We note that other pathways have also been considered as alternative substrate proton routes based on structural data . These pathways originate at the surface of the protein on the N side of the membrane and connect to Q binding site 1 and/or to N2 cluster via water molecules and protein residues. Site-directed mutagenesis studies will be required to identify the importance of these pathways in substrate proton transfer, including the gating mechanism that would prevent premature bulk protonation of anionic species.