Computational study of the activated O H state in the catalytic mechanism of cytochrome c oxidase

Abstract

Complex IV in the respiratory chain of mitochondria and bacteria catalyzes reduction of molecular oxygen to water, and conserves much of the liberated free energy as an electrochemical proton gradient, which is used for the synthesis of ATP. Photochemical electron injection experiments have shown that reduction of the ferric/cupric state of the enzyme’s binuclear heme a₃/Cu_B center is coupled to proton pumping across the membrane, but only if oxidation of the reduced enzyme by O₂ immediately precedes electron injection. In contrast, reduction of the binuclear center in the “as-isolated” ferric/cupric enzyme is sluggish and without linkage to proton translocation. During turnover, the binuclear center apparently shuttles via a metastable but activated ferric/cupric state (O_H), which may decay into a more stable catalytically incompetent form (O) in the absence of electron donors. The structural basis for the difference between these two states has remained elusive, and is addressed here using computational methodology. The results support the notion that Cu_B[II] is either three-coordinated in the O_H state or shares an OH⁻ ligand with heme a₃ in a strained μ-hydroxo structure. Relaxation to state O is initiated by hydration of the binuclear site. The redox potential of Cu_B is expected, and found by density functional theory calculations, to be substantially higher in the O_H state than in state O. Our calculations also suggest that the neutral radical form of the cross-linked tyrosine in the binuclear site may be more significant in the catalytic cycle than suspected so far.