An approximate dynamics method, based on donor and acceptor quantum trajectory ensembles, is employed to model hydrogen tunneling and the kinetic isotope effect (KIE) in soybean lipoxygenase-1. The proton is treated as a three-dimensional quantum-mechanical particle moving between the donor and acceptor wells for multiple configurations of the active site. Substitution of the proton with a deuteron reduces the transmission probability, integrated over enzyme configurations, by a factor of 51, which is in reasonable agreement with the experimental value of KIE equal to 81, validating the applicability of the current approach in biological systems. (C) 2012 Elsevier B. V. All rights reserved.