Mechanisms and kinetics of b-hairpin formation

Thermodynamics and kinetics of off-lattice models with side chains for the b-hairpin fragment of immunoglobulin-binding protein and its variants are reported. For all properties (except refolding time tF) there are no qualitative differences between the full model and the Go# version. The validity of the models is established by comparison of the calculated native structure with the Protein Data Bank coordinates and by reproducing the experimental results for the degree of cooperativity and tF. For the full model tF ' 2 ms at the folding temperature (experimental value is 6 ms); the Go# model folds 50 times faster. Upon refolding, structural changes take place over three time scales. On the collapse time scale compact structures with intact hydrophobic cluster form. Subsequently, hydrogen bonds form, predominantly originating from the turn by a kinetic zipping mechanism. The assembly of the hairpin is complete when most of the interstrand contacts (the rate-limiting step) is formed. The dominant transition state structure (located by using cluster analysis) is compact and structured. We predict that when hydrophobic cluster is moved to the loop tF marginally increases, whereas moving the hydrophobic cluster closer to the termini results in significant decrease in tF relative to wild type. The mechanism of hairpin formation is predicted to depend on turn stiffness.