Efficient Sampling Of Protein Conformational Dynamics And Prediction Of Mutation Effects
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Efficient Sampling Of Protein Conformational Dynamics And Prediction Of Mutation Effects
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Author : Hongbin Wan
language : en
Publisher:
Release Date : 2019
Efficient Sampling Of Protein Conformational Dynamics And Prediction Of Mutation Effects written by Hongbin Wan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with categories.
Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; however, MD simulations are typically limited to the microsecond timescale, whereas biological motions can take seconds or longer. Because of this, it remains extremely challenging to restrain simulations using ensemble-averaged experimental observables. Among various approaches to elucidate the kinetics of molecular simulations, Markov State Models (MSMs) have proven their ability to extract both kinetic and thermodynamic properties of long-timescale motions using ensembles of shorter MD simulation trajectories. In this dissertation, we have implemented an MSM path-entropy method, based on the idea of maximum-caliber, to efficiently predict the changes in protein folding behavior upon mutation. Next, we explore the accuracy of different MSM estimators applied to trajectory data obtained by adaptive seeding, in which new rounds of short MD simulations are collected from states of interest, and propose a simple method to build accurate models by population re-weighting of the transition count matrix. Finally, we explore ways to reconcile simulated ensembles with Hydrogen/Deuterium exchange (HDX) protection measurements, by constructing multi-ensemble Markov State Models (MEMMs) from biased MD simulations, and reconciling these predictions against the experimental data using the BICePs (Bayesian Inference of Conformational Populations) algorithm. We apply this approach to model the native-state conformational ensemble of apomyoglobin at neutral pH.
Molecular Dynamics And Electrostatic Modeling Of Proteins
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Author : Jeanmarie Guenot
language : en
Publisher:
Release Date : 1993
Molecular Dynamics And Electrostatic Modeling Of Proteins written by Jeanmarie Guenot and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1993 with Molecular biology categories.
Prediction Of Protein Structure And The Principles Of Protein Conformation
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Author : G.D. Fasman
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
Prediction Of Protein Structure And The Principles Of Protein Conformation written by G.D. Fasman and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Science categories.
The prediction of the conformation of proteins has developed from an intellectual exercise into a serious practical endeavor that has great promise to yield new stable enzymes, products of pharmacological significance, and catalysts of great potential. With the application of predic tion gaining momentum in various fields, such as enzymology and immunology, it was deemed time that a volume be published to make available a thorough evaluation of present methods, for researchers in this field to expound fully the virtues of various algorithms, to open the field to a wider audience, and to offer the scientific public an opportunity to examine carefully its successes and failures. In this manner the practitioners of the art could better evaluate the tools and the output so that their expectations and applications could be more realistic. The editor has assembled chapters by many of the main contributors to this area and simultaneously placed their programs at three national resources so that they are readily available to those who wish to apply them to their personal interests. These algorithms, written by their originators, when utilized on pes or larger computers, can instantaneously take a primary amino acid sequence and produce a two-or three-dimensional artistic image that gives satisfaction to one's esthetic sensibilities and food for thought concerning the structure and function of proteins. It is in this spirit that this volume was envisaged.
Biomolecular Simulations
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Author : Massimiliano Bonomi
language : en
Publisher: Humana
Release Date : 2020-08-14
Biomolecular Simulations written by Massimiliano Bonomi and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-08-14 with Science categories.
This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.
Protein Simulations
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Author : Valerie Daggett
language : en
Publisher: Elsevier
Release Date : 2003-11-26
Protein Simulations written by Valerie Daggett and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-11-26 with Medical categories.
Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
Protein Conformational Dynamics
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Author : Ke-li Han
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-01-20
Protein Conformational Dynamics written by Ke-li Han and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-01-20 with Medical categories.
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.
Computational Protein Design
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Author : Ilan Samish
language : en
Publisher: Humana
Release Date : 2016-12-03
Computational Protein Design written by Ilan Samish and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-12-03 with Science categories.
The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Directed Enzyme Evolution Advances And Applications
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Author : Miguel Alcalde
language : en
Publisher: Springer
Release Date : 2017-02-14
Directed Enzyme Evolution Advances And Applications written by Miguel Alcalde and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-02-14 with Science categories.
This book focuses on some of the most significant advances in enzyme engineering that have been achieved through directed evolution and hybrid approaches. On the 25th anniversary of the discovery of directed evolution, this volume is a tribute to the pioneers of this thrilling research field, and at the same time provides a comprehensive overview of current research and the state of the art. Directed molecular evolution has become the most reliable and robust method to tailor enzymes, metabolic pathways or even whole microorganisms with improved traits. By mirroring the Darwinian algorithm of natural selection on a laboratory scale, new biomolecules of invaluable biotechnological interest can now be engineered in a manner that surpasses the boundaries of nature. The volume is divided into two sections, the first of which provides an update on recent successful cases of enzyme ensembles from different areas of the biotechnological spectrum, including tryptophan synthases, unspecific peroxygenases, phytases, therapeutic enzymes, stereoselective enzymes and CO2-fixing enzymes. This section also provides information on the directed evolution of whole cells. The second section of the book summarizes a variety of the most applicable methods for library creation, together with the future trends aimed at bringing together directed evolution and in silico/computational enzyme design and ancestral resurrection.
An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation
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Author : Gregory R. Bowman
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-12-02
An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation written by Gregory R. Bowman and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-12-02 with Science categories.
The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Protein Conformation
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Author : Derek J. Chadwick
language : en
Publisher: John Wiley & Sons
Release Date : 2008-04-30
Protein Conformation written by Derek J. Chadwick and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-04-30 with Science categories.
How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.