Computational Approaches To Understand The Atomistic Drivers Of Enzyme Catalysis

Author by : Natasha Seelam
Languange : en
Publisher by : Unknown
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Description : 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.


From Enzyme Models To Model Enzymes

Author by : Anthony John Kirby
Languange : en
Publisher by : Royal Society of Chemistry
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Description : This introduction to the exciting area of artificial enzymes is suitable for students and more senior researchers.


Enzyme Kinetics Catalysis And Control

Author by : Daniel L. Purich
Languange : en
Publisher by : Elsevier
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Description : 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


New Trends In Enzyme Catalysis And Biomimetic Chemical Reactions

Author by : Gertz I. Likhtenshtein
Languange : en
Publisher by : Springer Science & Business Media
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Description : "This book is a view of enzyme catalysis by a physico-chemist with long-term experience in the investigation of structure and action mechanism of biological catalysts. This book is not intended to provide an exhaustive survey of each topic but rather a discussion of their theoretical and experimental background, and recent developments. The literature of enzyme catalysis is so vast and many scientists have made important contribution in the area, that it is impossible in the space allowed for this book to give a representative set of references. The author has tried to use reviews, and general principles of articles. He apologizes to those he has not been able to include. . [...] The monograph is intended for scientists working on enzyme catalysis and adjacent areas such as chemical modeling of biological processes, homogeneous catalysis, biomedical research and biotechnology. The book can be use as a subsidiary manual for instructors, graduate and undergraduate students of university biochemistry and chemistry departments."--Pages ix-x.


A Study Of Enzymes

Author by : Stephen A. Kuby
Languange : en
Publisher by : CRC Press
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Description : 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.


The Enzyme Catalysis Process

Author by : A. Cooper
Languange : en
Publisher by : Springer
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Description : 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.


Enzymes Catalysis Kinetics And Mechanisms

Author by : N.S. Punekar
Languange : en
Publisher by : Springer
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Description : This enzymology textbook for graduate and advanced undergraduate students covers the syllabi of most universities where this subject is regularly taught. It focuses on the synchrony between the two broad mechanistic facets of enzymology: the chemical and the kinetic, and also highlights the synergy between enzyme structure and mechanism. Designed for self-study, it explains how to plan enzyme experiments and subsequently analyze the data collected. The book is divided into five major sections: 1] Introduction to enzymes, 2] Practical aspects, 3] Kinetic Mechanisms, 4] Chemical Mechanisms, and 5] Enzymology Frontiers. Individual concepts are treated as stand-alone chapters; readers can explore any single concept with minimal cross-referencing to the rest of the book. Further, complex approaches requiring specialized techniques and involved experimentation (beyond the reach of an average laboratory) are covered in theory with suitable references to guide readers. The book provides students, researchers and academics in the broad area of biology with a sound theoretical and practical knowledge of enzymes. It also caters to those who do not have a practicing enzymologist to teach them the subject.


The Organic Chemistry Of Enzyme Catalyzed Reactions

Author by : Richard B. Silverman
Languange : en
Publisher by : Academic Press
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Description : 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


Enzyme Kinetics And Mechanism Part D Developments In Enzyme Dynamics

Author by : Anonim
Languange : en
Publisher by : Academic Press
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Description : General Description of the Volume: This volume, as do the other Enzyme Kinetics and Mechanism volumes in the Methods in Enzymology series, provides treatment of dynamic and chemical approaches for investigating enzyme catalysis and regulation, as well as designing metabolic inhibitors. It will greatly interest those involved in enzyme chemistry, metabolic control, and drug design. It should also interest those developing commercial applications for enzymes whose properties have been re-engineered using recombinant DNA technology and site-directed mutagenesis. General Description of the Series: The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences. Mechanisms of enzyme catalysis and inhibition Enzyme structure and function Regulatory control of enzymes Action of catalytic antibodies and ribozymes


Reaction Rate Theory And Rare Events

Author by : Baron Peters
Languange : en
Publisher by : Elsevier
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Description : Reaction Rate Theory and Rare Events bridges the historical gap between these subjects because the increasingly multidisciplinary nature of scientific research often requires an understanding of both reaction rate theory and the theory of other rare events. The book discusses collision theory, transition state theory, RRKM theory, catalysis, diffusion limited kinetics, mean first passage times, Kramers theory, Grote-Hynes theory, transition path theory, non-adiabatic reactions, electron transfer, and topics from reaction network analysis. It is an essential reference for students, professors and scientists who use reaction rate theory or the theory of rare events. In addition, the book discusses transition state search algorithms, tunneling corrections, transmission coefficients, microkinetic models, kinetic Monte Carlo, transition path sampling, and importance sampling methods. The unified treatment in this book explains why chemical reactions and other rare events, while having many common theoretical foundations, often require very different computational modeling strategies. Offers an integrated approach to all simulation theories and reaction network analysis, a unique approach not found elsewhere Gives algorithms in pseudocode for using molecular simulation and computational chemistry methods in studies of rare events Uses graphics and explicit examples to explain concepts Includes problem sets developed and tested in a course range from pen-and-paper theoretical problems, to computational exercises


Simulating Enzyme Reactivity

Author by : Inaki Tunon
Languange : en
Publisher by : Royal Society of Chemistry
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Description : The simulation of enzymatic processes is a well-established field within computational chemistry, as demonstrated by the 2013 Nobel Prize in Chemistry. It has been attracting increasing attention in recent years due to the potential applications in the development of new drugs or new environmental-friendly catalysts. Featuring contributions from renowned authors, including Nobel Laureate Arieh Warshel, this book explores the theories, methodologies and applications in simulations of enzyme reactions. It is the first book offering a comprehensive perspective of the field by examining several different methodological approaches and discussing their applicability and limitations. The book provides the basic knowledge for postgraduate students and researchers in chemistry, biochemistry and biophysics, who want a deeper understanding of complex biological process at the molecular level.


Enzymes

Author by : Robert A. Copeland
Languange : en
Publisher by : John Wiley & Sons
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Description : Fully updated and expanded-a solid foundation for understandingexperimental enzymology. This practical, up-to-date survey is designed for a broadspectrum of biological and chemical scientists who are beginning todelve into modern enzymology. Enzymes, Second Editionexplains the structural complexities of proteins and enzymes andthe mechanisms by which enzymes perform their catalytic functions.The book provides illustrative examples from the contemporaryliterature to guide the reader through concepts and data analysisprocedures. Clear, well-written descriptions simplify the complexmathematical treatment of enzyme kinetic data, and numerouscitations at the end of each chapter enable the reader to accessthe primary literature and more in-depth treatments of specifictopics. This Second Edition of Enzymes: A Practical Introductionto Structure, Mechanism, and Data Analysis features refinedand expanded coverage of many concepts, while retaining theintroductory nature of the book. Important new featuresinclude: A new chapter on protein-ligand binding equilibria Expanded coverage of chemical mechanisms in enzyme catalysisand experimental measurements of enzyme activity Updated and refined discussions of enzyme inhibitors andmultiple substrate reactions Coverage of current practical applications to the study ofenzymology Supplemented with appendices providing contact information forsuppliers of reagents and equipment for enzyme studies, as well asa survey of useful Internet sites and computer software forenzymatic data analysis, Enzymes, Second Edition isthe ultimate practical guide for scientists and students inbiochemical, pharmaceutical, biotechnical, medicinal, andagricultural/food-related research.


Enzyme Catalysis And Regulation

Author by : Gorden Hammes
Languange : en
Publisher by : Elsevier
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Description : 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.


Enzyme Catalysis In Organic Synthesis

Author by : Karlheinz Drauz
Languange : en
Publisher by : Wiley-VCH
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Description : How to succeed with enzymes in organic synthesis Comprehensive in coverage, this handbook provides a thorough understanding of enzyme-catalyzed organic transformations. Using it, readers can easily apply the principles of enzyme catalysis to new chemical reactions. All techniques described are directly transferable to applications, from laboratory to industrial scale. Benefits for the user: * synthetic applications organized according to reaction type * tabular survey of all commercially available enzymes * two indexes offering easy access to enzymes, compounds, and reaction types * the latest synthetic methods, including use of catalytic antibodies and protein engineering


Large Scale Quantum Mechanical Enzymology

Author by : Greg Lever
Languange : en
Publisher by : Springer
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Description : This work establishes linear-scaling density-functional theory (DFT) as a powerful tool for understanding enzyme catalysis, one that can complement quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations. The thesis reviews benchmark studies demonstrating techniques capable of simulating entire enzymes at the ab initio quantum-mechanical level of accuracy. DFT has transformed the physical sciences by allowing researchers to perform parameter-free quantum-mechanical calculations to predict a broad range of physical and chemical properties of materials. In principle, similar methods could be applied to biological problems. However, even the simplest biological systems contain many thousands of atoms and are characterized by extremely complex configuration spaces associated with a vast number of degrees of freedom. The development of linear-scaling density-functional codes makes biological molecules accessible to quantum-mechanical calculation, but has yet to resolve the complexity of the phase space. Furthermore, these calculations on systems containing up to 2,000 atoms can capture contributions to the energy that are not accounted for in QM/MM methods (for which the Nobel prize in Chemistry was awarded in 2013) and the results presented here reveal profound shortcomings in said methods.


Physical Organic Chemistry Ii

Author by : Th. J. De Boer
Languange : en
Publisher by : Elsevier
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Description : Physical Organic Chemistry—II provides information pertinent to the fundamental aspects of physical organic chemistry. This book discusses the common phenomenon in ionic organic chemistry. Organized into seven chapters, this book begins with an overview of electrochemical methods to obtain thermodynamic information on unstable species. This text then presents a brief summary of the experimental method in low temperature photochemical studies. Other chapters consider the general approach to understanding the molecular basis of enzyme catalysis and regulation. This book discusses as well the reactivity model for concerted cycloaddition reactions, which allows a systematization of substituent effects. The final chapter deals with the relative stabilities of phosphoranes in terms of the relative apicophilicities of groups, ring strain and steric factors, and experiments. This book is a valuable resource for organic and inorganic chemists. Postdoctoral students and scientists who are interested in physical organic chemistry will also find this book extremely useful.


Bioorganic Chemistry

Author by : H. Dugas
Languange : en
Publisher by : Springer Science & Business Media
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Description : Springer Advanced Texts in Chemistry New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical ther modynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the graduate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses. New York, New York CHARLES R.


Bioorganic Chemistry

Author by : Hermann Dugas
Languange : en
Publisher by : Springer Science & Business Media
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Description : This widely-praised textbook is particularly suited for advanced undergraduates or graduates in chemistry, biochemistry, medicinal chemistry, and pharmacology. The third edition has been substantially revised to reflect new research in the field, and features a major new chapter on self-assembly, auto-organization, and molecular devices. The outstanding figures remain a highlight of the book, and were described in an earlier edition as "the best I've seen for showing the organic chemistry of biomolecules." (Quart. Rev. Biol.)


Bioorganic Chemistry In Healthcare And Technology

Author by : Upendra K. Pandit
Languange : en
Publisher by : Springer Science & Business Media
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Description : In current thinking, Bioorganic Chemistry may be defined as the area of chemistry which lies in the border region between organic chemistry and biology and which describes and analyzes biological phenomena in terms of detailed molecular structures and molecular mechanisms. This molecular-level view of biological processes is not only essential to their fuller understanding but also serves as the platform for the application of the principles of such processes to areas of health care and technology. The objective of the ASI workshop on " Bioorganic Chemistry in Healthcare and Technology", held in the Hengelhoef Congress Centre in Houthalen-Helchteren, Belgium, from September 18-21, 1990, was to bring together most of the international experts in the field to discuss the current developments and new trends in bioorganic chemistry, especially in relation to the selected theme. The book presents nineteen invited plenary and session lectures and eighteen posters. These cover areas of (i) molecular design of therapeutic and agronomical agents based npon mechanistic rationale or drug-receptor interactions, (ii) production of substances of commercial value via combined organic chemical and bio-chemical methodologies, (iii) fundamental studies on the molecular mechanisms of enzymes and (iv) the evolution of conceptually new molecular systems which are programmed to execute specific recognition and/or catalytic functions. An abstracted version of the plenary discussion held at the end of the workshop is also included. We feel confident that the subject matter of this book will be of interest to a broad group of chemists engaged in academic or industrial research.


Simulating Enzyme Reactivity Computational Methods In Enzyme Catalysis

Author by : John Maclane
Languange : en
Publisher by : Createspace Independent Publishing Platform
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Description : The simulation of enzymatic processes is a well-established field within computational chemistry, as demonstrated by the 2013 Nobel Prize in Chemistry. It has been attracting increasing attention in recent years due to the potential applications in the development of new drugs or new environmental-friendly catalysts. Featuring contributions from renowned authors, including Nobel Laureate Arieh Warshel, this book explores the theories, methodologies and applications in simulations of enzyme reactions. It is the first book offering a comprehensive perspective of the field by examining several different methodological approaches and discussing their applicability and limitations. The book provides the basic knowledge for postgraduate students and researchers in chemistry, biochemistry and biophysics, who want a deeper understanding of complex biological process at the molecular level.


Synthesis Of Lactam Antibiotics

Author by : Alle Bruggink
Languange : en
Publisher by : Springer Science & Business Media
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Description : Penicillins and cephalosporins have a long history in combating bacterial infections. Despite new infectious diseases and occurring resistance, beta-lactam antibiotics will for many years to come continue to play a prominent role in our therapeutic arsenal. This book covers the industrial development of the chemical and biochemical processes used to manufacture these products, as well as looking ahead to possible future processes. The interplay between synthetic organic chemistry with the understanding and application of enzymes, modeling of fermentation processes and integration through (bio-) chemical process engineering is illustrated. In-depth scientific approaches to biocatalysis and biocatalyst development including enzyme kinetics, enzyme crystal studies and semi-rational enzyme mutations are also presented. Metabolic pathway analysis and modeling of fermentation process are treated as well as molecular precision in synthetic approaches to beta-lactams, their precursors and derivatives. Process technology studies including new reactor concepts, possible short-cut routes and improved down-stream-processing methods complete a broad view on the scope and limitations of the presently developed industrial processes including an intriguing insight into future process possibilities. This book represents an excellent case study on the transformation of traditional, stoïchiometric, organic synthesis and classical fermentations into modern (bio-) catalysis and biosynthesis based on insights in metabolic pathways and enzyme actions.


Concerted Organic And Bio Organic Mechanisms

Author by : Andrew Williams
Languange : en
Publisher by : CRC Press
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Description : The concept of concerted mechanisms was formulated nearly 90 years ago and virtually all general organic chemistry texts mention it. Until now, however, no monograph has addressed the concept explicitly. Over the last two decades, substantial advancements made in the development of precise methods for elucidating concerted mechanisms have heightened the need for a comprehensive text on the subject. Concerted Organic and Bio-organic Mechanisms gathers the salient materials related to this emerging field into a single text. It sets forth the precise definition of concertedness-along with working sub-definitions-and describes rigorous experimental tools chemists can use to diagnose the existence or absence of concerted mechanisms. Advances in our understanding of concerted mechanisms lead to further questions. Concerted Organic and Bio-organic Mechanisms provides the background and the tools researchers need to consider these important questions and further advance the frontiers of reactions, synthesis, and catalysis.


Computational Approaches To Biochemical Reactivity

Author by : Gábor Náray-Szabó
Languange : en
Publisher by : Springer Science & Business Media
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Description : A quantitative description of the action of enzymes and other biological systems is both a challenge and a fundamental requirement for further progress in our und- standing of biochemical processes. This can help in practical design of new drugs and in the development of artificial enzymes as well as in fundamental understanding of the factors that control the activity of biological systems. Structural and biochemical st- ies have yielded major insights about the action of biological molecules and the mechanism of enzymatic reactions. However it is not entirely clear how to use this - portant information in a consistent and quantitative analysis of the factors that are - sponsible for rate acceleration in enzyme active sites. The problem is associated with the fact that reaction rates are determined by energetics (i. e. activation energies) and the available experimental methods by themselves cannot provide a correlation - tween structure and energy. Even mutations of specific active site residues, which are extremely useful, cannot tell us about the totality of the interaction between the active site and the substrate. In fact, short of inventing experiments that allow one to measure the forces in enzyme active sites it is hard to see how can one use a direct experimental approach to unambiguously correlate the structure and function of enzymes. In fact, in view of the complexity of biological systems it seems that only computers can handle the task of providing a quantitative structure-function correlation.


Progress In Inorganic Chemistry

Author by : Stephen J. Lippard
Languange : en
Publisher by : John Wiley & Sons
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Description : This comprehensive series of volumes on inorganic chemistry provides inorganic chemists with a forum for critical, authoritative evaluations of advances in every area of the discipline. Every volume reports recent progress with a significant, up-to-date selection of papers by internationally recognized researchers, complemented by detailed discussions and complete documentation. Each volume features a complete subject index and the series includes a cumulative index as well.


Understanding Enzyme Catalysis Using Computer Simulation

Author by : Anonim
Languange : en
Publisher by : Unknown
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Description : Enzymes catalyze biochemical reactions with remarkable specificity and efficiency, usually under physiological conditions. Computer simulation is a powerful tool for understanding enzyme catalytic mechanisms, particularly in cases where standard experimental techniques may be of limited utility. Here, we present an overview of the application of computer simulation techniques to understanding enzyme catalytic mechanisms. Examples using quantum chemical methods, as well as combined quantum mechanical/classical mechanical approaches, are provided.


The Chemistry Of Enzyme Action

Author by : Anonim
Languange : en
Publisher by : Elsevier
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Description : The Chemistry of Enzyme Action