Proton-pumping mechanism of cytochrome c oxidase: A kinetic master-equation approach

► Kinetic-master equations model proton pumping in cytochrome c oxidase. ► Proton pumping at low efficiency can be achieved without kinetic gating. ► High thermodynamic efficiency of pumping requires kinetic gating. ► Internal proton transfer to pump site is key gated reaction step. ► Glu valve at the end of the D channel increases the pumping efficiency.