Theoretical elucidations of the reactions and the reaction-control mechanisms in enzymes

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Enzymes catalyze important chemical reactions in living systems. The enzyme reactions for material formations and energy conversions are highly efficient. Simple reactions are clarified by theoretical analyses, however, complicated reactions in many important enzymes are still unclear. Therefore, reactions of threonine synthase (ThrS), nitrite reductase (NiR), nitric oxide reductase (NOR) and DNA topoisomerase (Topo) are investigated by a mixed quantum mechanical and molecular mechanical (QM/MM) method. We utilized supercomputers and massive parallel simulations were performed. We elucidated the reaction mechanism by investigations for the protonation states, hydrogen-bonding network, existence of waters and possible reaction pathways.