VARIABILITY OF THE CANONICAL LOOP CONFORMATIONS IN SERINE PROTEINASESINHIBITORS AND OTHER PROTEINS

Canonical loops of protein inhibitors of serine proteinases occur in p roteins having completely different folds. In this article, conformati ons of the loops have been analyzed for inhibitors belonging to 10 str ucturally different families. Using deviation in C-alpha-C-alpha dista nces as a criterion for loop similarity, we found that the P3-P3' segm ent defines most properly the length of the loop. When conformational differences among loops of individual inhibitors were compared using r oot mean square deviation (rmsd) in atomic coordinates for all main ch ain atoms (Delta r method) and rmsd operating in main chain torsion an gles (Delta t method), differences of up to 2.1 Angstrom and 72.3 degr ees, respectively, were observed. Such large values indicate significa nt conformational differences among individual loops. Nevertheless, th e overall geometry of the inhibitor-proteinase interaction is very wel l preserved, as judged from the similarity of C-alpha-C-alpha distance s between C-alpha of catalytic Ser and C-alpha of P3-P3' residues in v arious enzyme-inhibitor complexes. The mode of interaction is very wel l preserved both in the chymotrypsin and subtilisin families, as dista nces calculated for subtilisin-inhibitor complexes are almost always w ithin the range of those for chymotrypsin-inhibitor complexes. Complex formation leads to conformational changes of up to 160 degrees for ch i(1) angle. Side chains of residue P1 and P2' adopt in different compl exes a similar orientation (chi(1) angle = -60 degrees and -180 degree s, respectively), To check whether the canonical conformation can be f ound among non-proteinase-inhibitor Brookhaven Protein Data Bank struc tures, two selection criteria-the allowed main chain dihedral angles a nd C-alpha-C-alpha distances for the P3-P3' segment-were applied to al l these structures. This procedure detected 132 unique hexapeptide seg ments in 121 structurally and functionally unrelated proteins. Partial preferences for certain amino acids occurring at particular positions in these hexapeptides could be noted, Further restriction of this set to hexapeptides with a highly exposed P1 residue side chain resulted in 40 segments. The possibility of complexes formation between these s egments and serine proteinases was ruled out in molecular modeling due to steric clashes. Several structural features that determine the can onical conformation of the loop both in inhibitors and in other protei ns can be distinguished. They include main chain hydrogen bonds both w ithin the P3-P3' segment and with the scaffold region, P3-P4 and P3'-P 4' hydrophobic interactions, and finally either hydrophobic or polar i nteractions involving the P1' residue. (C) 1998 Wiley-Liss, Inc.