Hybrid quantum and molecular mechanical (QM/MM) studies on the pyruvate to L-lactate interconversion in L-lactate dehydrogenase

Hybrid quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken to study the catalytic mechanism for the interconversion of pyruvate to L-lactate by the enzyme L-lactate dehydrogenase, in the presence of the cofactor nicotinamide adenine dinucleotide (NAD). The QM system comprised molecular species or fragments involved in the chemical bond-making and -breaking events: the substrate pyruvate, trans-1-methyldihydronicotinamide (a fragment of the cofactor), and His-195. The remainder of the enzyme, cofactor, and water molecules made up the MM system. The QM/MM potential energy surface was calculated as a grid of points for two reaction coordinates representing the transfers of a proton and of a hydride ion. From this surface, two transition states for the two transfers were identified, with the hydride-ion transfer step indicated as being rate-limiting and preceding the proton transfer. The intermediate is deprotonated L-lactate. This result disagrees with our earlier all-QM results for a ''supermolecule'' system consisting of substrate, cofactor and key active-site residue fragments ( Ranganathan, S.; Gready, J. E. Faraday Trans. 1994, 90 2047), which indicated protonation preceded hydride-ion transfer. Structures, energies, and atomic charges for reactant and product complexes and for the two transition states are reported.