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/CuB 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 CuB[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 CuB 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.

Keywords: electron transfer; oxygen reduction.

Fig. 1.

(A and B) The BNC of CcO from Bos taurus (PDB ID code 1V54). The T-shaped three-coordinate structure (A) and near planarity (B) of the Cu_B center are shown. The copper, its histidine ligands, heme, and cross-linked tyrosine are displayed in orange, blue, gray, and green, respectively. (C) The proposed catalytic cycle is drawn clockwise. The oxidation states of Fe, Cu_B, and the cross-linked tyrosine in the BNC are shown, along with protonation states of the cross-linked tyrosine and metal ligands. The name of each state is shown in the upper right corner of each yellow rectangle. Blue arrows show proton pumping, whereas electrons and protons consumed at the BNC are shown in red and black, respectively. O₂ binds to the BNC in the R→A transition.

Fig. 2.

Sequence of events leading to the formation of states O_H and O. The protonation of the –OH ligand of Cu_B in P_R leads to the formation of an activated state F_H, in which Cu is three-coordinated. Subsequent reduction and protonation of the BNC forms state O_H, which has a strained μ-hydroxo–bridged structure (dashed line indicates a weak bonding between Cu_B and the –OH ligand of Fe; Table S2). Diffusion of a water molecule toward Cu_B, structural relaxation (expansion) of the active site, and hydrogen bonding rearrangements (all depicted as a dashed vertical arrow) would lead to the formation of O from O_H.