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    Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I
    (Elsevier Science Bv, 2008) Goekoglu, Goekhan; Celik, Tank
    We have investigated the folding properties of tryptophan zipper-I molecule which folds into a stable beta-hairpin motif in aqueous solution as suggested by nuclear magnetic resonance (NMR) experiments. An all-atom presentation, including hydrogen, was used with an implicit solvent. As a simulation technique, simulated tempering algorithm was used to obtain equilibrium conformations of the molecule at ten distinct temperatures. Our minimum energy configuration obtained from simulated tempering algorithm is a beta-hairpin motif with 1.30 angstrom backbone root-mean-square deviation from the reference PDB structure (11e0.pdb). Several quantities and exhaustive folding free energy landscapes were determined and discussed in order to clarify the folding behavior. (c) 2008 Elsevier B.V. All rights reserved.