Redox-Activated Proton Transfer through a Redundant Network in the Q_o Site of Cytochrome bc₁

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. In this study, the energetics of the long-range proton transfers through multiple proton-conducting wires in the Q_o site of the bc₁ complex was investigated computationally 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 b as a plausible proton acceptor. Upon coenzyme-Q oxidation, a Grotthuss hopping mechanism is activated, facilitating proton transfer along three distinct pathways with comparable barriers and stability. These pathways operate redundantly, forming a robust proton-conducting network, and account for the unusual experimental behavior observed in single-point mutations. Energetic analyses exclude charged closed-shell species as likely intermediates and propose a reaction sequence for coenzyme-Q 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 redox-activated proton transfer in respiratory enzymes.