Binding of the Inhibitor Protein IF1 to Bovine F1-ATPase

In the structure of bovine F-1-ATPase inhibited with residues 1-60 of the bovine inhibitor protein IF1, the alpha-helical inhibitor interacts with five of the nine subunits of F-1-ATPase. In order to understand the contributions of individual amino acid residues to this complex binding mode, N-terminal deletions and point mutations have been introduced, and the binding properties of each mutant inhibitor protein have been examined. The N-terminal region of IF1 destabilizes the interaction of the inhibitor with F-1-ATPase and may assist in removing the inhibitor from its binding site when F1Fo-ATPase is making ATP. Binding energy is provided by hydrophobic interactions between residues in the long alpha-helix of IF1 and the C-terminal domains of the beta(DP)-subunit and beta(TP)-subunit and a salt bridge between residue E30 in the inhibitor and residue R408 in the C-terminal domain of the beta(DP)-subunit. Several conserved charged amino acids in the long a-helix of IF1 are also required for establishing inhibitory activity, but in the final inhibited state, they are not in contact with F-1-ATPase and occupy aqueous cavities in F-1-ATPase. They probably participate in the pathway from the initial interaction of the inhibitor and the enzyme to the final inhibited complex observed in the structure, in which two molecules of ATP are hydrolysed and the rotor of the enzyme turns through two 120 degrees steps. These findings contribute to the fundamental understanding of how the inhibitor functions and to the design of new inhibitors for the systematic analysis of the catalytic cycle of the enzyme. (C) 2010 Elsevier Ltd. All rights reserved.