Theoretical characterization of α-helix and β-hairpin folding kinetics

By means of the conformational free energy surface and corresponding diffusion coefficients, as obtained by long time scale atomistic molecular dynamics simulations (μs time scale), we model the folding kinetics of α-helix and β-hairpin peptides as a diffusive process over the free energy surface. The two model systems studied in this paper (the α-helical temporin L and β-hairpin prion protein H1 peptide) exhibit a funnel-like almost barrierless free energy profile, leading to nonexponential folding kinetics matching rather well the available experimental data. Moreover, using the free energy profile provided by Muñoz et al. [Muñoz et al. Nature 1997, 390: 196-199], this model was also applied to reproduce the two-state folding kinetics of the C-terminal β-hairpin of protein GB1, yielding an exponential folding kinetics with a time constant (∼5 μs) in excellent agreement with the experimentally observed one (∼6 μs). Finally, the folding kinetics obtained by solving the diffusion equation, considering either a one-dimensional or a two-dimensional free energy surface, are also compared in order to understand the relevance of the possible kinetic coupling between conformational degrees of freedom in the folding process. © 2005 American Chemical Society.