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

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dc.authoridGokoglu, Gokhan/0000-0002-2456-6397
dc.contributor.authorGoekoglu, Goekhan
dc.contributor.authorCelik, Tank
dc.date.accessioned2024-09-29T16:00:30Z
dc.date.available2024-09-29T16:00:30Z
dc.date.issued2008
dc.departmentKarabük Üniversitesien_US
dc.description.abstractWe 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.en_US
dc.identifier.doi10.1016/j.physa.2008.02.065
dc.identifier.endpage3545en_US
dc.identifier.issn0378-4371
dc.identifier.issue14en_US
dc.identifier.scopus2-s2.0-41649101790en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage3537en_US
dc.identifier.urihttps://doi.org/10.1016/j.physa.2008.02.065
dc.identifier.urihttps://hdl.handle.net/20.500.14619/5193
dc.identifier.volume387en_US
dc.identifier.wosWOS:000256126600018en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherElsevier Science Bven_US
dc.relation.ispartofPhysica A-Statistical Mechanics and Its Applicationsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjecttryptophan zipperen_US
dc.subjectbeta-hairpinen_US
dc.subjectgeneralized ensemblesen_US
dc.subjectsimulated temperingen_US
dc.titleSecondary structure prediction of beta-hairpin peptide tryptophan zipper-Ien_US
dc.typeArticleen_US

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