Water molecules participate in proteinase‐inhibitor interactions: Crystal structures of Leu 18 , Ala 18 , and Gly 18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B

Crystal structures of the complexes of Streptomyces griseus proteinase B (SGPB) with three P 1 variants of turkey ovomucoid inhibitor third domain (OMTKY3), Leu 18 , Ala 18 , and Gly 18 , have been determined and refined to high resolution. Comparisons among these structures and of each with native, uncomplexed SGPB reveal that each complex features a unique solvent structure in the S 1 binding pocket. The number and relative positions of water molecules bound in the S 1 binding pocket vary according to the size of the side chain of the P 1 residue. Water molecules in the S 1 binding pocket of SGPB are redistributed in response to the complex formation, probably to optimize hydrogen bonds between the enzyme and the inhibitor. There are extensive water‐mediated hydrogen bonds in the interfaces of the complexes. In all complexes, Asn 36 of OMTKY3 participates in forming hydrogen bonds, via water molecules, with residues lining the S 1 binding pocket of SGPB. For a homologous series of aliphatic straight side chains, Gly 18 , Ala 18 , Abu 18 , Ape 18 , Ahx 18 , and Ahp 18 variants, the binding free energy is a linear function of the hydrophobic surface area buried in the interface of the corresponding complexes. The resulting constant of proportionality is 34.1 cal mol −1 Å −2 . These structures confirm that the binding of OMTKY3 to the preformed S 1 pocket in SGPB involves no substantial structural disturbances that commonly occur in the site‐directed mutagenesis studies of interior residues in other proteins, thus providing one of the most reliable assessments of the contribution of the hydrophobic effect to protein‐complex stability.