Arantes, G. M.

Proton translocation catalyzed by cytochrome bc1 (respiratory complex III) during coenzyme-Q redox cycling is a critical bioenergetic process, yet its detailed molecular mechanism remains incompletely understood. Even the specific groups mediating proton transfer following coenzyme-Q oxidation have not been established. In this study, the energetics of proton transfer through multiple proton-conducting wires recently identified in the Qo site was investigated across various reactant redox states using hybrid QM/MM simulations and a specialized reaction coordinate. Key reactive groups and proton transfer mechanisms were characterized, confirming the propionate-A group of heme bL as a plausible proton acceptor. Upon quinol oxidation, a Grotthuss hopping mechanism is activated, facilitating proton transfer along three distinct pathways with comparable energetics. These pathways function redundantly, forming a robust proton-conducting network. A highly conserved tyrosine residue (Y147 in R. sphaeroides numbering) was found to be essential for complete proton transfer, whereas participation of H276 and D278 does not appear energetically feasible. Bioenergetic analyses exclude charged closed-shell species as likely intermediates and propose a reaction sequence for quinol oxidation proceeding as QH2 [->] QH* [->] Q0, either via coupled proton-electron transfers or stepwise mechanisms involving open-shell intermediates. These findings elucidate mechanistic details of the Q-cycle and improve our understanding of the catalytic reactions supporting coenzyme-Q redox cycling in respiratory complexes.