Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations

► Mechanism of proton transfer at Qo-site of cyt bc1 is proposed. ► Water molecules seem to play a crucial role in the binding of the quinol. ► The solvent is clearly not involved in the quinone binding after the oxidation. ► Predicted binding modes suggest that water is the primary acceptors of protons. ► The water coordination assures close iron sulfur protein-cyt b association.