Paper Citing NAMD - Abstract
Khalfa, Adil; Tarek, Mounir
On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2676-2684, MAR 4 2010
[RRKWLWLW] cyclic peptides have been shown to exhibit remarkable in vitro and in vivo antibacterial activity. Peptides alike seem to be promising for the development of new compounds to combat microbial pathogens, yet the molecular level understanding of their mechanism of action remains unclear. Here, we use coarse-grained (CG) molecular dynamics (MD) simulations of these cyclic peptides interacting with antibacterial cytoplasmic membrane models composed of a mixture or palmitoyl-oleoyl-phosphatidyl-ethamolamine (POPE) and palmitoyl-oleoyl-phospliatidylglycerol (POPG) lipid bilayers to provide a better understanding of their mode of action. Ill particular, the MD simulations performed at various concentrations of membrane-bound cyclic peptides reveal a novel type of mechanism in which the peptides first self-assemble at the membrane interface into amphipathic nanotubes. At high enough concentrations, coating of the membrane causes extrusion of lipids from the exposed bilayer leaflet, leading ultimately to a release of phospholipid micellar aggregates. Furthermore, the cyclic peptides also induce a drastic change in the lateral pressure profiles of the exposed leaflet, indicating a direct effect oil the mechanical properties of the bilayer.
