Redox-linked protonation state changes in cytochrome bc1 identified by Poisson–Boltzmann electrostatics calculations

Cytochrome bc1 is a major component of biological energy conversion that exploits an energetically favourable redox reaction to generate a transmembrane proton gradient. Since the mechanistic details of the coupling of redox and protonation reactions in the active sites are largely unresolved, we have identified residues that undergo redox-linked protonation state changes. Structure-based Poisson–Boltzmann/Monte Carlo titration calculations have been performed for completely reduced and completely oxidised cytochrome bc1. Different crystallographically observed conformations of Glu272 and surrounding residues of the cytochrome b subunit in cytochrome bc1 from Saccharomyces cerevisiae have been considered in the calculations. Coenzyme Q (CoQ) has been modelled into the CoQ oxidation site (Qo-site). Our results indicate that both conformational and protonation state changes of Glu272 of cytochrome b may contribute to the postulated gating of CoQ oxidation. The Rieske iron–sulphur cluster could be shown to undergo redox-linked protonation state changes of its histidine ligands in the structural context of the CoQ-bound Qo-site. The proton acceptor role of the CoQ ligands in the CoQ reduction site (Qi-site) is supported by our results. A modified path for proton uptake towards the Qi-site features a cluster of conserved lysine residues in the cytochrome b (Lys228) and cytochrome c1 subunits (Lys288, Lys289, Lys296). The cardiolipin molecule bound close to the Qi-site stabilises protons in this cluster of lysine residues.