Monte Carlo (MC) simulations of conformational changes and protonation of Glu-242, a key residue that shuttles protons in cytochrome c oxidase (CcO), are reported. Previous studies suggest that this residue may play a role of the valve of the enzyme proton pump. Here we examine how sensitive the results of simulations are to the computational method used. We applied both molecular mechanic (MM) and hybrid quantum mechanic:molecular mechanic (QM:MM) methods and find that the results are qualitatively different. The results indicate that the mechanism for proton gating in CcO is still an open issue.

The transition flux formula for the coupling matrix element of long-distance electron transfer reactions is discussed. Here we present a new derivation which is based on the Golden Rule approach. The electronic Franck–Condon factor that appears in the multielectronic formulation of the coupling element is discussed using the concept of tunneling time. An application of the tunneling flux theory to electron transfer reactions in a model system based on the low-potential heme and high-potential heme (heme bL)/(heme bH) redox pair of ubiquinol:cytochrome c oxidoreductase complex is described; the results are compared to those obtained by measuring energy splitting of the donor/acceptor multielectronic states and the direct calculation method.