The dynamic nature of proteins in solution is often an indispensable factor in biological function such as enzymatic catalysis. Complementary to the conventional structural analysis, computational simulations have the advantage to reflect the dynamic nature of proteins or enzymes. One of the computational simulation methods, the quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations, has been widely applied to the research in structural analysis, ligand-receptor binding and enzymatic catalysis.
In this dissertation, QM/MM MD simulations were applied to the studies on cytidine deaminase (CDA), yeast cytosine deaminase (yCD), and kumamolisin-As, as well as two protein lysine methyltransferases (PKMTs), DIM-5 and SET7/9. In the simulations of the transition state analogue (TSA) binding of zebularine 3, 4-hydrate to CDA and of 4-[R]-hydroxyl-3,4-dihydropyrimidine (DHP) to yCD, proton transfers were observed between the TSA and a catalytic Glu residue in both cases. Such general acidbase mechanism was also observed in the stabilization of the tetrahedral intermediate by a critical Asp residue during the acylation of kumamolisin-As. Moreover, dynamic substrate-assisted catalysis (DSAC) involving the His of the substrate at P1 site was proposed. It was suggested that DSAC may contribute to the transition state stabilizations and substrate specificity of kumamolisin-As. The origin of the product specificities of PKMTs was studied by comparison of QM/MM MD simulations on the first, second and third methyl transfers in the trimethylase DIM5 and the monomethylase SET7/9. The product specificities of the enzymes can be well explained by population distributions of well-aligned reactive structures and the relative free energy barriers for the methyl transfers. The structural and energetic reasons for the product specificities were discussed and a triplet code based on the relative free energy barriers for the three methyl transfers was proposed in the determination of product specificities of PKMTs
