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

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dc.citation.epage3545en_US
dc.citation.issueNumber14en_US
dc.citation.spage3537en_US
dc.citation.volumeNumber387en_US
dc.contributor.authorGökoǧlu G.en_US
dc.contributor.authorÇelik, T.en_US
dc.date.accessioned2016-02-08T10:09:02Z
dc.date.available2016-02-08T10:09:02Z
dc.date.issued2008en_US
dc.departmentDepartment of Physicsen_US
dc.description.abstractWe 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. © 2008 Elsevier Ltd. All rights reserved.en_US
dc.identifier.doi10.1016/j.physa.2008.02.065en_US
dc.identifier.issn0378-4371
dc.identifier.urihttp://hdl.handle.net/11693/23110
dc.language.isoEnglishen_US
dc.relation.isversionofhttp://dx.doi.org/10.1016/j.physa.2008.02.065en_US
dc.source.titlePhysica A: Statistical Mechanics and its Applicationsen_US
dc.subjectβ-hairpinen_US
dc.subjectGeneralized ensemblesen_US
dc.subjectSimulated temperingen_US
dc.subjectTryptophan zipperen_US
dc.subjectAlgorithmsen_US
dc.subjectHydrogenen_US
dc.subjectMolecular structureen_US
dc.subjectNuclear magnetic resonanceen_US
dc.subjectGeneralized ensemblesen_US
dc.subjectSimulated temperingen_US
dc.subjectTryptophan zipperen_US
dc.subjectPeptidesen_US
dc.titleSecondary structure prediction of beta-hairpin peptide tryptophan zipper-Ien_US
dc.typeArticleen_US

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