The hydrolysis of ATP by the ATP synthase in mitochondria is inhibited by a protein called IF 1. Bovine IF 1 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 IF 1 , the inhibitory region from residues 1-50 is mainly α-helical and buried deeply at the α DP β DP-catalytic interface, where it forms extensive interactions with five of the nine subunits of F 1-ATPase but mainly with the β 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 IF 1 and of a version of IF 1 with the mutation K39A, it appears that the in-trinsically disordered inhibitory region interacts first with the α E β E-catalytic interface, the most open of the three catalytic interfaces , where the available interactions with the enzyme allow it to form an α-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 α TP β TP state, the extent of the folded α-helical region of IF 1 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° rotation of the γ-subunit, the interface closes further to the α DP β DP-state, allowing more interactions to form between the enzyme and IF 1. The structure of IF 1 now extends to its maximally folded state found in the previously observed inhibited complex. rotary catalysis | inhibitory path | folding | binding site A small basic protein, known as IF 1 , found in the matrix of mitochondria, is a potent inhibitor of hydrolysis of ATP by mitochondrial F 1-ATPase (1). This protein also inhibits the ATP hydrolytic activity of the intact mitochondrial F 1 F o-ATPase, but not its ability to synthesize ATP in the presence of a proton motive force (2). Hence, IF 1 is a unidirectional inhibitor of ATP hydrolysis only. Bovine IF 1 is 84 amino acids long (3), and the active form is a homodimer held together by an antiparallel coiled-coil of α-helices from residues 49-81. Its N-terminal region from residues 1-45 provides the inhibitory part of the protein, and the dimeric inhibitor binds to two F 1-ATPase complexes simultaneously (4). A monomeric form of IF 1 comprising residues 1-60 is also an effective inhibitor, and in a structure (known as F 1-I1-60His) of bovine F 1-ATPase inhibited by this monomeric form, the inhibitor is buried deeply in a complex binding site in which the inhibitor interacts with five of the nine constituent subunits of F 1-ATPase (5). The structure of the bound inhibitor protein is dominated by an α-helix from residues 21-50, referred to as the long α-helix, and in the inhibited complex this α-helix occupies a deep groove at one of the three catalytic interfaces of F 1-ATPase, namely the one between the α DP-and β DP-subunits. This groove is lined with residues from α-helices and loops in the C-termina...