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  1. Horst and Graben | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTION J APPENDIXsource History View NewGuam: Energyarea,Magazine Jump to:II Wind FarmHorst and Graben

  2. John Horst | Department of Energy

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of Natural GasAdjustmentsShirleyEnergyTher i nA Guidephysics_today_article.pdf MoreEnergyJohn Coggin -John Horst -

  3. Genesis of fault hosted carbonate fracture cements in a naturally high CO2 province, South Viking Graben, UK North Sea 

    E-Print Network [OSTI]

    Lee, David Robert

    2013-07-01

    The Late Jurassic Brae oilfields in the South Viking Graben of the northern North Sea contain naturally high concentrations of carbon dioxide (up to 35 mol %). Fields immediately adjacent to the graben bounding fault ...

  4. Folding Photons

    SciTech Connect (OSTI)

    Gregg, B. A.; van de Lagemaat, J.

    2012-05-01

    Scientists have shown that wrinkles and folds can be used to maximize the absorption of low-energy photons by efficiently redirecting them into a thin absorbing film. This inexpensive technique for structuring photonic substrates could be used to increase the efficiency of many organic photovoltaic cells.

  5. Origami DNA model Mountain fold

    E-Print Network [OSTI]

    Csürös, Miklós

    Origami DNA model Mountain fold Solid lines are "mountains" and are to be folded away from you with the peak pointing towards you. 1. Fold all solid lines going lengthwise down the page into "mountain folds fold 2. Fold all dashed lines going lengthwise down the page into "valley folds". Mountain folds along

  6. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01

    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...

  7. Interpretation of recent seismic data from a frontier hydrocarbon province: western Rough Creek graben, southern Illinois and western Kentucky

    SciTech Connect (OSTI)

    Bertagne, A.J.; Pisasale, E.T.; Leising, T.C.

    1986-05-01

    The northern basement fault of the Rough Creek graben is seismically discernible and has surface expression in the Rough Creek fault zone. The southern basement fault is not clearly defined seismically, but can be inferred from shallow faulting and gravity data. This fault is roughly coincident with the Pennyrile fault zone. Extensional faults that formed the rift boundaries were the sites of late-stage compressional and extensional tectonics. Flower structures observed along the graben boundaries probably indicate post-Pennsylvanian wrench faulting. The basement within the graben plunges north-northwest, with the lowest point occurring south of the Rough Creek fault zone. Pre-Knox sediments thicken to approximately 12,000 in this area. The Knox Megagroup thickens toward the Mississippi Embayment, ranging from 4800 ft (southeastern graben area) to more than 7000 ft (west end of graben). Upper Ordovician to Devonian units also display westward thickening. The top of the Meramecian, New Albany, Maquoketa, and the base of the Knox generate continuous, high-amplitude seismic reflections due to large impedance contrasts between clastic and carbonate units. Shallow oil and gas production (Mississippian and Pennsylvanian) is present in this area. However, deep horizons (Knox, Lower Cambrian) remain relatively untested. Potential hydrocarbon traps in the pre-Knox sequence observed on seismic include fault blocks and updip pinch-outs.

  8. Algorithmic folding complexity

    E-Print Network [OSTI]

    Cardinal, Jean

    2009-01-01

    How do we most quickly fold a paper strip (modeled as a line) to obtain a desired mountain-valley pattern of equidistant creases (viewed as a binary string)? Define the folding complexity of a mountain-valley string as the ...

  9. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17

    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.

  10. INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION

    E-Print Network [OSTI]

    Halligan, Daniel

    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

  11. Protein folding and cosmology

    E-Print Network [OSTI]

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

    1997-06-04

    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.

  12. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12

    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.

  13. 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

  14. Computer Simulations of Protein Folding

    E-Print Network [OSTI]

    Sorin, Eric J.

    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

  15. Petaflop Computing for Protein Folding

    E-Print Network [OSTI]

    Izaguirre, Jesús A.

    "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

  16. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    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

  17. Protein folding in the ER.

    SciTech Connect (OSTI)

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

    1999-10-01

    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.

  18. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

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

    2010-07-18

    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.

  19. Graphene folding on flat substrates

    SciTech Connect (OSTI)

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong, E-mail: cke@binghamton.edu [Department of Mechanical Engineering, State University of New York at Binghamton, Binghamton, New York 13902 (United States); Zhang, Liuyang; Wang, Xianqiao [College of Engineering, University of Georgia, Athens, Georgia 30602 (United States)

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57?eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  20. Compact intermediates in RNA folding

    SciTech Connect (OSTI)

    Woodson, S.A. (JHU)

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

  1. Fast events in protein folding

    SciTech Connect (OSTI)

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

    1996-04-01

    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.

  2. Effective potentials for Folding Proteins

    E-Print Network [OSTI]

    Nan-yow Chen; Zheng-Yao Su; Chung-Yu Mou

    2006-01-28

    A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.

  3. Protein Folding Sculpting Evolutionary Change

    E-Print Network [OSTI]

    Lindquist, Susan

    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, ...

  4. Introduction to Grid computing Protein folding

    E-Print Network [OSTI]

    Boyar, Joan

    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

  5. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01

    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.

  6. A motion planning approach to protein folding 

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30

    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 ...

  7. A Novel Topology for Representing Protein Folds

    E-Print Network [OSTI]

    Segal, Mark R

    2009-01-01

    1993). Cooperativity in protein-folding kinetics. Proc NatlVoelz VA. (2007). The protein folding problem: when will itMS, Weikl TR. (2008). The protein folding problem. Annu Rev

  8. 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...

  9. SciTech Connect: "protein folding"

    Office of Scientific and Technical Information (OSTI)

    protein folding" Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: "protein folding" Semantic Semantic Term Title: Full Text: Bibliographic Data:...

  10. Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles, for Large-Scale Geologic Storage of CO?

    SciTech Connect (OSTI)

    Bruno, Michael

    2014-12-08

    Geomechanics Technologies has completed a detailed characterization study of the Wilmington Graben offshore Southern California area for large-scale CO? storage. This effort has included: an evaluation of existing wells in both State and Federal waters, field acquisition of about 175 km (109 mi) of new seismic data, new well drilling, development of integrated 3D geologic, geomechanics, and fluid flow models for the area. The geologic analysis indicates that more than 796 MMt of storage capacity is available within the Pliocene and Miocene formations in the Graben for midrange geologic estimates (P50). Geomechanical analyses indicate that injection can be conducted without significant risk for surface deformation, induced stresses or fault activation. Numerical analysis of fluid migration indicates that injection into the Pliocene Formation at depths of 1525 m (5000 ft) would lead to undesirable vertical migration of the CO? plume. Recent well drilling however, indicates that deeper sand is present at depths exceeding 2135 m (7000 ft), which could be viable for large volume storage. For vertical containment, injection would need to be limited to about 250,000 metric tons per year per well, would need to be placed at depths greater than 7000ft, and would need to be placed in new wells located at least 1 mile from any existing offset wells. As a practical matter, this would likely limit storage operations in the Wilmington Graben to about 1 million tons per year or less. A quantitative risk analysis for the Wilmington Graben indicate that such large scale CO? storage in the area would represent higher risk than other similar size projects in the US and overseas.

  11. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

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

    2006-07-27

    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.

  12. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Devadas, Srinivas

    Simultaneous Alignment and Folding of Protein Sequences J´er^ome Waldisp¨uhl1,2 , Charles W. O techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu. 1 Introduction The consensus fold of two proteins is their common minimum energy structure, given

  13. Disulfide-Linked Protein Folding Pathways

    E-Print Network [OSTI]

    Bardwell, James

    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

  14. ACCEPTED MANUSCRIPT Fold interaction and wavelength selection

    E-Print Network [OSTI]

    Kaus, Boris

    with the Fars region of the Zagros fold-and-thrust belt including a large range of fold aspect ratio, such as the Makran, appear to be dominated by thrusting, whereas others such as the Simply Folded Belt at Zagros is active which amplifies sufficiently fast. In the Zagros Simply Folded Belt, they argued that weak

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

    E-Print Network [OSTI]

    Plotkin, Steven S.

    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

  16. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21

    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.

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

    E-Print Network [OSTI]

    Croquette, Vincent

    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

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

    E-Print Network [OSTI]

    Horner, Geoffrey Ashworth

    2010-01-01

    Are there pathways for protein folding. J Chim Phys, 1968.p. Dobson, C.M. , Protein folding and misfolding. Nature,Bai, Y. , et al. , Protein folding intermediates: native-

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

    E-Print Network [OSTI]

    Horner, Geoffrey Ashworth

    2010-01-01

    Z. Zhou, and Y. Bai, A protein folding pathway with multipleintermediate state in protein folding by a hydrophobicAre there pathways for protein folding. J Chim Phys, 1968.

  20. Simultaneous alignment and folding of protein sequences

    E-Print Network [OSTI]

    Waldispuhl, Jerome

    Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first ...

  1. Topology to geometry in protein folding: -Lactoglobulin

    E-Print Network [OSTI]

    Berry, R. Stephen

    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

  2. Introduzione alle Proteine e al Protein Folding

    E-Print Network [OSTI]

    Giannozzi, Paolo

    Chapter 4 Introduzione alle Proteine e al Protein Folding 4.1 Proteine: propriet`a strutturali Le protein folding `e il cosiddetto modello HP, nel quale a ogni amino acido `e assegnata l'etichetta di

  3. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Will, Sebastian

    Simultaneous Alignment and Folding of Protein Sequences J´er^ome Waldisp¨uhl1,2 , Charles W. O-homology proteins. In this work, we present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is poly- nomial in time

  4. UNCORRECTED 3 Protein folding: Then and now

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    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

  5. 272 Dispatch Protein folding: Chaperones get Hip

    E-Print Network [OSTI]

    Craig, Elizabeth A

    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

  6. Approximate Inference and Protein-Folding

    E-Print Network [OSTI]

    Weiss, Yair

    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

  7. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    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

  8. EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS

    E-Print Network [OSTI]

    Guibas, Leonidas J.

    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

  9. Protein folding: not just another optimization

    E-Print Network [OSTI]

    Karplus, Kevin

    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

  10. Protein-Folding Dynamics: Overview of Molecular

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Protein-Folding Dynamics: Overview of Molecular Simulation Techniques Harold A. Scheraga, Mey folding in silico. Although just a few years ago the dynamic be- havior of a protein molecule could models of proteins now make it possible to study protein- folding pathways from completely unfolded

  11. Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures*

    E-Print Network [OSTI]

    Istrail, Sorin

    Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known technique to study protein folding pathways of several small proteins and obtained encouraging results. In this pa- per, we describe how our motion planning framework can be used to study protein folding kinetics

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

    E-Print Network [OSTI]

    Yang, Hui

    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

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    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

  14. 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

  15. Topological Solitons and Folded Proteins

    E-Print Network [OSTI]

    M. N. Chernodub; Shuangwei Hu; Antti J. Niemi

    2010-03-23

    We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by assembling the solitons together, one after another. We present a simple theoretical model that realizes our proposal and apply it to a number of biologically active proteins including 1VII, 2RB8, 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to construct solitons that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 0.7 Angstrom or less for the central alpha-carbons, i.e. within the limits of current experimental accuracy.

  16. Protein-Folding Landscapes in Multi-Chain Systems

    E-Print Network [OSTI]

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

    2005-01-01

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

  17. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

    W. A. (2004). The protein folding 'speed limit'. CurrentG. (1997). Theory of protein folding: the energy landscapeenergy landscape of protein folding: a synthesis. Proteins

  18. Protein-folding via divide-and-conquer optimization

    E-Print Network [OSTI]

    Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

    2004-01-01

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

  19. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

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

  20. Elucidating amyloid ?-protein folding and assembly: A multidisciplinary approach

    E-Print Network [OSTI]

    2006-01-01

    dynamics approach to protein folding and aggregation.study of amyloid ?-protein folding and oligomerization.nucleation of amyloid ?-protein folding. Proc. Natl. Acad.

  1. Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity

    E-Print Network [OSTI]

    Fernández-Vidal, Mónica; Jayasinghe, Sajith; Ladokhin, Alexey S; White, Stephen H

    2007-01-01

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

  2. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

    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-

  3. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

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

  4. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

    Stochastic Dynamics on a Protein Folding Energy Landscape .and J. N. Onuchic. Protein folding funnels: kinetic pathwaysand T. Head-Gordon. Protein folding by distributed computing

  5. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

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

    2010-05-25

    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.

  6. DMBC: Web Planning & Layouts Above the Fold

    E-Print Network [OSTI]

    Stowell, Michael

    DMBC: Web Planning & Layouts Above the Fold · Website width · Website Height · Important content · From an Image Web Layouts Photoshop · Canvas Size · Guide Lines · Shapes #12;· Text (Lorem Ipsum

  7. Insights into fold growth using fold-related joint patterns and mechanical stratigraphy

    E-Print Network [OSTI]

    Savage, Heather M.

    Insights into fold growth using fold-related joint patterns and mechanical stratigraphy Heather M Available online 17 September 2010 Keywords: Sheep Mountain Anticline Joint pattern Mechanical stratigraphy, we integrate mechanical stratigraphy with joint pattern analysis to determine relative timing

  8. STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS

    E-Print Network [OSTI]

    Dinner, Aaron

    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

  9. Thermodynamics of Protein Folding Erik Sandelin

    E-Print Network [OSTI]

    Sandelin, Erik

    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 sequence-independent local interactions which are found to strongly influence the thermodynamics

  10. Control of folding by gravity and matrix thickness: Implications for large-scale folding

    E-Print Network [OSTI]

    Podladchikov, Yuri

    and the Zagros Mountains but does control folding in central Asia. Applicability conditions of viscous and thin

  11. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1996-06-11

    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.

  12. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect (OSTI)

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A.

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  13. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, Rajeev R. (Mountain View, CA); Cowan, Thomas E. (Livermore, CA)

    1996-01-01

    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.

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

    E-Print Network [OSTI]

    Latombe, Jean-Claude

    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

  15. Multiple folding pathways of proteins with shallow knots and co-translational folding

    E-Print Network [OSTI]

    Chwastyk, Mateusz

    2015-01-01

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.

  16. Mechanical Models of Fault-Related Folding

    SciTech Connect (OSTI)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  17. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17

    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.

  18. Cotranslational folding of deeply knotted proteins

    E-Print Network [OSTI]

    Chwastyk, Mateusz

    2015-01-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

  19. Inverse Folding of RNA Pseudoknot Structures

    E-Print Network [OSTI]

    Gao, James Z M; Reidys, Christian M

    2010-01-01

    Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \\pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, {\\tt RNAinverse}, {\\tt RNA-SSD} as well as {\\tt INFO-RNA} are limited to RNA secondary structures, we present in this paper the inverse folding algorithm {\\tt Inv} which can deal with 3-noncrossing, canonical pseudoknot structures. Results: In this paper we present the inverse folding algorithm {\\tt Inv}. We give a detailed analysis of {\\tt Inv}, including pseudocodes. We show that {\\tt Inv} allows to...

  20. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01

    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 ...

  1. DMBC: Web Planning & Layouts Above the Fold

    E-Print Network [OSTI]

    Stowell, Michael

    DMBC: Web Planning & Layouts Above the Fold · · Website Heig Website width ht Important content - lipsum.com) Media Placeholders g & Organization · · Triad C C S· hades · Custom F Web Layouts Photosho

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

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-12-28

    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.

  3. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01

    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.

  4. Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments

    E-Print Network [OSTI]

    Haspel, Nurit

    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

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

    E-Print Network [OSTI]

    Zaki, Mohammed Javeed

    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

  6. DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS

    E-Print Network [OSTI]

    Langmead, Christopher James

    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

  7. FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    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

  8. 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

  9. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26

    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^{\

  10. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

    and the mechanism of protein folding. Ann Rev Biochem 1982;Baldwin RL. How does protein folding get started? TRENDS inNucleation mechanisms in protein folding. Current Opinion in

  11. 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

  12. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

    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

  13. THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES

    E-Print Network [OSTI]

    Sosnick, Tobin R.

    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

  14. Protein folding using contact maps Michele Vendruscolo and Eytan Domany

    E-Print Network [OSTI]

    Domany, Eytan

    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

  15. Predicting Protein Folding Kinetics via Temporal Logic Model Checking: Extended

    E-Print Network [OSTI]

    Langmead, Christopher James

    Predicting Protein Folding Kinetics via Temporal Logic Model Checking: Extended Abstract Abstract. We present a novel approach for predicting protein folding kinetics using techniques from checking. We tested our method on 19 test proteins. The quantitative predictions regarding folding rates

  16. Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios

    E-Print Network [OSTI]

    Berry, R. Stephen

    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

  17. Protein Folding: A New Geometric Analysis

    E-Print Network [OSTI]

    Walter A. Simmons; Joel L. Weiner

    2008-09-11

    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.

  18. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01

    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,...

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

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01

    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...

  20. CSAW: a dynamical model of protein folding

    E-Print Network [OSTI]

    Kerson Huang

    2006-01-12

    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.

  1. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01

    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.

  2. Resistance proof, folding-inhibitor drugs

    E-Print Network [OSTI]

    R. Broglia; G. Tiana; R. Berera

    2002-10-09

    Conventional drugs work, as a rule, by inhibiting the enzymatic activity of specific proteins, capping their active site. In this paper we present a model of non- conventional drug design based on the inhibiting effects small peptides obtained from segments of the protein itself have on the folding ability of the system. Such peptides attach to the newly expressed (unfolded) protein and inhibit its folding, inhibition which cannot be avoided but through mutations which in any case denaturate the enzyme. These peptides, or their mimetic molecules, can be used as effective alternative drugs to those already available, displaying the advantage of not suffering from the upraise of resistence.

  3. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

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

    2011-06-14

    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.

  4. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

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

    2008-06-24

    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.

  5. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

    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.

  6. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

    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.

  7. DNA Nanomechanical Switches under Folding Kinetics Control

    E-Print Network [OSTI]

    Meller, Amit

    DNA Nanomechanical Switches under Folding Kinetics Control Virgile Viasnoff,, Amit Meller operate at equilibrium under changes in solution composition. We propose an alternative DNA switch design after heat denaturation drives the switch to its lowest energy conformation, while rapid cooling (>100

  8. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

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

    1990-08-23

    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.

  9. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

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

    1998-01-13

    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.

  10. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

    Carangelo, R.M.; Wright, D.D.

    1995-08-08

    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 foci coincidence and thereby to increase the radiation energy throughput characteristic of the cell. 10 figs.

  11. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

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

    1995-01-01

    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.

  12. 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

  13. Cellular mechanisms of membrane protein folding William R Skach

    E-Print Network [OSTI]

    Cai, Long

    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

  14. Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics

    E-Print Network [OSTI]

    Santiago, Juan G.

    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

  15. 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

  16. COMMUNICATION First Principles Prediction of Protein Folding Rates

    E-Print Network [OSTI]

    Goddard III, William A.

    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

  17. Protein folding by zipping and assembly S. Banu Ozkan*

    E-Print Network [OSTI]

    Southern California, University of

    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

  18. Automated Discovery of Structural Signatures of Protein Fold and Function

    E-Print Network [OSTI]

    Muggleton, Stephen H.

    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

  19. Can flat-ramp-flat fault geometry be inferred from fold shape?: A comparison of kinematic and mechanical folds

    E-Print Network [OSTI]

    Savage, Heather M.

    in the suprajacent fold shapes. Differences between the kinematic and mechanical fault-fold relationships highlight rights reserved. Keywords: Fault-bend folding; Mechanical models; Kinematic models; Fault geometry and mechanical models have been used to analyze fault-cored folds. Kinematic models, which balance the geometry

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

    E-Print Network [OSTI]

    Roma "La Sapienza", Università di

    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. Gâ??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

  1. A simple theory of protein folding kinetics

    E-Print Network [OSTI]

    Pande, Vijay S

    2010-01-01

    We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical properties seen in detailed simulations as well as to serve as a model to easily compare why these simulations suggest a different kinetic mechanism than previous simple models. Specifically, we find that non-native contacts play a key role in determining the mechanism, which can shift dramatically as the energetic strength of non-native interactions is changed. For protein-like non-native interactions, our model finds that the native state is a kinetic hub, connecting the strength of relevant interactions directly to the nature of folding kinetics.

  2. Inverse folding of RNA pseudoknot structures

    E-Print Network [OSTI]

    Gao, James Z M; Reidys, Christian M

    2009-01-01

    Results: In this paper we present the inverse folding algorithm {\\tt inv} as well as two applications. We give a detailed analysis of {\\tt inv}, including pseudocodes. The algorithm is freely available at \\url{http://www.combinatorics.cn/cbpc/inv.html}. We show, using 3-noncrossing nonplanar RNA pseudoknot structures as an example, that {\\tt inv} allows to design specific 3-noncrossing RNA structures. Furthermore we use {\\tt inv} for estimating the distance of the neutral networks. Conclusions: The algorithm {\\tt inv} extends inverse folding capabilities to RNA pseudoknot structures. In comparison with {\\tt RNAinverse} it uses new ideas, for instance by taking sets of competing structures into consideration. As a result, {\\tt inv} is able to find novel sequences even for RNA secondary structures.

  3. The coarsening of folds in hanging drapes

    E-Print Network [OSTI]

    Peter Bella; Robert V. Kohn

    2015-07-29

    We consider the elastic energy of a hanging drape -- a thin elastic sheet, pulled down by the force of gravity, with fine-scale folding at the top that achieves approximately uniform confinement. This example of energy-driven pattern formation in a thin elastic sheet is of particular interest because the length scale of folding varies with height. We focus on how the minimum elastic energy depends on the physical parameters. As the sheet thickness vanishes, the limiting energy is due to the gravitational force and is relatively easy to understand. Our main accomplishment is to identify the "scaling law" of the correction due to positive thickness. We do this by (i) proving an upper bound, by considering the energies of several constructions and taking the best; (ii) proving an ansatz-free lower bound, which agrees with the upper bound up to a parameter-independent prefactor. The coarsening of folds in hanging drapes has also been considered in the recent physics literature, using a self-similar construction whose basic cell has been called a "wrinklon." Our results complement and extend that work, by showing that self-similar coarsening achieves the optimal scaling law in a certain parameter regime, and by showing that other constructions (involving lateral spreading of the sheet) do better in other regions of parameter space. Our analysis uses a geometrically linear F\\"{o}ppl-von K\\'{a}rm\\'{a}n model for the elastic energy, and is restricted to the case when Poisson's ratio is zero.

  4. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

    a unifying mechanism for protein folding? [Review]. TrendsOn the transition coordinate for protein folding. Journal ofMonoclonal Antibodies. Protein Science 6(1), 99-108. Strang,

  5. Why are MD simulated protein folding times wrong? Dmitry Nerukh

    E-Print Network [OSTI]

    Nerukh, Dmitry

    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

  6. On the Kinematics of Protein Folding SEAN CAHILL,1

    E-Print Network [OSTI]

    Cahill, Kevin

    On the Kinematics of Protein Folding SEAN CAHILL,1 MICHAEL CAHILL,2 KEVIN CAHILL3 1 Department words: protein folding; homology modeling; loops; Monte Carlo; kinematics; wriggling Three Kinematic

  7. Protein Folding Simulation in CCP Luca Bortolussi1

    E-Print Network [OSTI]

    Bortolussi, Luca

    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

  8. New Crystal Structures Lift Fog around Protein Folding

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

    may have found a new way to modify protein-folding activities. For example, engineering the nucleotide-sensing loop so that it promotes the desired rate of protein folding...

  9. Computational and experimental investigations of forces in protein folding 

    E-Print Network [OSTI]

    Schell, David Andrew

    2005-02-17

    Properly folded proteins are necessary for all living organisms. Incorrectly folded proteins can lead to a variety of diseases such as Alzheimer?s Disease or Bovine Spongiform Encephalitis (Mad Cow Disease). Understanding ...

  10. Experimental and Computational Studies on Protein Folding, Misfolding and Stability 

    E-Print Network [OSTI]

    Wei, Yun

    2010-07-14

    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...

  11. How paper folds: bending with local constraints

    E-Print Network [OSTI]

    Jemal Guven; Martin Michael Mueller

    2007-12-06

    A variational framework is introduced to describe how a surface bends when it is subject to local constraints on its geometry. This framework is applied to describe the patterns of a folded sheet of paper. The unstretchability of paper implies a constraint on the surface metric; bending is penalized by an energy quadratic in mean curvature. The local Lagrange multipliers enforcing the constraint are identified with a conserved tangential stress that couples to the extrinsic curvature of the sheet. The framework is illustrated by examining the deformation of a flat sheet into a generalized cone.

  12. Protein folding: Then and now Yiwen Chen 1

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    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

  13. Author's personal copy Protein folding: Then and now

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    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

  14. Predicting Protein Folding Kinetics via Temporal Logic Model Checking

    E-Print Network [OSTI]

    Predicting Protein Folding Kinetics via Temporal Logic Model Checking Christopher James Langmead award from the U.S. Department of Energy. #12;Keywords: protein folding, model checking, temporal logic #12;Abstract We present a novel approach for predicting protein folding kinetics using techniques from

  15. Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao

    E-Print Network [OSTI]

    Bystroff, Chris

    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

  16. Protein Folding Simulation by Two-Stage Optimization

    E-Print Network [OSTI]

    Will, Sebastian

    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

  17. Protein Folding Challenge and Theoretical Computer Science Somenath Biswas

    E-Print Network [OSTI]

    Biswas, Somenath

    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

  18. Evolutionary Monte Carlo for protein folding simulations Faming Lianga)

    E-Print Network [OSTI]

    Liang, Faming

    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

  19. Combinatorial Problems on Strings with Applications to Protein Folding

    E-Print Network [OSTI]

    Newman, Alantha

    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

  20. A Complete and Effective Move Set for Simplified Protein Folding

    E-Print Network [OSTI]

    Whitesides, Sue

    A Complete and Effective Move Set for Simplified Protein Folding Neal Lesh Mitsubishi Electric­13, 2003, Berlin, Germany. Copyright 2003 ACM 1-58113-635-8/03/0004 ...$5.00. Keywords protein folding, it captures the main features of the protein folding prob- lem. This problem is NP-complete, and hence

  1. Protein folding with stochastic L-systems Gemma Danks1

    E-Print Network [OSTI]

    Stepney, Susan

    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

  2. Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding

    E-Print Network [OSTI]

    Michalet, Xavier

    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

  3. MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix

    E-Print Network [OSTI]

    Dix, Daniel B.

    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

  4. Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives

    E-Print Network [OSTI]

    Janke, Wolfhard

    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

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

    E-Print Network [OSTI]

    Smith, J. MacGregor

    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

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

    E-Print Network [OSTI]

    Weston, Ken

    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

  7. Polymer Collapse, Protein Folding, and the Percolation Threshold

    E-Print Network [OSTI]

    Meirovitch, Hagai

    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

  8. John von Neumann Institute for Computing Monte Carlo Protein Folding

    E-Print Network [OSTI]

    Hsu, Hsiao-Ping

    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

  9. COMMUNICATION Are Residues in a Protein Folding Nucleus

    E-Print Network [OSTI]

    Dai, Yang

    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

  10. Self-folding miniature elastic electric devices Shuhei Miyashita1

    E-Print Network [OSTI]

    Wood, Robert

    , inspired by Origami art work and protein folding, have been exploited for the con- struction of various folds using global heating [9]. Whitney et al developed m-scale robots based on pop- up methods [10], and Abel et al presented a theoretical fra- mework for designing pop-up parallel folds [11]. Techniques

  11. Protein Folding in Contact Map Space Eytan Domany

    E-Print Network [OSTI]

    Domany, Eytan

    Protein Folding in Contact Map Space Eytan Domany Department of Physics of Complex Systems to the free energy is unable to stabilize the native fold of a single protein against a set of carefully dimensional structure determines the biological function of a protein. The pro­ tein folding problem, i

  12. 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. In the completely sequenced genomes, folds could be automatically identified for 20%­30% of the proteins, with 3

  13. Folding simulations of small proteins Seung-Yeon Kima

    E-Print Network [OSTI]

    Lee, Jooyoung

    Folding simulations of small proteins Seung-Yeon Kima , Julian Leeb , Jooyoung Leea,* a School Abstract Understanding how a protein folds is a long-standing challenge in modern science. We have used an optimized atomistic model (united- residue force field) to simulate folding of small proteins of various

  14. Folding energy landscape and network dynamics of small globular proteins

    E-Print Network [OSTI]

    Berry, R. Stephen

    Folding energy landscape and network dynamics of small globular proteins Naoto Horia , George for review September 17, 2008) The folding energy landscape of proteins has been suggested to be funnel coordinates Proteins fold on large-dimensional energy landscapes through myriads of conformations. One energy

  15. Protein Folding in the Endoplasmic Reticulum Ineke Braakman1

    E-Print Network [OSTI]

    Hebert, Daniel N.

    Protein Folding in the Endoplasmic Reticulum Ineke Braakman1 and Daniel N. Hebert2 1 Cellular Correspondence: i.braakman@uu.nl; dhebert@biochem.umass.edu In this article, wewill cover the folding of proteins­trans isomerase families. We will conclude with the perspective of the folding protein: a comparison

  16. Structure Learning for Generative Models of Protein Fold Families

    E-Print Network [OSTI]

    Structure Learning for Generative Models of Protein Fold Families Sivaraman Balakrishnan composition of the proteins within a fold family are widely used in science and engineering. Existing composition of the proteins within a fold family provide insights into the constraints that govern structure

  17. Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble

    E-Print Network [OSTI]

    Stanley, H. Eugene

    Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble Feng Ding for the interpretation of experimental results and understanding of protein folding mechanics, which has at- tracted, 1999; Guerois and Serrano, 2000) have been proposed to predict the transition states in protein folding

  18. Folding simulations of a three-stranded antiparallel -sheet peptide

    E-Print Network [OSTI]

    Caflisch, Amedeo

    for review May 11, 2000) Protein folding is a grand challenge of the postgenomic era. In this paper, 58 in general for antiparallel -sheets with short turns. protein folding energy landscape implicit solvation model Theoretical and experimental studies have provided insights into the protein folding process (1

  19. PeriodicitiesinSequenceResidueHydropathyandtheImplicationsonProteinFolds Nancy Zhang

    E-Print Network [OSTI]

    Brutlag, Doug

    1 PeriodicitiesinSequenceResidueHydropathyandtheImplicationsonProteinFolds Nancy Zhang March, 2000 algorithms is that there are hidden variables effecting the protein folding mechanism and explain why it is crucial to a protein's fold. In section III, I will explain how the Fourier transform

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

    E-Print Network [OSTI]

    Ali R. Mohazab; Steven S. Plotkin

    2012-11-30

    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-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation "alignment". The consensus minimal pathway is constructed and shown schematically for representative cases of an $\\alpha$, $\\beta$, and knotted protein. An overlap parameter is defined between pathways; we find that $\\alpha$ proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and $\\beta$ proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding.

  1. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13

    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.

  2. Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins

    E-Print Network [OSTI]

    Janke, Wolfhard

    parts of the sequence. Moreover, for most proteins, the folding process is relatively slow (microsecTwo-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins Stefan Schnabel,* Michael Bachmann, and Wolfhard Janke Institut fu¨r Theoretische

  3. Effects of Familial Alzheimer's Disease Mutations on the Folding Nucleation of the Amyloid ?-Protein

    E-Print Network [OSTI]

    2008-01-01

    nucleation of amyloid ?-protein folding. Proc. Natl Acad.dynamics method for protein folding. Chem. Phys. Lett. 314,Atomic simulations of protein folding using the replica

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

    E-Print Network [OSTI]

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

    2014-01-01

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

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

    E-Print Network [OSTI]

    Cho, Samuel Sung-Il

    2007-01-01

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

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

    E-Print Network [OSTI]

    Capraro, Dominique T.

    2008-01-01

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

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

    E-Print Network [OSTI]

    Polinkovsky, Mark E.; Polinkovsky, Mark E.

    2012-01-01

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

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

    E-Print Network [OSTI]

    Sagle, Laura B.

    2006-01-01

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

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

    E-Print Network [OSTI]

    Connell, Katelyn Blair

    2010-01-01

    Unifying features in protein- folding mechanisms. Proc NatlDramatic acceleration of protein folding by stabilization ofL. & Englander, S. W. (1995). Protein folding intermediates:

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

    E-Print Network [OSTI]

    Weinkam, Patrick

    2009-01-01

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

  11. A biochemical analysis of the complex protein folding machinery in algal chloroplasts

    E-Print Network [OSTI]

    Tran, Miller

    2012-01-01

    1992). "Hsp90 chaperones protein folding in vitro." NatureMolecular chaperones in protein folding and proteostasis."analysis of the complex protein folding machinery in algal

  12. Amyloid ?-Protein Monomer Folding: Free-Energy Surfaces Reveal Alloform-Specific Differences

    E-Print Network [OSTI]

    Yang, M; Teplow, DB

    2008-01-01

    study of amyloid ?-protein folding and oligomerization.Elucidating amyloid ?-protein folding and assembly: A multi-of Alzheimer's amyloid ?-protein folding and assembly. Curr.

  13. Inferring the Rate-Length Law of Protein Folding

    E-Print Network [OSTI]

    Lane, Thomas J

    2013-01-01

    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.

  14. An energy landscape theory for cotranslational protein folding

    E-Print Network [OSTI]

    Tourigny, David S

    2013-01-01

    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...

  15. Dodging the crisis of folding proteins with knots

    E-Print Network [OSTI]

    Joanna I. Su?kowska; Piotr Su?kowski; José N. Onuchic

    2009-12-30

    Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, which involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in around 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.

  16. Accordian-folded boot shield for flexible swivel connection

    DOE Patents [OSTI]

    Hoh, Joseph C. (Naperville, IL)

    1986-01-01

    A flexible swivel boot connector for connecting a first boot shield section to a second boot shield section, both first and second boot sections having openings therethrough, the second boot section having at least two adjacent accordian folds at the end having the opening, the second boot section being positioned through the opening of the first boot section such that a first of the accordian folds is within the first boot section and a second of the accordian folds is outside of the first boot, includes first and second annular discs, the first disc being positioned within and across the first accordian fold, the second disc being positioned within and across the second accordian fold, such that the first boot section is moveably and rigidly connected between the first and second accordian folds of the second boot section.

  17. When pigs fly: a study of computer generated paper folding 

    E-Print Network [OSTI]

    Nitsch, Elizabeth Jeanette

    2009-05-15

    of folds form bases, or starting shapes, which are common to the construction of more than one figure. The classic, or best-known bases, are the kite base, fish base, bird base, and frog base [5] (Fig. 5). 4 Fig. 4. Basic origami folds... suitable for everything from clothing and architecture to lanterns, kites, and, of course, origami [11]. 6 HISTORY OF ORIGAMI Given that paper originated in China, many historians trace the development of artistic paper folding to that country...

  18. A dynamical approach to protein folding

    E-Print Network [OSTI]

    Alessandro Torcini; Roberto Livi; Antonio Politi

    2001-03-13

    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.

  19. VERIFI code optimization yields three-fold increase in engine...

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

    for parallel readwrite processes. (Click image to view larger.) VERIFI code optimization yields three-fold increase in engine simulation speed By Greg Cunningham * May 7,...

  20. New Crystal Structures Lift Fog around Protein Folding

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

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

  1. Hundred-Fold Improvement in Temperature Mapping Reveals the Stresses...

    Office of Science (SC) Website

    Hundred-Fold Improvement in Temperature Mapping Reveals the Stresses Inside Tiny Transistors Basic Energy Sciences (BES) BES Home About Research Facilities Science Highlights...

  2. Protein folding: A complex potential for the driving force

    E-Print Network [OSTI]

    Chekmarev, Sergei F

    2013-01-01

    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.

  3. Thermodynamics of protein folding: a random matrix formulation

    E-Print Network [OSTI]

    Pragya Shukla

    2010-10-16

    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.

  4. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    Conference: MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title:...

  5. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Kane, A; Hertzog, D; Baumgartel, P; Lengefeld, J; Horsley,...

  6. Folded inflatable protective device and method for making same

    DOE Patents [OSTI]

    Behr, V.L.; Nelsen, J.M.; Gwinn, K.W.

    1998-10-20

    An apparatus and method are disclosed for making an inflatable protective device made of lightweight material that can withstand the initial stress from inflation and enhance radial inflation. The device includes a cushion and an inflator port. The invention further includes several stacks of folded cushion material including a combination of full-width stacks and half-width stacks: a first full-width stack defined by one or more fan folds in a first lateral half of the cushion wherein the folds are substantially centered above a first center line and are substantially over the inflator port; a second full-width stack defined by one or more fan folds in a second lateral half of the cushion wherein the folds are substantially centered above the first center line and substantially over the inflator port in the first full-width stack; a first half-width stack defined by a plurality of fan folds in the bottom of the cushion where neither edge of each fold extends substantially over the second center line; and a second half-width stack defined by a plurality of fan folds in the top of the cushion wherein neither edge of each fold extends substantially over the second center line. 22 figs.

  7. Folded inflatable protective device and method for making same

    DOE Patents [OSTI]

    Behr, Vance L. (Albuquerque, NM); Nelsen, James M. (Albuquerque, NM); Gwinn, Kenneth W. (Cedar Crest, NM)

    1998-01-01

    An apparatus and method for making an inflatable protective device made of lightweight material that can withstand the initial stress from inflation and enhance radial inflation. The device includes a cushion and an inflator port. The invention further includes several stacks of folded cushion material including a combination of full-width stacks and half-width stacks: a first full-width stack defined by one or more fan folds in a first lateral half of the cushion wherein the folds are substantially centered above a first center line and are substantially over the inflator port; a second full-width stack defined by one or more fan folds in a second lateral half of the cushion wherein the folds are substantially centered above the first center line and substantially over the inflator port in the first full-width stack; a first half-width stack defined by a plurality of fan folds in the bottom of the cushion where neither edge of each fold extends substantially over the second center line; and a second half-width stack defined by a plurality of fan folds in the top of the cushion wherein neither edge of each fold extends substantially over the second center line.

  8. Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2007-10-24

    Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are permutations of each other. Despite the simplicity of the model, the knowledge of the free-energy landscape in dependence of a suitable system order parameter enables us to reveal complex folding characteristics known from real bioproteins and synthetic peptides, such as two-state folding, folding through weakly stable intermediates, and glassy metastability.

  9. Folding Mechanisms Earth Structure (2nd Edition), 2003

    E-Print Network [OSTI]

    Maryland Appalachians Swiss Alps #12;© EarthStructure (2nd ed) 311/7/2010 Bending and Buckling CompressionFolding Mechanisms Earth Structure (2nd Edition), 2003 W.W. Norton & Co, New York Slide show by Ben van der Pluijm © WW Norton; unless noted otherwise #12;© EarthStructure (2nd ed) 211/7/2010 Folds

  10. Counting Mountain-Valley Assignments for Flat Folds

    E-Print Network [OSTI]

    Hull, Thomas C.

    Counting Mountain-Valley Assignments for Flat Folds Thomas Hull Department of Mathematics Merrimack), a mountain-valley (MV) assignment is a function f : E {M,V} which indicates which crease lines are con- vex can be thought of as a structural blueprint of the fold.) Creases come in two types: mountain creases

  11. Coarsely resolved topography along protein folding pathways Ariel Fernandez

    E-Print Network [OSTI]

    Berry, R. Stephen

    Coarsely resolved topography along protein folding pathways Ariel Ferna´ndez Instituto de Matema . The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting

  12. Statistical Analysis of Protein Folding Kinetics Aaron R. Dinner

    E-Print Network [OSTI]

    Dinner, Aaron

    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

  13. Multi-Agent Simulation of Protein Folding Luca Bortolussi1

    E-Print Network [OSTI]

    Bortolussi, Luca

    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

  14. A Gauge Field Theory of Chirally Folded Homopolymers with Applications to Folded Proteins

    E-Print Network [OSTI]

    Ulf H. Danielsson; Martin Lundgren; Antti J. Niemi

    2010-08-26

    We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. We find that in its low temperature phase the model is in the same universality class with proteins that are deposited in the Protein Data Bank, in the sense of the compactness index. We apply the model to analyze various statistical aspects of folded proteins. Curiously we find that it can produce results that are a very good good match to the data in the Protein Data Bank.

  15. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1994-12-27

    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 figures.

  16. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, Rajeev R. (Mountain View, CA); Cowan, Thomas E. (Livermore, CA)

    1994-01-01

    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.

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

    E-Print Network [OSTI]

    Mohazab, Ali R

    2012-01-01

    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...

  18. Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design

    E-Print Network [OSTI]

    AhYoung, AP; Koehl, A; Cascio, D; Egea, PF

    2015-01-01

    falciparum: Targeting protein folding and secretion forfalciparum: targeting protein folding and secretion for

  19. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-08-13

    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.

  20. Water dynamics clue to key residues in protein folding

    SciTech Connect (OSTI)

    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)

    2010-01-29

    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.

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

    E-Print Network [OSTI]

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

    2013-01-01

    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.

  2. PCB origami : folding circuit boards into electronic products

    E-Print Network [OSTI]

    Sterman, Yoav

    2013-01-01

    PCB origami is a concept for an alternative manufacturing process of electronic products, in which the electronic material will be manufactured flat and folded into functional 3D graspable products by the user. PCBs will ...

  3. UFO (UnFold Operator) computer program abstract

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F.

    1982-11-01

    UFO (UnFold Operator) is an interactive user-oriented computer program designed to solve a wide range of problems commonly encountered in physical measurements. This document provides a summary of the capabilities of version 3A of UFO.

  4. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01

    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 ...

  5. Determining the role of hydration forces in protein folding

    SciTech Connect (OSTI)

    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)

    1999-07-01

    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.

  6. Low energy pathways for reproducible in vivo protein folding

    E-Print Network [OSTI]

    Leonor Cruzeiro

    2011-01-03

    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.

  7. Early Events in Protein Folding Explored by Rapid Mixing Methods

    E-Print Network [OSTI]

    Roder, Heinrich

    of unfolded or partially folded states, (V7 10/11 12:16) VCH/G J-1079 Buchner I PMU: WSL(W) 19/08/04 AC1: WSL

  8. Investigation of Peptide Folding by Nuclear Magnetic Resonance Spectroscopy 

    E-Print Network [OSTI]

    Hwang, SoYoun

    2012-07-16

    . 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...

  9. Mechanisms of protein-folding diseases at a glance

    E-Print Network [OSTI]

    Valastyan, Julie Suzanne

    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 ...

  10. SOFTWARE Open Access RNAexinv: An extended inverse RNA folding from

    E-Print Network [OSTI]

    Barash, Danny

    SOFTWARE Open Access RNAexinv: An extended inverse RNA folding from shape and physical attributes problem that aims to predict the secondary structure of a given RNA sequence. Software packages are nowa

  11. Energy landscapes, folding mechanisms and kinetics of RNA tetraloop hairpins

    E-Print Network [OSTI]

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

    2014-12-02

    of its biological functions, are poorly understood. 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...

  12. 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]

    Regan, Lynne

    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

  13. Master equation approach to protein folding and kinetic traps

    E-Print Network [OSTI]

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

    1998-04-21

    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.

  14. 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

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

    E-Print Network [OSTI]

    Langmead, Christopher James

    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

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

    E-Print Network [OSTI]

    Mukamel, Shaul

    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

  17. RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki

    E-Print Network [OSTI]

    Moll, Mark

    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

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

    E-Print Network [OSTI]

    California at Irvine, University of

    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

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

    E-Print Network [OSTI]

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

    2006-01-01

    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

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

    E-Print Network [OSTI]

    Neumaier, Arnold

    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

  1. Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding

    E-Print Network [OSTI]

    Neumaier, Arnold

    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

  2. THE UNIVERSITY OF CHICAGO UNIFYING FRAMEWORK FOR THE PREDICTION OF PROTEIN FOLDING

    E-Print Network [OSTI]

    Sosnick, Tobin R.

    THE UNIVERSITY OF CHICAGO UNIFYING FRAMEWORK FOR THE PREDICTION OF PROTEIN FOLDING PATHWAYS the protein folding problem challenging? . . . . . . . . . . . . . 5 1.2 Some essential concepts: Ingredients of a protein folding algorithm . . . . . . . 15 1.4 Some useful formalisms regarding protein

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

    E-Print Network [OSTI]

    Cecconi, Fabio

    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

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

    E-Print Network [OSTI]

    Bernstein, Rachel Simma

    2011-01-01

    and the mechanism of protein folding in cytochrome C. Int Jstructure analysis of a protein folding transition state;of a three-state protein folding pathway by NMR relaxation

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

    E-Print Network [OSTI]

    Sagle, Laura B.

    2006-01-01

    for Mechanisms of Protein Folding. Proc. Natl. Acad. Sci. U.Ptitsyn, O. B. , Protein Folding: Hypothesis andEvidenc for Barrier-Limited Protein Folding Kinetics on the

  6. Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping

    E-Print Network [OSTI]

    Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping distances between proteins. This method shows significant improvement in protein fold recognition. Overall March 2014 Keywords: Protein sequence Fold recognition Alignment method Feature extraction

  7. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    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.

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

    E-Print Network [OSTI]

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

    2012-01-01

    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

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

    E-Print Network [OSTI]

    DeVries, Ingrid L.

    2011-01-01

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

  10. Concentration-Temperature Superposition of Helix Folding Rates in Gelatin

    E-Print Network [OSTI]

    J. L. Gornall; E. M. Terentjev

    2006-03-05

    We study the kinetics of helix-coil transition in water solutions of gelatin (collagen protein) by optical rotation techniques combined with thermal characterization. By examining the rates of secondary helix folding, and covering a very wide range of solution concentrations, we are able to identify a universal exponential dependence of folding rate on concentration and quench temperature. We demonstrate a new concentration-temperature superposition of data at all temperatures and concentrations, and build the corresponding master curve. The results support the concept of a diffuse helix-coil transition. We find no concentration dependance of the normalized rate constant, suggesting first order (single) kinetics of secondary helix folding dominate in the early stages of renaturation.

  11. Collective aspects of protein folding illustrated by a toy model

    SciTech Connect (OSTI)

    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)

    1995-09-01

    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.

  12. Heteropolymer freezing and design: Towards physical models of protein folding

    SciTech Connect (OSTI)

    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)

    2000-01-01

    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.

  13. Enhanced sampling and applications in protein folding in explicit solvent

    E-Print Network [OSTI]

    Zhang, Cheng

    2010-01-01

    We report a single-copy tempering method for enhancing sampling in simulating large complex systems. A continuous temperature space random walk is achieved by a Langevin equation, which is guided by a runtime estimate of the thermal average energy through a novel integral identity. We first validated the method in a two-dimensional Ising model and a Lennard-Jones liquid system. Then the method was applied to folding of three small proteins, trpzip2, trp-cage, and villin headpiece in explicit solvent. Within 0.5~1 microsecond, all three systems were folded into atomic accuracy: the alpha carbon root mean square deviation of the best folded conformations from the native states are 0.2 A, 0.4 A, and 0.4 A, for trpzip2, trp-cage, and villin headpiece, respectively.

  14. Minimal models for proteins and RNA: From folding to function

    E-Print Network [OSTI]

    D. L. Pincus; S. S. Cho; C. Hyeon; D. Thirumalai

    2008-08-22

    We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key applications ranging from folding of proteins with disulfide bonds to functions of molecular machines. After presenting the theoretical basis that justifies the use of CG models, we explore the biophysical basis for the emergence of a finite number of folds from lattice models. The lattice model simulations of approach to the folded state show that non-native interactions are relevant only early in the folding process - a finding that rationalizes the success of structure-based models that emphasize native interactions. Applications of off-lattice $C_{\\alpha}$ and models that explicitly consider side chains ($C_{\\alpha}$-SCM) to folding of $\\beta$-hairpin and effects of macromolecular crowding are briefly discussed. Successful application of a new class of off-lattice model, referred to as the Self-Organized Polymer (SOP), is shown by describing the response of Green Fluorescent Protein (GFP) to mechanical force. The utility of the SOP model is further illustrated by applications that clarify the functions of the chaperonin GroEL and motion of the molecular motor kinesin. We also present two distinct models for RNA, namely, the Three Site Interaction (TIS) model and the SOP model, that probe forced unfolding and force quench refolding of a simple hairpin and {\\it Azoarcus} ribozyme. The predictions based on the SOP model show that force-induced unfolding pathways of the ribozyme can be dramatically changed by varying the loading rate. We conclude with a discussion of future prospects for the use of coarse-grained models in addressing problems of outstanding interest in biology.

  15. Characterization of Protein Folding by Dominant Reaction Pathways

    E-Print Network [OSTI]

    Pietro Faccioli

    2008-06-23

    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.

  16. Topology, Geometry, and Stability: Protein Folding and Evolution

    E-Print Network [OSTI]

    Simmons, Walter

    2015-01-01

    The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows that features without length scales, i.e. topological features, are potentially of central importance. Topology is a natural mathematical tool for the study of shape and we avail ourselves of that tool to examine the relationship between the amino acid sequence and the shapes of protein molecules. We apply what we learn to conjectures about their biological evolution.

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

    E-Print Network [OSTI]

    Neary, Tiffany Jonean

    2008-01-01

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

  18. Neurobiology of Disease Cortical Folding Abnormalities in Autism Revealed by

    E-Print Network [OSTI]

    Van Essen, David

    Neurobiology of Disease Cortical Folding Abnormalities in Autism Revealed by Surface-based morphometry across a range of autism spectrum disorders (7.5­18 years of age). We generated sulcal depth maps autism spectrum disorder subgroups: low-functioning autism, high-functioning autism, and Asperger

  19. Modeling Learningless Vulnerability Discovery using a Folded Distribution

    E-Print Network [OSTI]

    Malaiya, Yashwant K.

    model is logistic, and thus the increase and decrease in the discovery process is assumedModeling Learningless Vulnerability Discovery using a Folded Distribution Awad A. Younis1 , Hyun, CO 80523, USA Abstract ­ A vulnerability discovery model describes the vulnerability discovery rate

  20. Folded-Light-Path Colloidal Quantum Dot Solar Cells

    E-Print Network [OSTI]

    Sargent, Edward H. "Ted"

    Folded-Light-Path Colloidal Quantum Dot Solar Cells Ghada I. Koleilat*, Illan J. Kramer*, Chris T-processed solar cells offer the promise of low cost, large-area processing, and, prospectively, high solar power solar cell performance20,21 . Results In the present work, we sought to increase the interaction

  1. Thermal and Kinematic Evolution of the Eastern Cordillera Fold and

    E-Print Network [OSTI]

    Toro, Jaime

    Thermal and Kinematic Evolution of the Eastern Cordillera Fold and Thrust Belt, Colombia Jaime Toro and then calculated the conductive thermal state of key steps of the kinematic history using ThrustpackR 4.0. The models were constrained by well, seismic, apatite fission-track, and thermal-maturity data. The main

  2. NICMOS OPTICS OffAxis Conicoids Fold Mirrors

    E-Print Network [OSTI]

    Schneider, Glenn

    NICMOS OPTICS Off­Axis Conicoids Fold Mirrors Cameras 3, 1, 2 Pupil Al ignment Mirror Reimaging Optics (and Witness Samples) Before Installation The integrated NICMOS optical system is comprised of the fifteen NICMOS mirrors are mounted to a graphite epoxy truss, called the Fore­Optics Bracket (FOB

  3. Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives

    E-Print Network [OSTI]

    Michael Bachmann; Wolfhard Janke

    2007-10-25

    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.

  4. The Mathematics of Wrinkles and Folds Robert V. Kohn

    E-Print Network [OSTI]

    and Folds #12;Paper, deformed smoothly Essential mechanics of paper: it resists bending. If midline") prefers isometry. It is nonconvex (for paper: many smooth minimizers). Second term ("bending energy inextensible sheets (like paper) extensible sheets (rubber or cloth) thin crystalline films on substrates

  5. POLYMER PROGRAM SEMINAR Folding gels and shells: Designing reconfigurable

    E-Print Network [OSTI]

    Alpay, S. Pamir

    POLYMER PROGRAM SEMINAR Folding gels and shells: Designing reconfigurable 3D shapes and `mechanical and reconfigurable 3D shapes and properties. In particular, we have studied the use of photo-crosslinkable polymer films to prepare polymer sheets and multilayers containing stimuli-responsive hydrogel elements

  6. Folding Reporter Not 4 Profit BMTA LANL Agreement Number: LOS ALAMOS NATIONAL SECURITY, LLC

    E-Print Network [OSTI]

    , Berendzen J, Terwilliger TC (1999) "Rapid protein folding assay using Green Fluorescent Protein" Nat Biotech

  7. Folding Reporter Foreign Not 4 Profit BMTA LANL Agreement Number: LOS ALAMOS NATIONAL SECURITY, LLC

    E-Print Network [OSTI]

    , Berendzen J, Terwilliger TC (1999) "Rapid protein folding assay using Green Fluorescent Protein" Nat Biotech

  8. RESEARCH ARTICLE Open Access Probing the folding of mini-protein Beta3s by

    E-Print Network [OSTI]

    Mukamel, Shaul

    RESEARCH ARTICLE Open Access Probing the folding of mini-protein Beta3s by two-dimensional infrared-dimensional correlation spectroscopy (2DCS) to characterize the folding mechanism of the mini-protein Beta3s with experimental 2DCS to study the folding mechanism of proteins. In addition to exploring the folding mechanism

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

    E-Print Network [OSTI]

    Emmerich, Michael

    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

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

    E-Print Network [OSTI]

    Lebendiker, Mario

    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

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

    E-Print Network [OSTI]

    Stanley, H. Eugene

    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

  12. 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

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

    E-Print Network [OSTI]

    Bachmann, Michael

    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

  14. BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum

    E-Print Network [OSTI]

    Petzold, Linda R.

    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

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

    E-Print Network [OSTI]

    Hebert, Daniel N.

    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

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

    E-Print Network [OSTI]

    Bachmann, Michael

    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

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

    E-Print Network [OSTI]

    Fidanova, Stefka

    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

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

    E-Print Network [OSTI]

    Istrail, Sorin

    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

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

    E-Print Network [OSTI]

    Dai, Yang

    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

  20. The energy landscape for protein folding and possible connections to function

    E-Print Network [OSTI]

    Onuchic, José

    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

  1. Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation

    E-Print Network [OSTI]

    Latombe, Jean-Claude

    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

  2. Membrane protein folding on the example of outer membrane protein A of Escherichia coli

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    Membrane protein folding on the example of outer membrane protein A of Escherichia coli J. H and mechanisms by which membrane proteins insert and fold into a biomem- brane have mostly been studiedA that involves at least three struc- turally distinct folding intermediates. Key words. Membrane protein folding

  3. Protein Fold Class Prediction using Neural Networks with Tailored Early-Stopping

    E-Print Network [OSTI]

    Igel, Christian

    Protein Fold Class Prediction using Neural Networks with Tailored Early-Stopping Thomas fold class given the primary sequence of a protein. Different feature spaces for primary sequences the fold class of proteins [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]. A fold class contains

  4. The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity

    E-Print Network [OSTI]

    Berry, R. Stephen

    The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity links protein fold and biological function: the conservation of the fold across distant homol- ogous hydrogen bond (3­9), recently termed dehydron (7), which is encoded in the 3D structure of protein folded

  5. Origami-like Folded MEMS for Realization of TIMU: Fabrication Technology and Initial

    E-Print Network [OSTI]

    Chen, Zhongping

    single-axis sensors and then folding them into a 3-D Fig. 1. Commercial MEMS IMUs Performance Fig. 2 for assembly of the integrated MEMS sensor cluster in a 3-D configuration, or folding in a 3-D shape. FoldedOrigami-like Folded MEMS for Realization of TIMU: Fabrication Technology and Initial Demonstration

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

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM)

    2007-09-18

    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.

  7. RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki

    E-Print Network [OSTI]

    Kavraki, Lydia E.

    RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki Abstract--Protein folding reviews a class of methods for studying the folding process called roadmap methods. e goal. It is assumed that the folded state is known. Roadmap methods build a graph representation of sampled

  8. The effects of nonnative interactions on protein folding rates: Theory and simulation

    E-Print Network [OSTI]

    Plotkin, Steven S.

    The effects of nonnative interactions on protein folding rates: Theory and simulation CECILIA interaction energy can actually assist the folding to the native structure. Keywords: protein folding: see www.proteinscience.org The mechanism of protein folding is of central importance to structural

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

    E-Print Network [OSTI]

    Istrail, Sorin

    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

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

    E-Print Network [OSTI]

    Clark, Patricia L.

    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

  11. Funnel-Like Organization in Sequence Space Determines the Distributions of Protein Stability and Folding Rate

    E-Print Network [OSTI]

    Levitt, Michael

    determinants of protein folding, we map out the complete organization of thermody- namic and kinetic properties simplified models of protein folding. We obtain a stability map and a folding rate map in sequence space. Proteins 2004;55:107­114. © 2004 Wiley-Liss, Inc. Key words: protein folding; protein sequence struc- ture

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

    E-Print Network [OSTI]

    Zhou, Yaoqi

    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

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

    E-Print Network [OSTI]

    Yang, Hui

    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

  14. Manipulating and Visualizing Proteins Simon, Horst D. 59 BASIC...

    Office of Scientific and Technical Information (OSTI)

    ACIDS; CALIFORNIA; CHAINS; CHEMISTRY; DISEASES; FIBROSIS; FORECASTING; GENETICS; OPTIMIZATION; PROTEIN STRUCTURE; PROTEINS; QUEUES; SHAPE; SIMULATION PROTEIN STRUCTURE...

  15. PLANAR ROTATION SEQUENCES AND DOMAIN EXCHANGE HORST BRUNOTTE

    E-Print Network [OSTI]

    by the authors [1]. The proof in [5] is based on a torus map which is described in detail by Kouptsov, Lowenstein

  16. Microsoft PowerPoint - Horst Simon.BitstoBuidings2

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass map shines light on darkMicroorganisms toPalladium/28/2008Hentschel

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

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2009-02-16

    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.

  18. Fold and thrust partitioning in a contracting fold belt: Insights from the 1931 Mach earthquake in Baluchistan

    E-Print Network [OSTI]

    Bilham, Roger

    models of the earthquake cycle in this fold and thrust belt suggest that slip on the frontal thrust fault is $5 mm/yr. Hence the minimum renewal time between earthquakes with 1.2-m mean displacement should is taken into account the minimum renewal time may exceed 2000 years. Citation: Szeliga, W., R. Bilham, D

  19. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01

    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.

  20. Strong Nernst-Ettingshausen effect in folded graphene

    E-Print Network [OSTI]

    Friedemann Queisser; Ralf Schützhold

    2013-01-17

    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.

  1. Experimental continuation of periodic orbits through a fold

    E-Print Network [OSTI]

    J. Sieber; A. Gonzalez-Buelga; S. A. Neild; D. J. Wagg; B. Krauskopf

    2008-06-12

    We present a continuation method that enables one to track or continue branches of periodic orbits directly in an experiment when a parameter is changed. A control-based setup in combination with Newton iterations ensures that the periodic orbit can be continued even when it is unstable. This is demonstrated with the continuation of initially stable rotations of a vertically forced pendulum experiment through a fold bifurcation to find the unstable part of the branch.

  2. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S.

    1995-12-11

    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.

  3. Combined approach to the inverse protein folding problem. Final report

    SciTech Connect (OSTI)

    Ruben A. Abagyan

    2000-06-01

    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).

  4. Living With Radical Uncertainty. The Exemplary case of Folding Protein

    E-Print Network [OSTI]

    Ignazio Licata

    2010-04-21

    Laplace's demon still makes strong impact on contemporary science, in spite of the fact that Logical Mathematics outcomes, Quantum Physics advent and more recently Complexity Science have pointed out the crucial role of uncertainty in the World's descriptions. We focus here on the typical problem of folding protein as an example of uncertainty, radical emergence and a guide to the "simple" principles for studying complex systems.

  5. Elastic energy of proteins and the stages of protein folding

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01

    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^{\

  6. Creases and folds : applying geometry to a pop-up fashion pavilion

    E-Print Network [OSTI]

    Li, Yujing, S.B. Massachusetts Institute of Technology

    2010-01-01

    This thesis explores the architectural opportunities embedded in geometric folding by studying the limitations and possibilities of a variety of patterns. In particular; the thesis focuses on the Yoshimura or diamond folding ...

  7. Techniques for modeling and analyzing RNA and protein folding energy landscapes 

    E-Print Network [OSTI]

    Tang, Xinyu

    2009-05-15

    RNA and protein molecules undergo a dynamic folding process that is important to their function. Computational methods are critical for studying this folding pro- cess because it is difficult to observe experimentally. In ...

  8. Optimal fold symmetry of LH2 rings on a photosynthetic membrane

    E-Print Network [OSTI]

    Cleary, Liam

    An intriguing observation of photosynthetic light-harvesting systems is the N-fold symmetry of light-harvesting complex 2 (LH2) of purple bacteria. We calculate the optimal rotational configuration of N-fold rings on a ...

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

    E-Print Network [OSTI]

    Dinc, Huseyin

    2002-01-01

    Design of an 8-bit current mode, ripple-folding analog to digital (A/D) converter is discussed. The ripple folding technique and the possible implementations in different process technologies are summarized. To have an A/D ...

  10. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect (OSTI)

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

    2005-02-10

    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.

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

    E-Print Network [OSTI]

    Januar, M; Handoko, L T; 10.1142/9789814335614_0047

    2011-01-01

    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.

  12. Directed transport as a mechanism for protein folding in vivo

    E-Print Network [OSTI]

    Ernesto Gonzalez-Candela; Victor Romero-Rochin

    2009-09-23

    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.

  13. Directed transport as a mechanism for protein folding in vivo

    E-Print Network [OSTI]

    Gonzalez-Candela, Ernesto

    2009-01-01

    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.

  14. Kinematics of fault-related folding derived from a sandbox experiment Sylvain Bernard,1,2

    E-Print Network [OSTI]

    Avouac, Jean-Philippe

    be used to determine incremental defor- mation associated with active folds [e.g., Rockwell et al., 1988

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

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2007-10-25

    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.

  16. Protein-Folding Landscapes in Multi-Chain Systems Cellmer, Troy...

    Office of Scientific and Technical Information (OSTI)

    37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; FREE ENERGY; MELTING; PROTEINS; THERMODYNAMICS; TOPOLOGY protein folding protein...

  17. 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

  18. Structural genomics of minimal organisms and protein fold space Sung-Hou Kim1,2,

    E-Print Network [OSTI]

    Structural genomics of minimal organisms and protein fold space Sung-Hou Kim1,2, *, Dong Hae Shin2: Berkeley Structural Genomics Center, minimal organisms, molecular function, protein fold space, structural determination. The results from the pipeline substantially increased the coverage of the protein fold space of M

  19. Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-

    E-Print Network [OSTI]

    Snow, Christopher

    Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide protein-folding theory. q 2002 Elsevier Science Ltd. All rights reserved Keywords: molecular dynamics; protein folding; villin headpiece; ensemble averaging; distributed computing*Corresponding author

  20. Outer membrane protein A of E. coli folds into detergent micelles, but not in the

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    Outer membrane protein A of E. coli folds into detergent micelles, but not in the presence-barrel membrane proteins, folding of OmpA was studied as a function of the hydrophobic chain length, the chemical; membrane protein folding; outer membrane protein A; porin; protein­detergent interaction; protein

  1. Parallel Folding Pathways in the SH3 Domain Protein , J. M. Borreguero2

    E-Print Network [OSTI]

    Buldyrev, Sergey

    Parallel Folding Pathways in the SH3 Domain Protein A. R. Lam1 , J. M. Borreguero2 , F. Ding3 , N of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an understanding of the folding process. We determined the TSE of the src-SH3 domain protein by using extensive

  2. Discrete molecular dynamics studies of the folding of a protein-like model

    E-Print Network [OSTI]

    Buldyrev, Sergey

    Discrete molecular dynamics studies of the folding of a protein-like model Nikolay V Dokholyan1 to resolve in time the folding of model proteins in computer simulations. Different computational approaches). Results: We used the recently proposed approach of Zhou and Karplus to study the folding of a protein

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

    E-Print Network [OSTI]

    Lindquist, Susan

    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

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

    E-Print Network [OSTI]

    Unger, Ron

    1996-01-01

    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

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

    E-Print Network [OSTI]

    Chen, Kuang-Yu

    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

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

    E-Print Network [OSTI]

    Gräter, Frauke

    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

  7. Nano Res. 2011, 4(12): 124212471242 Chemical Versus Thermal Folding of Graphene Edges

    E-Print Network [OSTI]

    Simons, Jack

    Nano Res. 2011, 4(12): 1242­12471242 Chemical Versus Thermal Folding of Graphene Edges Ninghai Su dynamics (MD) simulations, we have investigated the kinetics of the graphene edge folding processV/Å (or about 120 meV per edge atom) for folding the edges of intrinsic clean single-layer graphene (SLG

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

    E-Print Network [OSTI]

    Bigelow, Stephen

    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

  9. Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms

    E-Print Network [OSTI]

    Okamoto, Yuko

    Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms Yuji Sugita1 uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two simulation algorithms have been intro- duced to the protein folding problem (for reviews see, e.g., Refs. [1

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

    E-Print Network [OSTI]

    LaValle, Steven M.

    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

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

    E-Print Network [OSTI]

    Santiago, Juan G.

    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

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

    E-Print Network [OSTI]

    Levine, Alex J.

    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

  13. Protein Folding in Contact Map Space M. Vendruscolo, R. Najmanovich and E. Domany

    E-Print Network [OSTI]

    Domany, Eytan

    Protein Folding in Contact Map Space M. Vendruscolo, R. Najmanovich and E. Domany Department the contact map representation for protein folding. We devel­ oped an efficient search procedure in the space­ tational physics, chemistry and biology is that of protein folding; e.g. to predict the conformation

  14. 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

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

    E-Print Network [OSTI]

    Berne, Bruce J.

    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

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

    E-Print Network [OSTI]

    Mukamel, Shaul

    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

  17. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence and theoretical studies have revealed that protein folding kinetics can be quite complex and diverse depending theoretical understanding of the kinetics of protein folding [1­8]. The general scenarios that have emerged

  18. Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks Gregg Lois,1,2

    E-Print Network [OSTI]

    O'Hern, Corey S.

    Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks Gregg a protein fold reliably to its native conforma- tion even though a large number of metastable states exist the funneled energy landscape may explain how some proteins fold reliably 7 , a different picture, i.e., rugged

  19. Single-molecule spectroscopy of protein folding in a chaperonin cage

    E-Print Network [OSTI]

    Lipman, Everett A.

    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

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

    E-Print Network [OSTI]

    Stepney, Susan

    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

  1. Fast tree search for enumeration of a lattice model of protein folding Henry Cejtin,a)

    E-Print Network [OSTI]

    Li, Hao

    Fast tree search for enumeration of a lattice model of protein folding Henry Cejtin,a) Jan Edler conformations structures for a protein folding model on a cubic lattice of size 4 3 3. We used two types. © 2002 American Institute of Physics. DOI: 10.1063/1.1423324 I. INTRODUCTION The protein folding problem1

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

    E-Print Network [OSTI]

    Hoos, Holger H.

    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

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

    E-Print Network [OSTI]

    Hoos, Holger H.

    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

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

    E-Print Network [OSTI]

    Istrail, Sorin

    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

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

    E-Print Network [OSTI]

    Newman, Alantha

    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

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

    E-Print Network [OSTI]

    Harries, Daniel

    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

  7. Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics

    E-Print Network [OSTI]

    Morozov, Alexandre V.

    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

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

    E-Print Network [OSTI]

    Berry, R. Stephen

    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

  9. Modulation of the Maladaptive Stress Response to Manage Diseases of Protein Folding

    E-Print Network [OSTI]

    Morimoto, Richard

    Modulation of the Maladaptive Stress Response to Manage Diseases of Protein Folding Daniela Martino homeostasis components that direct protein folding and function. To identify global principles of misfolding. In diseased cells, maladaptation alters protein structure­function relationships, impacts protein folding

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

    E-Print Network [OSTI]

    Croquette, Vincent

    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

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

    E-Print Network [OSTI]

    Istrail, Sorin

    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

  12. A New Constraint Solver for 3D Lattices and its Application to the Protein Folding Problem

    E-Print Network [OSTI]

    Dal Palù, Alessandro

    A New Constraint Solver for 3D Lattices and its Application to the Protein Folding Problem protein folding) problem can be defined as the problem of determining, given the molecular composition of a protein. The predominant strategy in solving #12;the protein folding problem has been to determine a state

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

    E-Print Network [OSTI]

    Fleming, Patrick

    ­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

  14. Identification of the protein folding transition state from molecular dynamics trajectories

    E-Print Network [OSTI]

    Caflisch, Amedeo

    Identification of the protein folding transition state from molecular dynamics trajectories S. Muff The rate of protein folding is governed by the transition state so that a detailed characterization of its. INTRODUCTION Proteins fold from the heterogeneous set of denatured conformations to the structurally well

  15. Protein folding: from theory to practice D Thirumalai1,2

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    Protein folding: from theory to practice D Thirumalai1,2 , Zhenxing Liu3 , Edward P O'Brien4 and Govardhan Reddy1 A quantitative theory of protein folding should make testable predictions using theoretical globules represent major advances in the proteins folding field. Addresses 1 Biophysics Program, Institute

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

    E-Print Network [OSTI]

    Croquette, Vincent

    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

  17. "New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations

    E-Print Network [OSTI]

    Lazaridis, Themis

    "New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations Themis folding with a preferred pathway on a funnel-like average energy surface. A "new view" of protein folding is the primary unfolding event. The results suggest a synthesis of the "new" and the classical view of protein

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

    E-Print Network [OSTI]

    Cheng, Jianlin Jack

    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

  19. PHYSICAL REVIEW E VOLUME 48, NUMBER 2 AUGUST 1993 Toy model for protein folding

    E-Print Network [OSTI]

    Stillinger, Frank

    PHYSICAL REVIEW E VOLUME 48, NUMBER 2 AUGUST 1993 Toy model for protein folding Frank H. Stillinger (Received 1 March 1993) A conceptually simple model for protein-folding phenomena has been created thus far suggest that protein folding has a more complex cooperative character than has been embodied

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

    E-Print Network [OSTI]

    Haller, Gary L.

    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

  1. Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity

    E-Print Network [OSTI]

    Bachmann, Michael

    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

  2. Matching Simulation and Experiment: A New Simplified Model for Simulating Protein Folding (extended abstract)

    E-Print Network [OSTI]

    Istrail, Sorin

    Matching Simulation and Experiment: A New Simplified Model for Simulating Protein Folding (extended, Berkeley, CA 94720 T LHead-Gordon@lbl.gov, Abstract Simulations of simplified protein folding models have provided much insight into solving the protein folding problem. We propose here a new off-lattice bead

  3. Predicting protein folding rates from geometric contact and amino acid sequence

    E-Print Network [OSTI]

    Dai, Yang

    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

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

    E-Print Network [OSTI]

    Weston, Ken

    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

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

    E-Print Network [OSTI]

    Weston, Ken

    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

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

    E-Print Network [OSTI]

    Thorpe, Michael

    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

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

    E-Print Network [OSTI]

    Sørensen, Michael

    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

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

    E-Print Network [OSTI]

    Schlick, Tamar

    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

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

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    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

  10. Combination of Multiple Distance Measures for Protein Fold Classification Chendra Hadi Suryanto, Hideitsu Hino, Kazuhiro Fukui

    E-Print Network [OSTI]

    Fukui, Kazuhiro

    Combination of Multiple Distance Measures for Protein Fold Classification Chendra Hadi Suryanto. In this paper, we propose a new approach to protein fold classification, by introducing the concept of large demonstrate the effectiveness of the proposed method by classifying 27 fold classes of proteins in the Ding

  11. Predicting Protein Folds with Structural Repeats Using a Chain Graph Model

    E-Print Network [OSTI]

    Carbonell, Jaime

    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

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

    E-Print Network [OSTI]

    Erdogan, Hakan

    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- ture. Protein threading or fold recognition refers to a class of compu- tational methods for predicting

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

    E-Print Network [OSTI]

    Carbonell, Jaime

    Protein Quaternary Fold Recognition Using Conditional Graphical Models Yan Liu Jaime Carbonell 02139 pweigele@mit.edu Abstract Protein fold recognition is a crucial step in infer- ring biological structural folds, which consist of multiple protein chains that form chemical bonds among side chains

  14. Structural and energetic heterogeneity in protein folding. I. Theory Steven S. Plotkina)

    E-Print Network [OSTI]

    Plotkin, Steven S.

    Structural and energetic heterogeneity in protein folding. I. Theory Steven S. Plotkina) and Jose-energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein protein, both structural and energetic heterogeneity lower the thermodynamic barrier to folding. When

  15. How Does a Simplified-Sequence Protein Fold? Enrico Guarnera, Riccardo Pellarin, and Amedeo Caflisch*

    E-Print Network [OSTI]

    Caflisch, Amedeo

    How Does a Simplified-Sequence Protein Fold? Enrico Guarnera, Riccardo Pellarin, and Amedeo a putatively primordial protein we have simplified the sequence of a 56-residue a/b fold (the immu- noglobulin folding of the simplified protein suggest that evolution has enriched the primordial alphabet of amino

  16. Folding minimal sequences: the lower bound for sequence complexity of globular proteins

    E-Print Network [OSTI]

    Obradovic, Zoran

    Folding minimal sequences: the lower bound for sequence complexity of globular proteins Pedro of sequence complexity, are herein applied to two prior studies on the folding of minimal proteins.9. These values are therefore suggested to be necessary and sufficient for folding into globular proteins having

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

    E-Print Network [OSTI]

    Moll, Mark

    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 the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular

  18. Cooperativity, Smooth Energy Landscapes and the Origins of Topology-dependent Protein Folding Rates

    E-Print Network [OSTI]

    Levine, Alex J.

    Cooperativity, Smooth Energy Landscapes and the Origins of Topology-dependent Protein Folding Rates Barbara Santa Barbara, CA 93106-9510 USA The relative folding rates of simple, single-domain proteins, proteins whose folding energy landscapes are smooth, are highly dispersed and strongly correlated

  19. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving taxonomy-based protein fold

    E-Print Network [OSTI]

    Chen, Xin

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving taxonomy-based protein fold recognition INTRODUCTION Protein fold recognition from amino acid sequences is one of the funda- mental problems in structural bioinformatics, as fold information could facilitate the identification of a protein's tertiary

  20. Three-body interactions improve the prediction of rate and mechanism in protein folding models

    E-Print Network [OSTI]

    Plotkin, Steven S.

    Three-body interactions improve the prediction of rate and mechanism in protein folding models M. R-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations that stabilize protein structures and govern protein folding mechanisms is a fundamental problem in molecular

  1. Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model

    E-Print Network [OSTI]

    Buldyrev, Sergey

    Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model Feng Ding molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended is not necessary to reach the native state of a protein. Our results also suggest that the success of folding Trp

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

    E-Print Network [OSTI]

    Devadas, Srinivas

    Efficient traversal of beta-sheet protein folding pathways using ensemble models Solomon Shenker1. Molecular Dynamics (MD) simulations can now predict ms- timescale folding processes of small proteins peptides with few long-range interactions. Larger and slower- folding proteins, such as many with extended

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

    E-Print Network [OSTI]

    Domany, Eytan

    Pairwise contact potentials are unsuitable for protein folding Michele Vendruscolo and Eytan Domany that pairwise contact potentials alone cannot be used to predict the native fold of a protein. Ideally one would hope that a universal energy function exists, for which the native folds of all proteins

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

    E-Print Network [OSTI]

    Muggleton, Stephen H.

    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 to analyse (and determine the principles responsible for) the distribution of proteins in fold space

  5. Identification and Applications of Three-dimensional Non-local Structural Motifs in Protein Folding Data

    E-Print Network [OSTI]

    Yang, Hui

    Identification and Applications of Three-dimensional Non-local Structural Motifs in Protein Folding Francisco State University, U.S.A. 1 Background How does a protein fold into its biologically functional]. The product of such simulations is a collection of folding trajectories of the protein under study, where each

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

    E-Print Network [OSTI]

    Berry, R. Stephen

    Self-organization and mismatch tolerance in protein folding: General theory and an application The folding of a protein is a process both expeditious and robust. The analysis of this process presented here of their discretized configuration space. The properties ``expeditious and robust'' imply that the folding protein must

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

    E-Print Network [OSTI]

    Shorter, James

    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 into the effect of crowding on the stability and folding rate of protein tertiary structures, very little is known

  8. INVESTIGATING EVOLUTIONARY LINES OF LEAST RESISTANCE USING THE INVERSE PROTEIN-FOLDING

    E-Print Network [OSTI]

    Naylor, Gavin

    INVESTIGATING EVOLUTIONARY LINES OF LEAST RESISTANCE USING THE INVERSE PROTEIN-FOLDING PROBLEM J sequences that fold to a specified target protein conformation based on Sun et al's Grand Canonical (GC There is a large body of work devoted to solving the protein folding problem, which is defined as follows: Given

  9. The Backbone Conformational Entropy of Protein Folding: Experimental Measures from Atomic

    E-Print Network [OSTI]

    Hansma, Paul

    The Backbone Conformational Entropy of Protein Folding: Experimental Measures from Atomic Force range of proteins.1 ­ 15 When applied to a protein comprised of multiple independent folding units of information regarding the mechanical properties, folding kinetics and thermodynamics of proteins, some

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

    E-Print Network [OSTI]

    Dinner, Aaron

    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

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

    E-Print Network [OSTI]

    Di Mauro, Nicola

    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

  12. Folding Free Energies of 59-UTRs Impact Post-Transcriptional Regulation

    E-Print Network [OSTI]

    Ringnér, Markus

    Folding Free Energies of 59-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast. Here, the aim is to study genome-wide regulatory effects of mRNA 59-UTR folding free energies. We performed computations of secondary structures in 59-UTRs and their folding free energies for all verified

  13. 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

  14. Implementation and Characterization of Protein Folding on a Desktop Computational Grid

    E-Print Network [OSTI]

    Taufer, Michela

    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

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

    E-Print Network [OSTI]

    Taufer, Michela

    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

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

    E-Print Network [OSTI]

    Chan, Hue Sun

    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

  17. The FASEB Journal FASEB SRC Commentary Protein Folding in the Cell, from Atom to Organism

    E-Print Network [OSTI]

    Clark, Patricia L.

    The FASEB Journal · FASEB SRC Commentary Protein Folding in the Cell, from Atom to Organism Jeffrey Dame, Indiana, USA Proper cell function requires proper protein fold- ing. Misfolding of specific--as well as unique support systems--for protein folding that cannot be captured easily in test- tube

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

    E-Print Network [OSTI]

    Palczewski, Krzysztof

    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

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

    E-Print Network [OSTI]

    Istrail, Sorin

    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

  20. 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

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

    E-Print Network [OSTI]

    Demaine, Erik

    is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino to answer qualitative questions about the protein folding process. In this paper we consider a problem-MEC PB98- 0933. Preprint submitted to Elsevier Science 21 January 2002 #12;1 Introduction Protein folding

  2. Osnabrck University Neuer Graben 29/Schloss

    E-Print Network [OSTI]

    Steinhoff, Heinz-Jürgen

    programs for those who wish to specialize in just one subject, for example #12;2 Biology, Geoinformatics

  3. GEOLOGIC NOTE Fault linkage and graben

    E-Print Network [OSTI]

    Fossen, Haakon

    . Schultz $ Geomechanics-Rock Fracture Group, Department of Geological Sciences and Engineering/172 (1982), and his Ph.D. in geomechanics from Purdue University (1987). He worked at the Lunar

  4. Cooperative folding of muscle myosins: I. Mechanical model

    E-Print Network [OSTI]

    Matthieu Caruel; Jean-Marc Allain; Lev Truskinovsky

    2015-10-12

    Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an athermal perspective on such folding by analyzing the simplest purely mechanical prototype: a parallel bundle of bi-stable units attached to a common backbone. We show that in this analytically transparent model, characterized by a rugged energy landscape, the ground states are always highly coherent, single-phase configurations. We argue that such cooperative behavior, ensuring collective conformational change, is due to the dominance of long- range interactions making the system non-additive. The detailed predictions of our model are in agreement with experimentally observed non-equivalence of fast force recovery in skeletal muscles loaded in soft and hard devices. Some features displayed by the model are also recognizable in the behavior of other biological systems with passive multi-stability and long-range interactions including detaching adhesive binders and pulled RNA/DNA hairpins.

  5. Folding and insertion thermodynamics of the transmembrane WALP peptide

    E-Print Network [OSTI]

    Bereau, Tristan; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-01-01

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum---in contrast to both atomistic simulations and the alternative PLUM force field. Even tho...

  6. Folding and Function of Proteorhodopsins in Photoenergy Transducing Membranes

    SciTech Connect (OSTI)

    Spudich, John L

    2012-08-10

    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 world’s 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.

  7. Exploring the protein folding dynamics of beta3s with two-dimensional ultraviolet (2DUV) spectroscopy

    E-Print Network [OSTI]

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

    2014-01-01

    Wang* Exploring the Protein Folding Dynamics of Beta3s withExploring the Protein Folding Dynamics of Beta3s with Two-echo signals to monitor the protein folding pro- cess of the

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

    E-Print Network [OSTI]

    Sanchez, Katheryn Marie

    2010-01-01

    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

  9. Chaperone networks: Tipping the balance in protein folding diseases Cindy Voisine, Jesper Sndergaard Pedersen, Richard I. Morimoto

    E-Print Network [OSTI]

    Morimoto, Richard

    Review Chaperone networks: Tipping the balance in protein folding diseases Cindy Voisine, Jesper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Molecular chaperones and protein folding quality control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 C. elegans models of diseases of protein folding

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

    E-Print Network [OSTI]

    Zhu, L; Kaback, HR; Dalbey, RE

    2013-01-01

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

  11. Topological crossovers in the forced folding of self-avoiding matter

    E-Print Network [OSTI]

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

    2009-07-25

    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.

  12. Conformational Temperature Characterizing the Folding of a Protein

    E-Print Network [OSTI]

    Naoko Nakagawa

    2013-02-12

    The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for inherent structures are introduced and from these quantities a conformational temperature is defined. The conformational temperature follows the time evolution of a slow relaxation process and reaches the bath temperature when the system is equilibrated. We show that the nonequilibrium system is described by two temperatures, one for fast vibration and the other for slow configurational relaxation, while the equilibrium system is by one temperature. The proposed formalism is applicable widely for the systems with many metastable states.

  13. Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding

    SciTech Connect (OSTI)

    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)

    1996-12-01

    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.}

  14. Folding model calculations for 6He+12C Elastic Scattering

    E-Print Network [OSTI]

    Awad A. Ibraheem

    2015-11-02

    In the framework of the double folding model, we used the {\\alpha}+2n and di-triton configurations for the nuclear matter density of the 6He nucleus to generate the real part of the optical potential for the system 6He+12C. As an alternative, we also use the high energy approximation to generate the optical potential for the same system. The derived potentials are employed to analyze the elastic scattering differential cross section at energies of 38.3, 41.6 and 82.3 MeV/nucleon. For the imaginary part of the potential we adopt the squared Woods-Saxon form. The obtained results are compared with the corresponding measured data as well as with available results in literature. The calculated total reaction cross sections are investigated and compared with the optical limit Glauber model description.

  15. Folding model calculations for 6He+12C Elastic Scattering

    E-Print Network [OSTI]

    Ibraheem, Awad A

    2015-01-01

    In the framework of the double folding model, we used the {\\alpha}+2n and di-triton configurations for the nuclear matter density of the 6He nucleus to generate the real part of the optical potential for the system 6He+12C. As an alternative, we also use the high energy approximation to generate the optical potential for the same system. The derived potentials are employed to analyze the elastic scattering differential cross section at energies of 38.3, 41.6 and 82.3 MeV/nucleon. For the imaginary part of the potential we adopt the squared Woods-Saxon form. The obtained results are compared with the corresponding measured data as well as with available results in literature. The calculated total reaction cross sections are investigated and compared with the optical limit Glauber model description.

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

    E-Print Network [OSTI]

    Noel, Jeffrey Kenneth

    2012-01-01

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

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

    SciTech Connect (OSTI)

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

    2003-05-28

    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.

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

    E-Print Network [OSTI]

    Coluzza, Ivan

    2014-01-01

    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 ...

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

    E-Print Network [OSTI]

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

    2008-08-24

    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.

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

    SciTech Connect (OSTI)

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

    2006-02-17

    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.

  1. time algorithm for d-dimensional protein folding in the HP-model

    E-Print Network [OSTI]

    Istrail, Sorin

    A 2O(n 1-1 d log n) time algorithm for d-dimensional protein folding in the HP-model Bin Fu Wei Wang Abstract The protein folding problem in the HP-model is NP-hard in both 2D and 3D [4, 6 structure. By studying how proteins fold, their functions can be better understood. The study of protein

  2. Geometric, magnetic and electronic properties of folded graphene nanoribbons

    E-Print Network [OSTI]

    Chang, Shen-Lin; Yang, Po-Hua; Lin, Ming-Fa

    2015-01-01

    Geometric and electronic properties of folded graphene nanoribbons (FGNRs) are investigated by first-principles calculations. These properties are mainly dominated by the competition or cooperation among stacking, curvature and edge effects. For the zigzag FGNRs, the more stable structures are revealed to be AB stackings, while for the armchair types, AA" stackings are more stable. The interlayer interactions and hybridization of four orbitals lead to smaller energy gaps, anti-crossing bands, and more band-edge states. Specifically, the broken mirror symmetry in the odd-AB stacked zigzag FGNRs is responsible for the spin-up and spin-down splitting subbands. All FGNRs are direct-gap semiconductors except that the edge-edge interactions cause the even-AA stacked zigzag FGNRs to exhibit a pair of metallic linear bands. The width-dependent energy gaps in the armchair FGNRs can be classified into six groups. Furthermore, there exist rich features in density of states, including the form, number, intensity and ener...

  3. Effects of vocal fold epithelium removal on vibration in an excised human larynx model

    E-Print Network [OSTI]

    Tse, JR; Zhang, Z; Long, JL

    2015-01-01

    theory of vocal fold vibration,” in Speech Science: Recentclosure with in-phase vibration along the anterior-posteriorepithelium removal on vibration in an excised human larynx

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

    E-Print Network [OSTI]

    Elber, Ron

    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

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

    E-Print Network [OSTI]

    Dai, Yang

    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

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    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

  7. Entropic Folding Pathway of Human Epidermal Growth Factor Explored by Disulfide Scrambling and Amplified Collective Motion Simulations,

    E-Print Network [OSTI]

    Wriggers, Willy

    a predominantly entropic folding pathway governed by the disorder of three functional loop regions. Although EGF

  8. Enhancement of Chaperone-Mediated Protein Folding Through Substrate Protein Interactions with the Groel C-Termini 

    E-Print Network [OSTI]

    Weaver, Jeremy Scott

    2015-04-28

    aggregation is the basis of many neurodegenerative diseases, including Alzheimer’s, Parkinson’s, and Creutzfeldt–Jakob disease [115,117-119]. 9 Although Alzheimer’s and cystic fibrosis are very different pathologically, both of these diseases, as well... Folding............................................................................... 1 Troubled Folding and Protein Folding Diseases ................................................. 6 GroEL: the Essential Folding Machine...

  9. 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]

    Wirmer, Julia

    2005-01-01

    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 ...

  10. Eective detection of remote homologues by searching in sequence dataset of a protein domain fold

    E-Print Network [OSTI]

    Srinivasan, N.

    E¡ective detection of remote homologues by searching in sequence dataset of a protein domain fold S in protein sequence databases to detect evolutionary relationships. We describe here a sensitive protocol to a fold. We have assessed this protocol by exploring the relationships we detect among sequences known

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

    E-Print Network [OSTI]

    Bigelow, Stephen

    Topological Aspects of DNA Function and Protein Folding 523 Knotting pathways in proteins Joanna I Road, Santa Barbara, CA 93106, U.S.A. Abstract Most proteins, in order to perform their biological function, have to fold to a compact native state. The increasing number of knotted and slipknotted proteins

  12. Interplay between faulting and base level in the development of Himalayan frontal fold topography

    E-Print Network [OSTI]

    Interplay between faulting and base level in the development of Himalayan frontal fold topography] Fold topography preserves a potentially accessible record of the structure and evolution of an underlying thrust fault system, provided we understand the factors that shape that topography. Here we

  13. The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of

    E-Print Network [OSTI]

    Komives, Elizabeth A.

    The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding there are simple relations for the experimental observables: folding free-energy (DGwater) and the cooperativity of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction

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

    E-Print Network [OSTI]

    Nora Molkenthin; Shuangwei Hu; Antti J. Niemi

    2010-09-06

    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.

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

    SciTech Connect (OSTI)

    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

    1997-06-01

    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.

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

    E-Print Network [OSTI]

    Berry, R. Stephen

    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

  17. Single-molecule studies highlight conformational heterogeneity in the early folding steps of a

    E-Print Network [OSTI]

    Scherer, Norbert F.

    of Bacillus subtilis RNase P RNA is investigated by single-molecule fluorescence reso- nance energy transfer of the Mg2 -dependent single-molecule FRET efficiency reveals two previously undetermined folding of intermediates with different degrees of kinetic isolation and that folding occurs under kinetic control

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

    E-Print Network [OSTI]

    Linial, Nathan "Nati"

    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

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

    E-Print Network [OSTI]

    Gelfond, Michael

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

  20. The Thermodynamics and Kinetics of Protein Folding: A Lattice Model Analysis of Multiple Pathways with Intermediates

    E-Print Network [OSTI]

    Dinner, Aaron

    The Thermodynamics and Kinetics of Protein Folding: A Lattice Model Analysis of Multiple Pathways; In Final Form: May 5, 1999 The kinetics and thermodynamics of folding of a representative sequence of a 125-residue protein model subject to Monte Carlo dynamics on a simple cubic lattice were investigated

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

    E-Print Network [OSTI]

    Nerukh, Dmitry

    Controlling protein molecular dynamics: How to accelerate folding while preserving the native state state of the protein and at the same time, reduce the folding time in the simulation. We investigate 2008; accepted 14 October 2008; published online 11 December 2008 The dynamics of peptides and proteins

  2. 2780 IEEE SENSORS JOURNAL, VOL. 11, NO. 11, NOVEMBER 2011 Folded MEMS Pyramid Inertial Measurement Unit

    E-Print Network [OSTI]

    Chen, Zhongping

    2780 IEEE SENSORS JOURNAL, VOL. 11, NO. 11, NOVEMBER 2011 Folded MEMS Pyramid Inertial Measurement. A prototype of the folded MEMS pyramid IMU with co-fabricated iner- tial sensors, electrical interconnects-on-insulator (SOI) backbone with in-situ fabricated high-aspect-ratio sensors. A planar multi- sensor unit

  3. The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

    E-Print Network [OSTI]

    Michael C. Prentiss; David J. Wales; Peter G. Wolynes

    2010-07-02

    The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.

  4. View Dependence of 3D Recovery from Folded Pictures and Warped 3D Faces

    E-Print Network [OSTI]

    Cavanagh, Patrick

    View Dependence of 3D Recovery from Folded Pictures and Warped 3D Faces Patrick Cavanagh Department vertical lines through the nose and the eyes. When this folded picture is tilted back and forth, the same is true, over a more restricted range of angles, as we move in front of a picture of an object

  5. Mechanisms of active folding of the landscape (southern Tian Shan, China)

    E-Print Network [OSTI]

    Hubert-Ferrari, Aurélia

    ; accepted 28 November 2006; published 29 March 2007. [1] We explore the kinematic mechanisms of active largeMechanisms of active folding of the landscape (southern Tian Shan, China) Aure´lia Hubert-Ferrari,1-scale folding, based on analysis of two adjacent major anticlines in Tian Shan (central Asia) that share

  6. Investigation of routes and funnels in protein folding by free energy functional methods

    E-Print Network [OSTI]

    Plotkin, Steven S.

    Investigation of routes and funnels in protein folding by free energy functional methods Steven S, and approved March 20, 2000 (received for review December 17, 1999) We use a free energy functional theory the free energy barrier to folding. Correlating stronger contact energies with entropically likely contacts

  7. Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

    E-Print Network [OSTI]

    Ritort, Felix

    Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies D. Collin1 to thermodynamic free-energy differences. They have been shown to be applicable to single- molecule force measurements6 and have already provided infor- mation on the folding free energy of a RNA hairpin7,8 . Here we

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

    E-Print Network [OSTI]

    Kavraki, Lydia E.

    Low-Dimensional Free Energy Landscapes of Protein Folding Reactions by Nonlinear Dimensionality reaction has long been a controversial issue, even for the "simple" case where one single free energy dynamics simulations. The folding free energy landscape projected on the coordinates extracted from

  9. Late Cenozoic partitioning of oblique plate convergence in the Zagros fold-and-thrust belt (Iran)

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Late Cenozoic partitioning of oblique plate convergence in the Zagros fold-and-thrust belt (Iran 2 May 2006. [1] The NW trending Zagros fold-and-thrust belt is affected by two major dextral faults operating at the rear of the belt has become partitioned along the newly formed Main Recent Fault

  10. EDGE TESSELLATIONS AND THE STAMP FOLDING MATTHEW KIRBY AND RON UMBLE

    E-Print Network [OSTI]

    Umble, Ron

    ." How many ways can one con...gure the perforation lines on a sheet of postage stamps so that it folds that perforation lines in a sheet of postage stamps that folds into a stack of single stamps are lines of symmetry

  11. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect (OSTI)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

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

    E-Print Network [OSTI]

    Anders Irbäck; Carsten Peterson; Frank Potthast; Ola Sommelius

    1996-10-10

    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.

  13. Two-state protein-like folding of a homopolymer chain

    E-Print Network [OSTI]

    Mark P. Taylor; Wolfgang Paul; Kurt Binder

    2010-05-27

    Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple flexible homopolymer. Wang-Landau sampling is used to construct the 1D density of states for square-well chains of length 128. Analysis within both the micro-canonical and canonical ensembles shows that, for a chain with sufficiently short-range interactions, the usual polymer collapse transition is preempted by a direct freezing or "folding" transition. A 2D free-energy landscape, built via subsequent multi-canonical sampling, reveals a dominant folding pathway over a single free-energy barrier. This barrier separates a high entropy ensemble of unfolded states from a low entropy set of crystallite states and the transition proceeds via the formation of a transition-state folding nucleus. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to the thermodynamics of two-state protein folding. The model chain satisfies the van't Hoff calorimetric criterion for two-state folding and an Arrhenius analysis of the folding/unfolding free energy barrier yields a Chevron plot characteristic of small proteins.

  14. A Survey of lamba Repressor Fragments from Two-State to to Downhill Folding

    SciTech Connect (OSTI)

    Liu, F.; Gao, Y; Gruebele, M

    2010-01-01

    We survey the two-state to downhill folding transition by examining 20 {lambda}{sub 6-85}* mutants that cover a wide range of stabilities and folding rates. We investigated four new {lambda}{sub 6-85}* mutants designed to fold especially rapidly. Two were engineered using the core remodeling of Lim and Sauer, and two were engineered using Ferreiro et al.'s frustratometer. These proteins have probe-dependent melting temperatures as high as 80 C and exhibit a fast molecular phase with the characteristic temperature dependence of the amplitude expected for downhill folding. The survey reveals a correlation between melting temperature and downhill folding previously observed for the {beta}-sheet protein WW domain. A simple model explains this correlation and predicts the melting temperature at which downhill folding becomes possible. An X-ray crystal structure with a 1.64-{angstrom} resolution of a fast-folding mutant fragment shows regions of enhanced rigidity compared to the full wild-type protein.

  15. Comparison of amino acid occurrence and composition for predicting protein folds

    E-Print Network [OSTI]

    Y-h. Taguchi; M. Michael Gromiha

    2007-05-10

    Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein 3D structure prediction. Results: In this work, we propose a method based on linear discriminant analysis (LDA) for recognizing proteins belonging to 30 different folds using the occurrence of amino acid residues in a set of 1612 proteins. The present method could discriminate the globular proteins from 30 major folding types with the sensitivity of 37%, which is comparable to or better than other methods in the literature. A web server has been developed for predicting the folding type of the protein from amino acid sequence and it is available at http://granular.com/PROLDA/. Conclusions:Linear discriminant analysis based on amino acid occurrence could successfully recognize protein folds. The present method has several advantages such as, (i) it directly predicts the folding type of a protein without performing pair-wise comparisons, (ii) it can discriminate folds among large number of proteins and (iii) it is very fast to obtain the results. This is a simple method, which can be easily incorporated in any other structure prediction algorithms.

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

    SciTech Connect (OSTI)

    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)

    2001-05-21

    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.

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

    E-Print Network [OSTI]

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

    2009-06-24

    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.

  18. "Control of protein folding and misfolding in ionic liquid media, and a conjecture on early earth biology".

    E-Print Network [OSTI]

    Angell, C. Austen

    "Control of protein folding and misfolding in ionic liquid media, and a conjecture on early earth, such as protein folding and fibrillization, are reproduced (with little change from biological behavior

  19. Neural network analysis of sparse datasets ?? an application to the fracture system in folds of the Lisburne Formation, northeastern Alaska 

    E-Print Network [OSTI]

    Bui, Thang Dinh

    2005-11-01

    with conventional statistical analysis, were used to examine the effects of folding, bed thickness, structural position, and lithology on the fracture properties distributions in the Lisburne Formation, folded and exposed in the northeastern Brooks Range of Alaska...

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

    E-Print Network [OSTI]

    Caravella, Justin Andrew, 1974-

    2002-01-01

    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 ...

  1. Structure and evolution of the active fold and thrust belt of southwestern Taiwan using GPS geodesy 

    E-Print Network [OSTI]

    Hickman, John Bibb

    1999-01-01

    Using GPS and published geologic data, we have crographics. investigated the current deformation rates and local kinematic relationships for the southern region of the Taiwan fold-thrust belt. The GPS measurements suggest complex motions across...

  2. Impact of human vocal fold vibratory asymmetries on acoustic characteristics of sustained vowel phonation

    E-Print Network [OSTI]

    Mehta, Daryush (Daryush Dinyar)

    2010-01-01

    Clinical voice specialists make critical diagnostic, medical, therapeutic, and surgical decisions by coupling visual observations of vocal fold tissue motion with auditory-perceptual assessments of voice quality. The details ...

  3. STABILITY CONDITIONS ON DERIVED CATEGORIES OF CY 3-FOLDS (AFTER KONTSEVICHSOIBELMAN)

    E-Print Network [OSTI]

    Hacking, Paul

    STABILITY CONDITIONS ON DERIVED CATEGORIES OF CY 3-FOLDS (AFTER KONTSEVICH­SOIBELMAN) PAUL HACKING is OC(-1) OC(-1). 1 #12;2 PAUL HACKING One can contract C to get (locally) xy + zt = 0 and then flop

  4. Theoretical Studies on Proteins to Reveal the Mechanism of Their Folding and Biological Functions 

    E-Print Network [OSTI]

    Shao, Qiang

    2011-02-22

    The folding mechanism of several ?-structures (e.g., ?-hairpins and ?-sheets) was studied using newly developed enhanced sampling methods along with MD simulations in all implicit solvent environments. The influence of different implicit solvent...

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

    E-Print Network [OSTI]

    Waldispühl, Jerome

    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 ...

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

    SciTech Connect (OSTI)

    Bitto, E.

    2002-01-01

    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.

  7. 2D IR spectroscopy and computational modeling : application to protein folding and binding

    E-Print Network [OSTI]

    Ganim, Ziad

    2010-01-01

    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. ...

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

    E-Print Network [OSTI]

    Jeetain Mittal; Robert B. Best

    2009-02-26

    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.

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

    E-Print Network [OSTI]

    Dulin, Jennifer Natalie

    2013-02-22

    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...

  10. Site specific mutagenesis study of the protein folding process of luciferase 

    E-Print Network [OSTI]

    Wei, Ke

    1990-01-01

    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...

  11. Scale dependencies in structural analysis as illustrated by chevron folds along the Beartooth Front, Wyoming 

    E-Print Network [OSTI]

    Cook, Robert Annan

    1972-01-01

    of fracture sets found in folded layered rocks and their relationship with fold axis (modified from Stearns, 1968) ~ . 30 Kinking of laminae structures along set 4, fractures in shale . . . . . . . . . . . 31 lla, b, and c. Photographs of typical arcuate... are also under this category. The ductility is assessed by the intensity of layer descrip- tion from fractures and faults. The materials previously mentioned are nearly free of such structures. This ab- sence is not only true for the center...

  12. Mechanical characteristics of folds in Upper Cretaceous strata in the Disturbed Belt of northwestern Montana 

    E-Print Network [OSTI]

    Gilbert, Pat Kader

    1974-01-01

    MECHANICAL CHARACTERISTICS OF FOLDS IN UPPER CRETACEOUS STRATA IN THE DISTURBED BELT OF NORTHWESTERN MONTANA A Thesis by PAT KADER GILBERT Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements... for the degree of MASTER OF SCIENCE May 1974 Major Subject: Geology MECHANICAL CHARACTERISTICS OF FOLDS IN UPPER CRETACEOUS STRATA IN THE DISTURBED BELT OF NORTHWESTERN MONTANA A Thesis by PAT KADER GILBERT Approved as to style and content by: (Chairman...

  13. 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]

    Schuler, Ben

    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

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

    E-Print Network [OSTI]

    2014-01-01

    THE JOURNAL OF CHEMICAL PHYSICS 140, 204905 (2014) Precursory signatures of protein folding of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid

  15. The Major Outer Membrane Protein of Fusobacterium nucleatum (FomA) Folds and Inserts into Lipid Bilayers

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    The Major Outer Membrane Protein of Fusobacterium nucleatum (FomA) Folds and Inserts into Lipid-5020 Bergen, Norway Membrane protein insertion and folding was studied for the major outer membrane observation of parallel membrane insertion and folding pathways of a b-barrel membrane protein from

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

    E-Print Network [OSTI]

    Bedwell, David M.

    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

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

    E-Print Network [OSTI]

    Pedicini, Marco

    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

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

    E-Print Network [OSTI]

    Maclin, Rich

    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

  19. PHYSICAL REVIEW E VOLUME 52, NUMBER 3 Collective aspects of protein folding illustrated by a toy model

    E-Print Network [OSTI]

    Stillinger, Frank

    PHYSICAL REVIEW E VOLUME 52, NUMBER 3 Collective aspects of protein folding illustrated by a toy to illuminate some nonlocal, or collective, as- pects of protein folding phenomena. The model is two dimensional variables generated by the primary amino acid structure may be required for fully effective protein folding

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

    E-Print Network [OSTI]

    Wu, Jianzhong

    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

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

    E-Print Network [OSTI]

    Istrail, Sorin

    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

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

    E-Print Network [OSTI]

    Michalet, Xavier

    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

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

    E-Print Network [OSTI]

    Mirny, Leonid

    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

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

    E-Print Network [OSTI]

    Dai, Yang

    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

  5. Folding and Insertion of the Outer Membrane Protein OmpA Is Assisted by the Chaperone Skp and by Lipopolysaccharide*

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    Folding and Insertion of the Outer Membrane Protein OmpA Is Assisted by the Chaperone Skp have studied the folding pathway of a -barrel membrane protein using outer membrane protein A (Omp membrane proteins of bacteria. We investigated how Skp facilitates the insertion and folding of com

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

    E-Print Network [OSTI]

    Stepney, Susan

    Folding Protein-Like Structures with Open L-systems Gemma B. Danks, Susan Stepney, and Leo S. D501@york.ac.uk Abstract. Proteins, under native conditions, fold to specific 3D struc- tures according protein is a strong indicator of its function in the cell. The mechanisms involved in protein folding

  7. Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better Than 86% of Optimal

    E-Print Network [OSTI]

    Istrail, Sorin

    Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction This paper considers the protein structure prediction problem for lattice and off-lattice protein folding tools for reasoning about protein folding in unrestricted continuous space through anal- ogy. This paper

  8. Heavy oil reservoirs in the Tulare Fold Belt, Cymric-McKittrick fields, Kern County, California

    SciTech Connect (OSTI)

    Farley, T. (Chevron U.S.A., Bakersfield, CA (USA))

    1990-05-01

    The Tulare fold belt is a series of asymmetric, generally northeast-verging anticlines and synclines in the Pliocene-Pleistocene Tulare Formation that trend northwestward through the Cymric-McKittrick fields. Anticlines within the deformed belt generally originated as fault propagation folds above decollements, the most important of which is the regional decollement on top of the Amnicola sand, the basal Tulare unit. The Amnicola decollement is the northeast subsurface extension of the McKittrick thrust, a low-angle fault that has displaced the Miocene Antelope shale over the Pliocene San Joaquin Formation and locally over the Tulare Formation. The Amnicola decollement is itself deformed by folding related to a younger, deeper decollement near the base of the San Joaquin Formation that merges westward with the Amnicola decollement and defines a zone of faulting associated with the McKittrick thrust Heavy oil reservoirs in the Tulare Formation are currently undergoing active development by thermal recovery techniques. In general, the geometry of heavy oil reservoirs is determined by location within the Tulare fold belt combined with the position of a subhorizontal fluid level trap that forms the updip limit of fluid-saturated rock Reservoir geometry is complicated by complex local structure, discontinuous stratigraphy, and partial depletion of heavy oil reservoirs by fluid withdrawal due to gravity drainage. Proper resolution of fold geometry, fault geometry, and position of the fluid level trap is crucial to the design and monitoring of thermal recovery projects within the Tulare fold belt.

  9. Three-dimensional folding of pre-strained polymer sheets via absorption of laser light

    SciTech Connect (OSTI)

    Liu, Ying; Genzer, Jan, E-mail: mjescuti@ncsu.edu, E-mail: mddickey@ncsu.edu, E-mail: jan-genzer@ncsu.edu; Dickey, Michael D., E-mail: mjescuti@ncsu.edu, E-mail: mddickey@ncsu.edu, E-mail: jan-genzer@ncsu.edu [Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina 27695 (United States); Miskiewicz, Matthew; Escuti, Michael J., E-mail: mjescuti@ncsu.edu, E-mail: mddickey@ncsu.edu, E-mail: jan-genzer@ncsu.edu [Department of Electrical and Computer Engineering, North Carolina State University, 2410 Campus Shore Drive, Raleigh, North Carolina 27695 (United States)

    2014-05-28

    Patterned light from a laser can induce rapid self-folding of pre-strained polymer sheets. Black ink coated on the sheet absorbs the light, which converts the photon energy into thermal energy that heats the sheet locally; the temperature of the sheet is highest at the surface where the light impinges on the sheet and decreases through the sheet thickness. The gradient of temperature induces a gradient of strain relaxation through the depth of the sheet, which causes folding within seconds of irradiation. The pattern of laser light that irradiates the compositionally homogeneous two-dimensional (2D) substrate dictates the resulting three-dimensional (3D) shape. Unlike most approaches to self-folding, the methodology described here requires no patterning of pre-defined hinges. It opens up the possibility of using a patterning technique that is inherently 2D to form 3D shapes. The use of lasers also enables systematic control of key process parameters such as power, intensity, and the pattern of light (i.e., beam width and shape). The rate of folding and folding angle measured with respect to these parameters provide an indirect quantification of heat loss in the sample and thereby identify the threshold power and power intensity that must be delivered to the hinge for folding to occur.

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

    E-Print Network [OSTI]

    Nan-yow Chen

    2006-07-17

    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.

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

    SciTech Connect (OSTI)

    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)

    2014-05-28

    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.

  12. Characterization of fold defects in AZ91D and AE42 magnesium alloy permanent mold castings

    SciTech Connect (OSTI)

    Bichler, L. [Centre for Near-net-shape Processing of Materials, Ryerson University, 101 Gerrard St. E., Toronto, M5B 2K3 (Canada); Ravindran, C., E-mail: rravindr@ryerson.ca [Centre for Near-net-shape Processing of Materials, Ryerson University, 101 Gerrard St. E., Toronto, M5B 2K3 (Canada)

    2010-03-15

    Casting premium-quality magnesium alloy components for aerospace and automotive applications poses unique challenges. Magnesium alloys are known to freeze rapidly prior to filling a casting cavity, resulting in misruns and cold shuts. In addition, melt oxidation, solute segregation and turbulent metal flow during casting contribute to the formation of fold defects. In this research, formation of fold defects in AZ91D and AE42 magnesium alloys cast via the permanent mold casting process was investigated. Computer simulations of the casting process predicted the development of a turbulent metal flow in a critical casting region with abrupt geometrical transitions. SEM and light optical microscopy examinations revealed the presence of folds in this region for both alloys. However, each alloy exhibited a unique mechanism responsible for fold formation. In the AZ91D alloy, melt oxidation and velocity gradients in the critical casting region prevented fusion of merging metal front streams. In the AE42 alloy, limited solubility of rare-earth intermetallic compounds in the {alpha}-Mg phase resulted in segregation of Al{sub 2}RE particles at the leading edge of a metal front and created microstructural inhomogeneity across the fold.

  13. Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein

    SciTech Connect (OSTI)

    Wu, Ying; Kondrashkina, Elena; Kayatekin, Can; Matthews, C. Robert; Bilsel, Osman (NWU); (UMASS, Amherst)

    2008-09-29

    The earliest kinetic folding events for ({beta}{alpha}){sub 8} barrels reflect the appearance of off-pathway intermediates. Continuous-flow microchannel mixing methods interfaced to small-angle x-ray scattering (SAXS), circular dichroism (CD), time-resolved Foerster resonant energy transfer (trFRET), and time-resolved fluorescence anisotropy (trFLAN) have been used to directly monitor global and specific dimensional properties of the partially folded state in the microsecond time range for a representative ({beta}{alpha}){sub 8} barrel protein. Within 150 {micro}s, the {alpha}-subunit of Trp synthase ({alpha}TS) experiences a global collapse and the partial formation of secondary structure. The time resolution of the folding reaction was enhanced with trFRET and trFLAN to show that, within 30 {micro}s, a distinct and autonomous partially collapsed structure has already formed in the N-terminal and central regions but not in the C-terminal region. A distance distribution analysis of the trFRET data confirmed the presence of a heterogeneous ensemble that persists for several hundreds of microseconds. Ready access to locally folded, stable substructures may be a hallmark of repeat-module proteins and the source of early kinetic traps in these very common motifs. Their folding free-energy landscapes should be elaborated to capture this source of frustration.

  14. Erratum: Effects of the arctic (E22?G) mutation on amyloid ?-protein folding: Discrete molecular dynamics study (Journal of the American Chemical Society (2008) 130 (17413-17422) DOI: 10.1021/ja804984h)

    E-Print Network [OSTI]

    Lam, AR; Teplow, DB; Stanley, HE; Urbanc, B

    2011-01-01

    play key roles in protein folding and assembly. In the DMDMutation on Amyloid ?-Protein Folding: Discrete Molecular2006, 1, 322–328. Amyloid ?-Protein Folding implicit solvent

  15. Geometry of wrapped M5-branes in Calabi-Yau 2-folds

    SciTech Connect (OSTI)

    Fayyazuddin, Ansar; Husain, Tasneem Zehra; Pappa, Ioanna

    2006-06-15

    We study the geometry of M5-branes wrapping a 2-cycle which is special Lagrangian with respect to a specific complex structure in a Calabi-Yau 2-fold. Using methods recently applied to the 3-fold case, we are again able to find a characterization of the geometry, in terms of a nonintegrable almost complex structure and a (2,0) form. This time, however, due to the hyper-Kaehler nature of the underlying 2-fold, we also have the freedom of choosing a different almost complex structure with respect to which the wrapped 2-cycle is holomorphic. We show that this latter almost complex structure is integrable. We then relate our geometry to previously found geometries of M5-branes wrapping holomorphic cycles and go further to prove some previously unknown results for M5-branes on holomorphic cycles.

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

    E-Print Network [OSTI]

    Hinczewski, Michael; Dzubiella, Joachim; Netz, Roland R

    2010-01-01

    The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We analyze extensive simulation data of an alpha-helix in explicit water solvent as it stochastically folds and unfolds. The free energy profiles for different RCs exhibit significant variation, some having an activation barrier, others not. We show that this variation has little effect on the predicted folding kinetics if the diffusivity profiles are properly taken into account. This kinetic quasi-universality is rationalized by an RC rescaling, which, due to the reparameterization invariance of the Fokker-Planck equation, allows the combination of free energy and diffusivity effects into a single function, the rescaled free energy profile. This rescaled free energy indeed shows less variation among different RCs than the bare free energy and diffusivity profiles separately d...

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

    SciTech Connect (OSTI)

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

    1994-12-31

    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.

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

    SciTech Connect (OSTI)

    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

    2008-02-22

    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.

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

    SciTech Connect (OSTI)

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

    1996-12-31

    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.

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

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2013-01-01

    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.

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

    SciTech Connect (OSTI)

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

    2007-01-01

    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.

  2. RNA Folding

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMassR&D100 Winners * Impacts on Global TechnologyProceeding SignPriceRL's3,16, Rev22,;3

  3. FOLDING AND DEPLOYMENT OF ULTRA-THIN COMPOSITE H.M.Y.C. Mallikarachchi(1)

    E-Print Network [OSTI]

    Pellegrino, Sergio

    @caltech.edu ABSTRACT This paper presents an optimization study of thin-walled tape spring hinges made from carbon fiber of two-ply ±45 plain weave carbon fiber reinforced polymer (CFRP) material. The focus of the present reinforced plastic. Previously developed numerical simulation tech- niques to analyze the folding

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

    E-Print Network [OSTI]

    Chan, Hue Sun

    ¨ 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

  5. Nylon 6 Crystal Structures, Folds, and Lamellae from Theory Youyong Li and William A. Goddard III*

    E-Print Network [OSTI]

    Goddard III, William A.

    material with applications ranging from carpet and automotive parts to intimate apparel.1 In addition force field developed by Dasgupta et al.3 to carry out theoreti- cal calculations (quantum mechanics, molecular dynam- ics, and molecular mechanics) to determine the optimum packing and fold structures of nylon

  6. Translation efficiency is determined by both codon bias and folding energy

    E-Print Network [OSTI]

    Ruppin, Eytan

    Translation efficiency is determined by both codon bias and folding energy Tamir Tullera,b,1 studies have suggested that codon bias is the most important determinant of translation efficiency a genome-scale study aiming at dissecting the determi- nants of translation efficiency

  7. Statistical mechanics of a correlated energy landscape model for protein folding funnels

    E-Print Network [OSTI]

    Plotkin, Steven S.

    Statistical mechanics of a correlated energy landscape model for protein folding funnels Steven S correlations in conjunction with the a priori specification of the existence of a particularly low energy state provide a method of introducing the aspect of minimal frustration to the energy landscapes of random

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

    E-Print Network [OSTI]

    Pal, Debnath

    Estimates of the Loss of Main-Chain Conformational Entropy of Different Residues on Protein Folding of the main-chain (torsion angles, and ) conformational entropy by taking its side-chain into account. The analysis shows that the main-chain component of the total conformational entropy loss for a residue

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

    E-Print Network [OSTI]

    Dimakopoulos, Vassilios

    Task-parallel global optimization with application to protein folding C. Voglis, P. E. Hadjidoukas, Greece, {voglis,phadjido,dimako,lagaris}@cs.uoi.gr D. G. Papageorgiou Department of Materials Science a software framework for high perfor- mance numerical global optimization. At the core, a run- time library

  10. Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide into a

    E-Print Network [OSTI]

    Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide- residue Ebola virus fusion peptide into a membrane bilayer. We applied a multi-resolution computational viruses, the filoviruses contain a highly compact genome, consisting of only seven encoded proteins

  11. Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field

    E-Print Network [OSTI]

    Beccara, Silvio a; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro

    2013-01-01

    We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native beta-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappr...

  12. COMMUNICATION Proteins with Class a/b Fold Have High-level

    E-Print Network [OSTI]

    Gough, Julian

    COMMUNICATION Proteins with Class a/b Fold Have High-level Participation in Fusion Events Sujun Hua association of the component proteins. Here, we took a new approach to the analysis of the structural features of the proteins involved in fusion events. An exhaustive survey of fusion events within 30 completely sequenced

  13. 10D to 4D Euclidean Supergravity over a Calabi-Yau three-fold

    E-Print Network [OSTI]

    Sabra, Wafic

    2015-01-01

    We dimensionally reduce the bosonic sector of 10D Euclidean type IIA supergravity over a Calabi-Yau three-fold. The resulting theory describes the bosonic sector of 4D, N = 2 Euclidean supergravity coupled to vector- and hyper-multiplets.

  14. Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity

    E-Print Network [OSTI]

    Tristan Bereau; Michael Bachmann; Markus Deserno

    2011-07-01

    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.

  15. The chromosome folding problem: How to organize a 2 meter genome into a 20 micron nucleus?

    E-Print Network [OSTI]

    Poonen, Bjorn

    ;#12;#12;#12;Why study chromosome organization? #12;Human genome project-- now that we know our ATCGs, what do they mean? #12;Goal: Develop a parts list of functional elements in the human genome httpsThe chromosome folding problem: How to organize a 2 meter genome into a 20 micron nucleus? #12

  16. Buffed energy landscapes: Another solution to the kinetic paradoxes of protein folding

    E-Print Network [OSTI]

    Plotkin, Steven S.

    Buffed energy landscapes: Another solution to the kinetic paradoxes of protein folding Steven S, February 6, 2003 The energy landscapes of proteins have evolved to be different from most random structure that is stable at biological temperatures leads to energy landscapes having a single dominant

  17. Euler buckling-induced folding and rotation of red blood cells in an optical trap

    E-Print Network [OSTI]

    Sharma, Shobhona

    Euler buckling-induced folding and rotation of red blood cells in an optical trap A Ghosha 005, India Abstract. We investigate the physics of an optically-driven micromotor of biological origin. When a single, live red blood cell is placed in an optical trap, the normal biconcave disk shape

  18. The Hepatitis C Virus Internal Ribosome Entry Site Adopts an Ion-dependent Tertiary Fold

    E-Print Network [OSTI]

    Doudna, Jennifer A.

    The Hepatitis C Virus Internal Ribosome Entry Site Adopts an Ion-dependent Tertiary Fold Jeffrey S-0539, USA Hepatitis C virus (HCV) contains an internal ribosome entry site (IRES) located in the 5H entry site (IRES); hepatitis C virus (HCV); chemical and enzymatic probing*Corresponding author

  19. Familial Parkinson's Disease-associated L166P Mutation Disrupts DJ-1 Protein Folding and Function*

    E-Print Network [OSTI]

    Li, Lian

    Familial Parkinson's Disease-associated L166P Mutation Disrupts DJ-1 Protein Folding and Function by which loss-of-function mutations in DJ-1 lead to Par- kinson's disease. Parkinson's disease (PD)1 of this devastating disease. Recent evidence indi- cates that at least 10 distinct genetic loci, PARK1­PARK10

  20. Weak Temperature Dependence of the Free Energy Surface and Folding Pathways of Structured Peptides

    E-Print Network [OSTI]

    Caflisch, Amedeo

    Weak Temperature Dependence of the Free Energy Surface and Folding Pathways of Structured Peptides a thermodynamic description of minima and transi- tion states on the free energy surface, which is determined near equilibrium by counting popula- tions. The free energy surface, plotted as a function of two-order parameters