Experiment and theory highlight role of native state topology in SH3 folding

We use a combination of experiments, computer simulations and simple model calculations to characterize, first, the folding transition state ensemble of the src SH3 domain, and second, the features of the protein that determi ne its folding mechanism. Kinetic analysis of mutations at 52 of the 57 res idues in the src SH3 domain revealed that the transition state ensemble is even more polarized than suspected earlier: no single alanine substitution in the N-terminal 15 residues or the C-terminal 9 residues has more than a two-fold effect on the folding rate, while such substitutions at 15 sites i n the central three-stranded beta-sheet cause significant decreases in the folding rate. Molecular dynamics (MD) unfolding simulations and ab initio f olding simulations on the src SH3 domain exhibit a hierarchy of folding sim ilar to that observed in the experiments. The similarity in folding mechani sm of different SH3 domains and the similar hierarchy of structure formatio n observed in the experiments and the simulations can be largely accounted for by a simple native state topology-based model of protein folding energy landscapes.