The Catalytic Mechanism of LDH An analysis of the thermal properties of the promoting vibration and tunneling

Abstract

This work explores the role of dynamic motions in enzymatic catalysis and examines their contribution to the reaction mechanism. In the first project, the thermal properties of the "promoting vibration" of lactate dehydrogenase are examined. Previously, this coordinated fluctuation of several key residues in the LDH complex was shown to reduce donor acceptor distances in the hydride transfer step of LDH complex and was identified as part of the reaction coordinate of the enzyme. To study the thermal properties of the promoting vibration, the nicotinamide ring of the NADH cofactor was continuously heated using a coupled Nose-Hoover thermostat. As the experiment progressed over the course of 2 ps, the comparative temperatures of residues in equidistant shells from the center of the reaction were examined. The results of the experiments showed a favored direction of energy transport along the axis of the promoting vibration of LDH. By examining the lifetime of thermal fluctuations parallel and orthogonal to the axis of the promoting vibration, it was determined that at thermal equilibrium residues along the axis of the promoting vibration had fluctuations which were much longer lived than residues that were orthogonal to this axis. These results suggested that the promoting vibration in addition to being important in reducing distances between two reactant species, also, plays a role in channeling thermal fluctuations towards the active site. In the second project, the role of nuclear quantum effects in the reaction mechanism of LDH was examined. Nuclear quantum effects were successfully added into the molecular dynamics program CHARMM using the centroid approximation to the Feynman path integral formulation of quantum mechanics. In this method, the proton and hydride are replaced by a necklace of fictitious head particles, which each represent imaginary time slices along the cyclic path integral. The effect of the centroid molecular dynamics is to lower the potential barrier for potentials with small widths. After the averaging process of the necklace is taken into account, the force felt by the hydride particle is effectively reduced and a tunneling event can be simulated.