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

Gökhan Gökoğlu and Tarık Çelik

Physica A: Statistical Mechanics and its Applications, 2008, vol. 387, issue 14, 3537-3545

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.

Keywords: Tryptophan zipper; β-hairpin; Generalized ensembles; Simulated tempering (search for similar items in EconPapers)
Date: 2008
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S037843710800246X
Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:387:y:2008:i:14:p:3537-3545

DOI: 10.1016/j.physa.2008.02.065

Access Statistics for this article

Physica A: Statistical Mechanics and its Applications is currently edited by K. A. Dawson, J. O. Indekeu, H.E. Stanley and C. Tsallis

More articles in Physica A: Statistical Mechanics and its Applications from Elsevier
Bibliographic data for series maintained by Catherine Liu ().