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Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I

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  • Gökoğlu, Gökhan
  • Çelik, Tarık

Abstract

We have investigated the folding properties of tryptophan zipper-I molecule which folds into a stable β-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 β-hairpin motif with 1.30 Å backbone root-mean-square deviation from the reference PDB structure (1le0.pdb). Several quantities and exhaustive folding free energy landscapes were determined and discussed in order to clarify the folding behavior.

Suggested Citation

  • Gökoğlu, Gökhan & Çelik, Tarık, 2008. "Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(14), pages 3537-3545.
    • Handle: RePEc:eee:phsmap:v:387:y:2008:i:14:p:3537-3545
    DOI: 10.1016/j.physa.2008.02.065
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