Fast kinetics in beta-sheet protein folding

Protein folding is one of the most fundamental problems in biophysics and structural biology. Despite extensive efforts devoted to in the past, many fundamental questions still exist, such as: How do specific and nonspecific interactions determine the folding pathways, the roughness of the energy landscape, as well as the thermally and kinetically accessible conformation sub-states? On what range of timescales do particular conformational and folding events occur? To provide new insight into the physical mechanism of β-sheet protein folding, we have studied the folding dynamics of several peptide model systems that fold into well-defined β-sheet conformations in solution. Firstly, using several spectroscopic techniques, especially the laser-induced temperature jump initiation method coupled with infrared spectroscopy and site-specific mutagenesis, we have characterized the folding stability and mechanism of a β-hairpin. Our results show that the folding of this β-hairpin takes place on the sub-microsecond timescale and its folding free energy barrier is largely determined by the entropic cost associated with the formation of the reverse turn, while other factors, such as the strength of cross-strand hydrophobic interactions, mostly affect the unfolding free energy barrier. Secondly, we have studied the folding dynamic of a three-stranded β-sheet that contains two rigid reverse turns. As expected, this β-sheet exhibits ultrafast relaxation kinetics, suggestive of a folding scenario wherein the conformational relaxation encounters only a small free energy barrier (compared to kBT) or even proceeds in a downhill manner. Further Langevin dynamics simulations suggest that the observed T-jump relaxation kinetics could be modeled by a conformational diffusion process along a single-well free energy profile, which allowed us to further determine the effective diffusion constant and also the roughness of the folding energy landscape of this β-sheet. Thirdly, we have demonstrated the folding mechanism of a β-hairpin that exhibits cold denaturation. Our results showed that the folding free energy barrier separating the cold denatured state from the folded state is different from that separating the heat denatured state from the folded state. The latter coincides with the idea that the mechanism leading to cold denaturation is different from that leading to heat denaturation. Finally, we have investigated how the folding kinetics of a β-sheet varies with the complexity of the system, e.g., the number of β-strands. Our results suggest that size is an important determinant of the folding rate of β-sheets and formation of a β-sheet is very complex and depends largely on the peptide sequence