Author: James Bertell Watney
Publisher:
ISBN:
Category :
Languages : en
Pages : 288

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Book Description

Author: Inaki Tunon
Publisher: Royal Society of Chemistry
ISBN: 1782624295
Category : Science
Languages : en
Pages : 558

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Book Description
Exploring the theories, methodologies and applications in simulations of enzymatic reactions, this book is a great resource for postgraduate students and researchers.

Author: Yao Fan
Publisher:
ISBN:
Category : Catalysis
Languages : en
Pages : 358

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Author: Ian F. Thorpe
Publisher:
ISBN: 9780542279218
Category : Immune complexes
Languages : en
Pages : 390

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Book Description
During the course of my studies, I have examined the relationships between structure, function and dynamics in proteins using theoretical and computational methods to better comprehend the underlying physical principles involved. One aspect of this work involved the study of enzyme catalysis in dihydrofolate reductase (DHFR). In the case of DHFR, I was particularly interested in the mechanisms by which mutations some distance from the site of chemistry impact the rate of hydride transfer in the enzyme. Prior computational studies indicate that reduced hydride transfer efficacy is linked to changes in the fluctuations occurring in the protein. These results suggested that the long range effects of deleterious mutations in DHFR are mediated by mediating these dynamical changes. I sought to evaluate this suggestion and determine the source of these observations. I found that the deleterious effects of mutations can be well represented by appealing strictly to conformational distributions without explicit consideration of dynamics. I further demonstrated that alterations in the fluctuations of the enzyme were merely coincident with changes in hydride transfer efficacy. Another focus of my doctoral work has involved the study of ligand binding in the 4-4-20 antibody. Work by the Floyd Romeseberg and colleagues indicates that gains in affinity as a result of maturation are associated with decreased flexibility in 4-4-20. I sought to identify the molecular properties governing flexibility and affinity in 4-4-20. The results of my investigations demonstrate the correlation between enhanced affinity and rigidity in 4-4-20 and allow for the identification of detailed molecular mechanisms that determine these effects. The changes observed to occur in 4-4-20 upon maturation serve as a useful model for processes of molecular evolution and recognition in biological systems.

Author: Judith Klinman
Publisher: Springer
ISBN: 3642389627
Category : Science
Languages : en
Pages : 217

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Book Description
Christopher M. Cheatum and Amnon Kohen, Relationship of Femtosecond–Picosecond Dynamics to Enzyme-Catalyzed H-Transfer. Cindy Schulenburg and Donald Hilvert, Protein Conformational Disorder and Enzyme Catalysis. A. Joshua Wand, Veronica R. Moorman and Kyle W. Harpole, A Surprising Role for Conformational Entropy in Protein Function. Travis P. Schrank, James O. Wrabl and Vincent J. Hilser, Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations. Buyong Ma and Ruth Nussinov, Structured Crowding and Its Effects on Enzyme Catalysis. Michael D. Daily, Haibo Yu, George N. Phillips Jr and Qiang Cui, Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Karunesh Arora and Charles L. Brooks III, Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Steven D. Schwartz, Protein Dynamics and the Enzymatic Reaction Coordinate.

Author: Amit Kessel
Publisher: CRC Press
ISBN: 1498747213
Category : Computers
Languages : en
Pages : 1423

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Book Description
Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, thermodynamics, mechanisms, and applications in medicine and other industries. These are accompanied by multiple animations of biochemical reactions and mechanisms, accessible via embedded QR codes (which can be viewed by smartphones) An in-depth discussion of G-protein-coupled receptors (GPCRs) A wider-scale description of biochemical and biophysical methods for studying proteins, including fully accessible internet-based resources, such as databases and algorithms Animations of protein dynamics and conformational changes, accessible via embedded QR codes Additional features Extensive discussion of the energetics of protein folding, stability and interactions A comprehensive view of membrane proteins, with emphasis on structure-function relationship Coverage of intrinsically unstructured proteins, providing a complete, realistic view of the proteome and its underlying functions Exploration of industrial applications of protein engineering and rational drug design Each chapter includes a Summary, Exercies, and References Approximately 300 color images Downloadable solutions manual available at www.crcpress.com For more information, including all presentations, tables, animations, and exercises, as well as a complete teaching course on proteins' structure and function, please visit the author's website: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Introduction_to_Proteins_Book. Praise for the first edition "This book captures, in a very accessible way, a growing body of literature on the structure, function and motion of proteins. This is a superb publication that would be very useful to undergraduates, graduate students, postdoctoral researchers, and instructors involved in structural biology or biophysics courses or in research on protein structure-function relationships." --David Sheehan, ChemBioChem, 2011 "Introduction to Proteins is an excellent, state-of-the-art choice for students, faculty, or researchers needing a monograph on protein structure. This is an immensely informative, thoroughly researched, up-to-date text, with broad coverage and remarkable depth. Introduction to Proteins would provide an excellent basis for an upper-level or graduate course on protein structure, and a valuable addition to the libraries of professionals interested in this centrally important field." --Eric Martz, Biochemistry and Molecular Biology Education, 2012

Author: Monika Fuxreiter
Publisher: CRC Press
ISBN: 9781498703536
Category : Science
Languages : en
Pages : 479

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Book Description
The Latest Developments on the Role of Dynamics in Protein Functions Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, and biology show how these advanced methods provide insights into dynamic aspects of biochemical processes. A particular focus is on intrinsically disordered proteins (IDPs), which lack a well-defined three-dimensional structure and function as dynamic ensembles. The book covers a wide spectrum of dynamics, from electronic structure-based to coarse-grained techniques via multiscaling at different levels. After an introduction to dynamics and historical overview of basic methodologies, the book addresses the following issues: Is there a quantitative relationship between enzymatic catalysis and protein dynamics? Which are the functionally relevant motions of proteins? How can structural properties and partner recognition mechanisms of IDPs be simulated? How can we speed up molecular dynamics? How can we describe conformational ensembles by the synergistic effort of computations and experiments? While dynamics is now considered essential for interpreting protein action, it is not yet an integral component in establishing structure–function relationships of proteins. Helping to reshape this classical view in biochemistry, this groundbreaking book explores advances in computational methodology and contributes to the new, ensemble way of studying proteins.

Author: Rudolf K. Allemann
Publisher: Royal Society of Chemistry
ISBN: 0854041222
Category : Science
Languages : en
Pages : 412

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Book Description
In recent years, there has been an explosion in knowledge and research associated with the field of enzyme catalysis and H-tunneling. Rich in its breath and depth, this introduction to modern theories and methods of study is suitable for experienced researchers those new to the subject. Edited by two leading experts, and bringing together the foremost practitioners in the field, this up-to-date account of a rapidly developing field sits at the interface between biology, chemistry and physics. It covers computational, kinetic and structural analysis of tunnelling and the synergy in combining these methods (with a major focus on H-tunneling reactions in enzyme systems). The book starts with a brief overview of proton and electron transfer history by Nobel Laureate, Rudolph A. Marcus. The reader is then guided through chapters covering almost every aspect of reactions in enzyme catalysis ranging from descriptions of the relevant quantum theory and quantum/classical theoretical methodology to the description of experimental results. The theoretical interpretation of these large systems includes both quantum mechanical and statistical mechanical computations, as well as simple more approximate models. Most of the chapters focus on enzymatic catalysis of hydride, proton and H" transfer, an example of the latter being proton coupled electron transfer. There is also a chapter on electron transfer in proteins. This is timely since the theoretical framework developed fifty years ago for treating electron transfers has now been adapted to H-transfers and electron transfers in proteins. Accessible in style, this book is suitable for a wide audience but will be particularly useful to advanced level undergraduates, postgraduates and early postdoctoral workers.

Author: William P. Jencks
Publisher: Courier Corporation
ISBN: 9780486654607
Category : Science
Languages : en
Pages : 866

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Book Description
Exceptionally clear coverage of mechanisms for catalysis, forces in aqueous solution, carbonyl- and acyl-group reactions, practical kinetics, more.

Author: Alan Fersht
Publisher: World Scientific Publishing Company
ISBN: 9789813225190
Category : Catalysis
Languages : en
Pages : 0

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Book Description
The three-dimensional structure of proteins -- Chemical catalysis -- The basic equations of enzyme kinetics -- Measurement and magnitude of individual rate constants -- The pH dependence of enzyme catalysis -- Practical methods for kinetics and equilibria -- Detection of intermediates in enzymatic reactions -- Stereochemistry of enzymatic reactions -- Active-site-directed and enzyme-activated irreversible inhibitors : "affinity labels" and "suicide inhibitors" -- Conformational change, allosteric regulation, motors, and work -- Forces between molecules, and binding energies -- Enzyme-substrate complementarity and the use of binding energy in catalysis -- Specificity and editing mechanisms -- Recombinant DNA technology -- Protein engineering -- Case studies of enzyme structure and mechanism -- Protein stability -- Kinetics of protein folding -- Folding pathways and energy landscapes.