Theoretical Analysis of Enzymatic Functions based on Hybrid-Computational Modeling

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Owing to the rapid progress of computational architecture and the advance of new chemical theories for treating large molecular systems, understanding complex chemical reactions in the condensed phase is becoming one of the important issues in modern theoretical chemistry. Before the mid 90's, mainly due to a lack of computational power, the major target of quantum chemistry was limited to simple chemical reactions in the gas phase. At present, however, various types of chemical reactions in the condensed phase (e.g.reactions in solutions, on surfaces, inside proteins, and so on) have become realistic targets for theoretical and computational studies.In the field of biochemistry, understanding the nature of enzyme functions at atomistic level is one of the most important issues. Despite the intensive work over past decades, however, there is still no quantitative understanding of how enzymes work. Now, understanding the structure-function relationships of enzyme reactions is becoming a more and more important problem. In this research project, we developed a hybrid QM/MM modeling procedure combined with MD simulations and all-electron QM calculations for the entire protein matrix. By selecting typical protein systems, we then performed a systematic computational analyses based on QM/MM computations and discussed the major catalytic factors in typical enzyme reactions.