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Statistical Models Of Protein Conformational Dynamics
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Book Synopsis Metastability and Markov State Models in Molecular Dynamics by : Christof Schütte
Download or read book Metastability and Markov State Models in Molecular Dynamics written by Christof Schütte and published by American Mathematical Soc.. This book was released on 2013-12-26 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applications in modern biotechnology and molecular medicine often require simulation of biomolecular systems in atomic representation with immense length and timescales that are far beyond the capacity of computer power currently available. As a consequence, there is an increasing need for reduced models that describe the relevant dynamical properties while at the same time being less complex. In this book the authors exploit the existence of metastable sets for constructing such a reduced molecular dynamics model, the so-called Markov state model (MSM), with good approximation properties on the long timescales. With its many examples and illustrations, this book is addressed to graduate students, mathematicians, and practical computational scientists wanting an overview of the mathematical background for the ever-increasing research activity on how to construct MSMs for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecular sensors to molecular aggregation. This book bridges the gap between mathematical research on molecular dynamics and its practical use for realistic molecular systems by providing readers with tools for performing in-depth analysis of simulation and data-analysis methods. Titles in this series are co-published with the Courant Institute of Mathematical Sciences at New York University.
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
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.
Book Synopsis An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation by : Gregory R. Bowman
Download or read book An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation written by Gregory R. Bowman and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Modulation of Protein Function written by and published by . This book was released on 1979 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Actions: Principles and Modeling by : Ivet Bahar
Download or read book Protein Actions: Principles and Modeling written by Ivet Bahar and published by Garland Science. This book was released on 2017-02-14 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.
Book Synopsis Prediction of Protein Structure and the Principles of Protein Conformation by : G.D. Fasman
Download or read book Prediction of Protein Structure and the Principles of Protein Conformation written by G.D. Fasman and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 796 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly by :
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 2020-03-05 with total page 554 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
Book Synopsis Understanding Protein Dynamics, Binding and Allostery for Drug Design by : Guang Hu
Download or read book Understanding Protein Dynamics, Binding and Allostery for Drug Design written by Guang Hu and published by Frontiers Media SA. This book was released on 2021-06-08 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :Alexander V. Yakubovich Publisher :Springer Science & Business Media ISBN 13 :3642225926 Total Pages :130 pages Book Rating :4.6/5 (422 download)
Book Synopsis Theory of Phase Transitions in Polypeptides and Proteins by : Alexander V. Yakubovich
Download or read book Theory of Phase Transitions in Polypeptides and Proteins written by Alexander V. Yakubovich and published by Springer Science & Business Media. This book was released on 2011-09-01 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are nearly 100 000 different protein sequences encoded in the human genome, each with its own specific fold. Understanding how a newly formed polypeptide sequence finds its way to the correct fold is one of the greatest challenges in the modern structural biology. The aim of this thesis is to provide novel insights into protein folding by considering the problem from the point of view of statistical mechanics. The thesis starts by investigating the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. This knowledge is then applied in the statistical mechanics description of helix↔coil transitions in polypeptides. Finally, the theoretical formalism is generalized to the case of proteins in an aqueous environment. The major novelty of this work lies in combining (a) a formalism based on fundamental physical properties of the system and (b) the resulting possibility of describing the folding↔unfolding transitions quantitatively. The clear physical nature of the formalism opens the way to further applications in a large variety of systems and processes.
Book Synopsis The Thermodynamic Machinery of Life by : Michal Kurzynski
Download or read book The Thermodynamic Machinery of Life written by Michal Kurzynski and published by Springer Science & Business Media. This book was released on 2006-07-09 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thermodynamics was created in the ?rst half of the 19th century as a theory designed to explain the functioning of heat engines converting heat into mechanical work. In the course of time, while the scope of research in this ?eld was being extended to a wider and wider class of energy transformations, thermodynamics came to be considered as a general theory of machines identi?ed with energy transducers. Imp- tant progress in biochemistry in the ?rst half of the 20th century, and in molecular biology in the second half, made it possible to think of treating even living organisms as machines, at least on the subcellular level. However, success in applying thermodynamics to elucidate the phenomenon of life has been rather mitigated. Two reasons seem to be responsible for this unsatisfactory s- uation. Nineteenth century thermodynamics dealt only with simple (homogeneous) systems in complete equilibrium. Although during the 20th century a nonequilibrium thermodynamics was developed, sta- ing with the Onsager theory of linear response and ending with the Prigogine nonlinear theory of dissipative structures, these theories still concern the originally homogeneous systems. Because living organisms are complex systems with a historically frozen spatial and functional structure, a thermodynamics of both nonequilibrium and complex s- tems is needed for their description. The ?rst goal of the present book is to formulate the foundations of such a thermodynamics.
Book Synopsis Nuclear Magnetic Resonance by : G A Webb
Download or read book Nuclear Magnetic Resonance written by G A Webb and published by Royal Society of Chemistry. This book was released on 2010-04-09 with total page 513 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a spectroscopic method, nuclear magnetic resonance (NMR) has seen spectacular growth, both as a technique and in its applications. Today's applications of NMR span a wide range of scientific disciplines, from physics to biology to medicine. Each volume of Nuclear Magnetic Resonance comprises a combination of annual and biennial reports which together provide comprehensive coverage of the literature on this topic. This Specialist Periodical Report reflects the growing volume of published work involving NMR techniques and applications, in particular NMR of natural macromolecules, which is covered in two reports: NMR of Proteins and Nucleic Acids and NMR of Carbohydrates, Lipids and Membranes. For those wanting to become rapidly aquainted with specific areas of NMR, Nuclear Magnetic Resonance provides unrivalled scope of coverage. Seasoned practitioners of NMR will find this an invaluable source of current methods and applications.
Book Synopsis Protein Homeostasis Diseases by : Angel L. Pey
Download or read book Protein Homeostasis Diseases written by Angel L. Pey and published by Academic Press. This book was released on 2020-02-13 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Homeostasis Diseases: Mechanisms and Novel Therapies offers an interdisciplinary examination of the fundamental aspects, biochemistry and molecular biology of protein homeostasis disease, including the use of natural and pharmacological small molecules to treat common and rare protein homeostasis disorders. Contributions from international experts discuss the biochemical and genetic components of protein homeostasis disorders, the mechanisms by which genetic variants may cause loss-of-function and gain-of-toxic-function, and how natural ligands can restore protein function and homeostasis in genetic diseases. Applied chapters provide guidance on employing high throughput sequencing and screening methodologies to develop pharmacological chaperones and repurpose approved drugs to treat protein homeostasis disorders. - Provides an interdisciplinary examination of protein homeostasis disorders, with an emphasis on treatment strategies employing small natural and pharmacological ligands - Offers applied approaches in employing high throughput sequencing and screening to develop pharmacological chaperones to treat protein homeostasis disease - Gathers expertise from a range of international chapter authors who work across various biological methods and disease specific disciplines of relevance
Book Synopsis A Study of Enzymes by : Stephen A. Kuby
Download or read book A Study of Enzymes written by Stephen A. Kuby and published by CRC Press. This book was released on 2019-07-23 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: First published in 1990, this comprehensive monograph consists of two parts: Volume I, entitled Enzyme Catalysis, Kinetics, and Substrate Binding; and Volume II, entitled Mechanism of Enzyme Action. Volume I focuses on several aspects of enzyme catalytic behavior, their steady-state and transient-state kinetics, and the thermodynamic properties of substrate binding. Packed with figures, tables, schemes, and photographs, this volume contains over 1,000 references, including references regarding enzymology's fascinating history. This comprehensive book is of particular interest to enzymology students, teachers, and researchers. Volume II presents selected "cutting edge" examples of techniques and approaches being pursued in biochemistry. This up-to-date resource includes 11 chapters, which illustrate important theoretical and practical aspects of enzyme mechanisms. It also features selected examples in which today's most important techniques, ideas, and theories are used to elaborate on the intricate nature of enzyme action mechanisms. This particular volume provides important information for both the novice and the seasoned investigator.
Book Synopsis Nanoscale Photonic Imaging by : Tim Salditt
Download or read book Nanoscale Photonic Imaging written by Tim Salditt and published by Springer Nature. This book was released on 2020-06-09 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book, edited and authored by a team of world-leading researchers, provides a broad overview of advanced photonic methods for nanoscale visualization, as well as describing a range of fascinating in-depth studies. Introductory chapters cover the most relevant physics and basic methods that young researchers need to master in order to work effectively in the field of nanoscale photonic imaging, from physical first principles, to instrumentation, to mathematical foundations of imaging and data analysis. Subsequent chapters demonstrate how these cutting edge methods are applied to a variety of systems, including complex fluids and biomolecular systems, for visualizing their structure and dynamics, in space and on timescales extending over many orders of magnitude down to the femtosecond range. Progress in nanoscale photonic imaging in Göttingen has been the sum total of more than a decade of work by a wide range of scientists and mathematicians across disciplines, working together in a vibrant collaboration of a kind rarely matched. This volume presents the highlights of their research achievements and serves as a record of the unique and remarkable constellation of contributors, as well as looking ahead at the future prospects in this field. It will serve not only as a useful reference for experienced researchers but also as a valuable point of entry for newcomers.
Book Synopsis Hydrogen Exchange Mass Spectrometry of Proteins by : David D. Weis
Download or read book Hydrogen Exchange Mass Spectrometry of Proteins written by David D. Weis and published by John Wiley & Sons. This book was released on 2016-01-12 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hydrogen exchange mass spectrometry is widely recognized for its ability to probe the structure and dynamics of proteins. The application of this technique is becoming widespread due to its versatility for providing structural information about challenging biological macromolecules such as antibodies, flexible proteins and glycoproteins. Although the technique has been around for 25 years, this is the first definitive book devoted entirely to the topic. Hydrogen Exchange Mass Spectrometry of Proteins: Fundamentals, Methods and Applications brings into one comprehensive volume the theory, instrumentation and applications of Hydrogen Exchange Mass Spectrometry (HX-MS) - a technique relevant to bioanalytical chemistry, protein science and pharmaceuticals. The book provides a solid foundation in the basics of the technique and data interpretation to inform readers of current research in the method, and provides illustrative examples of its use in bio- and pharmaceutical chemistry and biophysics In-depth chapters on the fundamental theory of hydrogen exchange, and tutorial chapters on measurement and data analysis provide the essential background for those ready to adopt HX-MS. Expert users may advance their current understanding through chapters on methods including membrane protein analysis, alternative proteases, millisecond hydrogen exchange, top-down mass spectrometry, histidine exchange and method validation. All readers can explore the diversity of HX-MS applications in areas such as ligand binding, membrane proteins, drug discovery, therapeutic protein formulation, biocomparability, and intrinsically disordered proteins.
Download or read book Physics Briefs written by and published by . This book was released on 1994 with total page 1264 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cumulated Index Medicus written by and published by . This book was released on 1999 with total page 1860 pages. Available in PDF, EPUB and Kindle. Book excerpt:
