A quantum chemical study of the mechanism for proton-coupled electron transfer leading to proton pumping in cytochrome c oxidase

• Published in: Molecular physics 2010-10, Vol.108 (19-20), p.2733-2743
• Main Authors: Blomberg, Margareta R.A., Siegbahn, Per E.M.
• Format: Article
• Language: English
• Subjects: Accuracy; Barriers; cytochrome c oxidase; Cytochromes; density functional theory; Enzymes; Gating and risering; Oxidase; proton pumping; Protons; Pumping; Quantum chemistry
• ISSN: 0026-8976; 1362-3028; 1362-3028
• DOI: 10.1080/00268976.2010.523017

The proton pumping mechanism in cytochrome c oxidase, the terminal enzyme in the respiratory chain, has been investigated using hybrid DFT with large chemical models. In previous studies, a gating mechanism was suggested based on electrostatic interpretations of kinetic experiments. The predictions from that analysis are tested here. The main result is that the suggestion of a positively charged transition state for proton transfer is confirmed, while some other suggestions for the gating are not supported. It is shown that a few critical relative energy values from the earlier studies are reproduced with quite high accuracy using the present model calculations. Examples are the forward barrier for proton transfer from the N-side of the membrane to the pump-loading site when the heme a cofactor is reduced, and the corresponding back leakage barrier when heme a is oxidised. An interesting new finding is an unexpected double-well potential for proton transfer from the N-side to the pump-loading site. In the intermediate between the two transition states found, the proton is bound to PropD on heme a. A possible purpose of this type of potential surface is suggested here. The accuracy of the present values are discussed in terms of their sensitivity to the choice of dielectric constant. Only one energy value, which is not critical for the present mechanism, varies significantly with this choice and is therefore less certain.