Monte Carlo simulations of beta-hairpin folding at constant temperature.
Monte Carlo simulations were applied to beta-hairpin folding of a valine-based peptide. Two valine residues in the middle of the peptide were substituted with glycine, to serve as turn residues. Unlike lattice model simulations, structure prediction methods, and unfolding simulations, our simulations used an atom-based model, constant temperature (274 K), and non-beta-hairpin initial conformations. Based on the concept of solvent reference, the effective energy function simplified the solvent calculation and overcame the multiple minima problem. Driven by the hydrophobic interaction, the peptide first folded into a compact U-shaped conformation with a central turn, in analogy to the initial collapse with simultaneous nucleation in protein folding. The peptide units in the U-shaped conformation then reoriented, gradually forming hydrogen bonds in the beta-hairpin pattern from the beta-turn to the ends of the strands. With the same energy function, an alanine-based peptide folded into helix-dominated structures. The basic structure types (alpha-helix or beta-hairpin) that formed during the simulations depended upon the amino acid sequence. Compared with helix, beta-hairpin folding is driven mainly by the hydrophobic interaction. Hydrogen bonding is necessary to maintain the ordered secondary structure.
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The Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195 USA.sungs@cesmpt.ccf.org
D000409:Alanine / Q000737:chemistry; D000595:Amino Acid Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics; D014633:Valine / Q000737:chemistry
D009842:Oligopeptides; D012997:Solvents; D014633:Valine; D000409:Alanine