Interscaffolding additivity: Binding of P-1 variants of bovine pancreatic trypsin inhibitor to four serine proteases

Different families of protein inhibitors of serine proteases share similar conformation of the enzyme-binding loop, while their scaffoldings are compl etely different. In the enzyme-inhibitor complex, the P-1 position of the l oop makes numerous contacts within the S-1 pocket and significantly influen ces the energy of the interaction. Here, we determine the association energ ies (Delta G(a) values) for the interaction of coded P-1 variants of bovine pancreatic trypsin inhibitor (BPTI) with bovine beta-trypsin (BT), anionic salmon trypsin (AST), bovine alpha-chymotrypsin (BCHYM), and human neutrop hil elastase (HNE). The respective Delta G(a) ranges are 15, 13, 9, and 8 k cal mol(-1) (1 cal = 4.18 J). Next through interscaffolding additivity cycl es, we compare our set of Delta G(a) values determined for BCHYM and HNE wi th similar data sets available in the literature for three other inhibitor families. The analysis of the cycles shows that 27 to 83% of cycles fulfil the criteria of additvity. In one particular case (comparison of associatio ns of P-1 variants of BPTI and OMTKY3 with BCHYM) there is a structural bas is for strongly non-additive behaviour. We argue that the interscaffolding additvity depends on sequential and conformational similarities of sites wh ere the mutation(s) are introduced and on the particular substitution. In t he second interscaffolding analysis, we compare binding of the same P-1 mut ants to BT and AST. The high correlation coefficient shows that both trypsi ns recognize with comparable strength the non-cognate side-chains. However, the cognate Arg and Lys sidechains are recognized significantly more stron gly by AST. (C) 1999 Academic Press.