Pathway of binding of the intrinsically disordered mitochondrial inhibitor protein to F1-ATPase

The hydrolysis of ATP by the ATP synthase in mitochondria is inhibited by a protein called IF1. Bovine IF1 has 84 amino acids, and its N-terminal inhibitory region is intrinsically disordered. In a known structure of bovine F-1-ATPase inhibited with residues 1-60 of IF1, the inhibitory region from residues 1-50 is mainly alpha-helical and buried deeply at the alpha(DP)beta(DP)-catalytic interface, where it forms extensive interactions with five of the nine subunits of F-1-ATPase but mainly with the beta(DP)-subunit. As described here, on the basis of two structures of inhibited complexes formed in the presence of large molar excesses of residues 1-60 of IF1 and of a version of IF1 with the mutation K39A, it appears that the intrinsically disordered inhibitory region interacts first with the alpha(E)beta(E)-catalytic interface, the most open of the three catalytic interfaces, where the available interactions with the enzyme allow it to form an alpha-helix from residues 31-49. Then, in response to the hydrolysis of an ATP molecule and the associated partial closure of the interface to the alpha(TP)beta(TP) state, the extent of the folded alpha-helical region of IF1 increases to residues 23-50 as more interactions with the enzyme become possible. Finally, in response to the hydrolysis of a second ATP molecule and a concomitant 120 degrees rotation of the gamma-subunit, the interface closes further to the alpha(DP)beta(DP)-state, allowing more interactions to form between the enzyme and IF1. The structure of IF1 now extends to its maximally folded state found in the previously observed inhibited complex.