A method to predict residues conferring functional differences between related proteins: Application to MAP kinase pathways

Physicochemical properties are potentially useful in predicting functional differences between aligned protein subfamilies. We present a method that c onsiders physicochemical properties from ancestral sequences predicted to h ave given rise to the subfamilies of interest by gene duplication. Comparis on between two map kinases subfamilies, p38 and ERK, revealed a region that had an excess of change in properties after gene duplication followed by c onservation within the two subfamilies. This region corresponded to that ex perimentally defined as important for substrate and pathway specificity. Th e derived scores for the region of interest were found to differ significan tly in their distribution compared to the rest of the protein when the Kolm ogorov-Smirnov test was applied (p = 0.005). Thus, the incorporation of anc estral physicochemical properties is useful in predicting functional differ ences between protein subfamilies. In addition, the method was applied to t he MKK and MAPK components of the p38 and JNK pathways. These proteins show ed a similar pattern in their evolution and regions predicted to confer fun ctional differences are discussed.