Simulating Enzyme Reactivity PDF Download
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Author | : Inaki Tunon |
Publisher | : Royal Society of Chemistry |
Total Pages | : 558 |
Release | : 2016-11-25 |
Genre | : Science |
ISBN | : 1782624295 |
Download Simulating Enzyme Reactivity Book in PDF, ePub and Kindle
Exploring the theories, methodologies and applications in simulations of enzymatic reactions, this book is a great resource for postgraduate students and researchers.
Author | : John Maclane |
Publisher | : Createspace Independent Publishing Platform |
Total Pages | : 446 |
Release | : 2017-06-07 |
Genre | : |
ISBN | : 9781548041595 |
Download Simulating Enzyme Reactivity Computational Methods in Enzyme Catalysis Book in PDF, ePub and Kindle
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.
Author | : Arieh Warshel |
Publisher | : Wiley-Interscience |
Total Pages | : 264 |
Release | : 1991-11-29 |
Genre | : Computers |
ISBN | : |
Download Computer Modeling of Chemical Reactions in Enzymes and Solutions Book in PDF, ePub and Kindle
This practical reference explores computer modeling of enzyme reations--techniques that help chemists, biochemists and pharmaceutical researchers understand drug and enzyme action.
Author | : Ishan Satish Patel |
Publisher | : |
Total Pages | : 119 |
Release | : 2015 |
Genre | : |
ISBN | : |
Download Large Scale Simulation and Analysis to Understand Enzymatic Chemical Mechanisms Book in PDF, ePub and Kindle
The full stack approach, from Biochemical Network Simulation to Quantum Mechanics, is developed and utilized to understand in this thesis to understand enzymatic mechanism. The story falls into two segments that highlight two different aspects of enzymatic mechanisms. The first is the determination of the kinetic complexity of one full enzymatic turnover can affect the system in ways that cannot be predicted by simplistic simulations, as evidenced by differential hydrolysis rates of VX and Paraoxon in the enzyme PTE. Over 4M CPU hours of thermodynamic integration simulations were performed to obtain free energy profiles, as a function of up to 6 dimensions, along a reaction path determined through a combination of knowledge from physical organic chemistry, local energetic optimizations, and experimental information. The activation barriers were converted to reaction rates and simulated with mass action kinetics. The results show the slow-down in one turnover for the enzyme is not exactly the one with the "highest barrier" but is instead the result of non-preferential product-facing equilibrium. We also show that active site poisoning by VX opens up new pathways that are an overall detriment to the enzyme. The second is the uncovering of the drivers of enzymatic reactivity for a purely electronic Claisen rearrangement of Chorismate in CM, CM mutants, 1 F7 antibody, Solvent, and Vacuum. Utilizing Transition Path Sampling (TPS), we performed large scale simulations totaling over I OM CPU hours and 1000 TB of storage space to arrive at an understanding of the causation behind differential reactivity from a quantum mechanical orbital point of view. Our results suggest differential catalytic capacity is driven by, and correlates with, greater capacity to generate the forming bond, and for faster enzymes, greater capacity to disrupt the breaking bond. Further orbital level decompositions were performed that demonstrated disruption of the breaking bond allows greater catalytic gains because orbital symmetry prevents strong intermolecular electronic delocalization of the breaking bond electrons. Our evidence suggests a combination of catalyzing the departure from the reactant basin and the transport through the transition region are both reasons why the WT CM is an extremely capable catalyst.
Author | : Gábor Náray-Szabó |
Publisher | : Springer Science & Business Media |
Total Pages | : 386 |
Release | : 2006-04-11 |
Genre | : Science |
ISBN | : 0306469340 |
Download Computational Approaches to Biochemical Reactivity Book in PDF, ePub and Kindle
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.
Author | : Philip Hanoian |
Publisher | : |
Total Pages | : |
Release | : 2014 |
Genre | : |
ISBN | : |
Download Computer Simulations Of Enzymes Book in PDF, ePub and Kindle
Enzymes are proteins that perform the essential function of facilitating chemical reactions within living organisms, and the rate enhancements provided by enzymes are so significant that they remain a marvel for chemists today. The study of enzymes is thus pervaded by attempts to understand the precise mechanisms by which enzymes achieve these rate enhancements, with additional focus on the impressive level of specificity and selectivity these protein catalysts display as well. In this thesis, four studies on enzymatic systems are presented with the goal of further elucidating the mechanisms by which enzymes confer enormous rate enhancements to chemical reactions. In the first study, mixed quantum mechanical/molecular mechanical calculations are applied to study a series of phenolate inhibitors of increasing pKa bound to ketosteroid isomerase to explore the catalytically relevant hydrogen bonds in the enzyme active site. The second study uses molecular dynamics simulations to explore the use of water in the active site in lieu of the native enzymatic hydrogen bonds. The third study focuses on the positioning of the catalytic base in ketosteroid isomerase using molecular dynamics simulations, and this positioning is suggested to arise from non-local contributions involving nearby hydrophobic residues and an active site loop. In the final study, an additional enzyme, dihydrofolate reductase is examined, and empirical valence bond molecular dynamics simulations are applied to evaluate the free energy barriers of the wild-type enzyme and several evolutionarily motivated mutants. Overall, these studies help to further our understanding of enzymes and the roles of individual factors in enzyme catalysis.
Author | : Charles Walter |
Publisher | : |
Total Pages | : 226 |
Release | : 1976 |
Genre | : Science |
ISBN | : |
Download Enzyme Reactions and Enzyme Systems Book in PDF, ePub and Kindle
Author | : Paolo Carloni |
Publisher | : John Wiley & Sons |
Total Pages | : 294 |
Release | : 2006-03-06 |
Genre | : Science |
ISBN | : 3527605304 |
Download Quantum Medicinal Chemistry Book in PDF, ePub and Kindle
Computational methods are transforming the work of chemical and pharmaceutical laboratories. Increasingly faster and more exact simulation algorithms have made quantum chemistry a valuable tool in the search for active substances. Written by a team of leading international quantum chemists, this book is aimed at both beginners as well as experienced users of quantum chemical methods. All commonly used quantum chemical methods are treated here, including Density Functional Theory, quantum and molecular mechanical approaches. Numerous examples illustrate the use of these methods for dealing with problems in pharmaceutical practice, whether the study of inhibitor binding, identifying the surface load of active substances or deriving molecular descriptors using quantum chemical tools. For anyone striving to stay ahead in this rapidly evolving field.
Author | : Xiaoyu Wang |
Publisher | : Springer |
Total Pages | : 134 |
Release | : 2016-07-27 |
Genre | : Technology & Engineering |
ISBN | : 3662530686 |
Download Nanozymes: Next Wave of Artificial Enzymes Book in PDF, ePub and Kindle
This book describes the fundamental concepts, the latest developments and the outlook of the field of nanozymes (i.e., the catalytic nanomaterials with enzymatic characteristics). As one of today’s most exciting fields, nanozyme research lies at the interface of chemistry, biology, materials science and nanotechnology. Each of the book’s six chapters explores advances in nanozymes. Following an introduction to the rise of nanozymes research in the course of research on natural enzymes and artificial enzymes in Chapter 1, Chapters 2 through 5 discuss different nanomaterials used to mimic various natural enzymes, from carbon-based and metal-based nanomaterials to metal oxide-based nanomaterials and other nanomaterials. In each of these chapters, the nanomaterials’ enzyme mimetic activities, catalytic mechanisms and key applications are covered. In closing, Chapter 6 addresses the current challenges and outlines further directions for nanozymes. Presenting extensive information on nanozymes and supplemented with a wealth of color illustrations and tables, the book offers an ideal guide for readers from disparate areas, including analytical chemistry, materials science, nanoscience and nanotechnology, biomedical and clinical engineering, environmental science and engineering, green chemistry, and novel catalysis.
Author | : Peter Vagedes |
Publisher | : |
Total Pages | : 112 |
Release | : 2000 |
Genre | : |
ISBN | : |
Download Simulation of Enzyme Reactions Book in PDF, ePub and Kindle