Mitochondrial ATP synthases, the major producers of ATP in higher eukaryotic cells, are known to be regulated by a peptide designated IF(1). In contrast, in yeast three such peptides have been identified, IF(1) and STF(1), which inhibit the reverse ATPase reaction, and STF(2), a modulator of the action of these inhibitors. Despite significant homology to IF(1), STF(1) exhibits less than half ( approximately 40%) its inhibitory potency. The two-fold purpose of this bioinformatic study was to gain structural insight into the different inhibitory potencies of IF(1) and STF(1) and to determine to what extent yeast are unique in employing multiple peptides to regulate the ATP synthase. Sequence and secondary structural analyses and comparison with the known structure of bovine IF(1) predicted a dimeric structure for yeast STF(1) in which the C-terminal regions form a coiled-coil. Moreover, sequence comparisons showed that within this C-terminal region a conserved acidic residue (Asp 59) in yeast IF(1) is replaced by Asn in STF(1). In the known structure of bovine IF(1), predicted to be very similar to that of yeast IF(1), the residue Glu 68 corresponding to Asp 59 participates in the formation of a four-residue conserved acidic cluster in the middle of the coiled-coil in the C-terminal region. It is deduced here that this acidic cluster is likely to be important in the regulation of IF(1)'s inhibitory capacity and that replacement of conserved Asp 59 by Asn in STF(1) may reduce its potency. Although other homologs to the inhibitors IF(1) and STF(1) were not found in searches of available eukaryotic genomes, including human, a new homolog, named STF(3), with 65% identity to the modulator STF(2), was discovered within the yeast genome and identified to be expressed by searching the yeast EST database. Thus, yeast appears unique in regulating the ATP synthase by involving multiple peptides (IF(1), STF(1), STF(2), and perhaps STF(3)).