Comparative Computational Approach To Study Enzyme ReactionsUsing QM and QM-MM Methods

摘要

Choline oxidase catalyzes oxidation of choline into glycine betaine through atwo-step reaction pathway employing flavin as the cofactor. On the light of kinetic studies,it is proposed that a hydride ion is transferred from α-carbon of choline/hydrated-betainealdehyde to the N5 position of flavin in the rate-determining step, which is preceded bydeprotonation of hydroxyl group of choline/hydrated-betaine aldehyde to one of thepossible basic side chains. Using the crystal structure of glycine betaine?choline oxidasecomplex, we formulated two computational systems to study the hydride-transfermechanism including main active-site amino acid side chains, flavin cofactor, and cholineas a model system. The first system used pure density functional theory calculations,whereas the second approach used a hybrid ONIOM approach consisting of densityfunctional and molecular mechanics calculations. We were able to formulate in silico modelactive sites to study the hydride-transfer steps by utilizing noncovalent chemicalinteractions between choline/betaine aldehyde and active-site amino acid chains usingan atomistic approach. We evaluated and compared the geometries and energetics ofhydride-transfer process using two different systems. We highlighted chemical interactions and studied the effect of protonationstate of an active-site histidine base on the energetics of transfer. Furthermore, we evaluated energetics of the second hydridetransfer process as well as hydration of betaine aldehyde.