Hydride transfer in liver alcohol dehydrogenase: Quantum dynamics, kineticisotope effects, and role of enzyme motion

The quantum dynamics of the hydride transfer reaction catalyzed by liver al cohol dehydrogenase (LADH) are studied with real-time dynamical simulations including the motion of the entire solvated enzyme. The electronic quantum effects are incorporated with an empirical valence bond potential, and the nuclear quantum effects of the transferring hydrogen are incorporated with a mixed quantum/classical molecular dynamics method in which the transferr ing hydrogen nucleus is represented by a three-dimensional vibrational wave function. The equilibrium transition state theory rate constants are deter mined from the adiabatic quantum free energy profiles, which include the fr ee energy of the zero point motion for the transferring nucleus. The nonequ ilibrium dynamical effects are determined by calculating the transmission c oefficients with a reactive flux scheme based on real-time molecular dynami cs with quantum transitions (MDQT) surface hopping trajectories. The values of nearly unity for these transmission coefficients imply that nonequilibr ium dynamical effects such as barrier recrossings are not dominant for this reaction. The calculated deuterium and tritium kinetic isotope effects for the overall rate agree with experimental results. These simulations elucid ate the fundamental nature of the nuclear quantum effects and provide evide nce of hydrogen tunneling in the direction along the donor-acceptor axis. A n analysis of the geometrical parameters during the equilibrium and nonequi librium simulations provides insight into the relation between specific enz yme motions and enzyme activity. The donor-acceptor distance, the catalytic zinc-substrate oxygen distance, and the coenzyme (NAD(+)/ NADH) ring angle s are found to strongly impact the activation free energy barrier, while th e donor-acceptor distance and one of the coenzyme ring angles are found to be correlated to the degree of barrier recrossing. The distance between VAL -203 and the reactive center is found to significantly impact the activatio n free energy but not the degree of barrier recrossing. This result indicat es that the experimentally observed effect of mutating VAL-203 on the enzym e activity is due to the alteration of the equilibrium free energy differen ce between the transition state and the reactant rather than nonequilibrium dynamical factors. The promoting motion of VAL-203 is characterized in ter ms of steric interactions involving THR-178 and the coenzyme.