The Proton/Electron Coupling Mechanism of Cytochrome C Oxidase

Abstract

Mitochondrial cytochrome c oxidases (CcOs) are members of a large haem-copper oxidase superfamily. They fall within the A1 branch which includes closely structurally-related bacterial CcOs and quinol oxidases. Three possible networks of amino acids and waters have been identified in subunit I for intra-protein transfer of substrate and translocated protons. The D and K channels are very similar in all structures. The H channel was firstly described in bovine CcO, though several of its features are evident bacterial A1-type CcOs. In bacterial systems, there is substantial evidence that the D channel provides the route for pumped protons to a temporary proton trap site, though the exit route into the P phase remains uncertain. In contrast, in mammalian mitochondrial CcO structural and functional data have suggested that the H channel may instead provide the route for pumped protons to a similar trap site location, and that its ‘top’ half provides the exit route from the trap into the P phase. Direct measurements of coupling efficiencies of yeast mitochondrial CcO with mutations in these potential proton pathways showed that pumped protons are transferred through its D channel. Furthermore, MD simulations indicate that the ‘lower’ region of its H channel could not provide a transfer route into the trap site. This is consistent with prior MD simulations of this region of the bovine CcO H channel which supported a dielectric well, but not a proton transfer, role. However, the ‘top’ part of the H channel may indeed form a facile route for proton exit from the trap, possibly gated around the region of two arginines that are close to the haem propionates. Hence, some degree of convergence of thought on the mechanism of the bacterial, yeast and bovine CcOs may be proposed.