Computational approaches: Reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency

This review aims to provide experimental enzymologists interested in structure, dynamics, and function in catalysis with a talking knowledge of the possibilities present in modern computational chemistry. Topics covered include the use of computational methods in enzymology, examples of what can be observed by molecular dynamic (MD) simulations that are not available by experimental methods, lessons from simple systems and dynamic motion in catalysis. Under the use of computational methods, focus is on application of MD simulation to account for static crystal structures as well as dynamic structures, reaction coordinates and the structures of states from QM/MM calculations and near attack conformers (NACs). As for examples, discussion is on specific self cleavage of hammerhead RNA, modeling of missing loop and structural clarification of unobservable high B-factor portions of a crystal lattice and determination of important protonation states. Under the dynamic motion topic, cross-correlation and normal mode analysis, hydride equivalent transfer reactions and M-Hhal methyltyransferase reaction are outlined.