Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance
2008 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 30(2009), 8 vom: 02. Juni, Seite 1334-43 |
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| Weitere Verfasser: | , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2009
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Antimicrobial Cationic Peptides protegrin-1 |
| Zusammenfassung: | 2008 Wiley Periodicals, Inc. 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-1 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 |
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| Beschreibung: | Date Completed 14.07.2009 Date Revised 07.04.2009 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.21154 |