ASSESSMENT OF CONFORMATIONAL PARAMETERS AS PREDICTORS OF LIMITED PROTEOLYTIC SITES IN NATIVE PROTEIN STRUCTURES

Despite the importance of limited proteolysis in biological systems it is often difficult to rationalize why a proteinase hydrolyses a parti cular bond, given a simple sequence specificity alone. Understanding o f the structural properties limiting the proteolysis represents a firs t step on the pathway to control and manipulation of this phenomena. A n expanded set of nick-sites in proteins of known tertiary structure, cut by both narrow and broad specificity proteinases, has been generat ed yielding a robust data set of strictly limited sites. A critical ev aluation of an expanded set of conformational parameters revealed a st rong correlation with limited proteolytic sites, although they are onl y modest predictors in isolation. The overall predictive power is sign ificantly improved when the conformational parameters are combined in a weighted predictive scheme that permits their relative importance to be compared via a Metropolis search protocol. A subset of the paramet ers performs equally well demonstrating the key determinants of suscep tibility. The derived predictive algorithm has been made available via the internet. Its utility for predicting other surface-correlated fea tures is also discussed.