The membrane-spanning F0 sector of the Escherichia coli H+-transporting ATP synthase (EC 18.104.22.168) contains multiple copies of subunit c, a 79 amino acid residue protein that is thought to insert in the membrane like a hairpin with two membrane traversing α-helices. The center of the protein is much more polar than the putative transmembrane α-helices and has been postulated to play a crucial role in coupling H+ translocation through F0 to ATP synthesis in the membrane extrinsic, F1 sector of the complex. However, the direction of insertion of subunit c in the membrane has not been established. We show here that the “polar loop” lies on the F1 binding side of the membrane. A peptide corresponding to Lys34 → Ile46 of the polar loop was synthesized. Antisera were generated to the Lys34 → Ile46 cognate peptide, and the polyclonal antipeptide IgG was shown to bind to a crude F0 fraction by using enzyme-linked immunosorbent assays. The antipeptide serum did not bind tightly enough to F0 to disrupt function. However, a polyclonal antiserum made to purified, whole subunit c was shown to block the binding of to the F0 exposed in F1-stripped membranes. Incubation of the antisubunit c serum with the peptide reduced the inhibitory effect of the antiserum on the binding of F1 to F0. The reversal of inhibition by the peptide was specific to the antisubunit c serum in that the peptide had no effect on inhibition of F1 binding to F0 by antiserum to subunit a of F0. We conclude that the antisubunit c serum blocks F1 binding to the cytoplasmic side of the inner membrane by recognizing epitope(s) in the Lys34 → Ile46 sequence.
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