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Author : Christopher Davis Snow
Publisher :
ISBN 13 :
Total Pages : 432 pages
Book Rating : 4.52/5 ( download)
Download or read book Protein Folding Kinetics with Ensemble Molecular Dynamics written by Christopher Davis Snow and published by . This book was released on 2006 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :
Publisher : Academic Press
ISBN 13 : 0128211350
Total Pages : 552 pages
Book Rating : 4.59/5 ( download)
Download or read book Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly written by and published by Academic Press. This book was released on 2020-03-18 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field
Author : Si Zhang
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.47/5 ( download)
Download or read book COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING written by Si Zhang and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The cellular function of proteins, and their targeting by drug applications, are both governed by biomolecular thermodynamics and kinetics. In order to make meaningful and efficient predictions of these mechanisms, molecular simulations must be able to estimate the binding affinity and rates of association and dissociation of a protein-ligand complex, or the populations and rates of exchange between distinct conformational states (i.e. folding and unfolding, binding and unbinding). The above studies are typically done using different, but complementary approaches. Alchemical methods, including free energy perturbation (FEP) and thermodynamic integration (TI), have become the dominant method for computing high-quality estimates of protein-ligand binding free energies. In particular, the widely-used approach of relative binding free energy calculation can deliver accuracies within 1 kcal mol−1. However, detailed physical pathways and kinetics are missing from these calculations. In principle, all-atom molecular dynamics (MD) simulation, with the help of Markov State Models (MSMs), can be used to obtain this information, yet finite sampling error still limits MSM approaches from making accurate predictions for very slow unfolding or unbinding processes. To overcome these issues, a new approach called multiensemble Markov models (MEMMs) have been developed, in which sampling from biased thermodynamic ensembles can be used to infer states populations and transition rates in unbiased ensembles. In this dissertation, two distinct biophysical problems are investigated. In the first part, we apply expanded ensemble (EE) methods to accurately predict relative binding free energies for a series of protein-ligand systems. Moreover, we propose a simple optimization scheme for choosing alchemical intermediates in free energy simulations. In the second part, we employ MEMMs to estimate the free energies and kinetics of protein folding and ligand binding, to achieve greatly improved predictions. Finally, we combine the above EE method and a maximum-caliber algorithm to study how sequence mutations perturb protein stability and folding kinetics. In summary, this work comprises a wide range of current methodology in biophysical simulation, complementing and improving upon existing approaches.
Author : Gregory Ross Bowman
Publisher : Stanford University
ISBN 13 :
Total Pages : 279 pages
Book Rating : 4.55/5 ( download)
Download or read book Markov State Models for Protein and RNA Folding written by Gregory Ross Bowman and published by Stanford University. This book was released on 2010 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the molecular bases of human health could greatly augment our ability to prevent and treat diseases. For example, a deeper understanding of protein folding would serve as a reference point for understanding, preventing, and reversing protein misfolding in diseases like Alzheimer's. Unfortunately, the small size and tremendous flexibility of proteins and other biomolecules make it difficult to simultaneously monitor their thermodynamics and kinetics with sufficient chemical detail. Atomistic Molecular Dynamics (MD) simulations can provide a solution to this problem in some cases; however, they are often too short to capture biologically relevant timescales with sufficient statistical accuracy. We have developed a number of methods to address these limitations. In particular, our work on Markov State Models (MSMs) now makes it possible to map out the conformational space of biomolecules by combining many short simulations into a single statistical model. Here we describe our use of MSMs to better understand protein and RNA folding. We chose to focus on these folding problems because of their relevance to misfolding diseases and the fact that any method capable of describing such drastic conformational changes should also be applicable to less dramatic but equally important structural rearrangements like allostery. One of the key insights from our folding simulations is that protein native states are kinetic hubs. That is, the unfolded ensemble is not one rapidly mixing set of conformations. Instead, there are many non-native states that can each interconvert more rapidly with the native state than with one another. In addition to these general observations, we also demonstrate how MSMs can be used to make predictions about the structural and kinetic properties of specific systems. Finally, we explain how MSMs and other enhanced sampling algorithms can be used to drive efficient sampling.
Author : R. A. Broglia
Publisher : IOS Press
ISBN 13 : 9781586031664
Total Pages : 378 pages
Book Rating : 4.6X/5 ( download)
Download or read book Protein Folding, Evolution and Design written by R. A. Broglia and published by IOS Press. This book was released on 2001 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text presents the results of broad interdisciplinary effort to study proteins in physical and evolutionary prospectives. Among the authors are physicists, chemists, crystallographers, and evolutionary biologists. Experimental and theoretical developments from molecules to cells are presented providing a broad picture of modern biophysical chemistry.
Author : Prakash Saudagar
Publisher : Springer Nature
ISBN 13 : 9819920795
Total Pages : 287 pages
Book Rating : 4.92/5 ( download)
Download or read book Protein Folding Dynamics and Stability written by Prakash Saudagar and published by Springer Nature. This book was released on 2023-05-27 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.
Author : Ke-li Han
Publisher : Springer Science & Business Media
ISBN 13 : 3319029703
Total Pages : 488 pages
Book Rating : 4.02/5 ( download)
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Author : Monika Fuxreiter
Publisher : CRC Press
ISBN 13 : 1482297868
Total Pages : 458 pages
Book Rating : 4.67/5 ( download)
Download or read book Computational Approaches to Protein Dynamics written by Monika Fuxreiter and published by CRC Press. This book was released on 2014-12-24 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an
Author : Sidney Paul Elmer
Publisher :
ISBN 13 :
Total Pages : 264 pages
Book Rating : 4.50/5 ( download)
Download or read book Molecular Dynamics Studies on the Folding Dynamics of Poly-phenylacetylene, a Non-biological Polymer with a Helical, Folded State written by Sidney Paul Elmer and published by . This book was released on 2004 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Yawen Bai
Publisher : Springer Science & Business Media
ISBN 13 : 1597451894
Total Pages : 332 pages
Book Rating : 4.95/5 ( download)
Download or read book Protein Folding Protocols written by Yawen Bai and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process. Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences.
