Computer Simulation of Electron Transfer between the Cytochrome Active Center and Reactive Oxygen and Nitrogen Species

Abstract

In this work, computer simulation at the level of density functional theory is carried out using the PBE functional and bases of the def2- group. The characteristics of the electron transfer reaction according to the Marcus theory from the bioradicals O2-, NO, and NO- to the active center of cytochrome c are calculated. The values of the activation energy ΔG≠, the overlapping matrix element of the donor and acceptor HDA molecular orbitals, the frequency transfer factor ket , and the second-order transfer rate constant k are obtained. The numerical values of k for three radicals make it possible to draw a conclusion about the efficiency of their neutralization by interaction with the active center of the enzyme. For instance, for superoxide ion O2- k=6.32·105 М-1-с-1 at a distance of 5.02 Å, for nitrogen monoxide NO k=6.96·106 М-1-с-1 at a distance of 5.60 Å and oxoazanide ion NO- k=4.45·101 М-1-с-1 at distances of 5.60 Å and 4.45 Å. The transfer distances are obtained from the potential energy curves when the radical approaches the iron ion. The obtained values allow us to conclude that the iron ion in the heme protein environment is the most effective in deactivating the superoxide ion and nitrogen monoxide.