What the structures of the cytochrome c oxidase tell us about its mechanism

Cytochrome c oxidase (CcO) reduces molecular oxygen in a process coupled with proton pumping [1,2]. Models for proton pumping activity of CcO can be divided into two groups: one in which haem a is the key player, and another where this role is covered by the oxygen reduction site [1-3]. However, all currently accepted models require, more or less explicitly, an ordered sequence of events. We show that available structures of CcO can be clustered in four groups. These structural observations, and the experimental data on which there is a general consensus, suggest a four-state, stochastic pump model [4]. This model implies the observed convex dependence of the stoichiometry of the pump on the electron transfer rate [5], while to explain this phenomenon strictly deterministic models require a series of ad hoc assumptions (e.g. slipping mechanisms) [1,3,5]. Therefore, these results lead us to conclude that a stochastic conformational coupling could be in action in the energy transduction operated by this protein machine [4]. [1] M. Wikström, K. Krab, V. Sharma, Oxygen activation and energy conservation by cytochrome c oxidase, Chem, Rev. 118 (2018) 2469-2490. [2] S. Yoshikawa, A. Shimada, Reaction mechanism of cytochrome c oxidase, Chem. Rev. 115 (2015) 1936-1989. [3] N. Capitanio, L.L. Palese, G. Capitanio, et al., Allosteric interactions and proton conducting pathways in proton pumping aa(3) oxidases: heme a as a key coupling element, Biochim. Biophys. Acta 1817 (2012) 558-566. [4] L.L. Palese, Cytochrome c oxidase structures suggest a four-state stochastic pump mechanism, Phys. Chem. Chem. Phys. 21 (2019) 4822-4830. [5] N. Capitanio, G. Capitanio, D.A. Demarinis, et al., Factors affecting the H+/e- stoichiometry in mitochondrial cytochrome c oxidase: influence of the rate of electron flow and transmembrane delta pH. Biochemistry 35 (1996) 10800-10806.