Folding Unfolding Kinetics Of Lattice Proteins By Applying A Simple Statistical Mechanical Model For Protein Folding

Author : Hiroshi Wako,Haruo Abe
Publisher : Nova Biomedical Books
Page : 0 pages
File Size : 43,8 Mb
Release : 2011
Category : Chemical models
ISBN : 1617619221

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Folding/unfolding Kinetics of Lattice Proteins by Applying a Simple Statistical Mechanical Model for Protein Folding by Hiroshi Wako,Haruo Abe Pdf

The folding/unfolding kinetics of a three-dimensional lattice protein was studied using a simple statistical mechanical model for protein folding that was previously developed. The model considers the specificity of an amino acid sequence and the native structure of a given protein. The characteristic relaxation rate on the free energy surface was calculated starting from a completely unfolded structure (or native structure) that is assumed to associate with a folding rate (or an unfolding rate). To elucidate the roles of individual amino acid residues in protein folding/unfolding kinetics, the kinetic properties for all possible single amino acid substitutions of these proteins were calculated and their responses were examined. This book presents and discusses research results in the kinetics of protein folding/unfolding.

Author : Sebastian Doniach
Publisher : Springer Science & Business Media
Page : 400 pages
File Size : 46,7 Mb
Release : 2013-11-22
Category : Science
ISBN : 9781489913494

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Statistical Mechanics, Protein Structure, and Protein Substrate Interactions by Sebastian Doniach Pdf

A number of factors have come together in the last couple of decades to define the emerging interdisciplinary field of structural molecular biology. First, there has been the considerable growth in our ability to obtain atomic-resolution structural data for biological molecules in general, and proteins in particular. This is a result of advances in technique, both in x-ray crystallography, driven by the development of electronic detectors and of synchrotron radiation x-ray sources, and by the development ofNMR techniques which allow for inference of a three-dimensional structure of a protein in solution. Second, there has been the enormous development of techniques in DNA engineering which makes it possible to isolate and clone specific molecules of interest in sufficient quantities to enable structural measurements. In addition, the ability to mutate a given amino acid sequence at will has led to a new branch of biochemistry in which quantitative measurements can be made assessing the influence of a given amino acid on the function of a biological molecule. A third factor, resulting from the exponential increase in computing power available to researchers, has been the emergence of a growing body of people who can take the structural data and use it to build atomic-scale models of biomolecules in order to try and simulate their motions in an aqueous environment, thus helping to provide answers to one of the most basic questions of molecular biology: the relation of structure to function.

Author : Raj Kumar,Bal Ram Singh
Publisher : Springer
Page : 145 pages
File Size : 40,8 Mb
Release : 2016-11-21
Category : Science
ISBN : 9783319435404

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Protein Toxins in Modeling Biochemistry by Raj Kumar,Bal Ram Singh Pdf

This succinct volume addresses the production of inactive, potentially toxic proteins in the absence of correct protein folding and the resultant neurodegenerative diseases. Other topics include intrinsic disorder in protein structure and function and the effects of molten globules on protein toxicity. This concise and yet thorough text also discusses using toxin structure as a model for studying structural and functional aspects of protein chemistry. Protein Toxins in Modeling Biochemistry, a SpringerBrief, is essential reading for advanced researchers, scientists and advanced graduate students interested in protein chemistry and related areas of biochemistry and molecular science.

Author : J S Davies
Publisher : Royal Society of Chemistry
Page : 402 pages
File Size : 45,7 Mb
Release : 2007-10-31
Category : Science
ISBN : 9781847552723

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Amino Acids, Peptides and Proteins by J S Davies Pdf

Specialist Periodical Reports provide systematic and detailed review coverage of progress in the major areas of chemical research. Written by experts in their specialist fields the series creates a unique service for the active research chemist, supplying regular critical in-depth accounts of progress in particular areas of chemistry. For over 90 years The Royal Society of Chemistry and its predecessor, the Chemical Society, have been publishing reports charting developments in chemistry, which originally took the form of Annual Reports. However, by 1967 the whole spectrum of chemistry could no longer be contained within one volume and the series Specialist Periodical Reports was born. The Annual Reports themselves still existed but were divided into two, and subsequently three, volumes covering Inorganic, Organic, and Physical Chemistry. For more general coverage of the highlights in chemistry they remain a 'must'. Since that time the SPR series has altered according to the fluctuating degree of activity in various fields of chemistry. Some titles have remained unchanged, while others have altered their emphasis along with their titles; some have been combined under a new name whereas others have had to be discontinued. The current list of Specialist Periodical Reports can be seen on the inside flap of this volume.

Author : P. Michael Conn
Publisher : Academic Press
Page : 301 pages
File Size : 41,7 Mb
Release : 2009-01-09
Category : Science
ISBN : 9780080923390

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Molecular Biology of Protein Folding, Part B by P. Michael Conn Pdf

Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume. Follow the new editor-in-chief, P. Michael Conn, as he introduces this second thematic volume in the series – an in-depth aid to researchers who are looking for the best techniques and tools for understanding the complexities of protein folding Understand the advantages of protein folding over other therapeutic approaches and see how protein folding plays a critical role in the development of diseases such as Alzheimer’s and diabetes Decipher the rules of protein folding through compelling and timely reviews combined with chapters written by international authors in engineering, biochemistry, physics and computer science

Author : Kim Sneppen,Giovanni Zocchi
Publisher : Cambridge University Press
Page : 328 pages
File Size : 55,8 Mb
Release : 2005-08-25
Category : Science
ISBN : 0521844193

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Physics in Molecular Biology by Kim Sneppen,Giovanni Zocchi Pdf

This book, first published in 2005, is a discussion for advanced physics students of how to use physics to model biological systems.

Author : Tao Jiang,Ying Xu,Michael Q. Zhang
Publisher : MIT Press
Page : 570 pages
File Size : 46,8 Mb
Release : 2002
Category : Computers
ISBN : 0262100924

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Current Topics in Computational Molecular Biology by Tao Jiang,Ying Xu,Michael Q. Zhang Pdf

A survey of current topics in computational molecular biology. Computational molecular biology, or bioinformatics, draws on the disciplines of biology, mathematics, statistics, physics, chemistry, computer science, and engineering. It provides the computational support for functional genomics, which links the behavior of cells, organisms, and populations to the information encoded in the genomes, as well as for structural genomics. At the heart of all large-scale and high-throughput biotechnologies, it has a growing impact on health and medicine. This survey of computational molecular biology covers traditional topics such as protein structure modeling and sequence alignment, and more recent ones such as expression data analysis and comparative genomics. It combines algorithmic, statistical, database, and AI-based methods for studying biological problems. The book also contains an introductory chapter, as well as one on general statistical modeling and computational techniques in molecular biology. Each chapter presents a self-contained review of a specific subject. Not for sale in China, including Hong Kong.

Author : Kerson Huang
Publisher : World Scientific
Page : 159 pages
File Size : 42,8 Mb
Release : 2005
Category : Science
ISBN : 9789812561435

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Lectures on Statistical Physics and Protein Folding by Kerson Huang Pdf

This book introduces an approach to protein folding from the point of view of kinetic theory. There is an abundance of data on protein folding, but few proposals are available on the mechanism driving the process. Here, presented for the first time, are suggestion on possible research directions, as developed by the author in collaboration with C. C. Lin. The first half of this invaluable book contains a concise but relatively complete review of relevant topics in statistical mechanics and kinetic theory. It includes standard topics such as thermodynamics, the Maxwell-Boltzmann distribution, and ensemble theory. Special discussions include the dynamics of phase transitions, and Brownian motion as an illustration of stochastic processes. The second half develops topics in molecular biology and protein structure, with a view to discovering mechanisms underlying protein folding. Attention is focused on the energy flow through the protein in its folded state. A mathematical model, based on the Brownian motion of coupled harmonic oscillators, is worked out in the appendix.

Author : John H. Moore,Nicholas D. Spencer
Publisher : CRC Press
Page : 715 pages
File Size : 41,8 Mb
Release : 2023-07-03
Category : Science
ISBN : 9781003803232

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Encyclopedia of Chemical Physics and Physical Chemistry by John H. Moore,Nicholas D. Spencer Pdf

The Encyclopedia of Physical Chemistry and Chemical Physics introduces possibly unfamiliar areas, explains important experimental and computational techniques, and describes modern endeavors. The encyclopedia quickly provides the basics, defines the scope of each subdiscipline, and indicates where to go for a more complete and detailed explanation. Particular attention has been paid to symbols and abbreviations to make this a user-friendly encyclopedia. Care has been taken to ensure that the reading level is suitable for the trained chemist or physicist. The encyclopedia is divided in three major sections: FUNDAMENTALS: the mechanics of atoms and molecules and their interactions, the macroscopic and statistical description of systems at equilibrium, and the basic ways of treating reacting systems. The contributions in this section assume a somewhat less sophisticated audience than the two subsequent sections. At least a portion of each article inevitably covers material that might also be found in a modern, undergraduate physical chemistry text. METHODS: the instrumentation and fundamental theory employed in the major spectroscopic techniques, the experimental means for characterizing materials, the instrumentation and basic theory employed in the study of chemical kinetics, and the computational techniques used to predict the static and dynamic properties of materials. APPLICATIONS: specific topics of current interest and intensive research. For the practicing physicist or chemist, this encyclopedia is the place to start when confronted with a new problem or when the techniques of an unfamiliar area might be exploited. For a graduate student in chemistry or physics, the encyclopedia gives a synopsis of the basics and an overview of the range of activities in which physical principles are applied to chemical problems. It will lead any of these groups to the salient points of a new field as rapidly as possible and gives pointers as to where to read about the topic in more detail.

Author : Huzefa Rangwala,George Karypis
Publisher : John Wiley & Sons
Page : 611 pages
File Size : 40,8 Mb
Release : 2011-03-16
Category : Science
ISBN : 9781118099469

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Introduction to Protein Structure Prediction by Huzefa Rangwala,George Karypis Pdf

A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.

Author : Anonim
Publisher : Unknown
Page : 1846 pages
File Size : 51,7 Mb
Release : 1999
Category : Medicine
ISBN : OSU:32436010790556

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Cumulated Index Medicus by Anonim Pdf

Author : Richard A. Friesner
Publisher : John Wiley & Sons
Page : 544 pages
File Size : 53,7 Mb
Release : 2004-04-07
Category : Science
ISBN : 9780471465232

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Computational Methods for Protein Folding, Volume 120 by Richard A. Friesner Pdf

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.

Author : Alexei V. Finkelstein,Oleg Ptitsyn
Publisher : Elsevier
Page : 528 pages
File Size : 48,8 Mb
Release : 2016-06-22
Category : Science
ISBN : 9780081012369

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Protein Physics by Alexei V. Finkelstein,Oleg Ptitsyn Pdf

Protein Physics: A Course of Lectures covers the most general problems of protein structure, folding and function. It describes key experimental facts and introduces concepts and theories, dealing with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states. The book systematically summarizes and presents the results of several decades of worldwide fundamental research on protein physics, structure, and folding, describing many physical models that help readers make estimates and predictions of physical processes that occur in proteins. New to this revised edition is the inclusion of novel information on amyloid aggregation, natively disordered proteins, protein folding in vivo, protein motors, misfolding, chameleon proteins, advances in protein engineering & design, and advances in the modeling of protein folding. Further, the book provides problems with solutions, many new and updated references, and physical and mathematical appendices. In addition, new figures (including stereo drawings, with a special appendix showing how to use them) are added, making this an ideal resource for graduate and advanced undergraduate students and researchers in academia in the fields of biophysics, physics, biochemistry, biologists, biotechnology, and chemistry. Fully revised and expanded new edition based on the latest research developments in protein physics Written by the world's top expert in the field Deals with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states Summarizes, in a systematic form, the results of several decades of worldwide fundamental research on protein physics and their structure and folding Examines experimental data on protein structure in the post-genome era

Author : Victor Muñoz
Publisher : Royal Society of Chemistry
Page : 288 pages
File Size : 49,7 Mb
Release : 2008-06-24
Category : Science
ISBN : 9781847558282

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Protein Folding, Misfolding and Aggregation by Victor Muñoz Pdf

Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods have evolved to permit resolving fast processes of folding reactions and visualizing single molecules during folding. The findings from these novel experiments and detailed computer simulations have confirmed the main predictions of analytical theory of protein folding. In summary, protein folding research has finally acquired the status of a truly quantitative science, paving the way for more exciting developments in the near future. This unique book covers all the modern approaches and the many advances experienced in the field during the last 10 years. There is also much emphasis on computational methods and studies of protein aggregation which have really flourished in the last decade. It includes chapters in the areas that have witnessed major developments and are written by top experts including:computer simulations of folding, fast folding, single molecule spectroscopy, protein design, aggregation studies (both computational and experimental). Readers will obtain a unique perspective of the problems faced in the biophysical study of protein conformational behaviour in aqueous solution and how these problems are being solved with a multidisciplinary approach that combines theory, experiment and computer simulations. Protein Folding, Misfolding and Aggregation Classical Themes and Novel Approaches is essential reading for graduate students actively involved in protein folding research, other scientists interested in the recent progress of the field and instructors revamping the protein folding section of their biochemistry and biophysics courses.

Author : Hagai Meirovitch
Publisher : CRC Press
Page : 374 pages
File Size : 40,7 Mb
Release : 2020-08-14
Category : Computers
ISBN : 9781000072303

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Entropy and Free Energy in Structural Biology by Hagai Meirovitch Pdf

Computer simulation has become the main engine of development in statistical mechanics. In structural biology, computer simulation constitutes the main theoretical tool for structure determination of proteins and for calculation of the free energy of binding, which are important in drug design. Entropy and Free Energy in Structural Biology leads the reader to the simulation technology in a systematic way. The book, which is structured as a course, consists of four parts: Part I is a short course on probability theory emphasizing (1) the distinction between the notions of experimental probability, probability space, and the experimental probability on a computer, and (2) elaborating on the mathematical structure of product spaces. These concepts are essential for solving probability problems and devising simulation methods, in particular for calculating the entropy. Part II starts with a short review of classical thermodynamics from which a non-traditional derivation of statistical mechanics is devised. Theoretical aspects of statistical mechanics are reviewed extensively. Part III covers several topics in non-equilibrium thermodynamics and statistical mechanics close to equilibrium, such as Onsager relations, the two Fick's laws, and the Langevin and master equations. The Monte Carlo and molecular dynamics procedures are discussed as well. Part IV presents advanced simulation methods for polymers and protein systems, including techniques for conformational search and for calculating the potential of mean force and the chemical potential. Thermodynamic integration, methods for calculating the absolute entropy, and methodologies for calculating the absolute free energy of binding are evaluated. Enhanced by a number of solved problems and examples, this volume will be a valuable resource to advanced undergraduate and graduate students in chemistry, chemical engineering, biochemistry biophysics, pharmacology, and computational biology.