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Author: Giovanni Salvi
Publisher: Sudwestdeutscher Verlag Fur Hochschulschriften AG
ISBN: 9783838107714
Category :
Languages : de
Pages : 108
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Book Description
Protein folding stands as one of the major interdisciplinary challenges of the last fifteen years, involving biology, chemistry, medicine and physics. In this book solvent effects, and the related hydrophobic effect, on proteins are investigated. Using a simple lattice model of proteins, in which the solvent is semi-explicitly taken into account, thermodynamical quantities can be investigated and the crucial role the solvent plays in protein folding can be demonstrated. Of particular relevance is our observation that a simple model, in which the potential energy is described in terms of the interactions between amino-acids only, does not correctly reproduce solvent effects. Approaches like this, in which solvent effects are treated implicitly, are commonly employed in many of more sophisticated models for protein folding dynamics. Our results are then of great importance as they suggest the treatment of the solvent in these models may need to be re-examined.
Author: Giovanni Salvi
Publisher: Sudwestdeutscher Verlag Fur Hochschulschriften AG
ISBN: 9783838107714
Category :
Languages : de
Pages : 108
Get Book Here
Book Description
Protein folding stands as one of the major interdisciplinary challenges of the last fifteen years, involving biology, chemistry, medicine and physics. In this book solvent effects, and the related hydrophobic effect, on proteins are investigated. Using a simple lattice model of proteins, in which the solvent is semi-explicitly taken into account, thermodynamical quantities can be investigated and the crucial role the solvent plays in protein folding can be demonstrated. Of particular relevance is our observation that a simple model, in which the potential energy is described in terms of the interactions between amino-acids only, does not correctly reproduce solvent effects. Approaches like this, in which solvent effects are treated implicitly, are commonly employed in many of more sophisticated models for protein folding dynamics. Our results are then of great importance as they suggest the treatment of the solvent in these models may need to be re-examined.
Author: Jeremy L. England
Publisher:
ISBN:
Category :
Languages : en
Pages : 140
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Book Description
Author: Jennifer J. McManus
Publisher: Humana
ISBN: 9781493996803
Category : Science
Languages : en
Pages : 266
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Book Description
This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. 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. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.
Author: Benedetta Mennucci
Publisher: John Wiley & Sons
ISBN: 9780470515228
Category : Science
Languages : en
Pages : 636
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Book Description
This book covers the theory and applications of continuum solvation models. The main focus is on the quantum-mechanical version of these models, but classical approaches and combined or hybrid techniques are also discussed. Devoted to solvation models in which reviews of the theory, the computational implementation Solvation continuum models are treated using the different points of view from experts belonging to different research fields Can be read at two levels: one, more introductive, and the other, more detailed (and more technical), on specific physical and numerical aspects involved in each issue and/or application Possible limitations or incompleteness of models is pointed out with, if possible, indications of future developments Four-colour representation of the computational modeling throughout.
Author: Ivet Bahar
Publisher: Garland Science
ISBN: 1351815016
Category : Science
Languages : en
Pages : 337
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Book Description
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.
Author: Edward Amis
Publisher: Elsevier
ISBN: 0323148522
Category : Science
Languages : en
Pages : 487
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Book Description
Solvent Effects on Chemical Phenomena, Volume I discusses the developments in the understanding of solvent effects on chemical phenomena in solution. This five-chapter volume begins with a discussion on the general concepts of various solvation types, including positive and negative, inner and outer sphere, and mixed component. The subsequent chapter deals with the determination of the actual solvation number for single ions. A short list of the total effective hydration numbers of electrolytes determined from temperature dependence of proton shifts is also provided in this chapter. Another chapter presents a number of examples of the unusual properties of certain mixed aqueous systems. The solvent effects on reaction rates and mechanisms are highlighted in the concluding chapter. This chapter also covers various types of solvents, such as protic and dipolar aprotic. The enthalpy and entropy of activation in salvation and the Finkelstein reactions are also discussed. Research chemists and scientists, teachers, and students with courses in solution chemistry will greatly benefit from this volume.
Author: Valerie Daggett
Publisher: Elsevier
ISBN: 0080493785
Category : Medical
Languages : en
Pages : 477
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Book Description
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
Author: Reinhard Schweitzer-Stenner
Publisher: Elsevier
ISBN: 0443159653
Category : Science
Languages : en
Pages : 328
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Book Description
The Physics of Protein Structure and Dynamics looks at various aspects of protein structure and dynamics from a physico-chemical point of view. It goes into some depth regarding the description of non-covalent forces that determine the relative stability of folded and unfolded proteins. Anharmonic protein dynamics involving motions between different minima of a rugged Gibbs energy landscape is described in great detail. The book combines various aspects of the protein folding/unfolding processes with an overview of intrinsically disordered proteins, which have attracted considerable interest of the protein community over the last 25 years but are thus far underrepresented in classroom-oriented textbooks. The book looks at protein folding and intrinsically disordered proteins as heavily interrelated topics that need to be viewed together. Furthermore, it presents some basic physico-chemical aspects of protein/peptide self-assembly into nanoscale fibrils. Intrinsically disordered peptides and proteins play a major role particularly in aggregation and self-assembly processes that lead to various diseases (Alzheimer, Parkinson, Huntington, Mad-Cow). Therefore, the relevance of protein disorder for protein self-assembly deserves a closer look. Protein self-assembly cannot be separated from protein folding since it is frequently the product of misfolding. With regard to modern theories, the folding processes are linked to insights on protein dynamics and the discovered relationship between proteins and spin glasses. - The readers will benefit from being provided with an in-depth overview of the physical concepts that govern different aspects of protein folding, disorder and self-assembly. By emphasizing the relationship between these issues, the approach adds a holistic character to the book - The book is to a major extent mathematically based. Mathematics is part of the language of physicists and physical chemists which cannot be properly substituted by words - For instructors, the book will offer a unique source for her/his teaching of current protein physics issues - The way how the book will be constructed (multiple references to primary literature with DOI links, literature-based problem sets and topics for discussion) will facilitate a learning process suitable for research-oriented students - Problem solving frequently requires the writing of short computer programs, something that is underemphasized in chemistry and biochemistry education (with the exception of computationally trained students, of course)
Author: Andreas Klamt
Publisher: Elsevier
ISBN: 0080455530
Category : Technology & Engineering
Languages : en
Pages : 247
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Book Description
The COSMO-RS technique is a novel method for predicting the thermodynamic properties of pure and mixed fluids which are important in many areas, ranging from chemical engineering to drug design. COSMO-RS, From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design is about this novel technology, which has recently proven to be the most reliable and efficient tool for the prediction of vapour-liquid equilibria. In contrast to group contribution methods, which depend on an extremely large number of experimental data, COSMO-RS calculates the thermodynamic data from molecular surface polarity distributions, resulting from quantum chemical calculations of the individual compounds in the mixture. In this book, the author cleverly combines a vivid overview of the partly demanding theoretical steps with a deeper analysis of their scientific background and justification. Aimed at theoretical chemists, computational chemists, physical chemists, chemical engineers, thermodynamicists as well as students,academic and industrial experts, COSMO-RS, From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design provides a novel viewpoint to anyone looking to gain more insight into the theory and potential of the unique method, COSMO-RS. - The only book currently available on COSMO-RS technique - Provides a novel viewpoint for the scientific understanding and for the practical quantitative treatment of fluid phase thermodynamics - Includes illustrative examples of the COSMOtherm program
Author: Arieh Ben-Naim
Publisher: Springer Nature
ISBN: 3031318714
Category : Science
Languages : en
Pages : 185
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Book Description
This monograph presents the molecular theory and necessary tools for the study of solvent-induced interactions and forces. After introducing the reader to the basic definitions of solvent-induced interactions, the author provides a brief analysis of the statistical thermodynamics. The book thoroughly overviews the connection of those interactions with thermodynamics and consequently focuses on specifically discussing the hydrophobic-hydrophilic interactions and forces. The importance of the implementation of hydrophilic interactions and forces in various biochemical processes is thoroughly analyzed, while evidence based on theory, experiments, and simulated calculations supporting that hydrophilic interactions and forces are far more important than the corresponding hydrophobic effects in many biochemical processes such as protein folding, self-assembly of proteins, molecular recognitions, are described in detail. This title is of great interest to students and researchers working in the fields of chemistry, physics, biochemistry, and molecular biology.
