Download or read book Chemical Approaches to Understanding Enzyme Catalysis written by and published by . This book was released on 1982 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chemical Approaches to Understanding Enzyme Catalysis written by Bernard S. Green and published by Elsevier Publishing Company. This book was released on 1982 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Enzyme Kinetics Catalysis and Control written by Daniel L. Purich and published by Elsevier. This book was released on 2010-06-16 with total page 915 pages. Available in PDF, EPUB and Kindle. Book excerpt: Far more than a comprehensive treatise on initial-rate and fast-reaction kinetics, this one-of-a-kind desk reference places enzyme science in the fuller context of the organic, inorganic, and physical chemical processes occurring within enzyme active sites. Drawing on 2600 references, Enzyme Kinetics: Catalysis & Control develops all the kinetic tools needed to define enzyme catalysis, spanning the entire spectrum (from the basics of chemical kinetics and practical advice on rate measurement, to the very latest work on single-molecule kinetics and mechanoenzyme force generation), while also focusing on the persuasive power of kinetic isotope effects, the design of high-potency drugs, and the behavior of regulatory enzymes. - Historical analysis of kinetic principles including advanced enzyme science - Provides both theoretical and practical measurements tools - Coverage of single molecular kinetics - Examination of force generation mechanisms - Discussion of organic and inorganic enzyme reactions
Download or read book Enzyme Catalysis and Regulation written by Gorden Hammes and published by Elsevier. This book was released on 2012-12-02 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzyme Catalysis and Regulation is an introduction to enzyme catalysis and regulation and covers topics ranging from protein structure and dynamics to steady-state enzyme kinetics, multienzyme complexes, and membrane-bound enzymes. Case studies of selected enzyme mechanisms are also presented. This book consists of 11 chapters and begins with a brief overview of enzyme structure, followed by a discussion on methods of probing enzyme structure such as X-ray crystallography and optical spectroscopy. Kinetic methods are then described, with emphasis on the general principles of steady-state and transient kinetics. The chemical principles involved in enzyme catalysis are also discussed, and case studies of a few well-documented enzymes are presented. The regulation of enzyme activity is analyzed from a nongenetic viewpoint, with particular reference to binding isotherms and models for allosterism. Two particular enzymes, aspartate transcarbamoylase and phosphofructokinase, are used as examples of well-studied regulatory enzymes. The last two chapters focus on multienzyme complexes and membrane-bound enzymes. This monograph is intended for graduate students, advanced undergraduates, and research workers in molecular biology and biochemistry.
Download or read book Organic Chemistry of Enzyme Catalyzed Reactions Revised Edition written by Richard B. Silverman and published by Elsevier. This book was released on 2002-03-07 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Organic Chemistry of Enzyme-Catalyzed Reactions is not a book on enzymes, but rather a book on the general mechanisms involved in chemical reactions involving enzymes. An enzyme is a protein molecule in a plant or animal that causes specific reactions without itself being permanently altered or destroyed. This is a revised edition of a very successful book, which appeals to both academic and industrial markets. - Illustrates the organic mechanism associated with each enzyme-catalyzed reaction - Makes the connection between organic reaction mechanisms and enzyme mechanisms - Compiles the latest information about molecular mechanisms of enzyme reactions - Accompanied by clearly drawn structures, schemes, and figures - Includes an extensive bibliography on enzyme mechanisms covering the last 30 years - Explains how enzymes can accelerate the rates of chemical reactions with high specificity - Provides approaches to the design of inhibitors of enzyme-catalyzed reactions - Categorizes the cofactors that are appropriate for catalyzing different classes of reactions - Shows how chemical enzyme models are used for mechanistic studies - Describes catalytic antibody design and mechanism - Includes problem sets and solutions for each chapter - Written in an informal and didactic style
Download or read book New Trends in Enzyme Catalysis and Biomimetic Chemical Reactions written by Gertz I. Likhtenshtein and published by Springer Science & Business Media. This book was released on 2003 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzyme catalysis is an important and vigorously developing field of basic and applied research, posing challenging problems to biochemists and chemists. This volume embraces modern areas of enzyme catalysis where other books in the field concentrate mainly on kinetic, bioorganic and biochemical aspects of the enzyme catalysis and do not cover biophysical and physicochemical problems. Topics covered include: modern physical and kinetic methods of investigation;contemporary theories of elementary chemical processes in enzymes; structure, dynamics and action mechanism of enzyme active sites; concept of pretransition state; theory of long-range electron transfer and proton translocation;mechanisms of tough biochemical reactions (dinitrogen reduction, light energy conversation, water photooxidation, hydroxilation);the achievements and problems of biomimetic chemical reactions.
Download or read book From Enzyme Models to Model Enzymes written by Anthony John Kirby and published by Royal Society of Chemistry. This book was released on 2009 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: Designing artificial systems with catalytic efficiencies to rival those of natural enzymes is one of the great challenges facing science today. This introduction to the exciting area of artificial enzymes is suitable for both students and more senior researchers.
Download or read book Chemical Approaches to Intermediates of Enzyme Catalysis written by Philipp Christen and published by . This book was released on 1970 with total page 11 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Enzyme Catalysis Process written by A. Cooper and published by Springer Science & Business Media. This book was released on 2013-12-11 with total page 479 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume represents the proceedings of a NATO Advanced Studies Instituteheld near Barga (Italy), July 11-23, 1988, involving over 90 participants from more than twelve countries of Europe, North America and elsewhere. It was not our intention at this meeting to present a complete up-to-the-minute review of current research in enzyme catalysis but t·ather, in accord wi th the intended spiri t of NATO ASis, to gi ve an opportunity for advanced students and researchers in a wide variety of disciplines to meet tagether and study the problern from different points of view. Hence the lectures cover topics rauging from the purely theoretical aspects of chemical reaction kinetics in condensed matter through practical experimental approaches to enzyme structure, dynamics and mechanism, including the new experimental opportunities arising from genetic engineering techniques. Our approachwas unashamedly physical, both because the more biochemical aspects of enzymology are amply covered elsewhere and because progress in our understanding and application of the molecular basis of enzymic processes must ultimately come from advances in physical knowledge. We tried to cover as wide a spectrum as possible, and succeeded in gathering an expert and enthusiastic team of speakers, but there . are some inevitable omissions. In particular, and with hindsight, our discussions might have been enriched by more detailed coverage of general aspects of chemical catalysis - but readers requiring this background should find adequate references herein.
Download or read book Organic Chemistry of Enzyme Catalyzed Reactions Revised Edition written by Richard B. Silverman and published by Academic Press. This book was released on 2002-02-28 with total page 737 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Organic Chemistry of Enzyme-Catalyzed Reactions is not a book on enzymes, but rather a book on the general mechanisms involved in chemical reactions involving enzymes. An enzyme is a protein molecule in a plant or animal that causes specific reactions without itself being permanently altered or destroyed. This is a revised edition of a very successful book, which appeals to both academic and industrial markets. Illustrates the organic mechanism associated with each enzyme-catalyzed reaction Makes the connection between organic reaction mechanisms and enzyme mechanisms Compiles the latest information about molecular mechanisms of enzyme reactions Accompanied by clearly drawn structures, schemes, and figures Includes an extensive bibliography on enzyme mechanisms covering the last 30 years Explains how enzymes can accelerate the rates of chemical reactions with high specificity Provides approaches to the design of inhibitors of enzyme-catalyzed reactions Categorizes the cofactors that are appropriate for catalyzing different classes of reactions Shows how chemical enzyme models are used for mechanistic studies Describes catalytic antibody design and mechanism Includes problem sets and solutions for each chapter Written in an informal and didactic style
Download or read book Model Systems in Catalysis written by Robert Rioux and published by Springer Science & Business Media. This book was released on 2009-11-11 with total page 531 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is an excellent compilation of cutting-edge research in heterogeneous catalysis and related disciplines – surface science, organometallic catalysis, and enzymatic catalysis. In 23 chapters by noted experts, the volume demonstrates varied approaches using model systems and their successes in understanding aspects of heterogeneous catalysis, both metal- and metal oxide-based catalysis in extended single crystal and nanostructured catalytic materials. To truly appreciate the astounding advances of modern heterogeneous catalysis, let us first consider the subject from a historical perspective. Heterogeneous catalysis had its beginnings in England and France with the work of scientists such as Humphrey Davy (1778–1829), Michael Faraday (1791–1867), and Paul Sabatier (1854–1941). Sabatier postulated that surface compounds, si- lar to those familiar in bulk to chemists, were the intermediate species leading to catalytic products. Sabatier proposed, for example, that NiH moieties on a Ni sur- 2 face were able to hydrogenate ethylene, whereas NiH was not. In the USA, Irving Langmuir concluded just the opposite, namely, that chemisorbed surface species are chemically bound to surfaces and are unlike known molecules. These chemisorbed species were the active participants in catalysis. The equilibrium between gas-phase molecules and adsorbed chemisorbed species (yielding an adsorption isotherm) produced a monolayer by simple site-filling kinetics.
Download or read book Computational Approaches to Understand the Atomistic Drivers of Enzyme Catalysis written by Natasha Seelam and published by . This book was released on 2021 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzymes readily perform chemical reactions several orders of magnitude faster than their uncatalyzed versions in ambient conditions with high specificity, making them attractive design targets for industrial purposes. Traditionally, enzyme reactivity has been contextualized through transition-state theory (TST), in which catalytic strategies are described by their ability to minimize the activation energy to cross the reaction barrier through a combination of ground-state destabilization (GSD) and transition-state stabilization (TSS). While excellent progress has been made to rationally design enzymes, the complexity of the design space and the highly optimized nature of enzymes make general application of these approaches difficult. This thesis presents a set of computational methods and applications in order to investigate the larger perspective of enzyme-assisted kinetic processes. For the first part of the thesis, we analyzed the energetics and dynamics of proficient catalyst orotidine 5'-monophosphate decarboxylase (OMPDC), an enzyme that catalyzes decarboxylation nearly 17 orders of magnitude more proficiently than the uncatalyzed reaction in aqueous solvent. Potential-of-mean-force (PMF) calculations on wild type (WT) and two catalytically hindered mutants, S127A and V155D (representing TSS and GSD, respectively), characterized the energy barriers associated with decarboxylation as a function of two parameters: the distance between the breaking C–C bond and a proton-transfer coordinate from the nearby side chain of K72, a conserved lysine in the active site. Coupling PMF analyses with transition path sampling (TPS) approaches revealed two distinct decarboxylation strategies: a simultaneous, K72-assisted pathway and a stepwise, relatively K72-independent pathway. Both PMF and TPS rate calculations reasonably reproduced the empirical differences in relative rates between WT and mutant systems, suggesting these approaches can enable in silico inquiry into both pathway and mechanism identification in enzyme kinetics. For the second study, we investigated the electronic determinants of reactivity, using the enzyme ketol-acid reductoisomerase (KARI). KARI catalyzes first a methyl isomerization and then reduction with an active site comprised of several polar residues, two magnesium divalent cations, and NADPH. This study focused on isomerization, which is rate limiting, with two objectives: characterization of chemical mechanism in successful catalytic events (“reactive”) versus failed attempts to cross the barrier ("non-reactive"), and the interplay between atomic positions, electronic descriptors, and reactivity. Natural bonding orbital (NBO) analyses provided detailed electronic description of the dynamics through the reaction and revealed that successful catalytic events crossed the reaction barrier through a 3-center-2-electron (3C) bond, concurrent to isomerization of hydroxyl/carbonyls on the substrate. Interestingly, the non-reactive ensemble adopted a similar electronic pathway as the reactive ensemble, but its members were generally unable to form and sustain the 3C bond. Supervised machine learning classifiers then identified small subsets of geometric and electronic descriptors, “features”, that predicted reactivity; our results indicated that fewer electronic features were able to predict reactivity as effectively as a larger set of geometric features. Of these electronic features, the models selected diverse descriptors representing several facets of the chemical mechanism (charge, breaking–bond order, atomic orbital hybridization states, etc.). We then inquired how geometric features reported on electronic features with classifiers that leveraged pairs of geometric features to predict the relative magnitude of each electronic feature. Our findings indicated that the geometric, pair-feature models predicted electronic structure with comparable performance as cumulative geometric models, suggesting small subsets of features were capable of reporting on electronic descriptors, and that different subsets could be leveraged to describe various aspects of a chemical mechanism. Lastly, we revisited OMPDC in order to learn the key geometric features that distinguished between the simultaneous and stepwise pathways of decarboxylation, aggregating and labeling pathways drawn from WT and mutant systems ensembles. We leveraged classifiers that predicted between reactive pathways by selecting small subsets of structural features from 620 geometric features comprised of atoms from the active site. The classifiers performed comparably, with greater than 80% testing accuracy and AUC, between times starting from in the reactant basin to 30 fs into crossing the reaction barrier. Remarkably, model-selected features reported on chemically meaningful interactions despite no explicit prior knowledge of the mechanism in training. To illustrate this, we focused analyses on two particular features shown to be predictive while in the reactant basin, prior to crossing the barrier: a potential hydrogen-bond between D75*, an aspartate in the active site, and the 2'-hydroxyl of OMP, and electrostatic repulsion through the proximity of a different aspartate, D70, to the leaving group carboxylate of OMP. Analysis between the simultaneous and stepwise ensembles demonstrated that the simultaneous ensemble adopted shorter distances for both features, generally suggesting stronger interactions. Both features were additionally shown to be associated with the ability to distort the planarity of the orotidyl ring, where shorter distances for either feature were correlated with larger degrees of distortion. Taken together, this suggested the simultaneous ensemble was more effective at distorting the ground state structure prior to crossing the reaction barrier.
Download or read book Simulating Enzyme Reactivity written by Inaki Tunon and published by Royal Society of Chemistry. This book was released on 2016-11-25 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring the theories, methodologies and applications in simulations of enzymatic reactions, this book is a great resource for postgraduate students and researchers.
Download or read book Mechanisms of Catalysis written by and published by Academic Press. This book was released on 1991-01-28 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: The remarkable expansion of information leading to a deeper understanding of enzymes on the molecular level necessitated the development of this volume which not only introduces new topics to The Enzymes series but presents new information on some covered in Volume I and II of this edition.
Download or read book Understanding Enzymes written by Trevor Palmer and published by . This book was released on 1985 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: This clear and lucid book helps towards an understanding of the principles of enzymology, a subject with a somewhat undeserved reputation for being difficult. The subject is explained most carefully, without rushing or cutting corners, in a coverage which is balanced, readable and comprehensive, accounting for both theory and applications. The book will act as a bridge for those wishing to progress to more advanced and specialised areas. New material has been added since publication of the first edition, revealing advances made since 1980, including NMR spectroscopy, HPLC, immunoassay, genetic engineering and structures of oligomeric enzymes. Fresh and stimulating problems have been devised, diagrams redrawn and sections on obsolete techniques removed to make way for the new material. The approach taken throughout encourages, where appropriate, correct answers to problems, thereby reinforcing the reader's understanding of enzymology by facing real-life difficulties.
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.
Download or read book Dynamics in Enzyme Catalysis written by Judith Klinman and published by Springer. This book was released on 2013-09-14 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
