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P. Ferrara; A. Caflisch

Journal: J. Mol. Biol.
Year: 2001
Volume: 306
Issue: 4
Pages: 837-850
DOI: 10.1006/jmbi.2000.4400
Type of Publication: Journal Article

Computer Simulation; Hydrogen Bonding; Kinetics; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Peptides; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Thermodynamics


Fifty-five molecular dynamics runs of two three-stranded antiparallel β-sheet peptides were performed to investigate the relative importance of amino acid sequence and native topology. The two peptides consist of 20 residues each and have a sequence identity of 15 %. One peptide has Gly-Ser (GS) at both turns, while the other has d-Pro-Gly ((D)PG). The simulations successfully reproduce the NMR solution conformations, irrespective of the starting structure. The large number of folding events sampled along the trajectories at 360 K (total simulation time of about 5 micros) yield a projection of the free-energy landscape onto two significant progress variables. The two peptides have compact denatured states, similar free-energy surfaces, and folding pathways that involve the formation of a β-hairpin followed by consolidation of the unstructured strand. For the GS peptide, there are 33 folding events that start by the formation of the 2-3 β-hairpin and 17 with first the 1-2 β-hairpin. For the (D)PG peptide, the statistical predominance is opposite, 16 and 47 folding events start from the 2-3 β-hairpin and the 1-2 β-hairpin, respectively. These simulation results indicate that the overall shape of the free-energy surface is defined primarily by the native-state topology, in agreement with an ever-increasing amount of experimental and theoretical evidence, while the amino acid sequence determines the statistically predominant order of the events.