MD and QM/MM studies on long-chain L-α-hydroxy acid oxidase: substrate binding features and oxidation mechanism.

Long-chain l-α-hydroxy acid oxidase (LCHAO) is a flavin mononucleotide (FMN)-dependent oxidase that dehydrogenates l-α-hydroxy acids to keto acids. There were two different mechanisms, named as hydride transfer (HT) mechanism and carbanion (CA) mechanism, respectively, proposed about the catalytic process for the FMN-dependent l-α-hydroxy acid oxidases on the basis of biochemical data. However, crystallographic and kinetic studies could not provide enough evidence to prove one of the mechanisms or eliminate the alternative. In the present studies, theoretical computations were carried out to study the molecular mechanism for LCHAO-catalyzed dehydrogenation of l-lactate. Our molecular dynamics (MD) simulations indicated that l-lactate prefers to bind with LCHAO in a hydride transfer mode rather than a carbanion mode. Quantum mechanics/molecular mechanics (QM/MM) calculations were further carried out to obtain the optimized structures of reactants, transition states, and products at the level of ONIOM-EE (B...