Computational analysis of the binding of P1 variants of domain 3 of turkey ovomucoid inhibitor to Streptomyces griseus protease B

Abstract

Listen

Translate article

Binding constants for complexes of variants of the ovomucoid inhibitor domain 3 from turkey (OMTKY3) and Streptomyces griseus protease B (SGPB) have been computed. On the basis of the crystallographically determined structures of the complexes, continuum electrostatic calculations have been carried out to evaluate the electrostatic contribution to the binding energy. The hydrophobic component was computed based on the change in the solvent accessible surface area on complex formation. These two terms were combined linearly and the parameters for the protein dielectric, atomic solvation parameter and a constant term were derived using a multivariate fit to the observed binding energies. The resulting fit shows a high correlation with a multiple coefficient of determination of 0.79. This indicates that 79% of the variation in the observed binding energies is explained by the electrostatic and hydrophobic terms. The analysis results in a protein dielectric of 8.2 and an atomic solvation parameter of 30 cal/mol Å2. As a test, these parameters were used to calculate the binding energies of complexes of chymotrypsin and of leukocyte elastase OMTKY3, as well as three other variants of OMTKY3 bound to SGPB. As these structures were not used for the multivariate fit, they serve as an independent check on the derived parameters. The calculated energies for the three new variants of OMTKY3 are in good agreement with the observed values. However, the binding energies of the other complexes are poorly predicted. This implies that the parameters that were obtained are not transferable. The possible causes for this lack of transferability are discussed.