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Theoretical and Computational Chemistry Series
Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis
Edited by
Vicent Moliner
Vicent Moliner
Universitat Jaume I, Spain
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Hardback ISBN:
978-1-78262-429-5
PDF ISBN:
978-1-78262-683-1
EPUB ISBN:
978-1-78262-967-2
Special Collection:
2016 ebook collection
No. of Pages:
535
Published online:
16 Nov 2016
Published in print:
25 Nov 2016
About this book
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.
Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, The Royal Society of Chemistry, 2016.
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Digital access
$251.00
Print format
Simulating Enzyme Reactivity
$251.00
Table of contents
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Chapter 1: Perspective on Computer Modelling of Enzymatic Reactionsp1-30ByArieh Warshel;Arieh WarshelDepartment of Chemistry, University of Southern CaliforniaSGM 420, 3620 McClintock AvenueLos Angeles, CA 90089USA[email protected]Search for other works by this author on:Ram Prasad BoraRam Prasad BoraDepartment of Chemistry, University of Southern CaliforniaSGM 420, 3620 McClintock AvenueLos Angeles, CA 90089USA[email protected]Search for other works by this author on:
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Chapter 2: Fundamentals of Enzyme Catalysis: Determination of Rate Constantsp31-53ByRichard L. SchowenRichard L. SchowenSearch for other works by this author on:
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Chapter 3: A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applicationsp54-88ByJames T. Hynes;James T. HynesDepartment of Chemistry and Biochemistry, University of ColoradoBoulder, CO 80309-0215USA[email protected]Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC Univ. Paris 06, CNRS UMR 8640 PASTEUR24 rue Lhomond75005 ParisFrance[email protected]Search for other works by this author on:Damien Laage;Damien LaageEcole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC Univ. Paris 06, CNRS UMR 8640 PASTEUR24 rue Lhomond75005 ParisFrance[email protected]Search for other works by this author on:Iñaki Tuñón;Iñaki TuñónDepartament de Química Física, Universitat de ValènciaSpainSearch for other works by this author on:Vicent MolinerVicent MolinerDepartament de Química Física i Analítica, Universitat Jaume ISpainSearch for other works by this author on:
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Chapter 4: Electron Transfer Reactions in Enzymes: Seven Things that Might Break Down in Vanilla Marcus Theory and How to Fix Them if They Dop89-149ByAurélien de la Lande;Aurélien de la LandeLaboratoire de Chimie Physique, UMR8000, CNRS/Univ. Paris-Sud, Univ. Paris Saclay91405 OrsayFrance[email protected]Search for other works by this author on:Fabien Cailliez;Fabien CailliezLaboratoire de Chimie Physique, UMR8000, CNRS/Univ. Paris-Sud, Univ. Paris Saclay91405 OrsayFrance[email protected]Search for other works by this author on:Dennis R. SalahubDennis R. SalahubDepartment of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary2500 University Drive, N.W., CalgaryAlbertaCanadaT2N 1N4[email protected]College of Chemistry and Chemical Engineering, Henan University of TechnologyNo. 100, Lian Hua Street, High-Tech Development ZoneZhengzhou450001P.R. China[email protected]Search for other works by this author on:
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Chapter 5: Kinetic Isotope Effectsp150-184ByP. B. WilsonP. B. WilsonSearch for other works by this author on:
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Chapter 6: Free Energy Calculation Methods and Rare Event Sampling Techniques for Biomolecular Simulationsp185-214ByJens Smiatek;Jens SmiatekInstitute for Computational Physics, University of StuttgartAllmandring 370569 StuttgartGermany[email protected]Search for other works by this author on:Niels Hansen;Niels HansenInstitute of Thermodynamics and Thermal Process Engineering, University of StuttgartPfaffenwaldring 970569 StuttgartGermany[email protected]Search for other works by this author on:Johannes KästnerJohannes KästnerInstitute for Theoretical Chemistry, University of StuttgartPfaffenwaldring 5570569 StuttgartGermany[email protected]Search for other works by this author on:
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Chapter 7: Methods to Trace Conformational Transitionsp215-244ByPedro Sfriso;Pedro SfrisoInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and TechnologyBarcelonaSpain[email protected]Joint IRB-BSC Program in Computational BiologyBarcelonaSpainSearch for other works by this author on:Modesto OrozcoModesto OrozcoInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and TechnologyBarcelonaSpain[email protected]Joint IRB-BSC Program in Computational BiologyBarcelonaSpainSearch for other works by this author on:
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Chapter 8: Key Concepts and Applications of ONIOM Methodsp245-293ByHajime Hirao;Hajime HiraoDivision of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University21 Nanyang Link637371Singapore[email protected]Search for other works by this author on:Kai Xu;Kai XuDivision of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University21 Nanyang Link637371Singapore[email protected]Search for other works by this author on:Pratanphorn Chuanprasit;Pratanphorn ChuanprasitDivision of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University21 Nanyang Link637371Singapore[email protected]Search for other works by this author on:Adhitya Mangala Putra Moeljadi;Adhitya Mangala Putra MoeljadiDivision of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University21 Nanyang Link637371Singapore[email protected]Search for other works by this author on:Keiji MorokumaKeiji MorokumaFukui Institute for Fundamental Chemistry, Kyoto University34-4 Takano Nishihiraki-choSakyo, Kyoto 606-8103Japan[email protected]Search for other works by this author on:
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Chapter 9: First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanicsp294-339ByJens Dreyer;Jens DreyerComputational Biomedicine Institute (IAS-5/INM-9), Forschungszentrum JülichWilhelm-Johnen-Straßig;e52428 JülichGermany[email protected]Search for other works by this author on:Giuseppe Brancato;Giuseppe BrancatoScuola Normale Superiore (SNS)Piazza dei Cavalieri 756126 PisaItalySearch for other works by this author on:Emiliano Ippoliti;Emiliano IppolitiComputational Biomedicine Institute (IAS-5/INM-9), Forschungszentrum JülichWilhelm-Johnen-Straßig;e52428 JülichGermany[email protected]Search for other works by this author on:Vito Genna;Vito GennaLaboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di TecnologiaVia Morego 3016163 GenoaItalySearch for other works by this author on:Marco De Vivo;Marco De VivoComputational Biomedicine Institute (IAS-5/INM-9), Forschungszentrum JülichWilhelm-Johnen-Straßig;e52428 JülichGermany[email protected]Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di TecnologiaVia Morego 3016163 GenoaItalySearch for other works by this author on:Paolo Carloni;Paolo CarloniComputational Biomedicine Institute (IAS-5/INM-9), Forschungszentrum JülichWilhelm-Johnen-Straßig;e52428 JülichGermany[email protected]Computational Biophysics, German Research School for Simulation Sciences52425 JülichGermanySearch for other works by this author on:Ursula RothlisbergerUrsula RothlisbergerEcole polytechnique Fédérale de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BSPCH-1015 LausanneSwitzerlandSearch for other works by this author on:
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Chapter 10: Nuclear Quantum Effects in Enzymatic Reactionsp340-374ByReuven Eitan;Reuven EitanDepartment of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry and the Institute for Nanotechnology and Advanced Materials, Bar-Ilan UniversityRamat-Gan 52900Israel[email protected]Search for other works by this author on:Susanta Das;Susanta DasDepartment of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry and the Institute for Nanotechnology and Advanced Materials, Bar-Ilan UniversityRamat-Gan 52900Israel[email protected]Search for other works by this author on:Anil Mhashal;Anil MhashalDepartment of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry and the Institute for Nanotechnology and Advanced Materials, Bar-Ilan UniversityRamat-Gan 52900Israel[email protected]Search for other works by this author on:Vijay SinghVijay SinghDepartment of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry and the Institute for Nanotechnology and Advanced Materials, Bar-Ilan UniversityRamat-Gan 52900Israel[email protected]Search for other works by this author on:
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Chapter 11: QM/MM Methods for Simulating Enzyme Reactionsp375-403ByKara E. Ranaghan;Kara E. RanaghanCentre for Computational Chemistry, University of BristolClifton, Bristol, BS8 1TSUK[email protected]Search for other works by this author on:Adrian J. MulhollandAdrian J. MulhollandCentre for Computational Chemistry, University of BristolClifton, Bristol, BS8 1TSUK[email protected]Search for other works by this author on:
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Chapter 12: Ribozymesp404-435ByA. OlivaA. OlivaUniversitat Autònoma de Barcelona, Department of Chemistry, Edifici Cn08193 Bellaterra (Cerdanyola del Vallès)Spain[email protected]Search for other works by this author on:
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Chapter 13: Effects of Water and Non-aqueous Solvents on Enzyme Activityp436-452ByEva Pluhařová;Eva PluhařováEcole Normale Supérieure – PSL Research University, Chemistry Department, Sorbonne Universities – UPMC Univ Paris 06CNRS UMR 8640 PASTEUR24 rue Lhomond75005 ParisFrance[email protected]Search for other works by this author on:Nicolas Chéron;Nicolas ChéronEcole Normale Supérieure – PSL Research University, Chemistry Department, Sorbonne Universities – UPMC Univ Paris 06CNRS UMR 8640 PASTEUR24 rue Lhomond75005 ParisFrance[email protected]Search for other works by this author on:
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Chapter 14: Modelling Reactivity in Metalloproteins: Hydrogen Peroxide Decomposition by Haem Enzymesp453-480ByM. Alfonso-Prieto;M. Alfonso-PrietoDepartament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTC), Universitat de BarcelonaCarrer Martí i Franquès 1BarcelonaE-08028Spain[email protected]Search for other works by this author on:C. RoviraC. RoviraDepartament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTC), Universitat de BarcelonaCarrer Martí i Franquès 1BarcelonaE-08028Spain[email protected]Institució Catalana de Recerca i Estudis Avançats (ICREA)Passeig Lluís Companys, 23BarcelonaE-08018Spain[email protected]Search for other works by this author on:
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Chapter 15: Enzyme Designp481-521ByLur Alonso-Cotchico;Lur Alonso-CotchicoDepartament de Química, Universitat Autònoma de Barcelona08193 Cerdanyola del VallèsSpain[email protected]Search for other works by this author on:Jaime Rodríguez-Guerra;Jaime Rodríguez-GuerraDepartament de Química, Universitat Autònoma de Barcelona08193 Cerdanyola del VallèsSpain[email protected]Search for other works by this author on:Agustí Lledós;Agustí LledósDepartament de Química, Universitat Autònoma de Barcelona08193 Cerdanyola del VallèsSpain[email protected]Search for other works by this author on:
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