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.
|Titolo:||Theoretical characterization of α-helix and β-hairpin folding kinetics|
|Data di pubblicazione:||2005|
|Citazione:||Theoretical characterization of α-helix and β-hairpin folding kinetics / Daidone, Isabella; D'Abramo, Marco; DI NOLA, Alfredo; Amadei, Andrea. - In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. - ISSN 0002-7863. - STAMPA. - 127:42(2005), pp. 14825-14832.|
|Appare nella tipologia:||01a Articolo in rivista|