WorldCat Identities

Warshel, Arieh

Overview
Works: 19 works in 71 publications in 2 languages and 1,932 library holdings
Genres: Academic theses 
Roles: Author, Editor, Author of introduction, wpr, Other
Publication Timeline
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Most widely held works about Arieh Warshel
 
Most widely held works by Arieh Warshel
Computational approaches to biochemical reactivity by Gábor Náray-Szabó( )

21 editions published between 1997 and 2005 in English and held by 1,158 WorldCat member libraries worldwide

This book summarises recent results in the rapidly developing discipline of the computational aspects of biochemical reactivity. It presents a comprehensive and critical treatise on the subject, with numerous references covering practically all relevant and recent work. The chapters, written by eminent experts in the field, deal with quantum mechanical models for reactions in solution, ab initio molecular orbital studies on enzymatic reactions, combined quantum-classical models for proteins, force field approaches for modelling enzymes, electrostatic effects in proteins, electrostatic basis of enzyme catalysis, the mechanism of proteases, modelling of proton transfer reactions in enzymes and protein-ligand interactions. Audience: This volume will be of interest to graduate students and researchers working in molecular biophysics, structural biology or structure-based molecular design
Computer modeling of chemical reactions in enzymes and solutions by Arieh Warshel( Book )

24 editions published between 1991 and 2008 in English and Undetermined and held by 607 WorldCat member libraries worldwide

Annotation
Quantum tunnelling in enzyme-catalysed reactions( )

2 editions published in 2009 in English and held by 82 WorldCat member libraries worldwide

This accessible introduction to modern theories of enzyme catalysis presents the latest methods for studying quantum tunnelling in biological systems, 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
Theory and applications of the empirical valence bond approach : from physical chemistry to chemical biology by Fernanda Duarte( Book )

5 editions published in 2017 in English and held by 66 WorldCat member libraries worldwide

A comprehensive overview of current empirical valence bond (EVB) theory and applications, one of the most powerful tools for studying chemical processes in the condensed phase and in enzymes.-Discusses the application of EVB models to a broad range of molecular systems of chemical and biological interest, including reaction dynamics, design of artificial catalysts, and the study of complex biological problems -Edited by a rising star in the field of computational enzymology -Foreword by Nobel laureate Arieh Warshel, who first developed the EVB approach
Calculations of electrostatic interactions in biological systems and in solutions by Arieh Warshel( Book )

3 editions published in 1984 in English and held by 2 WorldCat member libraries worldwide

How do enzymes really work and how they do not work : what has been learnt from computer simulation studies by Arieh Warshel( Visual )

1 edition published in 2009 in English and held by 2 WorldCat member libraries worldwide

Computer Simulation of Chemical Reactions in Synthetic Model Compounds and Genetically Engineered Active Sites( Book )

2 editions published between 1988 and 1990 in English and held by 2 WorldCat member libraries worldwide

The primary objective of this project is to advance our understanding of the principles of biological recognition and specificity by using computer simulation approaches. We are interested in elucidating and analyzing the origin of the enormous power of biological catalysts, and exploiting this understanding in designing a new generation of highly specific molecular systems. Our computer simulation methods have approached the level where we can reproduce the effects of genetic modifications of enzymes in a semiquantitative way. We are also able to estimate in a reasonable way the overall catalytic free energies of enzymes. We are trying to utilize this progress in translating the rapidly accumulating experimental results about genetically modified enzymes into clear design principles. During the second year, we have progressed in several directions, ranging from simulations of several mutations in trypsin, subtilisin and Aspartateaminotransferase, simulations of chemical reactions in solutions, and preliminary studies of catalytic antibodies. These results and our plans for the next year are summarized in the report. Biological recognition, Enzyme catalysis, Computer aided, Enzyme engineering, Catalytic antibodies, Synthetic active sites
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1 edition published in 1969 in Hebrew and held by 1 WorldCat member library worldwide

Energetics of Cation Radical Formation at the Proximal Active Site Tryptophan of Cytochrome-c-Peroxidase and Ascorbate Peroxidase( )

1 edition published in 1998 in English and held by 1 WorldCat member library worldwide

Despite very similar protein structures, ascorbate peroxidase (APX) and yeast cytochrome-c-peroxidase (CCP) stabilize different radical species during enzyme turnover. Both enzymes contain similar active site residues, including the tryptophan that is oxidized to a stable cation radical in CCP. However, the analogous trytophan is not oxidized in APX, and the second oxidizing equivalent is retained as a porphyrin pi-cation radical. In this study, we provide an improved computational approach to estimate the contribution of solvent and protein electrostatics to the energetics of tryptophan cation radical formation in the two enzyme environments. The Protein Dipoles Langevin Dipoles (PDLD) model is combined with molecular dynamics to estimate the role of discrete solvation, atomic polarizabilitis, and dynamic motional averaging on the electrostatic potentials. The PDLD model shows that the protein environment of CCP stabilizes the tryptophan cation radical by 330 mV relative to that in APX. Analysis of the components contributing to this difference supports proposals that the cation binding site contributes to, but is not the sole cause of, the different sites of radical stabilization. The enzymes have thus evolved this distinction using several contributing interactions including the cation binding site, solvent access, and subtle differences in protein structure and dynamics
Quantum tunnelling in enzyme-catalysed reactions by Rudolf K Allemann( Book )

1 edition published in 2009 in Undetermined and held by 1 WorldCat member library worldwide

Sitting at the interface between biology, chemistry and physics, this introduction to modern theories of enzyme catalysis presents the latest methods used to study quantum tunnelling in biological systems
Catalytic effects of mutations of distant protein residues in human DNA polymerase [beta] : theory and experiment( )

1 edition published in 2012 in English and held by 1 WorldCat member library worldwide

Why nature really chose phosphate by Shina Caroline Lynn Kamerlin( )

1 edition published in 2013 in English and held by 1 WorldCat member library worldwide

Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it
Electron transfer in proteins : theory and experiment by Ralf Langen( Book )

1 edition published in 1995 in English and held by 1 WorldCat member library worldwide

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions by Andrew J Adamczyk( )

1 edition published in 2011 in English and held by 1 WorldCat member library worldwide

The proposal that enzymatic catalysis is due to conformational fluctuations has been previously promoted by means of indirect considerations. However, recent works have focused on cases where the relevant motions have components toward distinct conformational regions, whose population could be manipulated by mutations. In particular, a recent work has claimed to provide direct experimental evidence for a dynamical contribution to catalysis in dihydrofolate reductase, where blocking a relevant conformational coordinate was related to the suppression of the motion toward the occluded conformation. The present work utilizes computer simulations to elucidate the true molecular basis for the experimentally observed effect. We start by reproducing the trend in the measured change in catalysis upon mutations (which was assumed to arise as a result of a "dynamical knockout" caused by the mutations). This analysis is performed by calculating the change in the corresponding activation barriers without the need to invoke dynamical effects. We then generate the catalytic landscape of the enzyme and demonstrate that motions in the conformational space do not help drive catalysis. We also discuss the role of flexibility and conformational dynamics in catalysis, once again demonstrating that their role is negligible and that the largest contribution to catalysis arises from electrostatic preorganization. Finally, we point out that the changes in the reaction potential surface modify the reorganization free energy (which includes entropic effects), and such changes in the surface also alter the corresponding motion. However, this motion is never the reason for catalysis, but rather simply a reflection of the shape of the reaction potential surface
Special NIH lecture : 2013 Nobel laureate in chemistry : computer simulations of biological functions by Arieh Warshel( Visual )

1 edition published in 2013 in English and held by 1 WorldCat member library worldwide

(CIT): One of the challenges in molecular biology has been the ability to understand the action of biological systems on a well-defined molecular level, where the structural information is translated to clear functional description. Arieh Warshel, who has been advancing the frontiers of modeling biological functions for more that four decades, will describe the progress in the field since its early days. The lecture will include a discussion of the development of multiscale modeling of complex biological systems as well as a perspective of future directions
Computational Approaches to Biochemical Reactivity( )

2 editions published between 1997 and 2002 in English and held by 1 WorldCat member library worldwide

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
Calculations of chemical processes in solution by density-functional and other quantum-mechanical techniques by Richard P Muller( )

1 edition published in 1997 in English and held by 0 WorldCat member libraries worldwide

 
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Computational approaches to biochemical reactivity
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Computer modeling of chemical reactions in enzymes and solutionsQuantum tunnelling in enzyme-catalysed reactions
Alternative Names
Arieh Warshel biochimico israeliano naturalizzato statunitense

Arieh Warshel chemist, biochemist and biophysicist

Arieh Warshel chercheur en chimie

Arieh Warshel israelisch-amerikanischer Chemiker

Arieh Warshel israelisch-amerikanischer Chemiker und Nobelpreisträger

Arieh Warshel izraelsko-americký biochemik a biofyzik

Arieh Warshel scheikundige uit Israël

Waršel, ʾAryeh 1940-...

Warshel, A. 1940-

Ары Варшэль

Арі Варшель

Арје Варшел израелско-американски хемичар, биохемичар, биофизичар и нобеловец

Уоршел, Арье

אריה וואַרשל ישראליש־אמעריקאנער כעמיקער

אריה ורשל

אריה ורשל כימאי אמריקאי ישראלי

ורשל אריה 1940-....

أريه وارشيل

اری وارشل

اریا وارشل

آریه وارشل

एरिह वॉरशेल

এরিহ ওয়ারশেল

ஏரியே வார்செல்

അരിയ വാർഷൽ

아리에 와르셸

アリー・ウォーシェル

阿里耶·瓦舍尔

Languages
English (68)

Hebrew (1)