The potency and specificity of the interaction between the IA(3) inhibitorand its target aspartic proteinase from Saccharomyces cerevisiae

The yeast IA, polypeptide consists of only 68 residues, and the free inhibi tor has little intrinsic secondary structure. IA, showed subnanomolar poten cy toward its target, proteinase A from Saccharomyces cerevisiae, and did n ot inhibit any of a large number of aspartic proteinases with similar seque nces/structures from a wide variety of other species. Systematic truncation and mutagenesis of the IA, polypeptide revealed that the inhibitory activi ty is located in the N-terminal half of the sequence. Crystal structures of different forms of Lc, complexed with proteinase A showed that residues in the N-terminal half of the IA, sequence became ordered and formed an almos t perfect cr-helix in the active site of the enzyme. This potent, specific interaction was directed primarily by hydrophobic interactions made by thre e key features in the inhibitory sequence. Whereas IA,was cut as a substrat e by the nontarget aspartic proteinases, it mas not cleaved by proteinase A . The random coil IA, polypeptide escapes cleavage by being stabilized in a helical conformation upon interaction with the active site of proteinase A . This results, paradoxically, in potent selective inhibition of the target enzyme.