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Solute Solvent Interactions In Folded And Unfolded Proteins
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Book Synopsis Solute-Solvent Interactions in Folded and Unfolded Proteins by : Soyoung Lee
Download or read book Solute-Solvent Interactions in Folded and Unfolded Proteins written by Soyoung Lee and published by . This book was released on 2011 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis is devoted to understanding solute-solvent interactions in folded and unfolded proteins. To this end, we have studied partial molar volume, V°, and adiabatic compressibility, K°S, of 20 amino acid side chains using low weight molecular model compounds, N-acetyl amino acid amide and its derivatives, between 18°C and 55°C. We used our data to develop an additive scheme for calculating the partial specific volume and adiabatic compressibility of fully extended polypeptide chains as a function of pH and temperature. We compared our calculated volumetric characteristics of the fully extended conformations of apocytochrome c and apomyoglobin with the experimental values measured in neutral pH (for apocytochrome c) or acidic pH (for apomyoglobin). The comparison between the calculated and experimental volumetric characteristics suggested that neither apocytochrome c nor apomyoglobin are fully unfolded and retain solvent-inaccessible amino acid residues. To study cosolvent-solute interactions, we determined V° and K° S of amino acid side chains and glycyl units as a function of urea concentration. We analyzed these data within the framework of a statistical thermodynamic formalism to determine the association constants, k, for the reaction in which urea binds to each of the amino acid side chains and the glycyl unit replacing two water molecules in solvation shell. Our determined k range from 0.04 to 0.39 M with the average of 0.16 +/- 0.09 M. There was no apparent correlation between the values of k and the ratio of polar to nonpolar solvent accessible surface areas. This study supports a direct interaction model in which urea denatures a protein by concerted action via favorable interactions with a wide range of protein groups. In addition, we have presented buffer ionization effect on the volume of protein denaturation could be significant with the potential to affect not only its magnitude but also its sign using a pressure perturbation calorimetric technique. Our results identified buffer ionization as an important determinant of protein transition volume that needs to be carefully taken into account. Results described in this work provide fundamental understanding of solute-solvent interaction in both folded and unfolded proteins.
Book Synopsis Effect of Solute-solvent Interactions on Protein Stability and Ligand Binding by : Ikbae Son
Download or read book Effect of Solute-solvent Interactions on Protein Stability and Ligand Binding written by Ikbae Son and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Solvent-Induced Interactions and Forces in Protein Folding by : Arieh Ben-Naim
Download or read book Solvent-Induced Interactions and Forces in Protein Folding written by Arieh Ben-Naim and published by Springer Nature. This book was released on 2023-06-12 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein-Solvent Interactions by : Roger Gregory
Download or read book Protein-Solvent Interactions written by Roger Gregory and published by CRC Press. This book was released on 1995-01-04 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.
Download or read book Unfolded Proteins written by and published by Elsevier. This book was released on 2002-11-04 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt: A variety of complementary techniques and approaches have been used to characterize peptide and protein unfolding induced by temperature, pressure, and solvent. Volume 62, Unfolded Proteins, assembles these complementary views to develop a more complete picture of denatured peptides and proteins. The unifying observation common to all chapters is the detection of preferred backbone confirmations in experimentally accessible unfolded states. Peptide and protein unfolding induced by temperature, pressure, and solvent Denatured peptides and proteins Detection of preferred backbone confirmations in experimentally accessible unfolded states
Book Synopsis Solvation Thermodynamics by : Arieh Y. Ben-Naim
Download or read book Solvation Thermodynamics written by Arieh Y. Ben-Naim and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book deals with a subject that has been studied since the beginning of physical chemistry. Despite the thousands of articles and scores of books devoted to solvation thermodynamics, I feel that some fundamen tal and well-established concepts underlying the traditional approach to this subject are not satisfactory and need revision. The main reason for this need is that solvation thermodynamics has traditionally been treated in the context of classical (macroscopic) ther modynamics alone. However, solvation is inherently a molecular pro cess, dependent upon local rather than macroscopic properties of the system. Therefore, the starting point should be based on statistical mechanical methods. For many years it has been believed that certain thermodynamic quantities, such as the standard free energy (or enthalpy or entropy) of solution, may be used as measures of the corresponding functions of solvation of a given solute in a given solvent. I first challenged this notion in a paper published in 1978 based on analysis at the molecular level. During the past ten years, I have introduced several new quantities which, in my opinion, should replace the conventional measures of solvation thermodynamics. To avoid confusing the new quantities with those referred to conventionally in the literature as standard quantities of solvation, I called these "nonconventional," "generalized," and "local" standard quantities and attempted to point out the advantages of these new quantities over the conventional ones.
Book Synopsis Computational Methods for Protein Folding, Volume 120 by : Richard A. Friesner
Download or read book Computational Methods for Protein Folding, Volume 120 written by Richard A. Friesner and published by John Wiley & Sons. This book was released on 2004-04-07 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein Folding Protocols by : Yawen Bai
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.
Book Synopsis Biological Macromolecules and Polyelectrolytes in Solution by : Henryk Eisenberg
Download or read book Biological Macromolecules and Polyelectrolytes in Solution written by Henryk Eisenberg and published by Oxford University Press, USA. This book was released on 1976 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Folding written by Alka Dwevedi and published by Springer. This book was released on 2014-12-01 with total page 61 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book will discuss classes of proteins and their folding, as well as the involvement of bioinformatics in solving the protein folding problem. In vivo and in vitro folding mechanisms are examined, as well as the failures of in vitro folding, a mechanism helpful in understanding disease caused by misfolding. The role of energy landscapes is also discussed and the computational approaches to these landscapes.
Book Synopsis Protein Folding Dynamics and Stability by : Prakash Saudagar
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.
Book Synopsis Protein Dynamics, Function, and Design by : Oleg Jardetzky
Download or read book Protein Dynamics, Function, and Design written by Oleg Jardetzky and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of articles from the proceedings of the International School of Structural Biology and Magnetic Resonance 3rd Course: Protein Dynamics, Function, and Design. This NATO Advance Study Institute was held in Erice at the Ettore Majorana Centre for Scientific Culture on April 16-28, 1997. The aim of the Institute was to bring together experts applyipg different physical methods to problems of macro molecular dynamics-notably x-ray diffraction, NMR and other forms of spectroscopy, and molecular dynamics simulations. Emphasis was placed on those systems and types of problems-such as mechanisms of allosteric control, signal transmission, induced fit to different ligands with its implications for drug design, and the effects of dynamics on structure determination-where a correlation of findings obtained by different methods could shed the most light on the mechanisms involved and stimulate the search for new approaches. The individual articles represent the state of the art in each of the areas cov ered and provide a guide to the original literature in this rapidly developing field. v CONTENTS 1. Determining Structures of ProteinlDN A Complexes by NMR Angela M. Gronenbom and G. Marius Clore 2. Fitting Protein Structures to Experimental Data: Lessons from before Your Mother Was Born . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Jeffrey C. Hoch, Alan S. Stem, and Peter J. Connolly 3. Multisubunit Allosteric Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 William N. Lipscomb 4. Studying Protein Structure and Function by Directed Evolution: Examples with Engineered Antibodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Andreas Pliickthun 5. High Pressure Effects on Protein Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Book Synopsis Protein Folding and Drug Design by : Luis Serrano Romero
Download or read book Protein Folding and Drug Design written by Luis Serrano Romero and published by IOS Press. This book was released on 2007 with total page 333 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the great unsolved problems of science and also of physics is the prediction of the three dimensional structure of a protein from its amino acid sequence. It may be stated that the deep connection existing between physics and protein folding is not so much, or in any case not only, through physical methods, but through physical concepts.
Book Synopsis Thermodynamics of Preferential Solvation in Protein Unfolding by : Daniel J. Felitsky
Download or read book Thermodynamics of Preferential Solvation in Protein Unfolding written by Daniel J. Felitsky and published by . This book was released on 2003 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Modern Physical Organic Chemistry by : Eric V. Anslyn
Download or read book Modern Physical Organic Chemistry written by Eric V. Anslyn and published by University Science Books. This book was released on 2006 with total page 1148 pages. Available in PDF, EPUB and Kindle. Book excerpt: In additionto covering thoroughly the core areas of physical organic chemistry -structure and mechanism - this book will escortthe practitioner of organic chemistry into a field that has been thoroughlyupdated.
Download or read book Protein Folding in the Cell written by and published by Elsevier. This book was released on 2002-02-20 with total page 516 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume of Advances in Protein Chemistry provides a broad, yet deep look at the cellular components that assist protein folding in the cell. This area of research is relatively new--10 years ago these components were barely recognized, so this book is a particularly timely compilation of current information. Topics covered include a review of the structure and mechanism of the major chaperone components, prion formation in yeast, and the use of microarrays in studying stress response. Outlines preceding each chapter allow the reader to quickly access the subjects of greatest interest. The information presented in this book should appeal to biochemists, cell biologists, and structural biologists.
Book Synopsis Protein Folding, Misfolding and Aggregation by : Victor Muñoz
Download or read book Protein Folding, Misfolding and Aggregation written by Victor Muñoz and published by Royal Society of Chemistry. This book was released on 2008-06-24 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
