Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase.
The ability of using wave function propagation approaches to simulate isotope effects in enzymes is explored, focusing on the large H/D kinetic isotope effect of soybean lipoxygenase-1 (SLO-1). The H/D kinetic isotope effect (KIE) is calculated as the ratio of the rate constants for hydrogen and deuterium transfer. The rate constants are calculated from the time course of the H and D nuclear wave functions. The propagations are done using one-dimensional proton potentials generated as sections from the full multidimensional surface of the reacting system in the protein. The sections are obtained during a classical empirical valence bond (EVB) molecular dynamics simulation of SLO-1. Since the propagations require an extremely long time for treating realistic activation barriers, it is essential to use an effective biasing approach. Thus, we develop here an approach that uses the classical quantum path (QCP) method to evaluate the quantum free energy change associated with the biasing potential. This approach provides an interesting alternative to full QCP simulations and to other current approaches for simulating isotope effects in proteins. In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction.
Mavri
Janez
J
National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
Liu
Hanbin
H
Olsson
Mats H M
MH
Warshel
Arieh
A
D002384:Catalysis; D003198:Computer Simulation; D006859:Hydrogen / Q000737:chemistry; D008084:Lipoxygenase / Q000737:chemistry* / Q000378:metabolism*; D015394:Molecular Structure; D011789:Quantum Theory; D013025:Glycine max / Q000201:enzymology; D013499:Surface Properties
D006859:Hydrogen; C101084:lipoxygenase L-1; D008084:Lipoxygenase