Knowledge-based modeling of the serine protease triad into non-proteases

The Asp-His-Ser triad of serine proteases has been regarded, in the present study, as an independent catalytic motif, because in nature it has been in corporated at the active sites of enzymes as diverse as the serine protease s and the lipases, Incorporating this motif into non-protease scaffolds, by rational design and mutagenesis, might lead to the generation of novel cat alysts. As an aid to such experiments, a knowledge-based computer modeling procedure has been developed to model the protease Asp-His-Ser triad into n on-proteases, Catalytic triads from a set of trypsin family proteases have been analyzed and criteria that characterize the geometry of the triads hav e been obtained. Using these criteria, the modeling procedure first identif ies sites in non-proteases that are suitable for modeling the protease tria d, H-bonded Asp-His-Ser triads, that mimic the protease catalytic triad in geometry, are then modeled in at these sites, provided it is stereochemical ly possible to do so. Thus non-protease sites at which H-bonded Asp-His-Ser triads are successfully modeled in may be considered for mutagenesis exper iments that aim at introducing the protease triad into non-proteases, The t riad modeling procedure has been used to identify sites for introducing the protease triad in three binding proteins and an immunoglobulin. A scoring function, depending on inter-residue distances, solvent accessibility and t he substitution potential of amino acid residues at the modeling sites in t he host proteins, has been used to assess the quality of the model triads.