Sample records for folds grabens horst

  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 onYou are now leaving Energy.gov You are now leaving Energy.gov You are beingZealand Jump to: navigation, search OpenEIHesperia, California: EnergyHoloceneHonestHoosacHorseHorst and

  2. John Horst

    Broader source: Energy.gov [DOE]

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

  3. A New Approach to Component Testing Dr. Horst Brinkmeyer

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    of the entire electric/electronic system is done by the car manufacturers themselves. This job has become more, 70806 Kornwestheim horst.brinkmeyer@ibb-kwh.de Abstract Carefully tested electric/electronic components of electric/electronic systems in automotive environment has increased significantly in the last ten

  4. Volcanic rifting at Martian grabens Daniel Me`ge,1

    E-Print Network [OSTI]

    Mege, Daniel

    Volcanic rifting at Martian grabens Daniel Me`ge,1 Anthony C. Cook,2,3 Erwan Garel,4 Yves: Solar System Objects: Mars; 8121 Tectonophysics: Dynamics, convection currents and mantle plumes; 8010: Me`ge, D., A. C. Cook, E. Garel, Y. Lagabrielle, and M.-H. Cormier, Volcanic rifting at Martian

  5. Horst W. HamacherVorlesung, Lineare Optimierung, Sommersemester 2014 Page 1 6. Finiteness of Simplex Algorithm

    E-Print Network [OSTI]

    Krumke, Sven O.

    . Finiteness of Simplex Algorithm Finiteness of Bland's Rule 7. Revised Simplex Algorithm Horst W. Hamacher j with smallest index. · Choose the pivot row i such that B(i) is smallest. Then the simplexVorlesung, Lineare Optimierung, Sommersemester 2014 Page 3 Reduced Simplex Tableau Idea: Compute only a part of each

  6. Horst W. HamacherVorlesung, Lineare Optimierung, Sommersemester 2009 Page 1 15. Dual Simplex Algorithm

    E-Print Network [OSTI]

    Krumke, Sven O.

    Simplex Algorithm 16. Primal-Dual Simplex Algorithm Horst W. HamacherVorlesung, Lineare Optimierung, Sommersemester 2009 Page 2 Dual Simplex Algorithm Dual Simplex Given: Simplex tableau which is dual feasible If simplex tableau is also primal feasible: STOP - Tableau is optimal · Choose dual pivot column

  7. 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

    2013-07-01T23:59:59.000Z

    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 ...

  8. 3D numericalmodellingof grabeninteraction and linkage: a case studyof the Canyonlands grabens,

    E-Print Network [OSTI]

    Fossen, Haakon

    alongside each other with limited segment interaction; and (4) an abandoned graben segment in a system we understand fault growth in general and structurally complex hydrocarbon reservoirs in particular

  9. 3D numericalmodellingof grabeninteraction and linkage: a case studyof the Canyonlands grabens,

    E-Print Network [OSTI]

    Fossen, Haakon

    with limited segment interaction and (4) an abandoned graben segment in a sys- tem of multiple competing fault growth in general and structurally complex hydrocarbon reservoirs in particular (e.g., Morley

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

    E-Print Network [OSTI]

    Hurtado, José Miguel, 1974-

    2002-01-01T23:59:59.000Z

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

  11. Fluid-rock interactions in the Rhine Graben: A thermodynamic model of the hydrothermal alteration observed in deep drilling

    SciTech Connect (OSTI)

    Komninou, A.; Yardley, B.W.D. [Univ. of Leeds (United Kingdom)] [Univ. of Leeds (United Kingdom)

    1997-02-01T23:59:59.000Z

    Deep drilling at Soultz-sous-Forets, France, on the western flanks of the Rhine Graben, has penetrated Hercynian granite underlying Mesozoic sediments. Veins are present throughout the drilled granite, and there are flows of warm water localized in fractures within the granite. Detailed mineralogical study of core material from the research drillhole EPSI has been carried out in order to assess the alteration history of the Soultz granite, part of the crystalline basement of the Rhine Graben. The results of the study have been used, in conjunction with analyses of present-day fluids from deep drilling in the Rhine Graben reported in the literature, to model thermodynamically the alteration process, and in particular to evaluate if it is likely to be continuing today. Reaction-path calculations show that if deep basinal brines, such as are known from sediments of the central Rhine Graben, react with Hercynian granite, they will form different alteration assemblages depending on both the path that the fluid follows (e.g., descending through sediments or through granite) and the extent of preexisting alteration of the granite. The calculations suggest that fluid now sampled from granite in EPS-1 achieved its peak temperature, c. 200{degrees}C while within Permo-Triassic sandstone. The modeling also indicates that present-day fluids from the Rhine Graben system are capable of producing the vein quartz and possibly also the baryte veins, seen in the EPSI core. Much of the alteration present in the granite in the vicinity of veins and fractures may have been produced by a flow regime similar to that prevailing today. 48 refs., 15 figs., 4 tabs.

  12. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01T23:59:59.000Z

    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...

  13. Algorithmic folding complexity

    E-Print Network [OSTI]

    Cardinal, Jean

    2009-01-01T23:59:59.000Z

    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 ...

  14. ACCEPTED MANUSCRIPT Fold interaction and wavelength selection

    E-Print Network [OSTI]

    Kaus, Boris

    simulations the lateral growth of folds is studied, in particular with respect to fold segments interactions; folding modes; fold interactions; 3D folding; numerical modelling 1 Introduction Buckling or folding

  15. 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

  16. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17T23:59:59.000Z

    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.

  17. Protein folding and cosmology

    E-Print Network [OSTI]

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

    1997-06-04T23:59:59.000Z

    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.

  18. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12T23:59:59.000Z

    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.

  19. Ab initio RNA folding

    E-Print Network [OSTI]

    Tristan Cragnolini; Philippe Derreumaux; Samuela Pasquali

    2014-12-30T23:59:59.000Z

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  20. 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

  1. 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

  2. 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

  3. Petaflop Computing for Protein Folding

    E-Print Network [OSTI]

    Izaguirre, JesĂşs 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

  4. Protein folding in the ER.

    SciTech Connect (OSTI)

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

    1999-10-01T23:59:59.000Z

    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.

  5. Uncovering Allostery in a Uniquely Folded Metalloprotein /

    E-Print Network [OSTI]

    Baxter, Elizabeth Leigh

    2013-01-01T23:59:59.000Z

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

  6. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

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

    2010-07-18T23:59:59.000Z

    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.

  7. 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)

    2014-10-28T23:59:59.000Z

    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.

  8. Mesoscale Folding: A Physical Realization of an Abstract, 2D Lattice Model for Molecular Folding

    E-Print Network [OSTI]

    Prentiss, Mara

    . Protein Folding: Theoretical Studies of Thermodynamics and Dynamics. In Protein Folding; Creighton, T. E

  9. Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles, for Large-Scale Geologic Storage of CO2

    SciTech Connect (OSTI)

    Bruno, Michael

    2014-12-08T23:59:59.000Z

    Geomechanics Technologies has completed a detailed characterization study of the Wilmington Graben offshore Southern California area for large-scale CO2 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 CO2 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 CO2 storage in the area would represent higher risk than other similar size projects in the US and overseas.

  10. Fast events in protein folding

    SciTech Connect (OSTI)

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

    1996-04-01T23:59:59.000Z

    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.

  11. 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

  12. 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, ...

  13. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01T23:59:59.000Z

    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.

  14. A motion planning approach to protein folding

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

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

  15. A motion planning approach to protein folding 

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

    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 ...

  16. Biophysical characterization of protein folding and misfolding. 

    E-Print Network [OSTI]

    Schmittschmitt, Jason Peter

    2004-09-30T23:59:59.000Z

    The HPr proteins were characterized as folding by a two-state folding mechanism. Here, we present a comparison of the equilibrium and kinetic folding for the HPr protein from Bacillus subtilis, E coli and a key variant ...

  17. Search for: "protein folding" | DOE PAGES

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

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

  18. 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

  19. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

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

    2006-07-27T23:59:59.000Z

    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.

  20. 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

  1. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Horner, Geoffrey Ashworth

    2010-01-01T23:59:59.000Z

    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.

  3. 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

  4. 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

  5. Parametric analysis of RNA folding

    E-Print Network [OSTI]

    Hower, Valerie

    2009-01-01T23:59:59.000Z

    We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy model that are not determined experimentally. Our results indicate that variation of these specific parameters does not have a dramatic effect on the structures predicted by the free energy model. We additionally map a collection of known RNA secondary structures to the RNA polytope.

  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. 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

  8. 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

  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. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Snow, Christopher

    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

  11. 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

  12. 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 The protein folding and protein design problems are addressed, using coarse-grained models with only two types

  13. Introducing Protein Folding Using Simple Models

    E-Print Network [OSTI]

    D. Thirumalai; D. K. Klimov

    2001-01-04T23:59:59.000Z

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

  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. 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

  16. 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

  17. Structural and Energetic Heterogeneity in Protein Folding

    E-Print Network [OSTI]

    Steven S. Plotkin; Jose N. Onuchic

    2000-09-27T23:59:59.000Z

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

  18. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01T23:59:59.000Z

    Intermediates can accelerate protein folding. Proceedings ofunifying mechanism for protein folding? [Review]. Trends incoordinate for protein folding. Journal of Chemical Physics

  19. Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity

    E-Print Network [OSTI]

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

    2007-01-01T23:59:59.000Z

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

  20. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01T23:59:59.000Z

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

  1. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01T23:59:59.000Z

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

  2. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

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

    2010-05-25T23:59:59.000Z

    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.

  3. 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

  4. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1996-06-11T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Pratt, Vaughan

    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

  6. Mechanical Models of Fault-Related Folding

    SciTech Connect (OSTI)

    Johnson, A. M.

    2003-01-09T23:59:59.000Z

    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).

  7. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17T23:59:59.000Z

    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.

  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. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01T23:59:59.000Z

    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 ...

  15. Cooperativity and Contact Order in Protein Folding

    E-Print Network [OSTI]

    Marek Cieplak

    2004-01-11T23:59:59.000Z

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

  16. Self-folding with shape memory composites

    E-Print Network [OSTI]

    Felton, Samuel M.

    Origami-inspired manufacturing can produce complex structures and machines by folding two-dimensional composites into three-dimensional structures. This fabrication technique is potentially less expensive, faster, and ...

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

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-12-28T23:59:59.000Z

    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.

  18. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01T23:59:59.000Z

    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.

  19. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26T23:59:59.000Z

    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^{\

  20. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01T23:59:59.000Z

    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

  1. 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

  2. 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

  3. 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

  4. 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

  5. Protein Folding: A New Geometric Analysis

    E-Print Network [OSTI]

    Walter A. Simmons; Joel L. Weiner

    2008-09-11T23:59:59.000Z

    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.

  6. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01T23:59:59.000Z

    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,...

  7. What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

    E-Print Network [OSTI]

    Tawfik, Dan S.

    What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade not trading off, but instead promoting the acquisition of new activities. Indeed, computational analysis. It is often the case that activity and stability trade off.10,22 Many enzymes were, however, dramatically

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

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01T23:59:59.000Z

    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...

  9. Fast Gravitational Wave Radiometry using Data Folding

    E-Print Network [OSTI]

    Anirban Ain; Prathamesh Dalvi; Sanjit Mitra

    2015-04-07T23:59:59.000Z

    Gravitational Waves (GWs) from the early universe and unresolved astrophysical sources are expected to create a stochastic GW background (SGWB). The GW radiometer algorithm is well suited to probe such a background using data from ground based laser interferometric detectors. Radiometer analysis can be performed in different bases, e.g., isotropic, pixel or spherical harmonic. Each of these analyses possesses a common temporal symmetry which we exploit here to fold the whole dataset for every detector pair, typically a few hundred to a thousand days of data, to only one sidereal day, without any compromise in precision. We develop the algebra and a software pipeline needed to fold data, accounting for the effect of overlapping windows and non-stationary noise. We implement this on LIGO's fifth science run data and validate it by performing a standard anisotropic SGWB search on both folded and unfolded data. Folded data not only leads to orders of magnitude reduction in computation cost, but it results in a conveniently small data volume of few gigabytes, making it possible to perform an actual analysis on a personal computer, as well as easy movement of data. A few important analyses, yet unaccomplished due to computational limitations, will now become feasible. Folded data, being independent of the radiometer basis, will also be useful in reducing processing redundancies in multiple searches and provide a common ground for mutual consistency checks. Most importantly, folded data will allow vast amount of experimentation with existing searches and provide substantial help in developing new strategies to find unknown sources.

  10. Energetic Components of Cooperative Protein Folding

    E-Print Network [OSTI]

    Huseyin Kaya; Hue Sun Chan

    2000-10-11T23:59:59.000Z

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

  11. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12T23:59:59.000Z

    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.

  12. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

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

    2011-06-14T23:59:59.000Z

    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.

  13. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16T23:59:59.000Z

    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.

  14. Circular permutant GFP insertion folding reporters

    SciTech Connect (OSTI)

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

    2008-06-24T23:59:59.000Z

    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.

  15. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01T23:59:59.000Z

    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.

  16. CSAW: a dynamical model of protein folding

    E-Print Network [OSTI]

    Kerson Huang

    2006-01-12T23:59:59.000Z

    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.

  17. 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

  18. 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

  19. 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

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

    E-Print Network [OSTI]

    Roder, Heinrich

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

  1. 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

  2. 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

  3. 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

  4. 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

  5. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

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

    1998-01-13T23:59:59.000Z

    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.

  6. On the Complexity of Protein Folding

    E-Print Network [OSTI]

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

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

  7. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

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

    1995-08-08T23:59:59.000Z

    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.

  8. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

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

    1995-01-01T23:59:59.000Z

    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.

  9. Fast Gravitational Wave Radiometry using Data Folding

    E-Print Network [OSTI]

    Ain, Anirban; Mitra, Sanjit

    2015-01-01T23:59:59.000Z

    Gravitational Waves (GWs) from the early universe and unresolved astrophysical sources are expected to create a stochastic GW background (SGWB). The GW radiometer algorithm is well suited to probe such a background using data from ground based laser interferometric detectors. Radiometer analysis can be performed in different bases, e.g., isotropic, pixel or spherical harmonic. Each of these analyses possesses a common temporal symmetry which we exploit here to fold the whole dataset for every detector pair, typically a few hundred to a thousand days of data, to only one sidereal day, without any compromise in precision. We develop the algebra and a software pipeline needed to fold data, accounting for the effect of overlapping windows and non-stationary noise. We implement this on LIGO's fifth science run data and validate it by performing a standard anisotropic SGWB search on both folded and unfolded data. Folded data not only leads to orders of magnitude reduction in computation cost, but it results in a co...

  10. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

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

    1990-08-23T23:59:59.000Z

    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.

  11. RNAiFold: A web server for RNA inverse folding and molecular Juan Antonio Garcia-Martin, Peter Clote

    E-Print Network [OSTI]

    Clote, Peter

    RNAiFold: A web server for RNA inverse folding and molecular design Juan Antonio Garcia title: RNAiFold web server Key words: RNA, inverse folding, molecular design, synthetic biology, RNA to the 21st century. In this paper, we describe a new web server to support in silico RNA molecular design

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

    E-Print Network [OSTI]

    Roma "La Sapienza", UniversitĂ  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

  13. A simple theory of protein folding kinetics

    E-Print Network [OSTI]

    Pande, Vijay S

    2010-01-01T23:59:59.000Z

    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.

  14. Effects of interlayer slip on multilayered folds

    E-Print Network [OSTI]

    Casarta, Lawrence Joseph

    1980-01-01T23:59:59.000Z

    composed of Coconino Sandstone (brittle) or Indiana Limestone (ductile) interlayered with lead (very ductile) are folded by layer parallel compression at a confining pressure of 100 MPa, temperature of 24 C and axial displacement rate of 10 3 cm... differential stress-axial shortening curves. a, and b, specimens composed of Coconino Sandstone and lead. c, specimens composed of Indiana Limestone and lead. Each curve is for a different specimen a and b. Schematic illustration of double hinged...

  15. Simple Models of the Protein Folding Problem

    E-Print Network [OSTI]

    Chao Tang

    1999-12-26T23:59:59.000Z

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

  16. New Crystal Structures Lift Fog around Protein Folding

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

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

  17. Computational and experimental investigations of forces in protein folding

    E-Print Network [OSTI]

    Schell, David Andrew

    2005-02-17T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Wei, Yun

    2010-07-14T23:59:59.000Z

    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...

  19. 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

  20. 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

  1. abakaliki fold belt: Topics by E-print Network

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

    Cenozoic partitioning of oblique plate convergence in the Zagros fold-and-thrust belt (Iran) Physics Websites Summary: of oblique plate convergence in the Zagros fold-and-thrust...

  2. Folding simulations of small proteins Seung-Yeon Kima

    E-Print Network [OSTI]

    Lee, Jooyoung

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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2014-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Polinkovsky, Mark E.; Polinkovsky, Mark E.

    2012-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Sagle, Laura B.

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Weinkam, Patrick

    2009-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Capraro, Dominique T.

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Cho, Samuel Sung-Il

    2007-01-01T23:59:59.000Z

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

  6. An energy landscape theory for cotranslational protein folding

    E-Print Network [OSTI]

    Tourigny, David S

    2013-01-01T23:59:59.000Z

    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...

  7. Inferring the Rate-Length Law of Protein Folding

    E-Print Network [OSTI]

    Lane, Thomas J

    2013-01-01T23:59:59.000Z

    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.

  8. Accordian-folded boot shield for flexible swivel connection

    DOE Patents [OSTI]

    Hoh, Joseph C. (Naperville, IL)

    1986-01-01T23:59:59.000Z

    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.

  9. Variational theory for site resolved protein folding free energy surfaces

    E-Print Network [OSTI]

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

    1999-01-18T23:59:59.000Z

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

  10. Topological complexity, contact order and protein folding rates

    E-Print Network [OSTI]

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

    2002-05-29T23:59:59.000Z

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

  11. Mechanics of large folds in thin interfacial films

    E-Print Network [OSTI]

    Vincent Démery; Benny Davidovitch; Christian D. Santangelo

    2014-07-16T23:59:59.000Z

    A thin film at a liquid interface responds to uniaxial confinement by wrinkling and then by folding; its shape and energy have been computed exactly before self contact. Here, we address the mechanics of large folds, i.e. folds that absorb a length much larger than the wrinkle wavelength. With scaling arguments and numerical simulations, we show that the antisymmetric fold is energetically favorable and can absorb any excess length at zero pressure. Then, motivated by puzzles arising in the comparison of this simple model to experiments on lipid monolayers and capillary rafts, we discuss how to incorporate film weight, self-adhesion and energy dissipation.

  12. affecting protein folding: Topics by E-print Network

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

    or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape becomes...

  13. assisted protein folding: Topics by E-print Network

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

    or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape becomes...

  14. arrestin fold variations: Topics by E-print Network

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

    25 Next Page Last Page Topic Index 1 Variational theory for site resolved protein folding free energy surfaces Condensed Matter (arXiv) Summary: We present a microscopic...

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

    E-Print Network [OSTI]

    Chekmarev, Sergei F

    2013-01-01T23:59:59.000Z

    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.

  16. 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...

  17. Thermodynamics of protein folding: a random matrix formulation

    E-Print Network [OSTI]

    Pragya Shukla

    2010-10-16T23:59:59.000Z

    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.

  18. A dynamical approach to protein folding

    E-Print Network [OSTI]

    Alessandro Torcini; Roberto Livi; Antonio Politi

    2001-03-13T23:59:59.000Z

    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. PRELIMINARYREPORT41 110E 115 120 125 130 135 140 145 150

    E-Print Network [OSTI]

    , decarbonation, dehydration reactions Horst block Horst block Distance from trench axis (km) Graben Pacific plate Seamount South Chamorro Seamount Summit knoll Fault scarps Fault block Fault block Site 1200 B B' A A' 145;LEG 195 PRELIMINARY REPORT 48 Figure 8 T10 T4 T5 T7 T8 T9 T6 T2 T3 Stinger 6 joints 5.5 in Stinger

  20. Thermodynamic control and dynamical regimes in protein folding

    E-Print Network [OSTI]

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

    2001-10-07T23:59:59.000Z

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

  1. 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

  2. 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 ˇ , 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

  3. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1994-12-27T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Ah Young, AP; Koehl, A; Cascio, D; Egea, PF

    2015-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Mohazab, Ali R

    2012-01-01T23:59:59.000Z

    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...

  6. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-08-13T23:59:59.000Z

    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.

  7. Modeling two-state cooperativity in protein folding

    E-Print Network [OSTI]

    K. Fan; J. Wang; W. Wang

    2001-03-19T23:59:59.000Z

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

  8. 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)

    2010-01-29T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2013-01-01T23:59:59.000Z

    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.

  10. 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]

    Mochrie, Simon

    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

  11. DOI: 10.1002/cphc.200700247 Collapsed But Not Folded: Looking with

    E-Print Network [OSTI]

    Enderlein, Jörg

    at Protein Folding Jçrg Enderlein*[a] Protein folding, that is, the organization of proteins into a highly folded structure. To solve Levinthal's paradox it was postulated that proteins fold along specific path- ways (older view), or follow one of many parallel paths down the now famous protein folding funnel

  12. RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki

    E-Print Network [OSTI]

    Kavraki, Lydia E.

    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

  13. 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

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

    E-Print Network [OSTI]

    Carbonell, Jaime

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

  15. 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

  16. 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

  17. PCB origami : folding circuit boards into electronic products

    E-Print Network [OSTI]

    Sterman, Yoav

    2013-01-01T23:59:59.000Z

    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 ...

  18. Probing the Origins of Two-State Folding

    E-Print Network [OSTI]

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

    2013-01-01T23:59:59.000Z

    Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. To date, many theories for the prevalence of two-state kinetics have been presented, but none sufficiently explain the breadth of experimental observations. A model, making a minimum of assumptions, is introduced that suggests two-state behavior is likely for any system with an overwhelmingly populated native state. We show two-state folding is emergent and strengthened by increasing the occupancy population of the native state. Further, the model exhibits a hub-like behavior, with slow interconversions between unfolded states. Despite this, the unfolded state equilibrates quickly relative to the folding time. This apparent paradox is readily understood through this model. Finally, our results compare favorable with experimental measurements of protein folding rates as a function of chain length and Keq, and provide new insight into these result...

  19. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01T23:59:59.000Z

    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 ...

  20. Low energy pathways for reproducible in vivo protein folding

    E-Print Network [OSTI]

    Leonor Cruzeiro

    2011-01-03T23:59:59.000Z

    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.

  1. 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)

    1999-07-01T23:59:59.000Z

    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.

  2. UFO (UnFold Operator) computer program abstract

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F.

    1982-11-01T23:59:59.000Z

    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.

  3. Characterization of the vocal fold lamina propria towards voice restoration

    E-Print Network [OSTI]

    Hahn, Mariah S

    2004-01-01T23:59:59.000Z

    During normal speech, human vocal folds sustain greater than 100 high impact collisions each second. When the pliability of this complex biomechanical system is reduced by scarring, voice quality may be compromised. ...

  4. Master equation approach to protein folding and kinetic traps

    E-Print Network [OSTI]

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

    1998-04-21T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Bernstein, Rachel Simma

    2011-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Connell, Katelyn Blair

    2010-01-01T23:59:59.000Z

    intermediate state in protein folding by a hydrophobicThe Yin and Yang of protein folding. FEBS J Varley, P. ,H. (2006). Early events in protein folding explored by rapid

  7. 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

  8. 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

  9. 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

    2006-01-01T23:59:59.000Z

    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

  10. 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

  11. 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

  12. 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

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

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

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

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

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

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

  15. 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 Key words: artificial knot, chaperone, free energy landscape, knotted protein, protein folding

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

    E-Print Network [OSTI]

    DeVries, Ingrid L.

    2011-01-01T23:59:59.000Z

    in the transition state of protein folding: alternativeet al. (2008). "Protein folding and stability usingH. Rosner, et al. (2002). "Protein folding and stability of

  17. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    J. L. Gornall; E. M. Terentjev

    2006-03-05T23:59:59.000Z

    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.

  19. 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)

    2000-01-01T23:59:59.000Z

    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.

  20. 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)

    1995-09-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Zhang, Cheng

    2010-01-01T23:59:59.000Z

    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.

  2. Folded Compact Range Development and Coherent Change Detection Measurement Project

    SciTech Connect (OSTI)

    Sorensen, K.W.

    1995-03-01T23:59:59.000Z

    A novel, folded compact range configuration has been developed at the Sandia National Laboratories compact range antenna and radar cross section measurement facility, operated by the Radar/Antenna Department 2343, as a means of performing indoor, environmentally-controlled, far-field simulations of synthetic aperture radar (SAR) coherent change detection (CCD) measurements. This report describes the development of the folded compact range configuration, as well as the initial set of coherent change detection measurements made with the system. These measurements have been highly successful, and have demonstrated the viability of the folded compact range concept in simulating SAR CCD measurements. It is felt that follow-on measurements have the potential of contributing significantly to the body of knowledge available to the scientific community involved in CCD image generation and processing, and that this tool will be a significant aid in the research and development of change detection methodologies.

  3. 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

    2008-01-01T23:59:59.000Z

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

  4. The role of the energy gap in protein folding dynamics

    E-Print Network [OSTI]

    Estelle Pitard; Henri Orland

    1998-11-17T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2014-12-02T23:59:59.000Z

    41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 model, with the existence of several intermediates along the folding pathway. Recently, temper- ature jump in combination with microfluidic mixing techniques have revealed that the relaxation... with the recent experimental findings (for DNA hairpins) of Ansari and co-workers.41 In their study, the authors employed a combination of laser induced temperature jump and microfluidic techniques to initiate folding from different start- ing conditions...

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

    E-Print Network [OSTI]

    Simmons, Walter

    2015-01-01T23:59:59.000Z

    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.

  7. Characterization of Protein Folding by Dominant Reaction Pathways

    E-Print Network [OSTI]

    Pietro Faccioli

    2008-06-23T23:59:59.000Z

    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.

  8. Petrofabric analysis of experimentally folded multilithologic, layered rocks

    E-Print Network [OSTI]

    Pattison, Linda Jean

    1972-01-01T23:59:59.000Z

    of shortening and elongation parallel to the layering and normal to the fold axis and regions of relatively small differen- tial stress are located from the study of the orientations and positions of small thrust and normal faults, macro- and microfrac... to the bottom layer of the fold in the central anticline or to the top layer of the syncline. Movement on type G fractures creates a 0 thrust fault, and the displacement is at 20 to the direction of 25 loading (F'igure 6, p. 27 ). Type G fractures do...

  9. From genes to folds: a review of cortical gyrification theory

    E-Print Network [OSTI]

    Ronan, Lisa; Fletcher, Paul C

    2014-12-16T23:59:59.000Z

    REVIEW From genes to folds: a review of cortical gyrification theory Lisa Ronan • Paul C. Fletcher Received: 5 September 2014 / Accepted: 6 December 2014 #2; The Author(s) 2014. This article is published with open access at Springerlink.com Abstract... microcephaly. Curr Opin Neurol 14:151 Nonaka-Kinoshita M, Reillo I, Artegiani B, Martinez-Martinez MA, Nelson M, Borrell V, Calegari F (2013) Regulation of cerebral cortex size and folding by expansion of basal progenitors. EMBO J 32:1817–1828 O’Leary DDM, Chou...

  10. 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

  11. 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: protein folding; protein folding potential; contact map; neural networks; per­ ceptron. I. INTRODUCTION of protein folding [1] is to predict proteins' native structures from their amino acid sequences; solution

  12. 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

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

    E-Print Network [OSTI]

    Istrail, Sorin

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

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

    E-Print Network [OSTI]

    Hagen, Stephen J.

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

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

    E-Print Network [OSTI]

    Mirny, Leonid

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

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

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM)

    2007-09-18T23:59:59.000Z

    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.

  17. 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

  18. 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

  19. 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

  20. Structural Basis of Folding Cooperativity in Model Proteins: Insights from a Microcanonical Perspective

    E-Print Network [OSTI]

    Bachmann, Michael

    characteristic in protein folding. It is defined by a depletion of states that lie energetically between folded have been observed only in lattice models. INTRODUCTION Two-state protein folding is characterized (19,20), and protein folding (21­27). Two remarks are worthwhile: 1. If the transition

  1. Author's personal copy The Limited Role of Nonnative Contacts in the Folding

    E-Print Network [OSTI]

    Garrahan, Juan P.

    influential ideas on protein folding. Implicit in this simplification is a crucial assumption that has never been critically evaluated in a broad context: Detailed mechanisms of protein folding are not biased folding; principle of minimum frustration Introduction The current understanding of protein folding has

  2. 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

  3. 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

  4. 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(26):9885-9890, 2006 #12;Abstract The definition of reaction coordinates for the characterization of a protein folding along the main folding route. These results clearly show that a complex process such as protein folding

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

    E-Print Network [OSTI]

    Pratt, Vaughan

    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

  6. 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

  7. 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

  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 energy of protein folding is not well understood. We have developed empirical scales for the loss; protein folding; pro- tein engineering INTRODUCTION When a protein folds into a compact globule, the resi

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

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

    E-Print Network [OSTI]

    Janke, Wolfhard

    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

  16. 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

  17. 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

  18. Protein folding, the Levinthal paradox and rapidly mixing Markov chains

    E-Print Network [OSTI]

    Clote, Peter

    passage time) and (P) denote the energy gap between the lowest energy Ei0 (native state) and second lowest on a cubic lattice with normally distributed contact energies. Using a Monte-Carlo folding algorithm energy Ei1 of protein P with normally dis- tributed contact energy, Sali, Shakhnovich and Karplus

  19. Folding model description of reactions with exotic nuclei

    SciTech Connect (OSTI)

    Ibraheem, Awad A., E-mail: awad_ah_eb@hotmail.com [Al-Azhar University, Assiut Branch, Physics Department (Egypt); Hassanain, M. A. [King Khalid University, Physics Department (Saudi Arabia); Mokhtar, S. R. [Assiut University, Physics Department (Egypt); Zaki, M. A. [South-Valley University, Physics Department (Egypt); Mahmoud, Zakaria M. M. [Assiut University, Sciences Department, New-Valley Faculty of Education (Egypt); Farid, M. El-Azab [Assiut University, Physics Department (Egypt)

    2012-08-15T23:59:59.000Z

    Microscopic folding calculations based upon the effective M3Y nucleon-nucleon interaction and the nuclearmatter densities of the interacting nuclei have been carried out to explain recently measured experimental data of the {sup 6}He+{sup 120}Sn elastic scattering cross section at four different laboratory energies near the Coulomb barrier. The extracted reaction cross sections are also considered.

  20. The Highly Cooperative Folding of Small Naturally Occurring Proteins Is

    E-Print Network [OSTI]

    Baker, David

    Varani,2,3 Tobin Sosnick,4 and David Baker3,5, * 1 Molecular and Cellular Biology Program 2 Department 60637, USA 5 Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA 6 Present, this is now possible for protein folding (Kuhlman and Baker, 2004). Protein structures are stabilized

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

    E-Print Network [OSTI]

    Michael Bachmann; Wolfhard Janke

    2007-10-25T23:59:59.000Z

    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.

  2. * 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

  3. 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

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

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2009-02-16T23:59:59.000Z

    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.

  5. The competition between surface adsorption and folding of fibril-forming polypeptides

    E-Print Network [OSTI]

    Ni, Ran; Abeln, Sanne; Stuart, Martien A Cohen; Bolhuis, Peter G

    2015-01-01T23:59:59.000Z

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse grained model, we systematically studied the folding and adsorption behavior of a $\\beta$-roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a $\\beta$-roll before adsorbing onto the attractive surface, (ii) at higher temperature, the polypeptide first adsorbs in a disordered state, and folds while on the surface. The folding temperature increases with increasing attraction, as the folded $\\beta$-roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain t...

  6. Strong Nernst-Ettingshausen effect in folded graphene

    E-Print Network [OSTI]

    Friedemann Queisser; Ralf Schützhold

    2013-01-17T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Pierpaolo Bruscolini

    1997-07-24T23:59:59.000Z

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

  8. Learning to Fold Proteins Using Energy Landscape Theory

    E-Print Network [OSTI]

    Schafer, N P; Zheng, W; Wolynes, P G

    2014-01-01T23:59:59.000Z

    This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics protein folding models to illustrate the points covered in the first part of the article. Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes by reviewing how AWSEM has in recent years been able to elucidate questions related to the unusual kinetic behavior of artificially designed proteins, multidomain protein misfolding, and the initial stages of protein aggregation.

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

    SciTech Connect (OSTI)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S.

    1995-12-11T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01T23:59:59.000Z

    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^{\

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

    SciTech Connect (OSTI)

    Ruben A. Abagyan

    2000-06-01T23:59:59.000Z

    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).

  13. 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 approaches to the so-called protein folding problem, mainly because the microscopic models have no explicit

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

    E-Print Network [OSTI]

    Tang, Xinyu

    2009-05-15T23:59:59.000Z

    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 ...

  15. 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 ...

  16. Protein folding and phylogenetic tree reconstruction using stochastic approximation Monte Carlo

    E-Print Network [OSTI]

    Cheon, Sooyoung

    2007-09-17T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2007-10-25T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2011-01-01T23:59:59.000Z

    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.

  19. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect (OSTI)

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

    2005-02-10T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Ernesto Gonzalez-Candela; Victor Romero-Rochin

    2009-09-23T23:59:59.000Z

    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.

  1. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect (OSTI)

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

    2003-06-25T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Gonzalez-Candela, Ernesto

    2009-01-01T23:59:59.000Z

    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.

  3. Monitoring the Folding of Trp-Cage Peptide by Two-Dimensional Infrared (2DIR) Spectroscopy

    E-Print Network [OSTI]

    Mukamel, Shaul

    of China ABSTRACT: Protein folding is one of the most fundamental problems in modern molecular biology protein folding dynamics which accompany nanometer-scale conformational changes in the pico- to nanosecond bonding dynamics,17 fast chemical exchange in molecular complexes,18 and protein folding.7 According

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

    E-Print Network [OSTI]

    Mukamel, Shaul

    of the protein folding mechanism is of importance to pharmaceutical design and molecular biology [1-5]. Our understanding of protein folding has largely remained elusive due to the vast potential complexity framework for under- standing the global principles of protein folding in terms of funnels [9]. A greater

  5. 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-dimensional represen- tation of a complex process such as protein folding. reaction coordinate transition state

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

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

    E-Print Network [OSTI]

    Chakraborty, Debrup

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

  15. 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

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

    E-Print Network [OSTI]

    Xing, Eric P.

    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

  17. 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

  18. 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 arrangements and in the wider context of protein folding, function and evolution. Given the complicated nature

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

    E-Print Network [OSTI]

    Unger, Ron

    1996-01-01T23:59:59.000Z

    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

  20. THESIS FOR THE DEGREE OF LICENTIATE OF ENGINEERING Numerical Folding of Airbags

    E-Print Network [OSTI]

    Patriksson, Michael

    THESIS FOR THE DEGREE OF LICENTIATE OF ENGINEERING Numerical Folding of Airbags Based of Technology and G¨oteborg University G¨oteborg, Sweden 2007 #12;Numerical Folding of Airbags Based¨oteborg, Sweden 2007 #12;Numerical Folding of Airbags Based on Optimization and Origami Christoffer Cromvik

  1. 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

  2. Self-Folding Origami: Shape Memory Composites Activated by Uniform Heating

    E-Print Network [OSTI]

    Wood, Robert

    Self-Folding Origami: Shape Memory Composites Activated by Uniform Heating Michael T. Tolley1 systems. Here, self- folding origami are presented, which consist of shape memory composites materials and tools. The folding mechanism based on the in-plane contraction of a sheet of shape memory

  3. Temperature dependence of the folding rate in a simple protein model: Search for a ``glass'' transition

    E-Print Network [OSTI]

    Sali, Andrej

    the thermodynamics and kinetics of protein folding over a wide range of temperatures. Both random sequences are in qualitative disagreement with the conclusions of a theoretical analysis of protein folding kinetics based. INTRODUCTION The protein folding problem has both thermodynamic and kinetic aspects. The existence of a unique

  4. Kinetics of Folding of Proteins and RNA D. THIRUMALAI* AND S. A. WOODSON

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    protein folding is a self-assembly process; i.e., the information needed for obtaining the three of protein folding came from Levinthal6 who wondered how a protein molecule searches the astronomically large to general kinetic scenarios for protein folding which are just beginning to be con- firmed experimentally

  5. 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

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

    E-Print Network [OSTI]

    Levine, Alex J.

    folding of simple proteins. We demonstrate that tra- ditional GoŻ polymers lack the extreme cooperativityCooperativity, 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

  7. Using Loop Length Variants to Dissect the Folding Pathway of a Four-helix-bundle Protein

    E-Print Network [OSTI]

    Mochrie, Simon

    . These observations show that loop alteration may be useful as a general tech- nique for dissecting protein folding pathways. # 1999 Academic Press Keywords: protein folding; kinetics; Rop; loops; four-helix-bundle*Corresponding author Introduction A frequently debated question in the ®eld of protein folding is the importance

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

    E-Print Network [OSTI]

    Buldyrev, Sergey

    for studying theoretical aspects of protein folding. The MC algorithm is based on a set of rules, it is useful to study off-lattice models of protein folding. Thus far, several off-lattice simulations have been performed [19­21] that demonstrate the ability of the sim- plified models to study protein folding

  9. Characterization of folding the four-helix bundle protein Rop by real-time NMR

    E-Print Network [OSTI]

    Mochrie, Simon

    -loop-helix monomers. Protein folding moni- tored by stopped-flow fluorescence or CD exhibits biphasic kinetics when: protein folding/real-time NMR Introduction Rop is an RNA-binding protein that is involved in the regu of the effect on protein folding of the length of the connecting loop between the helices, led us to suggest

  10. 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

  11. [25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

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

  12. 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 about how crowding affects protein folding dynamics at the secondary structure level. In this study, we

  13. 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

  14. 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

  15. 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 parallelization of a real application case that concerns the protein folding problem. The experimental evaluation, cluster programming, numerical differentiation, global optimization, protein folding. 1. INTRODUCTION Many

  16. Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast

    E-Print Network [OSTI]

    Fayer, Michael D.

    Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR in the folded configuration. The dynamics of the folded HP35-đCNŢ2 are compared to that of the guanidine to differentiate the peptide dynamic contributions to the observables from those of the water solvent. Because

  17. 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

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

    E-Print Network [OSTI]

    Takada, Shoji

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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

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

    E-Print Network [OSTI]

    Sřrensen, 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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 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

  11. 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

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

    E-Print Network [OSTI]

    Tang, Xinyu

    2009-05-15T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Fraenkel, Aviezri

    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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

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

    E-Print Network [OSTI]

    Straub, John E.

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

  7. 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

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

    E-Print Network [OSTI]

    Lin, Andrew Tien-Shun

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

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

    E-Print Network [OSTI]

    Sanchez, Katheryn Marie

    2010-01-01T23:59:59.000Z

    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

  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

    2013-01-01T23:59:59.000Z

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

    E-Print Network [OSTI]

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

    2014-01-01T23:59:59.000Z

    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

  12. 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

    2012-01-01T23:59:59.000Z

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

  13. Dynamically Partitioning for Solving QBF Horst Samulowitz and Fahiem Bacchus

    E-Print Network [OSTI]

    Bacchus, Fahiem

    to increase the performance of search based solvers, sometimes significantly. Empirically our new solver offers performance that is superior to other search based solvers and in many cases superior to non-search comes from the solution learning techniques em- ployed in search based QBF solvers. Extending solution

  14. Kinetic mechanism of chain folding in polymer crystallization

    E-Print Network [OSTI]

    S. Stepanow

    2014-09-22T23:59:59.000Z

    I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled polymer melt, and the random coil structure of the polymer chains. Setting equal the average formation time of stems of length $% d_l$ with the Rouse time of a piece of polymer of the same arc length $d_l$ yields a lower bound for the thickness of stems and bundles. The estimated lamellar thickness is inversely proportional to the supercooling. The present approach emphasizes the importance of repulsive interactions in polymer crystallization, which are expected to be responsible for the logarithmic lamellar thickening and the increase of lamellar thickness with pressure. An expression for the growth rate is derived by considering the growth as a dynamic multistage process.

  15. 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)

    1996-12-01T23:59:59.000Z

    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.}

  16. 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.

    2003-05-28T23:59:59.000Z

    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.

  17. 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

    2008-08-24T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Coluzza, Ivan

    2014-01-01T23:59:59.000Z

    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. Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model

    E-Print Network [OSTI]

    Caraglio, Michele

    2011-01-01T23:59:59.000Z

    In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein folding to study the behavior of six different protein structures confined between two walls. Changing the distance 2R between the walls, we found, in accordance with previous studies, two confinement regimes: starting from large R and decreasing R, confinement first enhances the stability of the folded state as long as this is compact and until a given value of R; then a further decrease of R leads to a decrease of folding temperature and folding rate. We found that in the low confinement regime both unfolding temperatures and logarithm of folding rates scale as R-{\\gamma} where {\\gamma} values lie in between 1.42 and 2.35.

  20. 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

    2005-01-01T23:59:59.000Z

    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 ...

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

    E-Print Network [OSTI]

    Anna Kallias; Michael Bachmann; Wolfhard Janke

    2007-12-06T23:59:59.000Z

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

  2. 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

    2006-02-17T23:59:59.000Z

    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.

  3. 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

  4. 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

  5. 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

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

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

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

  7. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency

    E-Print Network [OSTI]

    Kranakis, Evangelos

    Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency Peter energy than random RNA" Key words: tRNA, folding energy, RNA secondary structure, structural RNA) and MITACS (Mathematics of Information Technology and Complex Systems) grants. § Department of Mathematics

  8. Predicting stress distributions in fold-and-thrust belts and accretionary wedges by optimization

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    element method (EEM) provides the stress distribution in geometrical models of folds, relevant to fold for discontinuities. The example chosen to illustrate the potential of the EEM and to validate our implementation is the thrusting of a rectangular sheet over a flat and weak de´collement. The EEM reproduces the solution proposed

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

    E-Print Network [OSTI]

    Folding and Strain Softening of Carbon Fiber Composites with an Elastomeric Matrix F. L´opez Jim damage. A possibility is the use of carbon fiber composites with a soft elastomeric matrix.M. Mikulas, Some micromechanics considera- tions of the folding of rigidizable composite materials, in

  10. 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

  11. 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

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

    E-Print Network [OSTI]

    Dinc, Huseyin

    2002-01-01T23:59:59.000Z

    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 converter compatible...

  13. 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

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

    E-Print Network [OSTI]

    Dinc, Huseyin

    2002-01-01T23:59:59.000Z

    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 converter compatible...

  15. Two-and three-dimensional folding of thin film single-crystalline silicon for photovoltaic

    E-Print Network [OSTI]

    Lewis, Jennifer

    Two- and three-dimensional folding of thin film single-crystalline silicon for photovoltaic power of a functional, nonpla- nar photovoltaic (PV) device. A mechanics model based on the theory of thin plates self-folding photovoltaics capillary force Silicon, in crystalline and amorphous forms, is currently

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

    E-Print Network [OSTI]

    Nora Molkenthin; Shuangwei Hu; Antti J. Niemi

    2010-09-06T23:59:59.000Z

    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.

  17. 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

  18. 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

    1997-06-01T23:59:59.000Z

    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.

  19. The Role of Climate in the Deformation of a Fold and Thrust Belt

    E-Print Network [OSTI]

    Steen, Sean Kristian

    2012-02-14T23:59:59.000Z

    and uplifted in large folds. In order to test this and related ideas in a natural example, we have compared modeled rainfall to measured thrust sheet displacement, geometry, and internal deformation in the Appalachian fold and thrust belt. We use mean annual...

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

    E-Print Network [OSTI]

    Anders Irbäck; Carsten Peterson; Frank Potthast; Ola Sommelius

    1996-10-10T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Huseyin Kaya; Hue Sun Chan

    2003-05-20T23:59:59.000Z

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

  2. Eigenvalues of the Homogeneous Finite Linear One Step Master Equation: Applications to Downhill Folding

    E-Print Network [OSTI]

    Lane, Thomas

    2012-01-01T23:59:59.000Z

    Motivated by claims about the nature of the observed timescales in protein systems said to fold downhill, we have studied the finite, linear master equation which is a model of the downhill process. By solving for the system eigenvalues, we prove the often stated claim that in situations where there is no free energy barrier, a transition between single and multi-exponential kinetics occurs at sufficient bias (towards the native state). Consequences for protein folding, especially the downhill folding scenario, are briefly discussed.

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

    E-Print Network [OSTI]

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

    2009-06-24T23:59:59.000Z

    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.

  4. 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)

    2001-05-21T23:59:59.000Z

    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.

  5. 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

    2012-01-01T23:59:59.000Z

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

  6. 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

  7. Discrete Applied Mathematics 127 (2003) 145161 The algorithmics of folding proteins on lattices

    E-Print Network [OSTI]

    Istrail, Sorin

    2003-01-01T23:59:59.000Z

    Institute of Science, Bangalore 560 012, India bStrand Genomics Pvt Ltd. India cKombinatorische Geometrie diagrams for collision-free motion of kinematic assemblies and robot arms). Proteins fold into compact

  8. Real-time detection of ambient aerosols using photothermal interferometry: Folded Jamin interferometer

    E-Print Network [OSTI]

    Real-time detection of ambient aerosols using photothermal interferometry: Folded Jamin of instrumentation that can directly measure ambient aerosol absorption through photothermal interferometry. The hallmark of this approach is its ability to directly measure aerosol absorption without interference from

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

    E-Print Network [OSTI]

    Dulin, Jennifer Natalie

    2013-02-22T23:59:59.000Z

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

    E-Print Network [OSTI]

    Jeetain Mittal; Robert B. Best

    2009-02-26T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Caravella, Justin Andrew, 1974-

    2002-01-01T23:59:59.000Z

    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 ...

  12. A NYQUIST FOLDING ANALOG-TO-INFORMATION RECEIVER Gerald L. Fudge1

    E-Print Network [OSTI]

    Haupt, Jarvis

    A NYQUIST FOLDING ANALOG-TO-INFORMATION RECEIVER Gerald L. Fudge1 , Ross E. Bland1 , Mark A. Chivers1 , Sujit Ravindran1 , Jarvis Haupt2 , P. E. Pace3 1 L-3 Communications Integrated Systems

  13. The folding Roboscooter : structural analysis for an electric scooter used in urban conditions

    E-Print Network [OSTI]

    Petron, Arthur J

    2008-01-01T23:59:59.000Z

    The Roboscooter is an electric, folding scooter designed for use in dense urban areas where congestion and pollution is a problem. Already heavily used in most European cities, scooters provide cheaper, faster transportation ...

  14. The effects of lithology and initial fault angle in physical models of fault-propagation folds

    E-Print Network [OSTI]

    McLain, Christopher Thomas

    2001-01-01T23:59:59.000Z

    Experimentally deformed physical rock models are used to examine the effects of changing mechanical stratigraphy and initial fault angle on the development of fault-propagation folds over a flat-ramp-flat thrust geometry. This study also...

  15. Splitting of Folded Strings in AdS_4*CP^3

    E-Print Network [OSTI]

    Jun-Bao Wu

    2012-08-04T23:59:59.000Z

    We study classically splitting of two kinds of folded string solutions in AdS_4*CP^3. Conserved charges of the produced fragments are computed for each case. We find interesting patterns among these conserved charges.

  16. 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 ...

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

    E-Print Network [OSTI]

    Mehta, Daryush (Daryush Dinyar)

    2010-01-01T23:59:59.000Z

    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 ...

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

    E-Print Network [OSTI]

    Dulin, Jennifer Natalie

    2013-02-22T23:59:59.000Z

    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...

  19. 2D IR spectroscopy and computational modeling : application to protein folding and binding

    E-Print Network [OSTI]

    Ganim, Ziad

    2010-01-01T23:59:59.000Z

    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. ...

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

    SciTech Connect (OSTI)

    Bitto, E.

    2002-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Stepney, Susan

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

  2. 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

  3. 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

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

    E-Print Network [OSTI]

    Straub, John E.

    2011-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2014-01-01T23:59:59.000Z

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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    E-Print Network [OSTI]

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-01-01T23:59:59.000Z

    ). 29 Aksel, T., Majumdar, A. & Barrick, D. The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding. Structure 19, 349-360 (2011). 30 Hilser, V. J. & Thompson, E. B. Intrinsic disorder as a... effects. Theor. Chem. Acc. 101, 426-434 (1999). 67 Best, R. B. & Hummer, G. Diffusive model of protein folding dynamics with Kramers turnover in rate. Phys. Rev. Lett. 96, 228104 (2006). 68 Hutter, J. L. & Bechhoefer, J. Calibration of atomic...

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

    E-Print Network [OSTI]

    Wei, Ke

    1990-01-01T23:59:59.000Z

    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...

  14. 40 Figure 9: Folded, brown weathering carbonate in purple and green slates.

    E-Print Network [OSTI]

    Kidd, William S. F.

    ;#12;#12;#12;#12;#12;#12;#12;#12;40 Figure 9: Folded, brown weathering carbonate in purple and green slates. Figure 10: dismembered folds of brown weathering sandy carbonate and light weathering arenite in purple, green and gray slates. #12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;58 Figure 14: Color laminated slate

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

    E-Print Network [OSTI]

    Gilbert, Pat Kader

    1974-01-01T23:59:59.000Z

    controlled cross section through a wave trai. n of these folds, The citations on these pages follow the style of the U. S. Geological Survey Bulletin. other field observations, laboratory analysis of collected samples, and theoretical considerations...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...

  16. Analysis of monoclinal folds associated with the Brittmore fault in northwest Houston, Texas

    E-Print Network [OSTI]

    Jones, Jayne Ann

    1988-01-01T23:59:59.000Z

    ANALYSIS OF MONOCLINAL FOLDS ASSOCIATED WITH THE BRITTMORE FAULT IN NORTHWEST HOUSTON, TEXAS A Thesis by JAYNE ANN JONES Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements for the degree... of MASTER OF SCIENCE August t988 Major Subject: Geology ANALYSIS OF MONOCUNAL FOLDS ASSOCIATED WITH THE BRITTMORE FAULT IN NORTHWEST HOUSTON, TEXAS A Thesis by JAYNE AhlN JONES Approved as to style and content by: Christ her C. Mathewson (Chairman...

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

    E-Print Network [OSTI]

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

    2000-08-30T23:59:59.000Z

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

  18. Triassic/Jurassic faulting patterns of Conecuh Ridge, southwest Alabama

    SciTech Connect (OSTI)

    Hutley, J.K.

    1985-02-01T23:59:59.000Z

    Two major fault systems influenced Jurassic structure and deposition on the Conecuh Ridge, southwest Alabama. Identification and dating of these fault systems are based on seismic-stratigraphic interpretation of a 7-township grid in Monroe and Conecuh Counties. Relative time of faulting is determined by fault geometry and by formation isopachs and isochrons. Smackover and Norphlet Formations, both Late Jurassic in age, are mappable seismic reflectors and are thus reliable for seismicstratigraphic dating. The earlier of the 2 fault systems is a series of horsts and grabens that trends northeast-southwest and is Late Triassic to Early Jurassic in age. The system formed in response to tensional stress associated with the opening of the Atlantic Ocean. The resulting topography was a series of northeast-southwest-trending ridges. Upper Triassic Eagle Mills and Jurassic Werner Formations were deposited in the grabens. The later fault system is also a series of horsts and grabens trending perpendicular to the first. This system was caused by tensional stress related to a pulse in the opening of the Gulf of Mexico. Faulting began in Early Jurassic and continued into Late Jurassic, becoming progressively younger basinward. At the basin margin, faulting produced a very irregular shoreline. Submerged horst blocks became centers for shoaling or carbonate buildups. Today, these blocks are exploration targets in southwest Alabama.

  19. 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)

    2014-05-28T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Thomas R. Weikl

    2005-02-15T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2004-07-14T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    T. Garel

    2003-05-03T23:59:59.000Z

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

  3. Wrinkles and folds in a fluid-supported sheet of finite size

    E-Print Network [OSTI]

    Oz Oshri; Fabian Brau; Haim Diamant

    2015-03-05T23:59:59.000Z

    A laterally confined thin elastic sheet lying on a liquid substrate displays regular undulations, called wrinkles, characterized by a spatially extended energy distribution and a well-defined wavelength $\\lambda$. As the confinement increases, the deformation energy is progressively localized into a single narrow fold. An exact solution for the deformation of an infinite sheet was previously found, indicating that wrinkles in an infinite sheet are unstable against localization for arbitrarily small confinement. We present an extension of the theory to sheets of finite length $L$, accounting for the experimentally observed wrinkle-to-fold transition. We derive an exact solution for the periodic deformation in the wrinkled state, and an approximate solution for the localized, folded state. We show that a second-order transition between these two states occurs at a critical confinement $\\Delta_F=\\lambda^2/L$.

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

    SciTech Connect (OSTI)

    Crawford, O.

    1997-10-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2010-01-01T23:59:59.000Z

    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...

  6. 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

    2008-02-22T23:59:59.000Z

    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.

  7. 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)

    1994-12-31T23:59:59.000Z

    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.

  8. The evolution and hydrocarbon habitat of the Papuan fold belt, PNG

    SciTech Connect (OSTI)

    Dalton, D.G.; Smith, R.I.; Cawley, S.J. (BP Australia Ltd., Melbourne, Victoria (Australia))

    1990-05-01T23:59:59.000Z

    After over 70 years of hydrocarbon exploration in the Papuan fold belt of PNG (Papua New Guinea) there have been a number of hydrocarbon discoveries over recent years that have confirmed its potential as a significant producing province. The Papuan basin developed during the early Mesozoic as part of the northeast corner of the Australian passive margin. The basin's tertiary evolution and the development of the Papuan fold belt within the Papuan basin has evolved in response to oblique convergence between the northerly moving Australian plate and westerly moving Pacific plate. Restacking of the Mesozoic passive margin sequence within the Papuan Basin was initiated in the early miocene by southward abduction of the Solomon Sea plate and the subsequent collision, in the late Miocene, of the Melanesian Island arc along the northeastern margin of PNG. This later collision provided the driving mechanism for the development of the papuan thrust belt. To date, all the significant hydrocarbon discoveries made within the Papuan fold belt have been located within the frontal zone of the fold belt, which is characterized by relatively simple ramp anticlines and thick-skinned inversion structures. The primary proven reservoir fairway is the Jurassic Toro formation, which is a sequence of stacked submarine bars prograding out across a shallow-marine low-gradient shelf. Geochemical analysis of produced hydrocarbons and samples collected from the many surface seeps found in the fold belt indicate two main families of oil. A model explains the distribution of hydrocarbons discovered to date, which involves Jurassic and Cretaceous source intervals and a complex history of secondary migration and entrapment. The unique technical problems associated with exploration of the Papuan fold belt leave many elements of the proven play systems uncertain, but in so doing, they present many challenges and opportunities for the future.

  9. 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

    1996-12-31T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2013-01-01T23:59:59.000Z

    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.

  11. 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.

    2007-01-01T23:59:59.000Z

    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.

  12. The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics

    E-Print Network [OSTI]

    Molin, J P Dal; Caliri, A

    2010-01-01T23:59:59.000Z

    Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process with two consecutive and independent stages, namely the search mechanism and the overall productive stabilization; ($ii$) the folding kinetics results from a mechanism as fast as can be; and ($iii$) at nanoscale dimensions, local thermal fluctuations may have important role on the folding kinetics. Here the first stage of folding process (search mechanism) is focused exclusively. The effects and consequences of local thermal fluctuations on the configurational kinetics, treated here in the context of non extensive statistical mechanics, is analyzed in detail through the dependence of the characteristic time of folding ($\\tau$) on the temperature $T$ and on the nonextensive parameter $q$.The model used consists of effective residues forming a chain of 27 beads, which occupy...

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

    E-Print Network [OSTI]

    Traub, Joseph F.

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

    Berry, R. Stephen

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

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

    SciTech Connect (OSTI)

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

    2001-07-23T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2002-03-31T23:59:59.000Z

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

  19. Folding model analysis of inelastic alfa particle scattering to giant resonances

    E-Print Network [OSTI]

    Simler, George F.

    1997-01-01T23:59:59.000Z

    % -2%) of the E2 energy-weighted sum rule (EWSR) for the folding (deformed potential) model, which were in good agreement with previous work. The experimental Ex=17.42 MeV peak was fit by a combination of 1=0 and 1=2 calculations corresponding to 19:t2...

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

    E-Print Network [OSTI]

    Roder, Heinrich

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

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

    E-Print Network [OSTI]

    Hickman, John Bibb

    1999-01-01T23:59:59.000Z

    ) from north to south, a dramatic change in the width of the deformation front of the fold and thrust belt which is accentuated across the Michih fault, and 4) the Tulungwan fault, a bounding fault between the Western Foothills and the Slate Belt, appears...

  2. 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

  3. 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 methods can be broadly classified into two categories, that is, template-based1­6 and taxonomy- based.7­13 In recent years, the taxonomy-based method has attracted great attention due to its encouraging performance

  4. 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

  5. Turn Scanning 133 From: Methods in Molecular Biology, vol. 168: Protein Structure, Stability, and Folding

    E-Print Network [OSTI]

    Ponder, Jay

    Turn Scanning 133 133 From: Methods in Molecular Biology, vol. 168: Protein Structure, Stability, and Folding Edited by: K. P. Murphy © Humana Press Inc., Totowa, NJ 7 Turn Scanning: Experimental extended structures. Here we present the use of turn scanning as an experimental method for assessing

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

    E-Print Network [OSTI]

    Dal PalĂą, Alessandro

    Department of Computer Science Universit`a di Udine New Mexico State University (dalpalu scientists have agreed that the answer to the folding problem lies in the concept of the energy state of the amino acid sequence in the 3D space with minimum energy state. According to this theory, the 3D

  7. 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

  8. Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity

    E-Print Network [OSTI]

    Baker, David

    Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch, conformational strain, and packing defects yielded new binding partners that exhibited specificities of at least of similar structure and sequence. Simple rules to identify protein recognition sites and predict energetic

  9. Phosphorylation of Photosystem II Controls Functional Macroscopic Folding of Photosynthetic Membranes

    E-Print Network [OSTI]

    Halazonetis, Thanos

    mobility of membrane proteins and sustained photosynthetic activity. The use of captured sunlight energy, Linko¨ ping University, SE-581 85 Linko¨ ping, Sweden b Departments of Molecular Biology and Plant contain highly folded membrane layers enriched in photosystem II, which uses light energy to oxidize water

  10. Differential Salt-induced Stabilization of Structure in the Initial Folding Intermediate Ensemble of Barstar

    E-Print Network [OSTI]

    Udgaonkar, Jayant B.

    Differential Salt-induced Stabilization of Structure in the Initial Folding Intermediate Ensemble of Fundamental Research, GKVK Campus, Bangalore 560 065 India The effects of two salts, KCl and MgCl2 mol21 in the absence of salt to a value of 6.9 kcal mol21 in the presence of 1 M KCl or 1 M MgCl2

  11. Salt Bridges Stabilize the Folded Structure of Barnase M. Vijayakumar and Huan-Xiang Zhou*

    E-Print Network [OSTI]

    Weston, Ken

    Salt Bridges Stabilize the Folded Structure of Barnase M. Vijayakumar and Huan-Xiang Zhou Form: May 19, 2001 Formation of salt bridges entails desolvation, and whether they stabilize protein structures is an open question. In this paper, the role of three Arg-Asp salt bridges in barnase was studied

  12. Microscopic Description of the Exotic Nuclei Reactions by Using Folding model Potentials

    SciTech Connect (OSTI)

    Ibraheem, Awad A. [Physics Department, Al-Azhar University, Assiut Branch, Assiut 71524 (Egypt); Physics Department, King Khalid University, Abha (Saudi Arabia); Hassanain, M. A. [Physics Department, King Khalid University, Abha (Saudi Arabia); Sciences Department, New-Valley Faculty of Education, Assiut University, El-Kharga, New-Valley (Egypt); Mokhtar, S. R.; El-Azab Farid, M. [Physics Department, Assiut University, Assiut 71516 (Egypt); Zaki, M. A. [Physics Department, South-Valley University, Aswan (Egypt); Mahmoud, Zakaria M. M. [Sciences Department, New-Valley Faculty of Education, Assiut University, El-Kharga, New-Valley (Egypt)

    2011-10-27T23:59:59.000Z

    A microscopic folding approach based upon the effective M3Y nucleon-nucleon interaction and the nuclear matter densities of the interacting nuclei has been carried out to explain recently measured experimental data of the {sup 6}He+{sup 120}Sn elastic scattering reaction at four different laboratory energies near the Coulomb barrier. The corresponding reaction cross sections are also considered.

  13. Self-folding and aggregation of amyloid nanofibrils Raffaella Paparcone*, Steven W. Cranford*,

    E-Print Network [OSTI]

    Buehler, Markus J.

    -617-452-23750, Fax: +1-617-324-4014 Abstract: Amyloids are highly organized protein filaments, rich in beta-grain model to analyze the competition between adhesive forces and elastic deformation of amyloid fibrils. We-folded nanorackets and nanorings and demonstrate that such aggregated amyloid fibrils are stable in such states even

  14. Rapid protein fold determination using unassigned Jens Meiler and David Baker*

    E-Print Network [OSTI]

    Baker, David

    Rapid protein fold determination using unassigned NMR data Jens Meiler and David Baker* Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, P.O. Box 357350, Seattle, WA 98195 algorithm, ROSETTA [Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209

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

    E-Print Network [OSTI]

    Tristan Bereau; Michael Bachmann; Markus Deserno

    2011-07-01T23:59:59.000Z

    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.

  16. Translocation of polymers with folded configurations across nanopores Stanislav Kotsev and Anatoly B. Kolomeiskya

    E-Print Network [OSTI]

    Translocation of polymers with folded configurations across nanopores Stanislav Kotsev and Anatoly August 2007; accepted 26 September 2007; published online 9 November 2007 The transport of polymers segment through the channel followed by the linear part of the polymer. The transition rates vary

  17. Extent of Hydrogen-Bond Protection in Folded Proteins: A Constraint on Packing Architectures

    E-Print Network [OSTI]

    Berry, R. Stephen

    Extent of Hydrogen-Bond Protection in Folded Proteins: A Constraint on Packing Architectures Ariel structuring and ultimately exclusion of water by hydrophobes surrounding backbone hydrogen bonds turn hydrophobes yields an optimal hydrogen-bond stabilization. This motif is shown to be nearly ubiquitous

  18. Coherent change detection and interferometric ISAR measurements in the folded compact range

    SciTech Connect (OSTI)

    Sorensen, K.W.

    1996-08-01T23:59:59.000Z

    A folded compact range configuration has been developed ant the Sandia National Laboratories` compact range antenna and radar-cross- section measurement facility as a means of performing indoor, environmentally-controlled, far-field simulations of synthetic aperture radar (SAR) measurements of distributed target samples (i.e. gravel, sand, etc.). The folded compact range configuration has previously been used to perform coherent-change-detection (CCD) measurements, which allow disturbances to distributed targets on the order of fractions of a wavelength to be detected. This report describes follow-on CCD measurements of other distributed target samples, and also investigates the sensitivity of the CCD measurement process to changes in the relative spatial location of the SAR sensor between observations of the target. Additionally, this report describes the theoretical and practical aspects of performing interferometric inverse-synthetic-aperture-radar (IFISAR) measurements in the folded compact range environment. IFISAR measurements provide resolution of the relative heights of targets with accuracies on the order of a wavelength. Several examples are given of digital height maps that have been generated from measurements performed at the folded compact range facility.

  19. Efficient Sampling of Protein Folding Pathways using HMMSTR and Probabilistic Roadmaps

    E-Print Network [OSTI]

    Bystroff, Chris

    of the samples to minimize van der Waals collisions (VDW), radius of gyration (RG) and hydrogen bond energy (HBEEfficient Sampling of Protein Folding Pathways using HMMSTR and Probabilistic Roadmaps *Yogesh A methods have used the knowledge of the true structure to sample conformational space. Our method uses only

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

    E-Print Network [OSTI]

    Avouac, Jean-Philippe

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

  1. An N-atom Collective State Atomic Clock with Root-N Fold Increase in Effective Frequency and Root-N Fold Reduction in Fringe Width

    E-Print Network [OSTI]

    May E. Kim; Resham Sarkar; Renpeng Fang; Selim M. Shahriar

    2014-12-15T23:59:59.000Z

    We describe a collective state atomic clock with Ramsey fringes narrowed by a factor of $\\sqrt{N}$ compared to a conventional clock, N being the number of non-interacting atoms, without violating the uncertainty relation. This narrowing is explained as being due to interferences among the collective states, representing an effective $\\sqrt{N}$ fold increase in the clock frequency, without entanglement. The detection process, which measures a collective state, can be used to increase the quantum efficiency of detection significantly, yielding a net improvement in stability by as much as a factor of 10.

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70COMMUNITYResponses:December 11,Release date:5, Rev9,222,;3

  3. High-resolution structure of a retroviral protease folded as a monomer

    SciTech Connect (OSTI)

    Gilski, Miroslaw [A. Mickiewicz University, 60-780 Poznan (Poland); Polish Academy of Sciences, 61-704 Poznan (Poland); Kazmierczyk, Maciej; Krzywda, Szymon [A. Mickiewicz University, 60-780 Poznan (Poland); Zábranská, Helena [Academy of Sciences of the Czech Republic, 166 10 Prague (Czech Republic); Cooper, Seth; Popovi?, Zoran [University of Washington, Box 352350, Seattle, WA 98195 (United States); Khatib, Firas; DiMaio, Frank; Thompson, James; Baker, David [University of Washington, Box 357350, Seattle, WA 98195 (United States); Pichová, Iva [Academy of Sciences of the Czech Republic, 166 10 Prague (Czech Republic); Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl [A. Mickiewicz University, 60-780 Poznan (Poland); Polish Academy of Sciences, 61-704 Poznan (Poland)

    2011-11-01T23:59:59.000Z

    The crystal structure of Mason–Pfizer monkey virus protease folded as a monomer has been solved by molecular replacement using a model generated by players of the online game Foldit. The structure shows at high resolution the details of a retroviral protease folded as a monomer which can guide rational design of protease dimerization inhibitors as retroviral drugs. Mason–Pfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerization of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldit. The structure indeed shows a monomeric protein, with the N- and C-termini completely disordered. On the other hand, the flap loop, which normally gates access to the active site of homodimeric retropepsins, is clearly traceable in the electron density. The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins. The overall fold of the protein follows the retropepsin canon, but the C{sup ?} deviations are large and the active-site ‘DTG’ loop (here NTG) deviates up to 2.7 Ĺ from the standard conformation. This structure of a monomeric retropepsin determined at high resolution (1.6 Ĺ) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections, including AIDS.

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

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2002-01-01T23:59:59.000Z

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

  6. Timing of granite emplacement and cooling in the SongpanGarze^ Fold Belt (eastern Tibetan Plateau) with tectonic implications

    E-Print Network [OSTI]

    Timing of granite emplacement and cooling in the Songpan­Garze^ Fold Belt (eastern Tibetan Plateau Abstract New U­Pb and Rb­Sr geochronology on syn- and post-orogenic granites provide constraints on the timing of major tectonic events in the Songpan­Garze^ fold belt, west Sichuan, China. The Ma Nai granite

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

    E-Print Network [OSTI]

    Olivier Collet

    1999-07-19T23:59:59.000Z

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

  8. BCL::MP-Fold: membrane protein structure prediction guided by EPR restraints

    E-Print Network [OSTI]

    Fischer, Axel Walter; Woetzel, Nils; Karakas, Mert; Weiner, Brian; Meiler, Jens

    2015-01-01T23:59:59.000Z

    For many membrane proteins the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold (BioChemical Library membrane protein fold) algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The RMSD100 value of the most accurate model is better than 8{\\AA} for twenty-seven, better than 6{\\AA} for twenty-two and better than 4{\\AA} for fifte...

  9. Curvature and folding dynamo effects in turbulent plasmas and ABC flux tubes

    E-Print Network [OSTI]

    de Andrade, L C Garcia

    2010-01-01T23:59:59.000Z

    Investigation of the eigenvalue spectra of dynamo solutions, has been proved fundamental for the knowledge of dynamo physics. Earlier, curvature-folding relation on dynamos in Riemannian spaces has been investigated [PPL 2008]. Here, analytical solutions representing general turbulent dynamo filaments are obtained in resistive plasmas. Turbulent diffusivity with vanishing kinetic helicity yields a fast mode for a steady dynamo eigenvalue. The magnetic field lays down on a local frame 2 plane along the filaments embedded in a 3D plasma. Curvature effects plays the role of folding in fast magnetic dynamos. In the present examples, plasma equipartition between normal and binormal components of the magnetic field components is considered. In the opposite case, oscillatory, purely imaginary, branches of the spectrum are found in dynamo manifold. Degenerate eigenvalues, are obtained when the dynamo growth rate coincides with the filaments curvature. Spectra of dynamo obtained are similar to the fast dynamo solution...

  10. When does TMAO fold a polymer chain and urea unfold it?

    E-Print Network [OSTI]

    Mondal, Jagannath; Berne, B J

    2013-01-01T23:59:59.000Z

    Longstanding mechanistic questions about the role of protecting osmolyte trimethylamine N- oxide (TMAO) which favors protein folding and the denaturing osmolyte urea are addressed by studying their effects on the folding of uncharged polymer chains. Using atomistic molecular dynamics simulations, we show that 1-M TMAO and 7-M urea solutions act dramatically differently on these model polymer chains. Their behaviors are sensitive to the strength of the attractive dispersion interactions of the chain with its environment: when these dispersion interactions are high enough, TMAO suppresses the formation of extended conformations of the hydrophobic polymer as compared to water, while urea promotes formation of extended conformations. Similar trends are observed experimentally on real protein systems. Quite surprisingly, we find that both protecting and denaturing osmolytes strongly interact with the polymer, seemingly in contrast with existing explanations of the osmolyte effect on proteins. We show that what rea...

  11. Phi-values in protein folding kinetics have energetic and structural components

    E-Print Network [OSTI]

    Claudia Merlo; Ken A. Dill; Thomas R. Weikl

    2005-07-14T23:59:59.000Z

    Phi-values are experimental measures of how the kinetics of protein folding is changed by single-site mutations. Phi-values measure energetic quantities, but are often interpreted in terms of the structures of the transition state ensemble. Here we describe a simple analytical model of the folding kinetics in terms of the formation of protein substructures. The model shows that Phi-values have both structural and energetic components. In addition, it provides a natural and general interpretation of "nonclassical" Phi-values (i.e., less than zero, or greater than one). The model reproduces the Phi-values for 20 single-residue mutations in the alpha-helix of the protein CI2, including several nonclassical Phi-values, in good agreement with experiments.

  12. Speeding protein folding beyond the Go model: How a little frustration sometimes helps

    E-Print Network [OSTI]

    Steven S. Plotkin

    2000-09-27T23:59:59.000Z

    Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and flexible. Eventually the rate drops rapidly towards zero when ruggedness significantly slows conformational transitions. Energy landscape arguments for thermodynamics and kinetics are coupled with a treatment of non-native collapse to elucidate this effect.

  13. Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem

    E-Print Network [OSTI]

    Hansmann, Uwe H E; Hansmann, Ulrich H.E.; Okamoto, Yuko

    1997-01-01T23:59:59.000Z

    We compare numerically the effectiveness of three recently proposed algorithms, multicanonical simulations, simulations in a 1/k-ensemble, and simulated tempering for the protein folding problem. For this we perform simulations with high statistics for one of the simplest peptides, Met-enkephalin. While the performances of all three approaches is much better than traditional methods, we find that the differences among the three are only marginal.

  14. The folding kinetics of ribonuclease Sa and a charge-reversal variant

    E-Print Network [OSTI]

    Trefethen, Jared M.

    2005-02-17T23:59:59.000Z

    Coulomb?s Law suggested that favorable electrostatic interactions in the denatured state were the cause for the decreased stability for the charge-reversed variant. Folding and unfolding kinetic studies were designed and conducted to study the iv charge... of the denatured state as suspected. Additionally, the results showed that the transition state was stabilized as well. These results show that a specific Coulombic interaction lowered the free energy in the denatured and transition state of the charge...

  15. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY

    SciTech Connect (OSTI)

    Kane, A; Hertzog, D; Baumgartel, P; Lengefeld, J; Horsley, D; Schuler, B; Bakajin, O

    2006-03-20T23:59:59.000Z

    The purpose of this study is to design, fabricate and optimize microfluidic mixers to investigate the kinetics of protein secondary structure formation with Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy. The mixers are designed to rapidly initiate protein folding reaction through the dilution of denaturant. The devices are fabricated out of fused silica, so that they are transparent in the UV. We present characterization of mixing in the fabricated devices, as well as the initial SRCD data on proteins inside the mixers.

  16. Oil springs and flat top anticlines, Carbon County Wyoming: An unusual fold pair

    SciTech Connect (OSTI)

    Blackstone, D.L. Jr. (Univ. of Wyoming, Laramie, WY (United States))

    1994-04-01T23:59:59.000Z

    Oil Springs Anticline, northwest of Medicine Bow, Wyoming, and located at the northeast corner of the Hanna Basin, lies near the junction of the Freezeout Hills Anticline, the Shirley thrust fault and the Flat Top Anticline. The surface fold as defined by the outcrop of the Wall Creek Sandstone Member of the Frontier Formation is disharmonic to deeper structure at the level of the Jurassic Sundance Formation. The fold is wedged between two major folds and is the result of a space problem between larger structural elements. The controlling Flat Top Anticline is an excellent example of a fold controlled by a well constrained fault in the Precambrian crystalline basement. The basement is bowed upward and outward to the northwest in the hanging wall of the Flat Top Anticline. The purpose of this paper is to describe the geologic structure of the Oil Springs and Flat Top anticlines and their relationship to the Freezeout Hills and the Hanna Basin. Commercial production of petroleum and natural gas occurs on the west flank of the Laramie-Cooper Lake Basin as far north as the northeast corner of the Hanna Basin. Stone reviewed the producing formations in the Laramie and eastern Hanna basins and noted that 11 commercial accumulations of petroleum and natural gas are directly related to anticlinal structures. Production derived from the Permian-Pennsylvanian Tensleep Sandstone in this region has a special geologic framework. Fields that produce from the Tensleep Sandstone are well defined anticlines bounded by faults or fault systems, a situation also reported by Biggs and Espach, Blackstone and in the Wyoming Geological Association Symposium. The Tensleep Sandstone reservoirs in these faulted anticlines are in juxtaposition to potential source rocks of either Jurassic or Cretaceous age in the footwalls of the faults. 17 refs., 9 figs., 1 tab.

  17. Oak Ridge fault, Ventura fold belt, and the Sisar decollement, Ventura basin, California

    SciTech Connect (OSTI)

    Yeats, R.S.; Huftile, G.J.; Grigsby, F.B. (Oregon State Univ. Corvallis (USA))

    1988-12-01T23:59:59.000Z

    The rootless Ventura Avenue, San Miguelito, and Rincon anticlines (Ventura fold belt) in Pliocene -Pleistocene turbidites are fault-propagation folds related to south-dipping reverse faults rising from a decollement in Miocene shale. To the east, the Sulfur Mountain anticlinorium overlies and is cut by the Sisar, Big Canyon, and Lion south-dipping thrusts that merge downward into the Sisar decollement in lower Miocene shale. Shortening of the Miocene and younger sequence is {approximately} 3 km greater than that of underlying competent Paleogens strata in the Ventura fold belt and {approximately} 7 km greater farther east at Sulfur Mountain. Cross-section balancing requires that this difference be taken up by the Paleogene sequence at the Oak Ridge fault to the south. Convergence is northeast to north-northeast on the base of earthquake focal mechanisms, borehole breakouts, and piercing-point offest of the South Mountain seaknoll by the Oak Ridge fault. A northeast-trending line connecting the west end of Oak Ridge and the east end of Sisar fault separates an eastern domain where late Quaternary displacement is taken up entirely on the Oak Ridge fault and a western domain where displacement is transferred to the Sisar decollement and its overlying rootless folds. This implies that (1) the Oak Ridge fault near the coast presents as much seismic risk as it does farther east, despite negligible near-surface late Quaternary movement; (2) ground-rupture hazard is high for the Sisar fault set in the upper Ojai Valley; and (3) the decollement itself could produce an earthquake analogous to the 1987 Whittier Narrows event in Low Angeles.

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

    E-Print Network [OSTI]

    D. K. Klimov; D. Thirumalai

    1998-04-22T23:59:59.000Z

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

  19. Structural Analysis of Protein Folding by the Long-Chain Archaeal Chaperone FKBP26

    SciTech Connect (OSTI)

    E Martinez-Hackert; W Hendrickson

    2011-12-31T23:59:59.000Z

    In the cell, protein folding is mediated by folding catalysts and chaperones. The two functions are often linked, especially when the catalytic module forms part of a multidomain protein, as in Methanococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. Here, we show that FKBP26 chaperone activity requires both a 50-residue insertion in the catalytic FKBP domain, also called 'Insert-in-Flap' or IF domain, and an 80-residue C-terminal domain. We determined FKBP26 structures from four crystal forms and analyzed chaperone domains in light of their ability to mediate protein-protein interactions. FKBP26 is a crescent-shaped homodimer. We reason that folding proteins are bound inside the large crescent cleft, thus enabling their access to inward-facing peptidyl-prolyl cis/trans isomerase catalytic sites and ipsilateral chaperone domain surfaces. As these chaperone surfaces participate extensively in crystal lattice contacts, we speculate that the observed lattice contacts reflect a proclivity for protein associations and represent substrate interactions by FKBP26 chaperone domains. Finally, we find that FKBP26 is an exceptionally flexible molecule, suggesting a mechanism for nonspecific substrate recognition.

  20. Group Theory of Chiral Photonic Crystals with 4-fold Symmetry: Band Structure and S-Parameters of Eight-Fold Intergrown Gyroid Nets

    E-Print Network [OSTI]

    Saba, Matthias; Mecke, Klaus; Gu, Min; Schröder-Turk, Gerd E

    2013-01-01T23:59:59.000Z

    The Single Gyroid, or srs, nanostructure has attracted interest as a circular-polarisation sensitive photonic material. We develop a group theoretical and scattering matrix method, applicable to any photonic crystal with symmetry I432, to demonstrate the remarkable chiral-optical properties of a generalised structure called 8-srs, obtained by intergrowth of eight equal-handed srs nets. Exploiting the presence of four-fold rotations, Bloch modes corresponding to the irreducible representations E- and E+ are identified as the sole and non-interacting transmission channels for right- and left-circularly polarised light, respectively. For plane waves incident on a finite slab of the 8-srs, the reflection rates for both circular polarisations are identical for all frequencies and transmission rates are identical up to a critical frequency below which scattering in the far field is restricted to zero grating order. Simulations show the optical activity of the lossless dielectric 8-srs to be large, comparable to met...

  1. The elasto-/hydro-dynamics of quasicrystals with 12- and 18-fold symmetries in some soft matters and mathematical solutions

    E-Print Network [OSTI]

    Tian You Fan

    2012-10-05T23:59:59.000Z

    The observation recently of 12-fold quasicrystals in polymers, nanoparticle mixture and 12-fold and 18-fold quasicrystals in colloidal solutions are important events for the study of quasicrystals. To describe the mechanical behaviour we propose a new solid-liquid phase quasicrystal model for some soft matters including polymers and colloids. The so-called new solid-liquid phase, is a new phase model of anisotropic fluid, but different from liquid crystal phase, here the structure presents quasiperiodic symmetry. Based on the model, the elasticity, fluidity and viscosity of the material have been studied, the relevant mathematical theory has also been proposed. Some mathematical solutions of the theory are discussed.

  2. Core-shell structures in single flexible-semiflexible block copolymers: Finding the free energy minimum for the folding transition

    E-Print Network [OSTI]

    Natsuhiko Yoshinaga; Kenichi Yoshikawa

    2007-06-11T23:59:59.000Z

    We investigate the folding transition of a single diblock copolymer consisting of a semiflexible and a flexible block. We obtain a {\\it Saturn-shaped} core-shell conformation in the folded state, in which the flexible block forms a core and the semiflexible block wraps around it. We demonstrate two distinctive features of the core-shell structures: (i) The kinetics of the folding transition in the copolymer are significantly more efficient than those of a semiflexible homopolymer. (ii) The core-shell structure does not depend on the transition pathway.

  3. Design of an individual vertex actuator and its use in understanding the effect of constraint location on Miura-Ori folding behavior

    E-Print Network [OSTI]

    Dias Carlson, Rachel (Rachel A.)

    2014-01-01T23:59:59.000Z

    The Miura-Ori fold is an origami pattern that can translate from a flat sheet to a compact folded state with a single degree of freedom. Currently little is understood about the relationship between the physical properties ...

  4. arXiv:0810.3042v1[physics.bio-ph]16Oct2008 Single-domain protein folding: a multi-faceted

    E-Print Network [OSTI]

    Ritort, Felix

    arXiv:0810.3042v1[physics.bio-ph]16Oct2008 Single-domain protein folding: a multi-faceted problem protein-like models can help to understand many controversial issues. Keywords: Protein folding, energy

  5. Two-and three-dimensional modeling and optimization applied to the design of a fast hydrodynamic focusing microfluidic mixer for protein folding

    E-Print Network [OSTI]

    Santiago, Juan G.

    focusing microfluidic mixer for protein folding Benjamin Ivorra, Juana L. Redondo, Juan G. Santiago, Pilar of a fast hydrodynamic focusing microfluidic mixer for protein folding Benjamin Ivorra,1,a) Juana L. Redondo

  6. Curvature-induced D-band Raman scattering in folded graphene This article has been downloaded from IOPscience. Please scroll down to see the full text article.

    E-Print Network [OSTI]

    Curvature-induced D-band Raman scattering in folded graphene This article has been downloaded from.1088/0953-8984/22/33/334205 Curvature-induced D-band Raman scattering in folded graphene* Awnish K Gupta1 , Cristiano Nisoli2 , Paul E Micro-Raman scattering from folds in single-layer graphene sheets finds a D-band at the fold for both

  7. Phonation thresholds as a function of laryngeal size in a two-mass model of the vocal folds (L)

    E-Print Network [OSTI]

    Lucero, Jorge Carlos

    Lucero and Koenig, 2005 and children Lucero and Koenig, 2003 in the vicinity of an abduction gesture the abduction- adduction gesture for /h/ is achieved by the combined action of vocal fold abduction, decrease

  8. Systematic Investigation of Hydrogel Material Properties on Cell Responses for Vocal Fold and Vascular Graft Tissue Engineering

    E-Print Network [OSTI]

    Bulick, Allen

    2010-01-14T23:59:59.000Z

    for this because of their biocompatibility and biological "blank slate" nature. This dissertation presents data investigating: the effects of glycosaminoglycans (GAGs) as biochemical stimuli on pig vocal fold fibroblasts (PVFfs); the effects of mechanical...

  9. Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation

    E-Print Network [OSTI]

    Chen, Mark

    N-linked glycosylation modulates protein folding and stability through a variety of mechanisms. As such there is considerable interest in the development of general rules to predict the structural consequences of site-specific ...

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

    E-Print Network [OSTI]

    Gilbert, Pat Kader

    1974-01-01T23:59:59.000Z

    -shape. The trough in S3 (see unit 23, Plate 2) is hi. ghly fractured in the sandstone and shows considerable flowage in the shale. From the air, it is readily apparent that these folds of the upper Two Medicine are much smaller in lateral extent along strike than... Formation (mostly shale), the Virgelle Sandstone, and the Two Medi. cine Formation (mostly shale), Montana Group, Upper Cretaceous. The Virgelle Sand- stone, about 54 meters thick, lies between the shales and behaved as the most competent member...

  11. Exact Solution of the Munoz-Eaton Model for Protein Folding

    E-Print Network [OSTI]

    Pierpaolo Bruscolini; Alessandro Pelizzola

    2002-05-30T23:59:59.000Z

    A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for a generic protein, for any choice of the energy and entropy parameters, and in principle allows the model to be used as a first tool to characterize the dynamics of a protein of known native state and equilibrium population. Applications to a $\\beta$-hairpin and to protein CI-2, with comparisons to previous results, are also shown.

  12. Protein folding and non-conventional drug design: a primer for nuclear structure physicists

    SciTech Connect (OSTI)

    Broglia, R.A. [Dipartimento di Fisica, Universita di Milano, Via Celoria 16, I-20133 Milan (Italy); INFN, Sezione di Milano, Via Celoria 16, I-20133 Milan (Italy); Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen (Denmark); Tiana, G.; Provasi, D. [Dipartimento di Fisica, Universita di Milano, Via Celoria 16, I-20133 Milan (Italy); INFN, Sezione di Milano, Via Celoria 16, I-20133 Milan (Italy)

    2004-02-27T23:59:59.000Z

    Some of the paradigms emerging from the study of the phenomena of phase transitions in finite many-body systems, like e.g. the atomic nucleus can be used at profit to solve the protein folding problem within the framework of simple (although not oversimplified) models. From this solution a paradigm emerges for the design of non-conventional drugs, which inhibit enzymatic action without inducing resistance (mutations). The application of these concepts to the design of an inhibitor to the HIV-protease central in the life cycle of the HIV virus is discussed.

  13. Overdamped thermal ratchets in one and more dimensions. Kinesin transport and protein folding

    E-Print Network [OSTI]

    Ernesto Gonzalez-Candela; Victor Romero-Rochin

    2006-05-26T23:59:59.000Z

    The overdamped thermal ratchet driven by an external (Orstein-Uhlenbeck) noise is revisited. The ratchet we consider is unbounded in space and not necessarily periodic . We briefly discuss the conditions under which current is obtained by analyzing the corresponding Fokker-Planck equation and its lack of stationary states. Next, two examples in more than one dimension and related to biological systems are presented. First, a two-dimensional model of a ``kinesin protein'' on a ``microtubule'' is analyzed and, second, we suggest that a ratchet mechanism may be behind the folding of proteins; the latter is elaborated with a multidimensional ratchet model.

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

    SciTech Connect (OSTI)

    Huang, David M.; Chandler, David

    2000-04-01T23:59:59.000Z

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

  15. Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

    E-Print Network [OSTI]

    Li, Ying Wai; Landau, David P; 10.1016/j.cpc.2010.12.049

    2011-01-01T23:59:59.000Z

    Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and are largely inaccessible to "standard" Monte Carlo methods.

  16. Protein-Folding Landscapes in Multi-Chain Systems Major Classification: Biological Sciences

    Office of Scientific and Technical Information (OSTI)

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItem Not Found Item Not Foundenhancer activity than histone30518theProtein-Folding

  17. Protein-folding via divide-and-conquer optimization | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOn AprilAElectronicCurvesSpeedingScientificof Scientific andPredictiveProtein-folding via

  18. Dr Marek Michalak leads a young team of biochemists whose cutting-edge research into protein folding in the endoplasmic reticulum has exciting implications for new treatments

    E-Print Network [OSTI]

    MacMillan, Andrew

    and protein folding. Consequently, our research has implications for a large number of human diseases.The main strategies for protein folding disorders. What would you say are some of the most exciting findings to come pathology.These chaperones play a critical role in the control of protein folding and are therefore key

  19. This paper is published in Bioinformatics, v.17, no.4, pp.349-358, April 2001. 1 Multi-class Protein Fold Recognition Using Support Vector

    E-Print Network [OSTI]

    Ding, Chris

    -class Protein Fold Recognition Using Support Vector Machines and Neural Networks Chris H.Q. Ding #3; and Inna, USA Abstract Motivation: Protein fold recognition is an important approach to structure discovery with discriminative methods for protein fold prediction use the one-against- others method, which has the well

  20. Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

    E-Print Network [OSTI]

    Snow, Christopher

    propose an efficient method for the prediction of protein folding rate constants and mechanisms. We use While experiments can yield a wealth of insight into protein folding, it is difficult for experiments of protein folding. The comparison of the rate prediction with experiment could be used as a test

  1. This journal is c the Owner Societies 2010 Phys. Chem. Chem. Phys., 2010, 12, 1175311762 11753 Colored noise, folding rates and departure from Kramers' behavior

    E-Print Network [OSTI]

    in a multidimensional problem. 1. Introduction Despite numerous advances in recent years,1,2 the protein folding problem, viscosity of the medium, etc. have a profound effect on protein folding rates.3,4 For example, from they were performed for restrict intervals of parameters. Protein folding kinetics is an example

  2. A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling

    E-Print Network [OSTI]

    Kou, Samuel

    A study of density of states and ground states in hydrophobic-hydrophilic protein folding models June 2006 We propose an equi-energy EE sampling approach to study protein folding in the two a detailed study of the thermodynamics of HP protein folding, in particular, on the temperature dependence

  3. 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]

    Caflisch, Amedeo

    225 From: Methods in Molecular Biology, vol. 350: Protein Folding Protocols Edited by: Y. Bai and R in the transition state. Key Words: Protein folding; energy landscape; transition state ensemble; denatured state- sively applied to the analysis of protein folding (1­5). Although proteins are essential macromolecules

  4. September 17, 2004 12:44 Proceedings Trim Size: 9.75in x 6.5in protfoldnew PROTEIN FOLDING TRAJECTORY ANALYSIS

    E-Print Network [OSTI]

    Wong, Limsoon

    September 17, 2004 12:44 Proceedings Trim Size: 9.75in x 6.5in protfoldnew PROTEIN FOLDING Research Center, Yorktown Heights, USA E-mail: {parida,ruhongz}@us.ibm.com Understanding how protein folds in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free

  5. L e t t e r A two-fold interpenetrated three-dimensional cobalt(II) complex with

    E-Print Network [OSTI]

    Gao, Song

    ; it consists of two-fold interpenetrated a-Po- like networks. The study of inorganic coordination polymersL e t t e r A two-fold interpenetrated three-dimensional cobalt(II) complex with dual dicyanamide(II) coordination polymer, Co(4,4ş- was constructed using dicyanamide and 4,4ş-bpy)[N(CN) 2 ] 2 , bipyridine bridges

  6. Protein Folding Dynamics Detected By Time-Resolved Synchrotron X-ray Small-Angle Scattering Technique

    SciTech Connect (OSTI)

    Fujisawa, Tetsuro; Takahashi, Satoshi [RIKEN Harima Institute, SPring-8 Center, Laboratory for Biometal Science, Hyogo 679-5148 (Japan); Institute for Protein Research, Osaka University Suita Osaka 565-0871/CREST, JST (Japan)

    2007-03-30T23:59:59.000Z

    The polypeptide collapse is an essential dynamics in protein folding. To understand the mechanism of the collapse, in situ observation of folding by various probes is necessary. The changes in secondary and tertiary structures in the folding process of globular proteins, whose chain lengths are less than 300 polypeptides, were observed by circular dichrosim and intrinsic fluorescence spectroscopies, respectively. On the other hand, those in protein compactness could be only detected by using time-resolved synchrotron x-ray small-angle scattering technique. The observed dynamics for several proteins with different topologies suggested a common folding mechanism termed 'collapse and search' dynamics, in which the polypeptide collapse precedes the formation of the native contact formation. In 'collapse and search' dynamics, the most outstanding feature lied in the compactness of the initial intermediates. The collapsed intermediates demonstrated the scaling relationship between radius of gyration (Rg) and chain length with a scaling exponent of 0.35 {+-} 0.11, which is close to the value (1/3) predicted by mechano-statistical theory for the collapsed globules of polymers in poor solvent. Thus, it was suggested that the initial collapse is caused by the coil-globule transition of polymers. Since the collapse is essential to the folding of larger proteins, further investigations on the collapse likely lead to an important insight into the protein folding phenomena.

  7. Structural geometry, strain distribution, and mechanical evolution of eastern Umtanum Ridge and a comparison with other selected localities within Yakima fold structures, south-central Washington

    SciTech Connect (OSTI)

    Price, E.H.

    1982-01-01T23:59:59.000Z

    The Yakima fold system of south-central Washington and north-central Oregon is a series of megascopic anticlinal ridge of multilayered basalt. Cross-sectional strain analyses were performed at five localities within three anticlines. The analyses show that the strain is consistent both laterally along a fold and within different folds. Folding strain is localized layer-internal faulting, extensive shattering, and limited layer-parallel faulting. Most strain is cataclastic, but glassy flow tops appear to have been more ductile. The strain distributions and structural geometries accord well with a flexural flow buckle model; however, the internal cataclastic flow is not inherently penetrative and limited flexural slip has occurred. This fold model suggests that most strain in the fold is by simple shear and it took place above the topographic surface of adjacent synclinal valleys. Large reverse faults associated with the anticlines are interpreted to be folding strain required by the concentric folding and their displacement is interpreted to have reached the surface late in the folding process. Therefore, the observed strain and its distribution are interpreted to be not directly the result of regional plateau shortening, but of local stresses and resultant strains related to fold geometry. A mechanical analysis of the Umtanum structure termination geometry, combined with slickenside striae movement directions from the study areas suggests that the Palouse slope has behaved as a rigid buttress around which the basalt has rotated clockwise into the folds from the southeast. Compression-box clay modeling of the Yakima fold system within the Pasco Basin shows that the buttress edge orientations control the localization and orientations of buckle folds. Fold orientations and three-dimensional shapes remarkably resembling the Yakima fold system in the Pasco Basin were produced under north-south compression.

  8. 3D synthetic aperture PIV measurements from artificial vibrating vocal folds

    E-Print Network [OSTI]

    Daily, Jesse; Belden, Jesse; Thomson, Scott; Truscott, Tadd

    2011-01-01T23:59:59.000Z

    During speech, air from the lungs is forced past the vocal folds which vibrate, producing sound. A pulsatile jet of air is formed downstream of the vibrating folds which interacts with the various structures in the airway. Currently, it is postulated that the way this jet interacts with the downstream structures in the airway directly affects the quality of human speech. In order to better understand this jet, it is desirable to visualize the jet in three dimensions. We present the results of a method that reconstructs the three dimensional velocity field using Synthetic aperture PIV (SAPIV) \\cite{Belden:2010}. SAPIV uses an array of high-speed cameras to artificially create a single camera with a variable focal length. This is accomplished by overlapping the images from the array to create a "focal stack". As the images are increasingly overlapped, more distant image planes come into focus. 3D PIV is then performed on the "refocused" focal stack to reconstruct the flow field in three dimensions. SAPIV has th...

  9. Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme

    SciTech Connect (OSTI)

    Matte, Allan; Grosse, Stephan; Bergeron, Hélčne; Abokitse, Kofi; Lau, Peter C.K. (Biotech Res.)

    2012-04-30T23:59:59.000Z

    The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavoring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a -barrel structure and two -helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the -barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site.

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

    E-Print Network [OSTI]

    Simmons, Walter

    2013-01-01T23:59:59.000Z

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

  11. Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding

    E-Print Network [OSTI]

    Guido Tiana; Carlo Camilloni

    2012-07-05T23:59:59.000Z

    The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations that build out the transition state is particularly cumbersome, mainly because of the large computational cost of generating a statistically-sound set of folding trajectories. Here we show that a biasing algorithm, based on the physics of the ratchet-and-pawl, can be used to identify efficiently the transition state. The basic idea is that the algorithmic ratchet exerts a force on the protein when it is climbing the free-energy barrier, while it is inactive when it is descending. The transition state can be identified as the point of the trajectory where the ratchet changes regime. Besides discussing this strategy in general terms, we test it within a protein model whose transition state can be studied independently by plain molecular dynamics simulations. Finally, we show its power in explicit-solvent simulations, obtaining and characterizing a set of transition--state conformations for ACBP and CI2.

  12. A New Scaffold of an Old Protein Fold Ensures Binding to the Bisintercalator Thiocoraline

    SciTech Connect (OSTI)

    Biswas, Tapan; Zolova, Olga E.; Lombó, Felipe; de la Calle, Fernando; Salas, Jose A.; Tsodikov, Oleg V.; Garneau-Tsodikova, Sylvie (Michigan); (Oviedo); (PharmaMar)

    2010-09-02T23:59:59.000Z

    Thiocoraline is a thiodepsipeptide with potent antitumor activity. TioX, a protein with an unidentified function, is encoded by a gene of the thiocoraline biosynthetic gene cluster. The crystal structure of the full-length TioX protein at 2.15 {angstrom} resolution reveals that TioX protomer shares an ancient {beta}{alpha}{beta}{beta}{beta} fold motif with glyoxalase I and bleomycin resistance protein families, despite a very low sequence homology. Intriguingly, four TioX monomers form a unique 2-fold symmetric tetrameric assembly that is stabilized by four intermolecular disulfide bonds formed cyclically between Cys60 and Cys66 of adjacent monomers. The arrangement of two of the four monomers in the TioX tetramer is analogous to that in dimeric bleomycin resistance proteins. This analogy indicates that this novel higher-order structural scaffold of TioX may have evolved to bind thiocoraline. Our equilibrium titration studies demonstrate the binding of a thiocoraline chromophore analog, quinaldic acid, to TioX, thereby substantiating this model. Furthermore, a strain of Streptomyces albus containing an exogenous thiocoraline gene cluster devoid of functional tioX maintains thiocoraline production, albeit with a lower yield. Taken together, these observations rule out a direct enzymatic function of TioX and suggest that TioX is involved in thiocoraline resistance or secretion.

  13. The Influence of fold and fracture development on reservoir behavior of the Lisburne Group of northern Alaska

    SciTech Connect (OSTI)

    Wesley K. Wallace; Catherine L. Hanks; Jerry Jensen: Michael T. Whalen; Paul Atkinson; Joseph Brinton; Thang Bui; Margarete Jadamec; Alexandre Karpov; John Lorenz; Michelle M. McGee; T.M. Parris; Ryan Shackleton

    2004-07-01T23:59:59.000Z

    The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is folded and thrust faulted where it is exposed throughout the Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study were to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of folds and their truncation by thrust faults. (2) The influence of folding on fracture patterns. (3) The influence of deformation on fluid flow. (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. Symmetrical detachment folds characterize the Lisburne in the northeastern Brooks Range. In contrast, Lisburne in the main axis of the Brooks Range is deformed into imbricate thrust sheets with asymmetrical hangingwall anticlines and footwall synclines. The Continental Divide thrust front separates these different structural styles in the Lisburne and also marks the southern boundary of the northeastern Brooks Range. Field studies were conducted for this project during 1999 to 2001 in various locations in the northeastern Brooks Range and in the vicinity of Porcupine Lake, immediately south of the Continental Divide thrust front. Results are summarized below for the four main subject areas of the study.

  14. MCAMC: An Advanced Algorithm for Kinetic Monte Carlo Simulations: from Magnetization Switching to Protein Folding

    E-Print Network [OSTI]

    M. A. Novotny; Shannon M. Wheeler

    2002-11-02T23:59:59.000Z

    We present the Monte Carlo with Absorbing Markov Chains (MCAMC) method for extremely long kinetic Monte Carlo simulations. The MCAMC algorithm does not modify the system dynamics. It is extremely useful for models with discrete state spaces when low-temperature simulations are desired. To illustrate the strengths and limitations of this algorithm we introduce a simple model involving random walkers on an energy landscape. This simple model has some of the characteristics of protein folding and could also be experimentally realizable in domain motion in nanoscale magnets. We find that even the simplest MCAMC algorithm can speed up calculations by many orders of magnitude. More complicated MCAMC simulations can gain further increases in speed by orders of magnitude.

  15. Relevant distance between two different instances of the same potential energy in protein folding

    E-Print Network [OSTI]

    Jose Luis Alonso; Pablo Echenique

    2005-04-21T23:59:59.000Z

    In the context of complex systems and, particularly, of protein folding, a physically meaningful distance is defined which allows to make useful statistical statements about the way in which energy differences are modified when two different instances of the same potential-energy function are used. When the two instances arise from the fact that different algorithms or different approximations are used, the distance herein defined may be used to evaluate the relative accuracy of the two methods. When the difference is due to a change in the free parameters of which the potential depends on, the distance can be used to quantify, in each region of parameter space, the robustness of the modeling to such a change and this, in turn, may be used to assess the significance of a parameters' fit. Both cases are illustrated with a practical example: the study of the Poisson-based solvation energy in the Trp-Cage protein (PDB code 1L2Y).

  16. Improvements in Mixing Time and Mixing Uniformity in Devices Designed for Studies of Protein Folding Kinetics

    SciTech Connect (OSTI)

    Yao, Shuhuai [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bakajin, Olgica [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2007-08-01T23:59:59.000Z

    Using a microfluidic laminar flow mixer designed for studies of protein folding kinetics, we demonstrate a mixing time of 1 +/- 1 micros with sample consumption on the order of femtomoles. We recognize two limitations of previously proposed designs: (1) size and shape of the mixing region, which limits mixing uniformity and (2) the formation of Dean vortices at high flow rates, which limits the mixing time. We address these limitations by using a narrow shape-optimized nozzle and by reducing the bend of the side channel streamlines. The final design, which combines both of these features, achieves the best performance. We quantified the mixing performance of the different designs by numerical simulation of coupled Navier-Stokes and convection-diffusion equations and experiments using fluorescence resonance energy-transfer (FRET)-labeled DNA.

  17. Systematic speedup of path integrals of a generic N-fold discretized theory

    SciTech Connect (OSTI)

    Bogojevic, A.; Balaz, A.; Belic, A. [Institute of Physics, P.O. Box 57, 11001 Belgrade (Serbia and Montenegro)

    2005-08-01T23:59:59.000Z

    We present and discuss a detailed derivation of an analytical method that systematically improves the convergence of path integrals of a generic N-fold discretized theory. We develop an explicit procedure for calculating a set of effective actions S{sup (p)}, for p=1,2,3,... which have the property that they lead to the same continuum amplitudes as the starting action, but converge to that continuum limit ever faster. Discretized amplitudes calculated using the p-level effective action differ from the continuum limit by a term of order 1/N{sup p}. We obtain explicit expressions for the effective actions for levels p{<=}9. We end by analyzing the speedup of Monte Carlo simulations of two different models: an anharmonic oscillator with quartic coupling and a particle in a modified Poeschl-Teller potential.

  18. Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

    SciTech Connect (OSTI)

    Martinez-Hackert, E.; Hendrickson, W

    2009-01-01T23:59:59.000Z

    Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.

  19. Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-06-01T23:59:59.000Z

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  20. Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-08-01T23:59:59.000Z

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.