Control of rotation of the F1FO-ATP synthase nanomotor by an inhibitory alpha-helix from unfolded epsilon or intrinsically disordered and IF1 proteins

The ATP synthase is a ubiquitous nanomotor that fuels life by the synthesis of the chemical energy of ATP. In order to synthesize ATP, this enzyme is capable of rotating its central rotor in a reversible manner. In the clockwise (CW) direction, it functions as ATP synthase, while in counter clockwise (CCW) sense it functions as an proton pumping ATPase. In bacteria and mitochondria, there are two known canonical natural inhibitor proteins, namely the epsilon and IF1 subunits. These proteins regulate the CCW F1FO-ATPase activity by blocking subunit rotation at the (DP)/(DP)/ subunit interface in the F-1 domain. Recently, we discovered a unique natural F-1-ATPase inhibitor in Paracoccus denitrificans and related -proteobacteria denoted the subunit. Here, we compare the functional and structural mechanisms of epsilon, IF1, and , and using the current data in the field, it is evident that all three regulatory proteins interact with the (DP)/(DP)/ interface of the F-1-ATPase. In order to exert inhibition, IF1 and contain an intrinsically disordered N-terminal protein region (IDPr) that folds into an -helix when inserted in the (DP)/(DP)/ interface. In this context, we revised here the mechanism and role of the subunit as a unidirectional F-ATPase inhibitor blocking exclusively the CCW F1FO-ATPase rotation, without affecting the CW-F1FO-ATP synthase turnover. In summary, the subunit has a mode of action similar to mitochondrial IF1, but in -proteobacteria. The structural and functional implications of these intrinsically disordered and IF1 inhibitors are discussed to shed light on the control mechanisms of the ATP synthase nanomotor from an evolutionary perspective.