Name
Title | ||
|---|---|---|
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance. |
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 |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1002/jcc.21154 | JOURNAL OF COMPUTATIONAL CHEMISTRY |
Keywords | Field | DocType |
molecular dynamics,implicit membrane model,protegrin-1 (PG-1),antimicrobial peptide,free energy decomposition,association energy | Peptide,Beta hairpin,Computational chemistry,Chemistry,Membrane,Solvent models,Molecular dynamics,Solvent,Dimer,Aqueous solution | Journal |
Volume | Issue | ISSN |
30 | 8 | 0192-8651 |
Citations | PageRank | References |
2 | 0.52 | 5 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Jin-hyuk Lee | 1 | 14 | 4.18 |
| Sihyun Ham | 2 | 5 | 1.63 |
| Wonpil Im | 3 | 163 | 17.39 |