Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis

With regards to enzyme dynamics, motions of residues near the active site can have an effect on the catalytic mechanism. These motions can influence the standard model of catalysis in different ways: (1) they may be extended motions related to conformational fluctuations; (2) they may be local subpicosecond motions near the active site and (3) they may force a revision of the view of thermodynamic cycles which is often used to describe catalysis. This review covers three kinds of dynamic effects: (1) rate-promoting quasi-harmonic motions, a fast subpicosecond effect usually for reactions that involve proton tunneling; (2) extended correlated motions involving several residues and the theoretical tools needed for studying them and (3) conformational fluctuations. Under the first effect, focus is on quantum theory of proton transfer, rate-promoting vibrations, computational diagnosis of promoting vibrations and experimental ramifications for promoting vibrations. As for conformational fluctuations, focus is on dihydrofolate reductase (DHFR) and conformation space.