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A. Cavalli; P. Ferrara; A. Caflisch

Journal: Proteins
Year: 2002
Volume: 47
Issue: 3
Pages: 305-314
DOI: 10.1002/prot.10041
Type of Publication: Journal Article

Amino Acid Sequence; Computer Simulation; Kinetics; Models, Molecular; Peptides; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Temperature


The thermodynamics and energetics of a 20-residue synthetic peptide with a stable three-stranded antiparallel β-sheet fold are investigated by implicit solvent molecular dynamics (MD) at 330 K (slightly above the melting temperature in the model) and compared with previous simulation results at 360 K. At both temperature values, the peptide folds reversibly to the NMR solution conformation, irrespective of the starting conformation. The sampling of the conformational space (2.3 µs and 25 folding events at 330 K, and 3 µs and 50 folding events at 360 K) is sufficient to obtain a thermodynamic description of minima and transition states on the free energy surface, which is determined near equilibrium by counting populations. The free energy surface, plotted as a function of two-order parameters that monitor formation of either of the β-hairpins, is similar at both temperature values. The statistically predominant folding pathway and its frequency (about two-thirds of the folding events) are the same at 330 K and 360 K. Furthermore, the main unfolding route is the reverse of the predominant folding pathway. The effective energy and its electrostatic and van der Waals contributions show a downhill profile at both temperatures, implying that the free energy barrier is of entropic origin and corresponds to the freezing of about two-thirds of the chain into a β-hairpin conformation. The average folding rate is nearly the same at 330 K and 360 K, while the unfolding rate is about four times slower at 330 K than at 360 K. Taken together with previous MD analysis of α-helices and β-hairpins, the present simulation results indicate that the free energy surface and folding mechanism of structured peptides have a weak temperature dependence.