Mechanisms and kinetics of beta-hairpin formation

Thermodynamics and kinetics of off-lattice models with side chains for the beta-hairpin fragment of immunoglobulin-binding protein and its variants ar e reported. For all properties (except refolding time tau(F)) there are no qualitative differences between the full model and the Gd version. The vali dity of the models is established by comparison of the calculated native st ructure with the Protein Data Bank coordinates and by reproducing the exper imental results for the degree of cooperativity and tau(F). For the full mo del tau(F) approximate to 2 mu s at the folding temperature (experimental v alue is 6 mu s); the Gb model folds 50 times faster. Upon refolding, struct ural changes take place over three time scales. On the collapse time scale compact structures with intact hydrophobic cluster form. Subsequently, hydr ogen bonds form, predominantly originating from the turn by a kinetic zippi ng mechanism. The assembly of the hairpin is complete when most of the inte rstrand contacts (the rate-limiting step) is formed. The dominant transitio n state structure (located by using cluster analysis) is compact and struct ured, We predict that when hydrophobic cluster is moved to the loop tau(F) marginally increases, whereas moving the hydrophobic cluster closer to the termini results in significant decrease in tau(F) relative to wild type. Th e mechanism of hairpin formation is predicted to depend on turn stiffness.