SIMULATION OF ELECTRON-TRANSFER SELF-EXCHANGE IN CYTOCHROME-C AND CYTOCHROME-B(5)

Brownian dynamics (BD) has been employed to simulate the kinetics of the electron-transfer self-exchange reactions of trypsin-solubilized bovine liver cytochrome b5 (cytb5) and horse heart cytochrome c (cytc). A structurally robust BD method simulating diffusional docking and electron transfer was employed to compute bimolecular rate constants, which were then compared with those obtained experimentally. BD provides a detailed description of the collision stage of the process, determined by the actual atomic scale irregularity of the proteins (steric factors) and the mutual electrostatic interactions. A realistic two-parameter model of the electron-transfer unimolecular rate constant was employed which is exponentially varying over donor-acceptor distance. The BD theory successfully reproduces the ionic strength dependence of the reaction. A slightly better fit was obtained than that afforded by van Leeuwen theory, with only two adjustable parameters. By fitting the BD-generated rate constants to the experimental curve and using Marcus theory, we extracted a reorganization energy lambda and distance decay factor beta for both self-exchange reactions. Values obtained were lambda = 1.06 and 0.69 eV for the cytb5 and cytc systems, respectively, and beta = 0.9 angstrom-1 was obtained for both systems. For the first time, BD was used in the limit where reaction is activation-controlled rather than diffusion-controlled. This was facilitated by a model that embodies an explicit coupling between the diffusion and chemical dynamics. In the activation-controlled regime the Brownian algorithm efficiently generates a Boltzmann distribution of docked conformers. A direct calculation of the entropy cost of forming docked complexes was performed by tallying the potential of mean force versus heme-heme distance.