Interscaffolding Additivity. Association of P1 Variants of Eglin c and of Turkey Ovomucoid Third Domain with Serine Proteinases

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Abstract
Standard mechanism protein inhibitors of serine proteinases share a common mechanism of interaction with their cognate enzymes. The P1 residue of the inhibitor interacts with the enzyme in a substrate-like manner. Its side chain becomes imbedded in the S1 cavity of the enzyme. The nature of P1, the primary specificity residue, greatly affects the strength and specificity of the enzyme inhibitor association. In canonical inhibitors, residues P4-P2'(P3'), where P1-P1' is the reactive site, share a common main chain conformation that does not change on complex formation. The remainder of the inhibitor's structure, the scaffolding, is not always common. Instead, there are at least 20 inhibitor families, each with a different scaffolding. In this paper, we ask whether the differences in standard free energy of association of enzyme-inhibitor complexes upon P1 mutations are independent of the nature of the scaffolding. We have already reported on 25 P1 variants of turkey ovomucoid third domain, a member of the Kazal inhibitor family, interacting with six different serine proteinases. Here, we report on seven different P1 variants of eglin c, a potato I family member, interacting with the same six serine proteinases under the same conditions. The differences in standard free energy on P1 mutations in the eglin c system agree very well, when P1 Pro is omitted. Complete agreement indicates that these P1 residues are interscaffolding additive. This is consistent with the superimposition of the high-resolution structures of eglin c and of turkey ovomucoid third domain with chymotrypsin. In both cases, the P1 Leu side chain is similarly oriented in almost indistinguishable specificity pockets of the enzyme.