Beta-Hairpin Restraint Potentials for Calculations of Potentials of Mean Force as a Function of Beta-Hairpin Tilt, Rotation, and Distance
DC Field | Value | Language |
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dc.contributor.author | Lee, Jinhyuk | - |
dc.contributor.author | Ham, Sihyun | - |
dc.contributor.author | Im, Wonpil | - |
dc.date.available | 2021-02-22T14:17:09Z | - |
dc.date.issued | 2009-06 | - |
dc.identifier.issn | 0192-8651 | - |
dc.identifier.issn | 1096-987X | - |
dc.identifier.uri | https://scholarworks.sookmyung.ac.kr/handle/2020.sw.sookmyung/13748 | - |
dc.description.abstract | We have developed a set of restraint potentials for beta-hairpin tilt relative to the membrane normal, beta-hairpin rotation around the beta-hairpin axis, and hairpin-hairpin distance. Such restraint potentials enable us to characterize the molecular basis of specific beta-hairpin tilt and rotation in membranes and hairpin-hairpin interactions at the atomic level by sampling their conformational space along these degrees of freedom, i.e., reaction coordinates, during molecular dynamics simulations. We illustrate the efficacy of the beta-hairpin restraint potentials by calculating the potentials of mean force (PMFs) as a function of tilt and rotation angles of protegrin-1 (PG-1), a beta-hairpin antimicrobial peptide, in an implicit membrane model. The peptide association in the membrane is also examined by calculating the PMFs as a function of distance between two PG-l peptides in various dimer interfaces. These novel restraint potentials are found to perform well in each of these cases and are expected to be a useful means to study the microscopic driving forces of insertion, tilting, and rotation of beta-hairpin peptides in membranes as well as their association in aqueous solvent or membrane environments particularly when combined with explicit solvent models. (C) 2008 Wiley Periodicals, Inc. J Comput Chem 30: 1334-1343, 2009 | - |
dc.format.extent | 10 | - |
dc.language | 영어 | - |
dc.language.iso | ENG | - |
dc.publisher | WILEY | - |
dc.title | Beta-Hairpin Restraint Potentials for Calculations of Potentials of Mean Force as a Function of Beta-Hairpin Tilt, Rotation, and Distance | - |
dc.type | Article | - |
dc.publisher.location | 미국 | - |
dc.identifier.doi | 10.1002/jcc.21154 | - |
dc.identifier.scopusid | 2-s2.0-66449133930 | - |
dc.identifier.wosid | 000265307300015 | - |
dc.identifier.bibliographicCitation | JOURNAL OF COMPUTATIONAL CHEMISTRY, v.30, no.8, pp 1334 - 1343 | - |
dc.citation.title | JOURNAL OF COMPUTATIONAL CHEMISTRY | - |
dc.citation.volume | 30 | - |
dc.citation.number | 8 | - |
dc.citation.startPage | 1334 | - |
dc.citation.endPage | 1343 | - |
dc.type.docType | Article | - |
dc.description.isOpenAccess | N | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Chemistry | - |
dc.relation.journalWebOfScienceCategory | Chemistry, Multidisciplinary | - |
dc.subject.keywordPlus | SOLID-STATE NMR | - |
dc.subject.keywordPlus | MOLECULAR-DYNAMICS SIMULATIONS | - |
dc.subject.keywordPlus | EFFECTIVE ENERGY FUNCTION | - |
dc.subject.keywordPlus | LIPID-BILAYERS | - |
dc.subject.keywordPlus | ANTIMICROBIAL PEPTIDE | - |
dc.subject.keywordPlus | HYDROPHOBIC MISMATCH | - |
dc.subject.keywordPlus | AMYLOID PROTOFILAMENTS | - |
dc.subject.keywordPlus | GRAMICIDIN CHANNEL | - |
dc.subject.keywordPlus | TACHYPLESIN-I | - |
dc.subject.keywordPlus | 3D STRUCTURE | - |
dc.subject.keywordAuthor | molecular dynamics | - |
dc.subject.keywordAuthor | implicit membrane model | - |
dc.subject.keywordAuthor | protegrin-1 (PG-1) | - |
dc.subject.keywordAuthor | antimicrobial peptide | - |
dc.subject.keywordAuthor | free energy decomposition | - |
dc.subject.keywordAuthor | association energy | - |
dc.identifier.url | https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21154 | - |
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