Topological studies suggest that the pathway of the protons through F0 is provided by amino acid residues accessible from the lipid phase.

The structure of the F0 part of ATP synthases from E. coli and Neurospora crassa was analyzed by hydrophobic surface labeling with [125I]TID. In the E. coli F0 all three subunits were freely accessible to the reagent, suggesting that these subunits are independently integrated in the membrane. Labeled amino acid residues were identified by Edman degradation of the dicyclohexylcarbodiimide binding (DCCD) proteins from E. coli and Neurospora crassa. The very similar patterns obtained with the two homologous proteins suggested the existence of tightly packed alpha-helices. The oligomeric structure of the DCCD binding protein appeared to be very rigid since little, if any, change in the labeling pattern was observed upon addition of oligomycin or DCCD to membranes from Neurospora crassa. When membranes were pretreated with DCCD prior to the reaction with [125I]TID an additionally labeled amino acid appeared at the position of Glu-65 which binds DCCD covalently, indicating the location of this inhibitor on the outside of the oligomer. It is suggested that proton conduction occurs at the surface of the oligomer of the DCCD binding protein. Possibly this oligomer rotates against the subunit alpha or beta and thus enables proton translocation. Conserved residues in subunit alpha, probably located in the lipid bilayer, might participate in the proton translocation mechanism.