Search results for: protein-folding-kinetics

A Motion Planning Approach to Protein Folding

Author : Guang Song
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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 known as the native state. There are two major problems in protein folding. One, usually called protein structure prediction, is to predict the structure of the protein's native state given only the amino acid sequence. Another important and strongly related problem, often called protein folding, is to study how the amino acid sequence dynamically transitions from an unstructured state to the native state. In this dissertation, we concentrate on the second problem. There are several approaches that have been applied to the protein folding problem, including molecular dynamics, Monte Carlo methods, statistical mechanical models, and lattice models. However, most of these approaches suffer from either overly-detailed simulations, requiring impractical computation times, or overly-simplified models, resulting in unrealistic solutions. In this work, we present a novel motion planning based framework for studying protein folding. We describe how it can be used to approximately map a protein's energy landscape, and then discuss how to find approximate folding pathways and kinetics on this approximate energy landscape. In particular, our technique can produce potential energy landscapes, free energy landscapes, and many folding pathways all from a single roadmap. The roadmap can be computed in a few hours on a desktop PC using a coarse potential energy function. In addition, our motion planning based approach is the first simulation method that enables the study of protein folding kinetics at a level of detail that is appropriate (i.e., not too detailed or too coarse) for capturing possible 2-state and 3-state folding kinetics that may coexist in one protein. Indeed, the unique ability of our method to produce large sets of unrelated folding pathways may potentially provide crucial insight into some aspects of folding kinetics that are not available to other theoretical techniques.

Protein Folding Kinetics with Ensemble Molecular Dynamics

Author : Christopher Davis Snow
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Computational Approaches for Understanding Dynamical Systems Protein Folding and Assembly

Author : David B. Teplow
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Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more.

Folding Kinetics of BPTI Variants and Development of a Model for the Relationship of Hydrogen Exchange to Protein Folding

Author : Renhao Li
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Old and New Views of Protein Folding

Author : Kunihiro Kuwajima
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Folding of B-lactoglobolin, a case of the inconsistency of local and non-local interactions. (Y. Goto, M. Hoshino, K. Kuwata and C. A. Batt). Dynamic stability of bovine B-lactoglobulin studied by hydrogen/deuterium exchange. (V. Forge, M. Hoshino, K. Kuwata, C. A. Batt, and Y. Goto). Folding intermediates of equine B-lactoglobulin. (M. Ikeguchi). Structural analysis of protein folding intermediates by solution X-ray scattering. (M. Arau, K. Ito, K. Maki, T. Ikura, T. Inobe, H. Kihara, Y. Amemiya and K. Kuwajima). Nonnative structure of proteins and its implications for protein folding. (K. Soda and Y. Seki). Dynamics of a-helices, B-hairpins and loops. (J. Hofrichter, P. A. Thompson, V. Muñoz, G. S. Jas, E. Henry, S. J. Hagen, L. Lapidus and W. A. Eaton). Kinetic and structural characterization of early events in protein folding. (H. Roder, M. C. R. Shastry, J. M. Sauder and S.-H. Park). CD measurements on the early folding intermediate of cytochrome c using the fast flow mixer. (S. Takahashi, S. Akiyama, K. Ishimori and I. Morishima). Fast protein dynamics probed by vibrational spectroscopy. (Y. Mizutani, K. Yamamoto and T. Kitagawa). The consistency principle revisited. (N. Go). Complete structure reconstruction for model proteins using mutation calorimetry. (M. P. Morrissey and E. I. Shakhnovich). Site resolved landscape theory of fast folding proteins. (S. Takada). Hierarchy and connectivity in the folding funnel. (H. K. Nakamura and M. Sasai). The folding mechanisms of a-lactalbumin and Ca - binding Iysozyme. (K. Kuwajima, M. Arai, M. Mizuguchi, T. Koshiba and K. Nitta). Determinants of the native-like tertiary topology in the a-lactakbumin molten globule. (Z.-y. Peng). Kinetic folding reactions and molecular dynamics simulations of a-lactalbumin. (T. Yoda, M. Saito, M. Arai, K. Horii, K. Tsumoto, M. Matsushima, I. Kumagai, T. K. Chaudhuri and K. Kuwajima). Folding-unfolding processes of four species of 3SS-variant of lysozyme - the role of an individual disulfide bridge. (A. Yakota, Y. Noda, H. Tachibana and S.-I. Segawa). Evaluation of some factors that contribute to conformational stability of a protein using database of stability/structure. (K. Yutani, K. Takano and J. Funahashi). Computational analysis of protein thermal stability and dennatured state. (Y. Sugita). Hydrophobic effects: roles of water and denaturants. /M. Ikeguchi, S. Nakamura and K. Shimizu). Effects of deletion or insertions on the structure, stability and function of staphylococcal nuclease. (M. Kataoka, J. Tunoki and H. Takahara). Statistical analysis of unfolding process of protein G BI domain with 50 runs of molecular dynamics simulations. (T. Takahashi, A. Tanaka and K. Nagayama). Protein folding simulations by generalized-ensemble algorithms. (Y. Okamoto). Protein folding and genome evolution. (M. Go and K. Yura). Symmetry in protein folds: implication in evolution and folding. (K. Kinoshita, A. Kidera and N. Go). Multistate kinetics of folding and unfolding of barstar. (A. K. Bhuyan and J. B. Udgaonkar). Equilibrium and kinetics of folding of staphylococcal nuclease and its proline mutants. (K. Maki, T. Ikura, A. Mohs and K. Kuwajima). Cold denaturation and folding/unfolding of a protein at low temperature. (A. Tamura). Folding elements in dihydrofolate reductase suggested by circular permutation analysis. (M. Iwakura). Thermodynamic analysis of protein induced folding upon DNA binding. (M. Oda, K. Furukawa, K. Ogata, A. Sarai and H. Nakamura). High pressure NMR study on protein dynamics and folding. (K. Akasaka).

Cumulated Index Medicus

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Computational Methods for Protein Folding

Author : Richard A. Friesner
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Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels. Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies. Computational Methods for Protein Folding is the 120th volume in the acclaimed series Advances in Chemical Physics, a compilation of scholarly works dedicated to the dissemination of contemporary advances in chemical physics, edited by Nobel Prize-winner Ilya Prigogine.

Early Events in Protein Folding Investigated Through Ultrarapid Microfluidic Mixing

Author : Steven Andrew Waldauer
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Computational Approaches to Understanding the Role of Hydration Forces in Protein Folding

Author : Jon Michael Sorenson
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Leucine Zipper Peptides as Models for Protein Folding

Author : Hans Wendt
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Topology and Protein Folding

Author : Leslie Lou Chavez
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Index Medicus

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Protein Folding Kinetics

Author : Bengt Nölting
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First methods book which includes many detailed descriptions Absolutely needed and thus timely for the scientific community Comprises 15% more content and includes the mentioned special features

Computer Simulations of Protein Folding

Author : Atipat Rojnuckarin
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Protein Folding Funnels

Author : Peter Evans Leopold
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Application of Time resolved Tryptophan Phosphoresence Spectroscopy to Protein Folding Studies

Author : Vinod Subramaniam
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Experimental and Computational Investigation of Early Events in Protein Folding

Author : Vijay R. Singh
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Protein Folding and Solvent

Author : Young Min Rhee
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Time Resolved Optical Methods for the Study of Protein Folding and Conformation

Author : Anne Gershenson
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Protein Folding and Protein protein Interactions

Author : Shyam S. Vangala
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