HP Model Alantha Newman #3; Abstract We consider the problem of protein folding in the HP model on the two-dimensional square lattice. This problem but not in the string) are present. The protein folding problem in the hydrophobic-hydrophilic (HP) model on the 2D

Newman, Alantha

317

Protein Folding, Spin Glass and Computational Complexity 1 Aviezri S. Fraenkel  

E-Print Network (OSTI)

Protein Folding, Spin Glass and Computational Complexity 1 Aviezri S. Fraenkel Abstract of protein folding to solve computationally intractable problems. One way of investigating this idea is to encode known NP­complete problems in terms of protein folding. The main content of this paper is to do

Fraenkel, Aviezri

318

An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem  

E-Print Network (OSTI)

An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem Alena hydrophobic-polar (2D HP) protein folding problem. We present an improved version of our recently proposed Ant search. Overall, the results presented here establish our new ACO algorithm for 2D HP protein folding

Hoos, Holger H.

319

Cotranslational protein folding with L-systems Gemma B. Danks1,2  

E-Print Network (OSTI)

Cotranslational protein folding with L-systems Gemma B. Danks1,2 , Susan Stepney2 , and Leo S. D-systems, parallel rewriting rules, to modelling protein folding using two complementary approaches: a physics an adaptive stochas- tic open L-systems model of protein folding. L-systems were originally developed to model

Stepney, Susan

320

Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines  

E-Print Network (OSTI)

Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support, Columbia, Missouri * Corresponding author: chengji@missouri.edu Abstract Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Here we developed a method

Cheng, Jianlin Jack

Note: This page contains sample records for the topic "folds grabens horst" 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

An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem  

E-Print Network (OSTI)

An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem Alena Shmygelska, Rosal, the two dimensional hydrophobic-polar (2D HP) protein folding problem. We introduce an ant colony algorithm closely approaches that of specialised, state-of-the methods for 2D HP protein folding. 1

Hoos, Holger H.

322

Patterns of Protein-Fold Usage in Eight Microbial Genomes: A Comprehensive Structural Census  

E-Print Network (OSTI)

Patterns of Protein-Fold Usage in Eight Microbial Genomes: A Comprehensive Structural Census Mark in terms of patterns of fold usage--whether a given fold occurs in a particular organism. Of the 340 be analyzed through trans- membrane-helix (TM) prediction. All the genomes appear to have similar usage

Gerstein, Mark

323

ORIGINAL RESEARCH PAPER Canyon-infilling and gas hydrate occurrences in the frontal fold  

E-Print Network (OSTI)

ORIGINAL RESEARCH PAPER Canyon-infilling and gas hydrate occurrences in the frontal fold to infer the canyon-infilling, fold uplift, and gas hydrate occurrences beneath the frontal fold at the toe simu- lating reflector (BSR) on seismic sections indicates the base of gas hydrate stability zone

Lin, Andrew Tien-Shun

324

BarMap: RNA Folding on Dynamics Energy Landscapes Ivo L. Hofacker,a  

E-Print Network (OSTI)

of pulling polymers through a pore. Key words: RNA folding kinetics, barrier tree, dynamic energy landscapeBarMap: RNA Folding on Dynamics Energy Landscapes Ivo L. Hofacker,a , Christoph Flamma , Christian required to analyse the folding energy landscapes to a one-time preprocessing step. The basic idea

Flamm, Christoph

325

Using Motion Planning to Study Protein Folding Pathways Department of Computer Science  

E-Print Network (OSTI)

Using Motion Planning to Study Protein Folding Pathways #3; Guang Song Department of Computer a framework for studying protein folding path- ways and potential landscapes which is based on techniques and study with other methods. Our focus in this work is to study the protein folding mech- anism assuming we

LaValle, Steven M.

326

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

327

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

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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

328

Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete  

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Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete Bonnie Berger* Tom Leightont Abstract One of the simplest and most popular biophysical mod- els of protein folding is the hydrophobic-hydrophilic (HP) model. The HP model abstracts the hydrophobic in- teraction in protein folding

Istrail, Sorin

329

Single-molecule spectroscopy of protein folding in a chaperonin cage  

E-Print Network (OSTI)

Single-molecule spectroscopy of protein folding in a chaperonin cage Hagen Hofmanna , Frank for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms In the recent past, a large number of components have been identified that control and modulate protein folding

Lipman, Everett A.

330

Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent  

E-Print Network (OSTI)

Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect understanding of protein folding and misfolding is critical to many problems in computational biology.1 Many

Berne, Bruce J.

331

Lattice Protein Folding With Two and Four-Body Statistical Hin Hark Gan,1  

E-Print Network (OSTI)

Lattice Protein Folding With Two and Four-Body Statistical Potentials Hin Hark Gan,1 Alexander/sequence compatibility of proteins,5,6 homology modeling,7 and protein folding simulations.8 ­10 Currently, most structures. Multibody potentials may help improve our understanding of the cooperativity of protein folding

Schlick, Tamar

332

Techniques for modeling and analyzing RNA and protein folding energy landscapes  

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techniques can be used to study RNA and protein fold- ing kinetics such as population kinetics, folding rates, and the folding of particular subsequences. In particular, a map-based Master Equation (MME) method can be used to analyze the population kinetics...

Tang, Xinyu

2009-05-15T23:59:59.000Z

333

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

E-Print Network (OSTI)

Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path Gregg Lois the dynamics of protein folding. The key insight is that the search for the native protein conformation. In the ``new view'' of protein folding (3,7), statistical fluctuations on an energy landscape give rise

O'Hern, Corey S.

334

Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study  

E-Print Network (OSTI)

Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study Re October 1998 In the framework of a lattice-model study of protein folding, we investigate the interplay model. Lattice models have been widely used in the study of protein folding dynamics.2­8 The main

Levine, Alex J.

335

A new approach to multi-modal diffusions with applications to protein folding  

E-Print Network (OSTI)

A new approach to multi-modal diffusions with applications to protein folding Julie Lyng Forman1 rates are estimated. The new models provide a better fit to this type of protein folding data than time; measurement error; martingale estimating func- tion; multi-modality; protein folding; stochastic

Sørensen, Michael

336

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

337

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability  

E-Print Network (OSTI)

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how on the effects of macro- molecular crowding on protein folding and binding stability has been reached. Crowders

Weston, Ken

338

Predicting protein folding rates from geometric contact and amino acid sequence  

E-Print Network (OSTI)

Predicting protein folding rates from geometric contact and amino acid sequence ZHENG OUYANG structural properties. Keywords: protein folding; geometric contact number; zippers model; folding rate, USA (RECEIVED January 22, 2008; FINAL REVISION April 4, 2008; ACCEPTED April 7, 2008) Abstract Protein

Dai, Yang

339

Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies  

E-Print Network (OSTI)

Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies for protein folding studies and has been extensively stud- ied, both experimentally (at the ensemble level concentration. It is shown that new infor- mation about different aspects of the protein folding reaction can

Croquette, Vincent

340

AN ANALYSIS OF PROTEIN FOLDING BY DECODING THE HIERARCHY OF NATIVE-STATE STRUCTURAL INTERACTIONS  

E-Print Network (OSTI)

AN ANALYSIS OF PROTEIN FOLDING BY DECODING THE HIERARCHY OF NATIVE-STATE STRUCTURAL INTERACTIONS and Department of Physics and Astronomy 2002 #12;ABSTRACT AN ANALYSIS OF PROTEIN FOLDING BY DECODING by which proteins fold is one of the most intensely studied prob- lems in science. Here, an analysis

Thorpe, Michael

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341

Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy  

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Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy Jun Jiang of the signals provides a quantitative marker of protein folding status, accessible by both theoretical calculations and experiments. SECTION: Biophysical Chemistry and Biomolecules Protein folding is an important

Mukamel, Shaul

342

The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding  

E-Print Network (OSTI)

­coil theories and protein folding. Contrary to the hypothesis, we find that systematic local steric effects can). The central thermodynamic question in protein folding is: How can a polypeptide chain overcome conformational­6) and protein-folding theories (7). It follows from the hypothesis that local structural transitions are ruled

Fleming, Patrick

343

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics  

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Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics John involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the preceding

Takada, Shoji

344

Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level  

E-Print Network (OSTI)

Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level coupled to the process of protein folding in vivo. While previous studies have provided invaluable insight about how crowding affects protein folding dynamics at the secondary structure level. In this study, we

Shorter, James

345

Semi-deterministic and genetic algorithms for global optimization of microfluidic protein folding  

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Semi-deterministic and genetic algorithms for global optimization of microfluidic protein folding of a fast microfluidic protein folding device. The aim of the latter design is to reduce mixing times protein folding devices design. Section 3 presents three global optimization algorithms with associated

Santiago, Juan G.

346

Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics  

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Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics Eric Alm1 underlying the protein-folding problem can be tested by developing and characterizing simple models that make prefactor for protein folding. Finally, we discuss the limitations of simple native-state-based models

Morozov, Alexandre V.

347

Gibbs Adsorption Isotherm Combined with Monte Carlo Sampling to See Action of Cosolutes on Protein Folding  

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Driven by conditions set by smaller solutes, proteins fold and unfold. Experimentally, these conditions stability. Proteins 2004;57:311­321. © 2004 Wiley-Liss, Inc. INTRODUCTION Inside cells, proteins fold poten- tials, to follow the process of protein folding or unfolding in response to its environment

Harries, Daniel

348

Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding \\Lambda  

E-Print Network (OSTI)

Parallel Continuation­Based Global Optimization for Molecular Conformation and Protein Folding­ pecially protein folding. Global minimization problems are difficult to solve when the objective functions­ cluding energy functions for molecular conformation and protein folding. Mathematical theory

Neumaier, Arnold

349

Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results  

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Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results a comprehensive survey of combinatorial algorithms and theorems about lattice protein folding models obtained in the almost 15 years since the publication in 1995 of the first protein folding approximation algorithm

Istrail, Sorin

350

Pathways for protein folding: is a "new view" needed? Vijay S Pande1  

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Pathways for protein folding: is a "new view" needed? Vijay S Pande1 , Alexander Yu Grosberg2 energy MG Molten globule Introduction How do proteins fold? While the thirty five years since Anfinsen has demonstrated the complexity of protein folding, the search continues for the general principles

Croquette, Vincent

351

A minimum-reaction-flux solution to master-equation models of protein folding  

E-Print Network (OSTI)

A minimum-reaction-flux solution to master-equation models of protein folding Huan-Xiang Zhoua; published online 20 May 2008 Master equations are widely used for modeling protein folding. Here- ceptual and quantitative models for protein folding.1­15 In such models, the conformational space

Weston, Ken

352

Relationship between protein folding thermodynamics and the energy landscape Jaegil Kim,* Thomas Keyes,  

E-Print Network (OSTI)

Relationship between protein folding thermodynamics and the energy landscape Jaegil Kim,* Thomas Received 23 September 2008; published 4 March 2009 The origin of protein folding thermodynamics is examined.15.Cc, 05.70. a, 87.15.A Protein folding--i.e., how a polypeptide chain reaches a unique native state

Straub, John E.

353

From residue matching patterns to protein folding topographies: General model and bovine  

E-Print Network (OSTI)

From residue matching patterns to protein folding topographies: General model and bovine pancreatic-grained model for protein-folding dynamics is introduced based on a discretized representation of torsional, pattern recognition, and general characteristics of protein folding kinetics. Topology here implies

Berry, R. Stephen

354

Protein Folding and Misfolding in Disease Instructors: Jean Baum and Ron Levy  

E-Print Network (OSTI)

Protein Folding and Misfolding in Disease Instructors: Jean Baum and Ron Levy Tuesday 2:30-5:00 PDB Training Room Syllabus Part I: Protein Folding 9/4: Introduction to Protein Architecture 9/11: Cooperative Transitions in Protein Molecules 9/16: Kinetics of Protein Folding and the Energy Landscape Model 9

Chen, Kuang-Yu

355

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity  

E-Print Network (OSTI)

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity¨lich, 52425 Ju¨lich, Germany Received June 14, 2010; E-mail: deserno@andrew.cmu.edu Abstract: Protein folding be difficult to measure. Therefore, protein folding cooperativity is often probed using the calorimetric

Bachmann, Michael

356

[25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures  

E-Print Network (OSTI)

[25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures By Nikolay V their unique three-dimensional structure. This ques- tion, known as the protein-folding problem,1­25 is of great importance because understanding protein-folding mechanisms is a key to success- ful manipulation

Dokholyan, Nikolay V.

357

Combining Task-and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform  

E-Print Network (OSTI)

Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform Is efficient protein folding possible with CHARMM on the United Devices MetaProcessor? B. Uk1 , M. Taufer1 parallelism and might not fit the needs for protein folding simulations with explicit water molecules. A short

Taufer, Michela

358

3D finite amplitude folding: Implications for stress evolution during crustal and lithospheric deformation  

E-Print Network (OSTI)

3D finite amplitude folding: Implications for stress evolution during crustal and lithospheric-layer folding to study this instability in 3D. It is demonstrated that linear theories correctly describe insensitive to the applied background shortening directions. Furthermore, the 3D folding instability reduces

Kaus, Boris

359

Some New Features for Protein Fold Prediction Nikhil Ranjan Pal and Debrup Chakraborty  

E-Print Network (OSTI)

Some New Features for Protein Fold Prediction Nikhil Ranjan Pal and Debrup Chakraborty Electronics}@isical.ac.in Abstract. In this paper we propose several sets of new features for protein fold prediction. The first discriminating powers in predicting protein folds. 1 Introduction One of the most important and challenging

Chakraborty, Debrup

360

Fluctuations of primary ubiquitin folding intermediates in a force clamp Frauke Grater, Helmut Grubmuller *  

E-Print Network (OSTI)

function of which is determined by their three-dimensional struc- ture, the protein fold. Understanding the basic mechanism and associated driving forces of protein folding remains a major task in biology and has., 1997; Marszalek et al., 1999). Along these lines, new insights into protein folding have been recently

Gräter, Frauke

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361

J. Mol. Biol. (1996) 259, 988994 Local Interactions Dominate Folding in a Simple  

E-Print Network (OSTI)

Unger1,2 * and John Moult2 Recent computational studies of simple models of protein folding have1 Press Limited Keywords: protein folding; lattice models; local interactions*Corresponding author Introduction What are the dominant contributions guiding the process of protein folding? The short life

Unger, Ron

362

Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential  

E-Print Network (OSTI)

the important contributions that computational methods can make in providing insights into protein folding. Understanding protein folding at the atomic level is a critical but elusive goal in structural biology. A protein's folded state can often be studied by x-ray crystallography or NMR spectroscopy, and recent

Chan, Hue Sun

363

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear  

E-Print Network (OSTI)

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality) The definition of reaction coordinates for the characterization of a protein-folding reaction has long been-dimensional represen- tation of a complex process such as protein folding. reaction coordinate transition state

Moll, Mark

364

Within the folds, outside the box Susan Lindquist uncovers the roles that misshapen proteins  

E-Print Network (OSTI)

a com- mon thread. "The one universal theme in our lab is protein folding and how changes in protein on a hazy day. "People didn't realize how broad the protein folding problems are. A lot of things that started out as basic research into protein folding are now translating into a direct interest in human

Lindquist, Susan

365

Implementation and Characterization of Protein Folding on a Desktop Computational Grid  

E-Print Network (OSTI)

Implementation and Characterization of Protein Folding on a Desktop Computational Grid Is CHARMM such as protein folding, desktop grids could become viable alter- natives to clusters of PCs. In this paper, we present a prototype and discuss the viabil- ity of a protein folding application with CHARMM on the United

Taufer, Michela

366

Molecular Dynamics Simulations: Methods and Value in the Folding Problem Devon Chandler-Brown  

E-Print Network (OSTI)

March 2013 Introduction The protein folding has been an outstanding problem in molecular biology for a long period of time. Stated simply, the question of protein folding is that of how the primary amino that govern protein folding are thought to be well established. Forces driven by ionic, Van der Waals

367

Multi-class Protein Fold Recognition Through a Symbolic-Statistical Framework  

E-Print Network (OSTI)

Multi-class Protein Fold Recognition Through a Symbolic-Statistical Framework Marenglen Biba, University of Bari, Italy {biba,esposito,ferilli,basile,ndm}@di.uniba.it Abstract. Protein fold recognition to a multi-class protein fold recognition problem. We compare the proposed approach to a symbolic

Di Mauro, Nicola

368

Task-parallel global optimization with application to protein folding C. Voglis, P. E. Hadjidoukas,  

E-Print Network (OSTI)

Task-parallel global optimization with application to protein folding C. Voglis, P. E. Hadjidoukas parallelization of a real application case that concerns the protein folding problem. The experimental evaluation, cluster programming, numerical differentiation, global optimization, protein folding. 1. INTRODUCTION Many

Dimakopoulos, Vassilios

369

Long Proteins with Unique Optimal Foldings in the H-P Model ?  

E-Print Network (OSTI)

state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state model designed to answer qualitative questions about the protein folding process. In this paper we; 1 Introduction Protein folding [14,22,30] is a central problem in molecular and computational

370

Predicting Protein Folds with Structural Repeats Using a Chain Graph Model  

E-Print Network (OSTI)

Predicting Protein Folds with Structural Repeats Using a Chain Graph Model Yan Liu yanliu, Carnegie Mellon University, Pittsburgh, PA 15213 USA Abstract Protein fold recognition is a key step to to accurately identify protein folds aris- ing from typical spatial arrangements of well-defined secondary

Xing, Eric P.

371

Face-centered cubic (FCC) lattice models for protein folding: energy function inference and biplane packing  

E-Print Network (OSTI)

Face-centered cubic (FCC) lattice models for protein folding: energy function inference and biplane simplified. The objective of PSP (also known as protein folding) is to select the molecule conformation which to infer general energy functions for the protein folding problem. While the general problem is intractable

Istrail, Sorin

372

Analysis of Methods for Predicting Protein Fold and Remote Homologue Recognition  

E-Print Network (OSTI)

Analysis of Methods for Predicting Protein Fold and Remote Homologue Recognition Prepared by Sanjay Stanford University #12;1. PROTEIN FOLD AND REMOTE HOMOLOGS 1.1 INTRODUCTION Life is a complex system-going efforts to learn biology, the protein folding has been one of those challenging areas in computational

373

Mechanical Properties of Bovine Rhodopsin and Bacteriorhodopsin: Possible Roles in Folding and Function  

E-Print Network (OSTI)

in rhodopsin but not in bacteriorhodopsin. This core may reflect differences in mechanisms of protein folding their adaptation to differing functions. Introduction Protein folding is one of the most challenging problems protein folding. For more than a decade, the atomic force microscope (AFM) has permitted the use of single

Palczewski, Krzysztof

374

Title: The automatic discovery of structural principles describing protein fold space  

E-Print Network (OSTI)

Title: The automatic discovery of structural principles describing protein fold space Adrian P author Short title Describing protein fold space #12;Summary The study of protein structure has largely arrangements and in the wider context of protein folding, function and evolution. Given the complicated nature

Muggleton, Stephen H.

375

Folding and Function of Proteorhodopsins in Photoenergy Transducing Membranes  

SciTech Connect

The overall research objectives are to develop proteorhodopsin (PR) proteins as a model system for {alpha}?-helical membrane protein insertion and folding, and to advance understanding of the diversity and mechanisms of PRs, a large family of photoenergy transducers (~4000 identified) abundant in the worlds oceans. Specific aims are: (1) To develop a highefficiency genetic selection procedure for light-driven proton-pumping in E. coli cells. Such a procedure would provide a positive selection method for proper folding and function of PRs in the E. coli membrane. (2) Characterize flash-induced absorption changes and photocurrents in PR variants in organisms from various environments, and their expression level and function when expressed in E. coli. Subaims are to: (a) elucidate the relationship of the transport mechanism to mechanisms of other microbial rhodopsins, some of which like PRs function as ion transporters and some of which use light energy to activate signaling pathways (sensory rhodopsins); and (b) identify important residues and chemical events in light-driven proton transport by PRs. In addition to their importance to the energy of the biosphere PRs have attracted interest for their potential for use in making photoenergy-transducing membranes for bioengineering applications.

Spudich, John L

2012-08-10T23:59:59.000Z

376

Ultraviolet resonance Raman and fluorescence studies of folded and unfolded conformations of the membrane protein OmpA  

E-Print Network (OSTI)

Thermodynamics of Membrane Protein Folding: Lessons from theA Model for Membrane Protein Folding, H. S. Shafaat, K. M.goals of membrane protein folding studies is to ascertain

Sanchez, Katheryn Marie

2010-01-01T23:59:59.000Z

377

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

378

Topological crossovers in the forced folding of self-avoiding matter  

E-Print Network (OSTI)

We study the scaling properties of forced folding of thin materials of different geometry. The scaling relations implying the topological crossovers from the folding of threedimensional plates to the folding of two-dimensional sheets, and further to the packing of one-dimensional strings, are derived for elastic and plastic manifolds. These topological crossovers in the folding of plastic manifolds were observed in experiments with predominantly plastic aluminum strips of different geometry. Elasto-plastic materials, such as paper sheets during the (fast) folding under increasing confinement force, are expected to obey the scaling force-diameter relation derived for elastic manifolds. However, in experiments with paper strips of different geometry, we observed the crossover from packing of one-dimensional strings to folding two dimensional sheets only, because the fractal dimension of the set of folded elasto-plastic sheets is the thickness dependent due to the strain relaxation after a confinement force is withdrawn.

Alexander S. Balankin; Daniel Morales Matamoros; Ernesto Pineda Leon; Antonio Horta Rangel; Miguel Angel Martinez Cruz; Didier Samayoa Ochoa

2009-07-25T23:59:59.000Z

379

Energy optimization for off-lattice protein folding  

Science Journals Connector (OSTI)

Two three-dimensional AB off-lattice protein models consisting of hydrophobic and hydrophilic monomers are studied in this paper. By incorporating an extra energy contribution into the original energy function, the protein folding is converted from a constraint optimization problem into an unconstrained one which can be solved by the well-known gradient method. From the initial configurations randomly generated by the heuristic strategy proposed in this paper, our algorithm can find better results than those by nPERM for the four Fibonacci sequences. Based on the initial configurations obtained by energy landscape paving (ELP) routine, some of our results for the lowest energies are better than the best values reported in the literature.

Wenqi Huang; Mao Chen; Zhipeng L

2006-10-09T23:59:59.000Z

380

Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding  

SciTech Connect

An information theory model of hydrophobic effects is used to construct a molecular explanation why hydrophobic solvation entropies of protein unfolding measured by high sensitivity calorimetry converge to zero at a common convergence temperature. The entropy convergence follows directly from the weak temperature dependence of occupancy fluctuations {l_angle}{delta}{ital n}{sup 2}{r_angle} for molecular-scale volumes in water. The macroscopic expression of the contrasting entropic behavior of water relative to common organic solvents is the {ital relative} temperature insensitivity of the water isothermal compressibility compared to hydrocarbon liquids. The information theory model used provides a quantitative description of small molecule hydration and, in addition, predicts that the value of the entropy at convergence is slightly {ital negative}. Interpretations of entropic contributions to protein folding should account for this result. {copyright} {ital 1996 The American Physical Society.}

Garde, S.; Hummer, G.; Garcia, A.E.; Paulaitis, M.E.; Pratt, L.R. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); [Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716 (United States); [Department of Chemical Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

1996-12-01T23:59:59.000Z

Note: This page contains sample records for the topic "folds grabens horst" 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

Contact order revisited: Influence of protein size on the folding rate  

SciTech Connect

Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical model of protein folding that predicts that logarithm of the folding rate decreases with the protein chain length L as L2/3, and by the finding that the folding rates of multistate folding proteins strongly correlate with their sizes and have very bad correlation with CO, we reexamined the dependence of folding rate on CO and L in attempt to find a structural parameter that determines folding rates for the totality of proteins. We show that the Abs{sub CO} = CO x L, is able to predict rather accurately folding rates for both two-state and multistate folding proteins, as well as short peptides, and that this Abs{sub CO} scales with the protein chain length as L0.70 {+-} 0.07 for the totality of studied single-domain proteins and peptides.

Ivankov, Dmitry N.; Garbuzynskiy, Sergiy O.; Alm, Eric; Plaxco, Kevin W.; Baker, David; Finkelstein, Alexei V.

2003-05-28T23:59:59.000Z

382

Development and application of all-atom structure-based models for studying the role of geometry in biomolecular folding and function  

E-Print Network (OSTI)

in Protein Folding . . . . . . . . . . . . . . . . . . . . .P. G. (2004) Theory of protein folding. Curr. Opin. Struct.statistical mechanics of protein folding. Proc. Nat. Acad.

Noel, Jeffrey Kenneth

2012-01-01T23:59:59.000Z

383

Power law scaling of lateral deformations with universal Poissons index for randomly folded thin sheets  

E-Print Network (OSTI)

We study the lateral deformations of randomly folded elastoplastic and predominantly plastic thin sheets under the uniaxial and radial compressions. We found that the lateral deformations of cylinders folded from elastoplastic sheets of paper obey a power law behavior with the universal Poissons index nu = 0.17 pm 0.01, which does not depend neither the paper kind and sheet sizes, nor the folding confinement ratio. In contrast to this, the lateral deformations of randomly folded predominantly plastic aluminum foils display the linear dependence on the axial compression with the universal Poissons ratio nu_e = 0.33 pm 0.01. This difference is consistent with the difference in fractal topology of randomly folded elastoplastic and predominantly plastic sheets, which is found to belong to different universality classes. The general form of constitutive stress-deformation relations for randomly folded elastoplastic sheets is suggested.

Alexander S. Balankin; Didier Samayoa Ochoa; Ernesto Pineda Leon; Rolando Cortes Montes de Oca; Antonio Horta Rangel; Miguel Angel Martinez Cruz

2008-08-24T23:59:59.000Z

384

Transferable coarse-grained potential for $\\textit{de novo}$ protein folding and design  

E-Print Network (OSTI)

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and folding is introduced. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences are not yet fully realistic and require further experimental testing. For an independent set of proteins, notoriously difficult to fold, the correct folding of both the designed and the natural sequences is also demonstrated. The folding properties are characterized by free energy calculations. which not only are consistent among natural and designed proteins, but we also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, this novel coarse-grained protein model ...

Coluzza, Ivan

2014-01-01T23:59:59.000Z

385

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

SciTech Connect

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

386

Thermodynamics and Kinetics of a Go Proteinlike Heteropolymer Model with Two-State Folding Characteristics  

E-Print Network (OSTI)

We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding behavior. It turns out that general, characteristic folding features of realistic proteins with a single free-energy barrier can also be observed in this simplified model, where the folding transition is primarily driven by the hydrophobic force.

Anna Kallias; Michael Bachmann; Wolfhard Janke

2007-12-06T23:59:59.000Z

387

An 8-bit current mode ripple folding analog to digital converter  

E-Print Network (OSTI)

. 3. 4 Noise IV. RIPPLE FOLDING TECHNIQUE 1. Conceptual Description of Ripple Folding. . 2. Topologies to Implement Minimum-Maximum Detection. . . . . 2. 1 The Diode Bridge 2. 2 Bipolar Realization. . 2. 3 CMOS Realization 2. 4 Switched Current... single pole system. 23 Noise bandwidth. 24 Traditional folding A/D converter 25 (a) Conceptual ripple lolding A/D converter. . . . . . 21 23 23 . . . 30 . . . . . . 35 36 . . . . . 37 . . . 41 FIGURE Page 26 27 28 Diode bridge...

Dinc, Huseyin

2012-06-07T23:59:59.000Z

388

Using Bit-Vector Decision Procedures for Analysis of Protein Folding Pathways  

E-Print Network (OSTI)

Abstract. We explore the use of bit-vector decision procedures for the analysis of protein folding pathways. We argue that the protein folding problem is not identical to the classical probabilistic model checking problem in verification. Motivated by the different nature of the protein folding problem, we present a translation of the protein folding pathways analysis problem into a bounded model checking framework with bit vector decision procedures. We also present initial results of our experiments using the UCLID bit-vector decision procedure. 1

Christopher James Langmead; Sumit Kumar Jha

389

Investigation of Protein Folding by Using Combined Method of Molecular Dynamics and Monte Carlo Simulations.  

E-Print Network (OSTI)

??We used the combination of molecular dynamics and Monte Carlo method to investigate protein folding problems. The environments of proteins are very big, and often (more)

Liao, Jun-min

2006-01-01T23:59:59.000Z

390

Use of Urea Solutions to Study Backbone Hydration in Protein Folding.  

E-Print Network (OSTI)

?? The focus of this research was to understand the role of bulk water in protein-folding equilibria. Several thermodynamic properties of bulk water were measured (more)

Sekaran Parthasarathy, Harini

2013-01-01T23:59:59.000Z

391

Large Protein Folding and Dynamics Studied by Advanced Hydrogen Exchange Methods.  

E-Print Network (OSTI)

??Protein folding studies over the past 50 years have been largely focused on small proteins (< 200 residues) leading to a dearth of information about (more)

Walters, Benjamin Thomas

2013-01-01T23:59:59.000Z

392

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

E-Print Network (OSTI)

??The Funneled Energy Landscape Theory is currently the most widely accepted theory of protein folding. In this dissertation, the basic concepts of the Energy Landscape (more)

Cho, Samuel Sung-Il

2007-01-01T23:59:59.000Z

393

Structural Basis for the Cooperation of Hsp110 and Hsp70 Molecular Chaperones in Protein Folding.  

E-Print Network (OSTI)

??Protein folding is a crucial process for cell survival. Only natively structured proteins can perform their essential biological functions. Although all structure-relevant information is principally (more)

Polier, Sigrun

2009-01-01T23:59:59.000Z

394

Simplified models for simulating replica exchange simulations and recovering kinetics of protein folding.  

E-Print Network (OSTI)

??Protein folding is a fundamental problem in modern structural biology. The nature of the problem poses challenges to the understanding of the process via computer (more)

Zheng, Weihua

2009-01-01T23:59:59.000Z

395

Structural Characterization of Protein Folding Intermediates by Oxidative Labeling and Mass Spectrometry.  

E-Print Network (OSTI)

??A key challenge associated with protein folding studies is the characterization of short-lived intermediates that become populated en route to the native state. In this (more)

Stocks, Bradley B

2012-01-01T23:59:59.000Z

396

A Study of the Protein Folding Dynamic Abstract--In this paper, we propose two means to  

E-Print Network (OSTI)

A Study of the Protein Folding Dynamic Omar GACI Abstract--In this paper, we propose two means to study the protein folding dynamic. We rely on the HP model to study the protein folding problem in a con algorithms is validated experimentally. Keywords: boids, protein folding problem, interaction networks

Paris-Sud XI, Université de

397

Protein Folding Dynamics via Quantification of Kinematic Energy Landscape Sema Kachalo, Hsiao-Mei Lu, and Jie Liang*  

E-Print Network (OSTI)

Protein Folding Dynamics via Quantification of Kinematic Energy Landscape Se¨ma Kachalo, Hsiao of protein folding has been studied ex- tensively [1,2]. A remarkable observation is that protein folding that protein folding rates are largely determined by the topology of their native structure [3]. Theoretical

Dai, Yang

398

Probing sequence-structure relationships in proteins: Application of simple energy functions to the inverse folding problem  

E-Print Network (OSTI)

A brief description of the protein-folding and inverse-folding problems is provided. Design of energy are applied to estimate the sequence capacity of all known protein folds, and to compute the evolutionary for recognition of protein folds, and conclude with an application to protein evolution, studying the sequence

Elber, Ron

399

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

E-Print Network (OSTI)

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

Wirmer, Julia

2005-01-01T23:59:59.000Z

400

How Does Folding Modulate Thermal Conductivity of Graphene? Nuo Yang1,2  

E-Print Network (OSTI)

of thermal conductivity is due to scattering of low frequency phonons by the folds. Our results suggest dimensional materials. Keywords Folded graphene ribbon, thermal conductivity, phonon transport, scattering #12 conductivity of low-dimensional silicon and carbon materials11 and graphene ribbons12 were studied by EMD

Li, Baowen

Note: This page contains sample records for the topic "folds grabens horst" from the National Library of EnergyBeta (NLEBeta).
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We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

10.1098/rspa.2001.0921 Folding energetics in thin-lm diaphragms  

E-Print Network (OSTI)

10.1098/rspa.2001.0921 Folding energetics in thin-¯lm diaphragms By G. Gioia1, A. DeSimone2, M to elucidate how the folding patterns of thin- lm dia- phragms subject to in-plane isotropic and anisotropic- lm diaphragms (Madou 1997). However, a thorough understanding of the mechanical behaviour

DeSimone, Antonio

402

CHARGE-BASED MOS CORRELATED DOUBLE SAMPLING COMPARATOR AND FOLDING CIRCUIT  

E-Print Network (OSTI)

CHARGE-BASED MOS CORRELATED DOUBLE SAMPLING COMPARATOR AND FOLDING CIRCUIT Roman Genov and Gert 21218-2686 E-mail: roman,gert¡ @bach.ece.jhu.edu ABSTRACT A novel charge-based comparator and folding circuit are pre- sented. Correlated double sampling comparison is performed using a log-domain integrator

Cauwenberghs, Gert

403

THE JOURNAL OF CHEMICAL PHYSICS 139, 121925 (2013) Unfolded protein ensembles, folding trajectories, and refolding  

E-Print Network (OSTI)

#12;THE JOURNAL OF CHEMICAL PHYSICS 139, 121925 (2013) Unfolded protein ensembles, folding) Computer simulations can provide critical information on the unfolded ensemble of proteins un- der, to characterize properties of the unfolded states of intrinsically disordered or intrinsically folded proteins

Plotkin, Steven S.

404

The structural basis of protein folding and its links with human disease  

Science Journals Connector (OSTI)

...to 134 C. M. Dobson Protein folding and human disease...of a 27-mer model protein as a function of the...collapses rapidly to a disordered globule. It then makes...Investigating the folding of a protein by experimental methods...heterogeneity of the ensembles of conformations that...

2001-01-01T23:59:59.000Z

405

Self-Consistent Approaches for the Protein Folding Problem: Kinetics and Equilibrium Properties of Random Copolymers  

Science Journals Connector (OSTI)

......One expression of the protein folding problem is to...structure of the folded protein, and to deduce the...brings a statistical ensemble of extended coils into...in the misfolding of proteins has arisen recently...homopolymeric, fl, and the disordered, Hdis, terms respectively......

Edward G. Timoshenko; Yuri A. Kuznetsov; Andrei Moskalenko; Kenneth A. Dawson

1997-01-01T23:59:59.000Z

406

Discrete Nonlinear Schrodinger Equation, Solitons and Organizing Principles for Protein Folding  

E-Print Network (OSTI)

We introduce a novel generalization of the discrete nonlinear Schr\\"odinger equation. It supports solitons that describe how proteins fold. As an example we scrutinize the villin headpiece HP35, an archetypal protein for testing both experimental and theoretical approaches to protein folding. Using explicit soliton profiles we construct its carbon backbone with an unprecedented accuracy.

Nora Molkenthin; Shuangwei Hu; Antti J. Niemi

2010-09-06T23:59:59.000Z

407

On the Design and Analysis of Protein Folding Potentials Dror Tobi,1  

E-Print Network (OSTI)

On the Design and Analysis of Protein Folding Potentials Dror Tobi,1 Gil Shafran,2 Nathan Linial,2) is to find a potential energy function using physical chemistry principles, trying to mimic the way proteins fold in nature. Another approach, more limited in scope, is to find an energy function that will set

Linial, Nathan "Nati"

408

Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations  

E-Print Network (OSTI)

Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding First principle models of protein folding gener- ally are preferred over statistical approaches because a knowledge-based approach and a more funda- mental methodology. Our present focus is on whether protein

Berry, R. Stephen

409

Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model  

SciTech Connect

We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill, which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail gave approximation algorithms for folding proteins on the cubic lattice under HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio which they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.

Agarwala, R. [National Institutes of Health, Bethesda, MD (United States); Batzoglou, S. [MIT, Cambridge, MA (United States); Dancik, V. [Univ. of Southern California, Los Angeles, CA (United States)] [and others

1997-06-01T23:59:59.000Z

410

Local Interactions and Protein Folding: A 3D Off-Lattice Approach  

E-Print Network (OSTI)

The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional proteins, the dominance of a native state for many sequences is observed. As in lattice model approaches, folding takes place by gradual compactification, followed by a sequence dependent folding transition. Our results differ from lattice approaches in that bimodal energy distributions are not observed and that high folding temperatures are accompanied by relatively low temperatures for the peak of the specific heat. Also, in contrast to earlier studies using lattice models, our results convincingly demonstrate that one does not need more than two types of residues to generate sequences with good thermodynamic folding properties in three dimensions.

Anders Irbck; Carsten Peterson; Frank Potthast; Ola Sommelius

1996-10-10T23:59:59.000Z

411

Extensional Tectonics | Open Energy Information  

Open Energy Info (EERE)

Extensional Tectonics Extensional Tectonics Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Print PDF Extensional Tectonics Dictionary.png Extensional Tectonics: No definition has been provided for this term. Add a Definition Crustal extension results in horst and graben topography (reference: geologycafe.com) Crustal extension (or lithospheric extension) results in a thinning of the crust, bringing the Earth's surface closer to the hot mantle which increases heat flow. This high heat flow often results in moderate temperature (190-230°C) geothermal resources. Extensional zones are exemplified by horst and graben structures such as those found in the Basin & Range province of the US. Retrieved from "http://en.openei.org/w/index.php?title=Extensional_Tectonics&oldid=599244"

412

Property:TopoFeatures | Open Energy Information  

Open Energy Info (EERE)

Property Property Edit with form History Facebook icon Twitter icon » Property:TopoFeatures Jump to: navigation, search Property Name TopoFeatures Property Type String Description Describes topographic features within the vicinity of the field (e.g. volcanic features, rift valleys, extensional features) that may be significant reflections of underlying geothermal resources. This is a property of type Page. Subproperties This property has the following 4 subproperties: G Geysers Geothermal Area L Lightning Dock Geothermal Area S Soda Lake Geothermal Area Stillwater Geothermal Area Pages using the property "TopoFeatures" Showing 23 pages using this property. A Amedee Geothermal Area + Horst and Graben + B Beowawe Hot Springs Geothermal Area + Horst and Graben +

413

Noninvasive Monitoring of Vocal Fold Vertical Vibration Using The Acoustic Doppler Effect  

Science Journals Connector (OSTI)

SummaryObjectives/Hypothesis To validate a proposed method of noninvasively monitoring vocal fold vertical vibration through utilization of the acoustic Doppler effect and the waveguide property of the vocal tract. Study Design Validation case-control study. Methods In this device, an ultrasound beam is generated and directed into the mouth. The vocal tract, acting as a natural waveguide, guides the ultrasound beam toward the vibrating vocal folds. The vertical velocity of vocal fold vibration is then recovered from the Doppler frequency of the reflected ultrasound. One subject (age 32, male) was studied and measurements were taken under three modes of vocal fold vibration: breathing (no vibration), whispering (irregular vibration), and normal phonation (regular vibration). Results The peak-to-peak amplitude of the measured velocity of vocal fold vertical vibration was about 0.16m/s, and the fundamental frequency was 172Hz; the extracted velocity information showed a reasonable waveform and value in comparison with the previous studies. In all three modes of phonation, the Doppler frequencies derived from the reflected ultrasound corresponded with the vertical velocity of vocal fold vibration as expected. Conclusions The proposed method can accurately represent the characteristics of different phonation modes such as no phonation, whisper and normal phonation. The proposed device could be used in daily monitoring and assessment of vocal function and vocal fold vibration.

Chao Tao; Jack J. Jiang; Dan Wu; Xiaojun Liu; Ann Chodara

2012-01-01T23:59:59.000Z

414

Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics  

E-Print Network (OSTI)

Chevron rollovers of some proteins imply that their logarithmic folding rates are nonlinear in native stability. This is predicted by lattice and continuum G\\=o models to arise from diminished accessibilities of the ground state from transiently populated compact conformations under strongly native conditions. Despite these models' native-centric interactions, the slowdown is due partly to kinetic trapping caused by some of the folding intermediates' nonnative topologies. Notably, simple two-state folding kinetics of small single-domain proteins are not reproduced by common G\\=o-like schemes.

Huseyin Kaya; Hue Sun Chan

2003-05-20T23:59:59.000Z

415

Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks  

Science Journals Connector (OSTI)

We perform simulations of model proteins to study folding on rugged energy landscapes. We construct first-passage networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to basins and transitions between them in the energy landscape. We find power-law relations between the folding time and the number of nodes and bonds. We show that these scalings are determined by the fractal properties of first-passage networks. Thus, we have identified a possible mechanismthe small fractal dimension of first passage networkswhich can give rise to reliable folding in proteins with rugged energy landscapes.

Gregg Lois; Jerzy Blawzdziewicz; Corey S. OHern

2010-05-06T23:59:59.000Z

416

Time Resolved Collapse of a Folding Protein Observed with Small Angle X-Ray Scattering  

SciTech Connect

High-intensity, ''pink'' beam from an undulator was used in conjunction with microfabricated rapid-fluid mixing devices to monitor the early events in protein folding with time resolved small angle x-ray scattering. This Letter describes recent work on the protein bovine {beta} -lactoglobulin where collapse from an expanded to a compact set of states was directly observed on the millisecond time scale. The role of chain collapse, one of the initial stages of protein folding, is not currently understood. The characterization of transient, compact states is vital in assessing the validity of theories and models of the folding process.

Pollack, L.; Tate, M. W.; Finnefrock, A. C.; Kalidas, C.; Trotter, S.; Darnton, N. C.; Lurio, L.; Austin, R. H.; Batt, C. A.; Gruner, S. M. (and others)

2001-05-21T23:59:59.000Z

417

Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks  

E-Print Network (OSTI)

We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to basins and transitions between them in the energy landscape. We find power-laws between the folding time and number of nodes and bonds. We show that these scalings are determined by the fractal properties of first-passage networks. Reliable folding is possible in systems with rugged energy landscapes because first passage networks have small fractal dimension.

Gregg Lois; J. Blawzdziewicz; Corey S. O'Hern

2009-06-24T23:59:59.000Z

418

Efficient traversal of beta-sheet protein folding pathways using ensemble models  

E-Print Network (OSTI)

Efficient traversal of beta-sheet protein folding pathways using ensemble models Solomon Shenker1 methodology to address these computational complexity limitations. Our approach aims to complement the range

Devadas, Srinivas

419

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models  

E-Print Network (OSTI)

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models Solomon Shenker1 methodology to address these com- putational complexity limitations. Our approach aims to complement the range of

Gifford, David K.

420

E-Print Network 3.0 - acute vocal fold Sample Search Results  

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

Properties of the Vocal Fold Mucosa In a Porcine Model Lei Xi (Christina) Chen... Advisor: Amir Miri 1.0 INTRODUCTION - Voice is produced by flow-induced self-oscillations of...

Note: This page contains sample records for the topic "folds grabens horst" 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

Electrostatics and packing in biomolecules : accounting for conformational change in protein folding and binding  

E-Print Network (OSTI)

The role of electrostatics and packing in protein folding and molecular association was assessed in different biomolecular systems. A continuum electrostatic model was applied to long-range electrostatic effects in the ...

Caravella, Justin Andrew, 1974-

2002-01-01T23:59:59.000Z

422

The use of single tryptophan variants to study protein folding and stability  

E-Print Network (OSTI)

Studies on the kinetics of protein folding of the histidine-containing phosphocarrier protein (HPr) from the thermophile Bacillus stearothermophilus (Bst) will contribute much to the understanding of the origins of its enhanced thermal stability...

Dulin, Jennifer Natalie

2013-02-22T23:59:59.000Z

423

Protein folding and misfolding: a paradigm of selfassembly and regulation in complex biological systems  

Science Journals Connector (OSTI)

...disorganized ensembles of conformations...single domains of proteins appear to be...unfolded state disordered aggregates degradation...accessible to a protein following its...ribosome. Globular proteins fold from their highly disordered unfolded states...

2003-01-01T23:59:59.000Z

424

From local structure to a global framework: recognition of protein folds  

Science Journals Connector (OSTI)

...flexible and disordered regions. The use...flexibility profiles of a protein structure may also...prediction of disordered protein regions from amino...structure space with ensemble fold recognition...program Phyre. Proteins 70, 611-625...

2014-01-01T23:59:59.000Z

425

Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in  

E-Print Network (OSTI)

Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems, volunteered by private citizens across the globe (Butler, 2000). For example, SETI@home has accumulated over

Snow, Christopher

426

The Kinetics and Magnesium Requirements for the Folding of Antigenomic Ribozymes  

E-Print Network (OSTI)

The Kinetics and Magnesium Requirements for the Folding of Antigenomic Ribozymes Sirinart of antigenomic ri- bozyme was studied, it is demonstrated that its L3 loop requires magnesium and, apparently

Perreault, Jean-Pierre

427

Three-Dimensional Hydrogel Model Using Adipose-Derived Stem Cells for Vocal Fold Augmentation  

E-Print Network (OSTI)

Adipose-derived stem cells (ASCs) may provide a clinical option for rebuilding damaged superficial lamina propria of the vocal fold. We investigated the effects of five hydrogels (hyaluronic acid [HA], collagen, fibrin, ...

Park, Hyoungshin

428

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

E-Print Network (OSTI)

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

Ganim, Ziad

2010-01-01T23:59:59.000Z

429

Theory and simulation of macromolecular crowding effects on protein folding stability and kinetics  

E-Print Network (OSTI)

We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta- and alpha/beta-proteins are well described by an adaptation of the scaled particle theory (SPT). In this approach, the native state, transition state, and the unfolded protein are treated as effective hard spheres with radii approximately independent of the size and concentration of the crowders. The same model predicts the effect of crowding on the folding barrier and therefore refolding rates with no adjustable parameters. A simple extension of the SPT model, assuming additivity, can also describe the behavior of mixtures of crowding particles.

Jeetain Mittal; Robert B. Best

2009-02-26T23:59:59.000Z

430

Crystallographic Structure of SurA, a Molecular Chaperone that Facilitates Folding of Outer Membrane Porins  

SciTech Connect

The SurA protein facilitates correct folding of outer membrane proteins in gram-negative bacteria. The sequence of Escherichia coli SurA presents four segments, two of which are peptidyl-prolyl isomerases (PPIases); the crystal structure reveals an asymmetric dumbbell, in which the amino-terminal, carboxy-terminal, and first PPIase segments of the sequence form a core structural module, and the second PPIase segment is a satellite domain tethered approximately 30 A from this module. The core module, which is implicated in membrane protein folding, has a novel fold that includes an extended crevice. Crystal contacts show that peptides bind within the crevice, suggesting a model for chaperone activity whereby segments of polypeptide may be repetitively sequestered and released during the membrane protein-folding process.

Bitto, E.

2002-01-01T23:59:59.000Z

431

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models  

E-Print Network (OSTI)

Molecular dynamics (MD) simulations can now predict ms-timescale folding processes of small proteins; however, this presently requires hundreds of thousands of CPU hours and is primarily applicable to short peptides with ...

Waldisphl, Jerome

432

Site specific mutagenesis study of the protein folding process of luciferase  

E-Print Network (OSTI)

SITE SPECIFIC MUTAGENESIS STUDY OF THE PROTEIN FOLDING PROCESS OF LUCIFERASE A Thesis KE WEI Submitted to the Office of Graduate Studies of Texas A8 M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE... MAY 1990 Major Subject: Genetics SITE SPECIFIC MUTAGENESIS STUDY OF THE PROTEIN FOLDING PROCESS OF LUCIFERASE A Thesis by KE WEI Approved as to style and content by: T. O. aldwin ( Chair of Committee ) C. N. Pace ( Member ) M. D. Manson...

Wei, Ke

2012-06-07T23:59:59.000Z

433

Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results  

E-Print Network (OSTI)

... a very nice step forward in the computerology of proteins. Ken Dill 1995[1] We present a comprehensive survey of combinatorial algorithms and theorems about lattice protein folding models obtained in the almost 15 years since the publication in 1995 of the first protein folding approximation algorithm with mathematically guaranteed error bounds [60]. The results presented here are mainly about the HP-protein folding model introduced by Ken Dill in 1985 [37]. The main topics of this survey include: approximation algorithms for linear-chain and side-chain lattice models, as well as off-lattice models, NP-completeness theorems about a variety of protein folding models, contact map structure of self-avoiding walks and HP-folds, combinatorics and algorithmics of side-chain models, bi-sphere packing and the Kepler conjecture, and the protein side-chain self-assembly conjecture. As an appealing bridge between the hybrid of continuous mathematics and discrete mathematics, a cornerstone of the mathematical difficulty of the protein folding problem, we show how work on 2D self-avoiding walks contact-map decomposition [56] can build upon the exact RNA contacts counting

Sorin Istrail; Fumei Lam

2009-01-01T23:59:59.000Z

434

Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics  

E-Print Network (OSTI)

The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction coordinates are identified as collective growth modes of the unstable fluctuations about the saddle-points in the free energy surface. The description of the chain dynamics incorporates internal friction (independent of the solvent viscosity) arising from the elementary isomerizations of the backbone dihedral angles. We find that the folding rate depends linearly on the solvent friction for high viscosity, but saturates at low viscosity because of internal friction. For $\\lambda$-repressor, the calculated folding rate prefactor, along with the free energy barrier from the variational theory, gives a folding rate that agrees well with the experimentally determined rate under highly stabilizing conditions, but the theory predicts too large a folding rate at the transition midpoint. This discrepancy obtained using a fairly complete quantitative theory inspires a new set of questions about chain dynamics, specifically detailed motions in individual contact formation.

John J. Portman; Shoji Takada; Peter G. Wolynes

2000-08-30T23:59:59.000Z

435

Protein folding by a quasi-static-like process: A first-order state transition  

Science Journals Connector (OSTI)

In this paper we report that quasi-static-like processes, in which stable intermediates were introduced carefully and deliberately, may be used to reversibly unfold and refold purified native porcine growth hormone. Through circular dichroism (CD) and dynamic light scattering (DLS), we were able to study the secondary structure conformational changes, tertiary structure thermal stabilities, and the particle size distributions of both the intermediates and the final folded product. The CD data showed that the secondary structure was restored in the initial folding stage, whereas the tertiary structure within the protein was restored one step before the last folding stage, as elucidated by thermal stability experiments. DLS analysis suggested that the average hydrodynamic radii of the folding intermediates shrunk to nativelike size immediately after the first folding stage. Our data suggested that the denaturant-containing protein folding reaction is a first-order-like state transition process. This quasi-static-like process may be useful in the prevention of aggregate formation in protein purification and thus can be used in protein engineering to improve the overall yield from harvesting proteins.

Chia-Ching Chang; Ya-Chi Su; Ming-Sung Cheng; Lou-Sing Kan

2002-08-09T23:59:59.000Z

436

Folding Proteins with Both Alpha and Beta Structures in a Reduced Model  

E-Print Network (OSTI)

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same time can predict the three dimensional structure of a protein with a given sequence in reasonable time. For this purpose, rather than focusing on the real folding dynamics or full structural details at the atomic scale, we adopt the Monte Carlo method and the coarse-grained representation of the protein in which both side-chains and the backbones are replaced by suitable geometrical objects in consistent with the known structure. On top of the coarse-grained representation, our effective potential can be developed. Two new interactions, the dipole-dipole interactions and the local hydrophobic interactions, are introduced and are shown to be as crucial as the hydrogen bonds for forming the secondary structures. In particular, for the first time, we demonstrate that the resulting reduced model can successfully fold proteins with both helix and sheet structures without using any biased potential. Further analyses show that this model can also fold other proteins in reasonable accuracy and thus provides a promising starting point for the problem of protein folding.

Nan-yow Chen

2006-07-17T23:59:59.000Z

437

Using Knowledge-Based Neural Networks to Improve Algorithms: Refining the Chou-Fasman Algorithm for Protein Folding  

E-Print Network (OSTI)

for Protein Folding Richard Maclin Jude W. Shavlik Computer Sciences Dept. University of Wisconsin 1210 W learning Theory refinement Neural networks Finite-state automata Protein folding Chou-Fasman algorithm-Fasman algorithm, a method for predicting how globular proteins fold. Empirical evidence shows

Maclin, Rich

438

Fast Protein Folding in the Hydrophobic-hydrophilic Model Within Three-eights of Optimal (Extended Abstract)  

E-Print Network (OSTI)

Fast Protein Folding in the Hydrophobic-hydrophilic Model Within Three-eights of Optimal (Extended for the protein folding problem in the hydrophobic- hydrophilic model, Dill (1985). To our knowledge, our al for this model, Dill (1994). The hydrophobic-hydrophilic model abstracts the dominant force of protein folding

Istrail, Sorin

439

Dynamic Control of Protein Folding Pathway with a Polymer of Tunable Hydrophobicity Diannan Lu, Jianzhong Wu, and Zheng Liu*,  

E-Print Network (OSTI)

Dynamic Control of Protein Folding Pathway with a Polymer of Tunable Hydrophobicity Diannan Lu ReceiVed: July 30, 2007 While the knowledge of protein folding in a dilute solution is now well of protein folding by using a thermally responsive polymer that varies its hydrophobicity concomitant

Wu, Jianzhong

440

Single-Molecule Fluorescence Studies of Protein Folding and Conformational Xavier Michalet,* Shimon Weiss, and Marcus Jager*  

E-Print Network (OSTI)

Single-Molecule Fluorescence Studies of Protein Folding and Conformational Dynamics Xavier Michalet. Single-Molecule Fluorescence Studies of Protein Folding and Conformations at Equilibrium 1796 4-Molecule Protein Folding under Nonequilibrium Conditions 1808 6. Conclusion 1809 7. Acknowledgments 1810 8

Michalet, Xavier

Note: This page contains sample records for the topic "folds grabens horst" from the National Library of EnergyBeta (NLEBeta).
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441

THE JOURNAL OF CHEMICAL PHYSICS 140, 204905 (2014) Precursory signatures of protein folding/unfolding: From time series  

E-Print Network (OSTI)

THE JOURNAL OF CHEMICAL PHYSICS 140, 204905 (2014) Precursory signatures of protein folding conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid the important role played by weaker correlations in such protein folding dynamics. © 2014 AIP Publishing LLC

442

THE JOURNAL OF CHEMICAL PHYSICS 134, 055107 (2011) Protein folding in a reverse micelle environment: The role of confinement  

E-Print Network (OSTI)

THE JOURNAL OF CHEMICAL PHYSICS 134, 055107 (2011) Protein folding in a reverse micelle environment made in the experimental observation1­6 and simulation of protein folding using min- imal coarse and mechanism of protein folding has been developed, including how the ki- netics may be related

Straub, John E.

443

Protein folding dynamics in lattice model with physical movement Sema Kachalo, Hsiao-Mei Lu and Jie Liang  

E-Print Network (OSTI)

Protein folding dynamics in lattice model with physical movement S¨ema Kachalo, Hsiao-Mei Lu analysis of the kinetic energy landscape. I. INTRODUCTION The dynamics of protein folding has been studied exten- sively [1, 3­5]; A remarkable empirical observation is that protein folding rates are well

Dai, Yang

444

Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model  

E-Print Network (OSTI)

Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of intermediates in protein folding has been a matter of great controversy. Although it was widely believed, experimental evidence has been accumulating that small proteins fold fast without any detectable intermediates

Mirny, Leonid

445

Folding Protein-Like Structures with Open Gemma B. Danks, Susan Stepney, and Leo S. D. Caves  

E-Print Network (OSTI)

protein is a strong indicator of its function in the cell. The mechanisms involved in protein folding. The protein folding process may be viewed as an emergent phenomenon, a result of underlying physics. In this spirit we present a model for investigating protein folding using open L-systems, local rewriting rules

Stepney, Susan

446

In eukaryotic cells, most secreted and transmembrane proteins fold and mature in the lumen of the endoplasmic  

E-Print Network (OSTI)

In eukaryotic cells, most secreted and transmembrane proteins fold and mature in the lumen conditions and the physiologicalstateofthecell.Tohandlethisdynamicsitu- ation, cells adjust the protein-folding transcriptional activation of UPR target genes, including those that function as part of the ER protein-folding

Bedwell, David M.

447

Florence, 28/02/2011: Two applied inverse problems: Introduction 1 -Problem #1: Studying the protein fold via NMR constraints.  

E-Print Network (OSTI)

the protein fold via NMR constraints. In collaboration with the CERM (Centre for Magnetic Resonance problems. #12;Florence, 28/02/2011: Two applied inverse problems: The problem of protein folding 2 H CCN) Backbone #12;Florence, 28/02/2011: Two applied inverse problems: The problem of protein folding 3 Genoma

Pedicini, Marco

448

From: Methods in Molecular Biology, vol. 350: Protein Folding Protocols Edited by: Y. Bai and R. Nussinov Humana Press Inc., Totowa, NJ  

E-Print Network (OSTI)

115 From: Methods in Molecular Biology, vol. 350: Protein Folding Protocols Edited by: Y. Bai and R to Protein Folding Benjamin Schuler Summary Protein folding is a process characterized by a large degree this method to protein folding. Key Words: Protein folding; fluorescence spectroscopy; single molecule

Schuler, Ben

449

Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms  

SciTech Connect

Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with ? helix and ? hairpin, but also the important role played by weaker correlations in such protein folding dynamics.

Hsu, P. J.; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320 Taiwan (China); Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Cheong, S. A. [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)

2014-05-28T23:59:59.000Z

450

THE INFLUENCE OF FOLD AND FRACTURE DEVELOPMENT ON RESERVOIR BEHAVIOR OF THE LISBURNE GROUP OF NORTHERN ALASKA  

SciTech Connect

The Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults. (2) The influence of folding and lithostratigraphy on fracture patterns. (3) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. (4) The influence of lithostratigraphy and deformation on fluid flow. The results of field work during the summer of 1999 offer some preliminary insights: The Lisburne Limestone displays a range of symmetrical detachment fold geometries throughout the northeastern Brooks Range. The variation in fold geometry suggests a generalized progression in fold geometry with increasing shortening: Straight-limbed, narrow-crested folds at low shortening, box folds at intermediate shortening, and folds with a large height-to-width ratio and thickened hinges at high shortening. This sequence is interpreted to represent a progressive change in the dominant shortening mechanism from flexural-slip at low shortening to bulk strain at higher shortening. Structural variations in bed thickness occur throughout this progression. Parasitic folding accommodates structural thickening at low shortening and is gradually succeeded by penetrative strain as shortening increases. The amount of structural thickening at low to intermediate shortening may be inversely related to the local amount of structural thickening of the Kayak Shale, the incompetent unit that underlies the Lisburne. The Lisburne Limestone displays a different structural style in the south, across the boundary between the northeastern Brooks Range and the main axis of the Brooks Range fold-and-thrust belt. The steep forelimbs of angular asymmetrical folds typically have been cut and displaced by thrust faults, resulting in superposition of a fault-bend fold geometry on the truncated folds. Remnant uncut folds within trains of thrust-truncated folds and the predominance of detachment folds to the north suggest that these folds originated as detachment folds. Fold asymmetry and a more uniformly competent Lisburne Limestone may have favored accommodation of a significant proportion of shortening by thrust faulting, in contrast with the dominance of fold shortening to the north. Two dominant sets of fractures are present in the least deformed Lisburne Limestone: Early extension fractures normal to the regional fold trend and late extension and shear fractures parallel to the regional fold trend. These two major fracture sets remain as deformation increases, but they are more variable in orientation, character, and relative age. Compared to fold limbs, the fold hinges display greater density and extent of fractures, more conjugate and shear fractures, and more evidence of penetrative strain. This suggests that hinges remained fixed during fold growth. Late extension fractures normal to the fold axis are common even where penetrative strain is greatest. Fracture density is greater in fine-grained carbonates than in coarse-grained carbonates over the entire spectrum of deformation.

Wesley K. Wallace; Catherine L. Hanks; Michael T. Whalen; Jerry Jensen; Paul K. Atkinson; Joseph S. Brinton

2000-05-01T23:59:59.000Z

451

Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions  

E-Print Network (OSTI)

In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes from native structures by minimizing the entropic loop-closure cost during folding. The model predicts characteristic folding sequences of structural elements such as helices and beta-strand pairings. Based on few simple rules, the kinetic impact of these structural elements is estimated from the routes and compared to average experimental Phi-values for the helices and strands of 15 small, well-characterized proteins. The comparison leads on average to a correlation coefficient of 0.62 for all proteins with polarized Phi-value distributions, and 0.74 if distributions with negative average Phi-values are excluded. The diffuse Phi-value distributions of the remaining proteins are reproduced correctly. The model shows that Phi-value distributions, averaged over secondary structural elements, can often be traced back to entropic loop-closure events, but also indicates energetic preferences in the case of a few proteins governed by parallel folding processes.

Thomas R. Weikl

2005-02-15T23:59:59.000Z

452

Tri-fold - Agencies Assisting with EEOICPA and the Former worker Program |  

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

Information Center » Worker » Former Worker Program » Tri-fold - Information Center » Worker » Former Worker Program » Tri-fold - Agencies Assisting with EEOICPA and the Former worker Program Tri-fold - Agencies Assisting with EEOICPA and the Former worker Program January 2014 Agencies Assisting with EEOICPA and the Former Worker Program FWP provides no-cost medical screenings to all former DOE Federal, contractor, and subcontractor employees. The screening focuses on the early detection of health conditions that may be related to occupational exposures such as beryllium, asbestos, radiation, silica, etc. Medical screenings include a physical exam, hearing test, Medical screenings include a physical exam, hearing test, blood and urine tests, and other special tests depending on the individual's work and exposure history.

453

Remarks on homo- and hetero-polymeric aspects of protein folding  

E-Print Network (OSTI)

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common approach to diversity is randomness, which is usually implemented in two body interactions (charges, polar character,..). On the other hand, the (almost) universal character of the protein backbone suggests that folding may also be viewed as the crystallization transition of an homopolymeric chain, the main ingredients of which are the peptide bond and chirality (proline and glycine notwithstanding). The model of a chiral dipolar chain leads to a unified picture of secondary structures, and to a possible connection of protein structures with ferroelectric domain theory.

T. Garel

2003-05-03T23:59:59.000Z

454

Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models  

E-Print Network (OSTI)

Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-wise interactions only, we have found 1) a significantly increased correlation with experimental phi-values and folding rates, 2) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ~ 20%, and 3) a considerably larger amount of 3-body energy present in Chymotripsin inhibitor than other proteins studied.

M. R. Ejtehadi; S. P. Avall; S. S. Plotkin

2004-07-14T23:59:59.000Z

455

A new tool for protein fold recognition: A Bayesian heuristic threading algorithm.  

SciTech Connect

This paper presents a new threading algorithm, designed to be used in protein fold recognition. Its purpose is to contribute toward the goal of predicting three-dimensional structures of proteins from knowledge of their amino-acid sequences alone. Sequences for new proteins are being discovered at a rapid rate, as a result of the Human Genome Project, and related genome research. Understanding of protein folding, and especially the ability to predict the 3D fold from the sequence, is crucial to the understanding of the function of these new proteins. This is considered by many to be the most important problem in contemporary molecular biology. Numerical tests of the speed and reliability of the algorithm are described, along with comparisons with two popular threading algorithms. For the systems examined, the new method constitutes a significant improvement.

Crawford, O.

1997-10-01T23:59:59.000Z

456

Parallel continuation-based global optimization for molecular conformation and protein folding  

SciTech Connect

This paper presents the authors` recent work on developing parallel algorithms and software for solving the global minimization problem for molecular conformation, especially protein folding. Global minimization problems are difficult to solve when the objective functions have many local minimizers, such as the energy functions for protein folding. In their approach, to avoid directly minimizing a ``difficult`` function, a special integral transformation is introduced to transform the function into a class of gradually deformed, but ``smoother`` or ``easier`` functions. An optimization procedure is then applied to the new functions successively, to trace their solutions back to the original function. The method can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation and protein folding. Mathematical theory for the method, as a special continuation approach to global optimization, is established. Algorithms with different solution tracing strategies are developed. Different levels of parallelism are exploited for the implementation of the algorithms on massively parallel architectures.

Coleman, T.F.; Wu, Z. [Cornell Univ., Ithaca, NY (United States)

1994-12-31T23:59:59.000Z

457

Femtosecond spectroscopy probes the folding quality of antibody fragments expressed as GFP fusions in the cytoplasm  

SciTech Connect

Time-resolved femtosecond spectroscopy can improve the application of green fluorescent proteins (GFPs) as protein-folding reporters. The study of ultrafast excited-state dynamics (ESD) of GFP fused to single chain variable fragment (scFv) antibody fragments, allowed us to define and measure an empirical parameter that only depends on the folding quality (FQ) of the fusion. This method has been applied to the analysis of genetic fusions expressed in the bacterial cytoplasm and allowed us to distinguish folded and thus functional antibody fragments (high FQ) with respect to misfolded antibody fragments. Moreover, these findings were strongly correlated to the behavior of the same scFvs expressed in animal cells. This method is based on the sensitivity of the ESD to the modifications in the tertiary structure of the GFP induced by the aggregation state of the fusion partner. This approach may be applicable to the study of the FQ of polypeptides over-expressed under reducing conditions.

Didier, P. [Faculte de Pharmacie, UMR 7175, 74, route du Rhin, 67412 Illkirch (France); Weiss, E.; Sibler, A.-P. [Ecole Superieure de Biotechnologie de Strasbourg, UMR 7175, Boulevard Sebastien Brant, F-67412 Illkirch (France); Philibert, P.; Martineau, P. [Centre de recherche en cancerologie de Montpellier, UMR 5160, Val d'Aurelle-Paul Lamarque, 34298 Montpellier cedex 5 (France); Bigot, J.-Y. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Guidoni, L. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Laboratoire Materiaux et Phenomenes Quantiques, UMR 7162, Batiment Condorcet, 10 rue Alice Domon et Leonie Duquet, 75205 Paris cedex 13 (France)], E-mail: luca.guidoni@univ-paris-diderot.fr

2008-02-22T23:59:59.000Z

458

The earliest events in protein folding: Helix dynamics in proteins and model peptides  

SciTech Connect

The earliest events in protein folding are critically important in determining the folding pathway, but have proved difficult to study by conventional approaches. We have developed new rapid initiation methods and structure-specific probes to interrogate the earliest events of protein folding. Our focus is the pathways. Folding or unfolding reactions are initiated on a fast timescale (10 ns) using a laser induced temperature jump (15 C) and probed with time-resolved infrared spectroscopy. We obtained the kinetics of the helix-coil transition for a model 21-residue peptide. The observed rate constant k{sub obs} = k{sub f} + k{sub u} for reversible kinetics; from the observed rate (6 x 10{sup 6} s{sup -1}) and the equilibrium constant favoring folding of 7.5 at 27 C, we calculate a folding lifetime of 180 ns and an unfolding lifetime of 1.4 {mu}s. The {open_quotes}molten globule{close_quotes} form of apomyoglobin (horse, pH*3, 0.15M NaCl) shows similar kinetics for helix that is unconstrained by tertiary structure (helix with an unusually low Amide I frequency, near 1633 cm{sup -1}). In {open_quotes}native{close_quotes} apomyoglobin (horse, pH*5.3, 10 mM NaCl) two very different rates (45 ns and 70 {mu}s) are observed and we infer that a third occurs on a timescales inaccessible to our experiment (> 1 ms). We suggest that the slower processes are due to helix formation that is rate-limited by the formation of tertiary structure.

Dyer, R.B.; Williams, S.; Woodruff, W.H. [Los Alamos National Lab., NM (United States)] [and others

1996-12-31T23:59:59.000Z

459

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

SciTech Connect

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

460

The statistical properties of protein folding in the {\\phi}^4 theory  

E-Print Network (OSTI)

The statistical properties of protein folding within the {\\phi}^4 model are investigated. The calculation is performed using statistical mechanics and path integral method. In particular, the evolution of heat capacity in term of temperature is given for various levels of the nonlinearity of source and the strength of interaction between protein backbone and nonlinear source. It is found that the nonlinear source contributes constructively to the specific heat especially at higher temperature when it is weakly interacting with the protein backbone. This indicates increasing energy absorption as the intensity of nonlinear sources are getting greater. The simulation of protein folding dynamics within the model is also refined.

Januar, M; Handoko, L T

2013-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "folds grabens horst" 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

RNA Folding  

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

3 3 Rick Russell, Ian S. Millett, Sebastian Doniach and Daniel Herschlag Stanford University One goal of genome projects is to systematically identify genes (1,2). The best current knowledge indicates that humans carry approximately 35000 genes. This number is an estimate that varies from expert to expert and range up to 100,000 (3-5). To anyone who has taken an elementary biology class, this ambiguity must seem strange. How hard can it be to count genes? After all, don't cells translate genes into proteins? Counting genes should be as easy as counting proteins. In fact, most estimates for the number of genes in the human genome exploit this strategy with researchers developing various ways of directly or indirectly counting proteins (6-10). The fundamental problem then is in the definition of a gene. A gene encodes an action - and not all the action in a cell is in the protein.

462

Protein folding  

Science Journals Connector (OSTI)

Finding pruning techniques to optimize a backtracking search is a good topic that arises in courses on Data Structures or Algorithms. The goal of this assignment is for students to experience how pruning can dramatically improve the runtime of a recursive ...

Carl Burch

2012-05-01T23:59:59.000Z

463

The Influence of Fold and Fracture Development on Reservoir Behavior of the Lisburne Group of Northern Alaska  

SciTech Connect

The objectives of this study were to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults, (2) The influence of folding and lithostratigraphy on fracture patterns, (3) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics, and (4) The influence of lithostratigraphy and deformation on fluid flow.

Wallace, W.K.; Hanks, C.L.; Whalen, M.T.; Jensen, J.; Atkinson, P.K.; Brinton, J.S.

2001-01-09T23:59:59.000Z

464

Department of Mechanical Engineering Fall 2012 Auto Folding Clothes Drying Rack Global Project  

E-Print Network (OSTI)

PENNSTATE Department of Mechanical Engineering Fall 2012 Auto Folding Clothes Drying Rack ­ Global, and rotating clothes drying rack. The main client for the rack is a woman in South Korea who is confined rack for our client that she can use easily from her wheelchair. A secondary objective is to develop

Demirel, Melik C.

465

Unimodal Maps as Boundary-Restrictions of Two-Dimensional Full-Folding Maps  

E-Print Network (OSTI)

Unimodal Maps as Boundary-Restrictions of Two-Dimensional Full-Folding Maps Hideki TSUIKI tsuiki-75-753-6744, Fax:+81-75-753-6694 Abstract It is shown that every unimodal map is realized as a restriction of a simple map defined on the unit disc to a part of its boundary. Our two-dimensional map is called a full

Tsuiki, Hideki

466

In vitro analysis of aggregation-disaggregation of the folding intermediate of Bacillus subtilis -amylase  

E-Print Network (OSTI)

in vivo. Keywords: Alpha-amylase, Bacillus subtilis protein secretion, aggregation-disaggregation, folding -amylase A. COLOMER-PALLAS, M.-F. PETIT-GLATRON and R. CHAMBERT* Institut Jacques Monod, Laboratoire chloride; FTIR, Fourier transform infrared; ATR, attenuated total reflexion Proteins and enzymes: -amylase

Boyer, Edmond

467

On Enhancing Power Benefits in 3D ICs: Block Folding and Bonding Styles Perspective  

Science Journals Connector (OSTI)

Low power is widely considered as a key benefit of 3D ICs, yet there have been few thorough design studies on how to maximize power benefits in 3D ICs. In this paper, we present design methodologies to reduce power consumption in 3D ICs using a large-scale ... Keywords: 3D IC, block folding, bonding style, power benefit

Moongon Jung, Taigon Song, Yang Wan, Yarui Peng, Sung Kyu Lim

2014-06-01T23:59:59.000Z

468

Simple Two-State Protein Folding Kinetics Requires Near-Levinthal Thermodynamic Cooperativity  

E-Print Network (OSTI)

¨ seyin Kaya and Hue Sun Chan* Protein Engineering Network of Centres of Excellence (PENCE), Department unfolding is less dependent on temperature than the interactions that drive the folding kinetics. Proteins importance. Quite obviously, the relationship between model energetics and conformational distribution can

Chan, Hue Sun

469

ARTICLE IN PRESS The folding pathway of ubiquitin from all-atom  

E-Print Network (OSTI)

, the shape of the energy landscape and the actual folding mechanism have been addressed in these studies to form a unique compact structure is directly proportional to the chain length of the polypep- tide [3]. Another factor that has been used to explain kinetic foldability is the random energy model (REM). The REM

Jackson, Sophie

470

Long range correlations and folding angle with applications to ?-helical proteins  

SciTech Connect

The conformational complexity of chain-like macromolecules such as proteins and other linear polymers is much larger than that of point-like atoms and molecules. Unlike particles, chains can bend, twist, and even become knotted. Thus chains might also display a much richer phase structure. Unfortunately, it is not very easy to characterize the phase of a long chain. Essentially, the only known attribute is the radius of gyration. The way how it changes when the degree of polymerization becomes different, and how it evolves when the ambient temperature and solvent properties change, is commonly used to disclose the phase. But in any finite length chain there are corrections to scaling that complicate the detailed analysis of the phase structure. Here we introduce a quantity that we call the folding angle to identify and scrutinize the phase structure, as a complement to the radius of gyration. We argue for a mean-field level relationship between the folding angle and the scaling exponent in the radius of gyration. We then estimate the value of the folding angle in the case of crystallographic ?-helical protein structures in the Protein Data Bank. We also show how the experimental value of the folding angle can be obtained computationally, using a semiclassical Born-Oppenheimer description of ?-helical chiral chains.

Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden)] [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Nicolis, Stam, E-mail: Stam.Nicolis@lmpt.univ-tours.fr [Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France)] [Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

2014-03-07T23:59:59.000Z

471

Monatshefte fur Chemie (Chemical Monthly) 125: 167188 (1994) Fast Folding and Comparison of RNA  

E-Print Network (OSTI)

Monatshefte f¨ur Chemie (Chemical Monthly) 125: 167­188 (1994) Fast Folding and Comparison of RNA¨ur Theoretische Chemie der Universit¨at Wien A­1090 Wien, Austria b Institut f¨ur Molekulare Biotechnologie D of Oxford South Parks Road, Oxford OX1 3PS, UK \\Lambda Mailing Address: Institut f¨ur Theoretische Chemie

Stadler, Peter F.

472

Structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein  

Science Journals Connector (OSTI)

...state. Folding studies on naturally occuring AR proteins have until now focused only...significantly more stable compared with naturally occurring AR proteins (29). Therefore we propose that ARs with the highest...collected in house at -180 C with Cu K a radiation ( l = 1.5418 a) using a rotating-anode...

Christian Lw; Ulrich Weininger; Piotr Neumann; Mirjam Klepsch; Hauke Lilie; Milton T. Stubbs; Jochen Balbach

2008-01-01T23:59:59.000Z

473

The Zagros folded belt (Fars, Iran): constraints from topography and critical wedge modelling  

Science Journals Connector (OSTI)

......Asmari Formation, which is one of the main oil reservoirs in the Zagros. The folded Meso-Cenozoic...neglect the contribution of radiogenic heating in the upper crust but which is consistent...A. , Connors C., Dahlen F.A., Price E.J., Suppe J.,1994. Effect of......

F. Mouthereau; O. Lacombe; B. Meyer

2006-04-01T23:59:59.000Z

474

PHYSICAL REVIEW E 89, 012407 (2014) Tuning the ordered states of folded rods by isotropic confinement  

E-Print Network (OSTI)

the production of self-deployable devices such as solar wings [7] through the reversible folding of ordered is of paramount importance concerning nucleic polymers (DNA, RNA). In the cell nucleus, DNA is embedded within and the organization of their veins [4,5]. This raises the question of interaction between mechanical stress

Adda-Bedia, Mokhtar

475

Folding and Strain Softening of Carbon Fiber Composites with an Elastomeric Matrix  

E-Print Network (OSTI)

Folding and Strain Softening of Carbon Fiber Composites with an Elastomeric Matrix F. L´opez Jim damage. A possibility is the use of carbon fiber composites with a soft elastomeric matrix the fibers on the compression side of the material to form elastic mi- crobuckles. Through this mechanism

476

A "loop entropy reduction" phage-display selection for folded amino acid sequences  

E-Print Network (OSTI)

is that insertion of a long disordered sequence into a loop of a host protein will substantially destabilize; ACCEPTED October 27, 2000) Abstract As a step toward selecting folded proteins from libraries of randomized the host because of the entropic cost of closing a loop in a disordered chain. If the inserted sequence

Baker, David

477

THE PROTEIN NON-FOLDING PROBLEM: AMINO ACID DETERMINANTS OF INTRINSIC ORDER AND DISORDER  

E-Print Network (OSTI)

THE PROTEIN NON-FOLDING PROBLEM: AMINO ACID DETERMINANTS OF INTRINSIC ORDER AND DISORDER R and disorder, three primary and one derivative database of intrinsically disordered proteins were compiled on homology. The three primary disordered databases have a combined total of 157 proteins or segments

Obradovic, Zoran

478

Internal Friction Controls the Speed of Protein Folding from a Compact Configuration  

E-Print Network (OSTI)

Internal Friction Controls the Speed of Protein Folding from a Compact Configuration Suzette A is independent of the cosolutes used to adjust solvent friction. Therefore, interactions within the interior. Interestingly, we find a very strong temperature dependence in these "internal friction"-controlled dynamics

Roder, Heinrich

479

Protein folding in contact map space Eytan Domany, Rafael Najmanovich and Michele Vendruscolo  

E-Print Network (OSTI)

assumption of all physical approaches to folding is that there exists some energy function, from which important, we present a method to derive contact energy parameters based on perceptron learning. The energy the proteins in a given database. We show that such an energy function exists if the candidates are produced

Domany, Eytan

480

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity  

E-Print Network (OSTI)

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is barrierless. A microcanonical analysis, where the energy is the natural variable, has shown better suited to unambiguously characterize the nature of the transition compared to its canonical counterpart. Replica exchange molecular dynamics simulations of a high resolution coarse-grained model allow for the accurate evaluation of the density of states, in order to extract precise thermodynamic information, and measure its impact on structural features. The method is applied to three helical peptides: a short helix shows sharp features of a two-state folder, while a longer helix and a three-helix bundle exhibit downhill and two-state transitions, respectively. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition.

Tristan Bereau; Michael Bachmann; Markus Deserno

2011-07-01T23:59:59.000Z

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481

Active folding of fluvial terraces across the Siwaliks Hills, Himalayas of central Nepal  

E-Print Network (OSTI)

Active folding of fluvial terraces across the Siwaliks Hills, Himalayas of central Nepal J. Lave´1 of central Nepal, south of the Kathmandu Basin. The Main Frontal Thrust fault (MFT), which marks the southern analysis, complemented by geological investiga- tions in central Nepal. Active deformation in the Himalaya

Avouac, Jean-Philippe

482

Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments  

E-Print Network (OSTI)

]. In order to render physical meaning to Áxz we address two questions here: (i) Does Áxz represent the physical meaning and relia- bility of the folding landscape parameters that are extracted from trajectories the behavior of the multiple degrees of freedom explored by the biomolecule. The structural meaning of Áxz

Thirumalai, Devarajan

483

Basinwide fold evolution and geometric development of cratonic - foreland basin interaction  

SciTech Connect

Latest results of the Williston Basin Project incorporate a north-south regional seismic line, which is crossing the deepest part of the Williston Basin from Saskatchewan to South Dakota. The integration of this new profile to the two, existing east-west regional seismic sections, gives a quasi-3D image of the basin. The combined seismic data illustrate alternating extensive and compressive phases during basin development, marked by basinwide circular and radial folds. This alternating pattern of basin subsidence is the very nature of crotonic basin evolution. The structural necessity for compressive phases during crotonic basin subsidence, is shown in a regional scale interpretation that has undergone an Earth-curvature correction. The geometrical evolution of the neighboring foreland basin is also interpreted from data that has been corrected with the Earth-curvature function. It shows that basinwide folds sub-parallel and perpendicular to the longitudinal axis of the basin are analogous to the circular and radial folds of the crotonic basins. These folds, in the foreland belt, are less pronounced because larger scale structural elements can overprint them. Where the crotonic and foreland basins overlap, a complex, deformed zone is present, and contains late stage volcanism, in this area. The geometry of the Williston Basin can be modeled by the Sloss-type [open quote]inverted Gaussian function[close quote] that is modified by the periodic westward tilting of the basin and the Earth-curvature function.

Redly, P.; Hajnal, Z. (Univ. of Saskatchewan, Saskatoon (Canada))

1996-01-01T23:59:59.000Z

484

Basinwide fold evolution and geometric development of cratonic - foreland basin interaction  

SciTech Connect

Latest results of the Williston Basin Project incorporate a north-south regional seismic line, which is crossing the deepest part of the Williston Basin from Saskatchewan to South Dakota. The integration of this new profile to the two, existing east-west regional seismic sections, gives a quasi-3D image of the basin. The combined seismic data illustrate alternating extensive and compressive phases during basin development, marked by basinwide circular and radial folds. This alternating pattern of basin subsidence is the very nature of crotonic basin evolution. The structural necessity for compressive phases during crotonic basin subsidence, is shown in a regional scale interpretation that has undergone an Earth-curvature correction. The geometrical evolution of the neighboring foreland basin is also interpreted from data that has been corrected with the Earth-curvature function. It shows that basinwide folds sub-parallel and perpendicular to the longitudinal axis of the basin are analogous to the circular and radial folds of the crotonic basins. These folds, in the foreland belt, are less pronounced because larger scale structural elements can overprint them. Where the crotonic and foreland basins overlap, a complex, deformed zone is present, and contains late stage volcanism, in this area. The geometry of the Williston Basin can be modeled by the Sloss-type {open_quote}inverted Gaussian function{close_quote} that is modified by the periodic westward tilting of the basin and the Earth-curvature function.

Redly, P.; Hajnal, Z. [Univ. of Saskatchewan, Saskatoon (Canada)

1996-12-31T23:59:59.000Z

485

Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin  

Science Journals Connector (OSTI)

...perspective, allowing us to determine the...the actin free-energy folding landscape...chaperonin free-energy surfaces may change...on the nucleotide status of CCT, first in...temperature (k us) due to the large activation energy of unfolding, measured...

2008-01-01T23:59:59.000Z

486

Stream response to repeated coseismic folding, Tiptonville dome, New Madrid seismic zone  

E-Print Network (OSTI)

Sciences, University of Colorado, Boulder, CO 80309-0399, USA c Environmental Dynamics Program, University River to small flood-plain streams. Fluvial response of these streams to repeated coseismic folding has migrated across the area forming the present flood plain. This surface comprises a sandy point-bar deposit

Mueller, Karl

487

The Influence of Fold and Fracture Development on Reservoir Behavior of the Lisburne Group of Northern Alaska  

SciTech Connect

The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively underformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults, (2) The influence of folding on fracture patterns, (3) The influence of deformation on fluid flow, and (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics.

Wallace, Wesley K.; Hanks, Catherine L.; Whalen, Michael T.; Jensen1, Jerry; Shackleton, J. Ryan; Jadamec, Margarete A.; McGee, Michelle M.; Karpov1, Alexandre V.

2001-07-23T23:59:59.000Z

488

Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse  

E-Print Network (OSTI)

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.

Margaret S. Cheung; Angel E. Garcia; Jose N. Onuchic

2002-03-31T23:59:59.000Z

489

Protein folding by distributed computing and the denatured state ensemble Neelan J. Marianayagam, Nicolas L. Fawzi, and Teresa Head-Gordon  

E-Print Network (OSTI)

July 26, 2005) The distributed computing (DC) paradigm in conjunction with the folding@home (FH) client from higher energy subpopulations in the DSE. folding mechanism folding@home two-state kinetics Poisson a particular strength of the distributed computing (DC) approach known as folding@home (FH), which compares

Head-Gordon, Teresa L.

490

Large-Scale Context in Protein Folding: Villin Headpiece Ariel Fernandez,*,, Min-yi Shen,| Andres Colubri, Tobin R. Sosnick,, R. Stephen Berry,| and Karl F. Freed*,|  

E-Print Network (OSTI)

Large-Scale Context in Protein Folding: Villin Headpiece Ariel Ferna´ndez,*,,§ Min-yi Shen,| Andre but that are predicted to affect the folding rates and dynamics dramatically. The problem of protein folding breaks the protein folding process that has to date made it difficult to develop an ab initio approach to describe

Berry, R. Stephen

491

Recently, I heard a researcher present a colloquium on computational aspects of protein-folding. Although this man was obviously an expert  

E-Print Network (OSTI)

of protein-folding. Although this man was obviously an expert on the topic, he casually mentioned in passing that, of course, #2;protein- folding is NP-complete.#1; Protein-folding is a biological process that a particular mathematical model (minimal energy) of protein-folding is NP-complete in the Turing machine model

Traub, Joseph F.

492

Four-State Folding of a SH3 Domain: Salt-Induced Modulation of the Stabilities of the Intermediates and Native State  

E-Print Network (OSTI)

the late intermediate M that forms after the rate-limiting transition of folding. Protein folding reactions. This simplistic picture of protein folding is supported by and in turn reinforces simplified computer simulations structure gradually over many small distributed barriers.29,30 This complexity of protein folding reactions

493

Long Proteins with Unique Optimal Foldings in the H-P Model Oswin Aichholzer David Bremner y Erik D. Demaine z Henk Meijer x  

E-Print Network (OSTI)

results about bonds in the H-P model. 1 Introduction Protein folding is a central problem such as drug de- sign. One of the most popular models of protein folding is the hydrophilic-hydrophobic (H of protein folding such as the tendency for the hydrophobic components to fold to the center of a globular

494

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

SciTech Connect

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

Eliezer, D.

1994-06-01T23:59:59.000Z

495

THE INFLUENCE OF FOLD AND FRACTURE DEVELOPMENT ON RESERVOIR BEHAVIOR OF THE LISBURNE GROUP OF NORTHERN ALASKA  

SciTech Connect

The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults. (2) The influence of folding on fracture patterns. (3) The influence of deformation on fluid flow. (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. The Lisburne in the main axis of the Brooks Range is characteristically deformed into imbricate thrust sheets with asymmetrical hanging wall anticlines and footwall synclines. In contrast, the Lisburne in the northeastern Brooks Range is characterized by symmetrical detachment folds. The focus of our 2000 field studies was at the boundary between these structural styles in the vicinity of Porcupine Lake, in the Arctic National Wildlife Refuge. The northern edge of thrust-truncated folds in Lisburne is marked by a local range front that likely represents an eastward continuation of the central Brooks Range front. This is bounded to the north by a gently dipping panel of Lisburne with local asymmetrical folds. The leading edge of the flat panel is thrust over Permian to Cretaceous rocks in a synclinal depression. These younger rocks overlie symmetrically detachment-folded Lisburne, as is extensively exposed to the north. Six partial sections were measured in the Lisburne of the flat panel and local range front. The Lisburne here is about 700 m thick and is interpreted to consist primarily of the Wachsmuth and Alapah Limestones, with only a thin veneer of Wahoo Limestone. The Wachsmuth (200 m) is gradational between the underlying Missippian Kayak Shale and the overlying Mississippian Alapah, and increases in resistance upward. The Alapah consists of a lower resistant member (100 m) of alternating limestone and chert, a middle recessive member (100 m), and an upper resistant member (260 m) that is similar to Wahoo in the northeastern Brooks Range. The Wahoo is recessive and is thin (30 m) due either to non-deposition or erosion beneath the sub-Permian unconformity. The Lisburne of the area records two major episodes of transgression and shallowing-upward on a carbonate ramp. Thicknesses and facies vary along depositional strike. Asymmetrical folds, mostly truncated by thrust faults, were studied in and south of the local range front. Fold geometry was documented by surveys of four thrust-truncated folds and two folds not visibly cut by thrusts. A portion of the local range front was mapped to document changes in fold geometry along strike in three dimensions. The folds typically display a long, non-folded gently to moderately dipping backlimbs and steep to overturned forelimbs, commonly including parasitic anticline-syncline pairs. Thrusts commonly cut through the anticlinal forelimb or the forward synclinal hinge. These folds probably originated as detachment folds based on their mechanical stratigraphy and the transition to detachment folds to the north. Their geometry indicates that they were asymmetrical prior to thrust truncation. This asymmetry may have favored accommodation of increasing shortening by thrust breakthrough rather than continued folding. Fracture patterns were documented in the gently dipping panel of Lisburne and the asymmetrical folds within it. Four sets of steeply dipping extension fractures were identified, with strikes to the (1) N, (2) E, (3) N to NW, and (4) NE. The relative timing of these fracture sets is complex and unclear. En echelon sets of fractures are common, and display normal or strike-slip sense. Mesoscopic and penetrative structures are locally well developed, and indicate bed-parallel shear within the flat panel and strain within folds. Three sets of normal faults are well developed in the area, and are unusual

Wesley K. Wallace; Catherine L. Hanks; Jerry Jensen; Michael T. Whalen

2002-01-01T23:59:59.000Z

496

The evolution of surface flow stripes and stratigraphic folds within Kamb Ice Stream: why don't they match?  

E-Print Network (OSTI)

from several processes or a combination of processes producing strains within the ice, and an extensive has been shown to produce folds of the internal stratigraphy depicted by ice- penetrating radarThe evolution of surface flow stripes and stratigraphic folds within Kamb Ice Stream: why don

Jacobel, Robert W.

497

Mechanical models of fracture reactivation and slip on bedding surfaces during folding of the asymmetric anticline at Sheep Mountain, Wyoming  

E-Print Network (OSTI)

Mechanical models of fracture reactivation and slip on bedding surfaces during folding June 2008 Accepted 5 June 2008 Available online 13 June 2008 Keywords: Fold Fracture reactivation Bed methods to investigate the reactivation of fractures (opening and shearing) and the development of bedding

Borja, Ronaldo I.

498

RNA Folding: A Little Cooperation Goes a Long Way | Advanced Photon Source  

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

A New Phase in Cellular Communication A New Phase in Cellular Communication Engineering Thin-Film Oxide Interfaces Novel Materials Become Multifunctional at the Ultimate Quantum Limit Outsmarting Flu Viruses How Lead-Free Solder (Mis)Behaves under Stress Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed RNA Folding: A Little Cooperation Goes a Long Way NOVEMBER 19, 2012 Bookmark and Share Shown here is the energy landscape for folding of a ribozyme, and how cooperation between tertiary interactions at different parts of the structure (red dots) help the RNA reach its unique native structure and avoid non-native intermediates. The nucleic acid RNA is an essential part of the critical process by which

499

Full-folding optical potential for preequilibrium nucleon scattering at low energies  

E-Print Network (OSTI)

The real part of the optical potential for the nucleon-nucleus scattering at lower energies (E_ienergy-dependent effective NN-interactions DDM3Y, BDM3Y and HLM3Y based on the Reid and Paris potentials are used in this respect. The effects of the nucleon density distribution and the average relative momentum on the folded potential have been analysed. A good agreement with the phenomenological potential of Lagrange-Lejeune, as well as with the parametrization of Jeukenne-Lejeune-Mahaux for both neutron and proton double-folded potentials is obtained. The results indicate that the strongly simplified model interactions used in preequilibrium reaction theory neglect important dynamical details of such processes.

M. Avrigeanu; A. N. Antonov; H. Lenske; I. Stetcu

1998-07-25T23:59:59.000Z

500

Monte Carlo procedure for protein folding in lattice model. Conformational rigidity  

E-Print Network (OSTI)

A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance condition. Its properties are discussed and its role during the folding process is elucidated. This method is applied on small chains on two-dimensional lattice. A Bortz-Kalos-Lebowitz type algorithm which allows to study the kinetic of the chains at very low temperature is implemented in the presented method. We show that the coefficients of the Arrhenius law are in good agreement with the value of the main potential barrier of the system.

Olivier Collet

1999-07-19T23:59:59.000Z