- Previous Article
- Next Article
- Table of Contents
Journal of Physical Chemistry B, Vol.101, No.28, 5614-5618, 1997
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.
Keywords:LIGAND-BINDING SITES;PROTON AFFINITIES;FREE-ENERGIES;SIMULATIONS;ABINITIO;COMPLEX;FRAMEWORK;SYSTEMS;STATES