Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis
Chapter 3: A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applications
Published:16 Nov 2016
Special Collection: 2016 ebook collection
James T. Hynes, Damien Laage, Iñaki Tuñón, Vicent Moliner, 2016. "A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applications", Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, Inaki Tunon, Vicent Moliner
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In this chapter we present the basic principles of transition state theory (TST) and a number of its applications to the study of enzymatic reactions. The assumptions of TST are discussed, as are the refinements to account for the failure of those assumptions, in particular that of no recrossing of the transition state surface. The selection of a reaction coordinate and the associated generation of free energy surfaces and their importance for TST receive special attention. While TST in its usual form assumes classical nuclear motion of the reaction coordinate, it can also be applied – with a special choice of classical reaction coordinate – for enzymatic reactions involving the transfer of light particles (proton, hydride and hydrogen atom transfers), where a quantum description of their motion is required. The theory and deviations from it are illustrated and discussed in detail via applications to a number of enzyme-catalysed reactions, indicating how TST and its variants can be successfully used to obtain rate constants for these reactions, to understand important aspects of their mechanism, and to identify the sources of the catalytic effect itself.