Simulating Enzyme Reactivity: Computational Methods in Enzyme CatalysisInaki Tunon, Vicent Moliner 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. |
Contents
Chapter 1 Perspective on Computer Modelling of Enzymatic Reactions | 1 |
Theory | 31 |
Methods | 215 |
Applications | 375 |
| 522 | |
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Common terms and phrases
A. J. Mulholland Acad acid active site adiabatic approach atoms binding Biochemistry Biol catalytic catalytic effect Chem chemical chorismate chorismate mutase classical cofactor complex Computational Chemistry configuration conformational coupling D. G. Truhlar density dynamics electronic electrostatic energy barrier environment enzymatic reactions enzyme catalysis example experimental Figure force fields free energy function geometry optimisation Hammes-Schiffer Hessian Hirao hydride hydrogen bond interactions isotope KatG kcal kcal molÀ1 KIEs kinetic Kohen Lett MD simulations mechanism model system molecular Moliner motion mutations Natl nucleophile obtained ONIOM pathway peroxidases Phys polarisation potential energy Proc protein proton QM region QM/MM QM/MM methods QM/MM simulations quantum rate constant reactant reaction coordinate reactive reorganisation energy residues ribozyme Rothlisberger sampling SN2 reaction solution solvent stabilisation Struct structure studies substrate Theory Comput trajectories transfer transition Tun˜ón tunnelling values vibrational Warshel water molecule