From Truncated Models to Full Protein QM/MM Analysis of the Reaction Catalyzed by Malate Dehydrogenase

Abstract

Our previous work on computational analysis of the reaction catalyzed by malate dehydrogenase involved gas phase reaction simulation using geometry optimization calculations. These revealed that the proton abstraction preceded the hydride transfer due to the activity of the arginine residues around the active site. These gas phase simulations tested two truncated models, one including the arginine residues (R124, R130, and R196), whereas the other one did not. The initial transition states were compared to determine the initial catalytic reaction. A hybrid quantum and molecular mechanics (QM/MM)method has now been used with the whole gMDH dimer, in explicit solvent, to simulate the catalytic reaction with the substrate malate and the cofactor NAD. The simulation analysis helps to give insight into the role of specific regions of gMDH that contribute to the mechanism. The relative changes in the position of malate and NAD during the simulation were studied to determine their interactions with gMDH. In particular the minimum energy pathway for proton and hydride transfer were investigated. In silico characterization of the roles of arginine residues is being correlated with the effects of in vitro site directed mutations to ascertain the precise roles of individual arginines in binding and catalysis.This work is supported by NSF Grant MCB 0448905 to EB.