Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance
✍ Scribed by Jinhyuk Lee; Sihyun Ham; Wonpil Im
- Publisher
- John Wiley and Sons
- Year
- 2009
- Tongue
- English
- Weight
- 632 KB
- Volume
- 30
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
We have developed a set of restraint potentials for β‐hairpin tilt relative to the membrane normal, β‐hairpin rotation around the β‐hairpin axis, and hairpin–hairpin distance. Such restraint potentials enable us to characterize the molecular basis of specific β‐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 β‐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 β‐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 β‐hairpin peptides in membranes as well as their association in aqueous solvent or membrane environments particularly when combined with explicit solvent models. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009