Paper Citing NAMD - Abstract
Saito, Hiroaki; Iwayama, Masashi; Takagi, Hiroyuki; Nishimura, Megumi; Miyakawa, Takeshi; Kawaguchi, Kazutomo; Takasu, Masako; Mizukami, Taku; Nagao, Hidemi
Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:3834-3839, DEC 15 2012
The structure and lateral pressure profile of the 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC) lipid bilayers in the absence and presence of gramicidin A (GA) are studied by molecular dynamics simulation. Due to the hydrophobic mismatch between the GA and DSPC lipid bilayer, the chain conformation became disordered, and the hydrophobic thickness around the GA largely decreased to fit the length of hydrophobic core region of the GA. The polar headgroup of lipid was found to orient toward the membrane normal as the lipid approaches the GA. The surface tension around the polar headgroup region in the DMPC/GA membrane decreased due to the decrease of electrostatic interactions between the headgroups. The larger lateral pressure in the hydrophobic region of the DSPC/GA membrane causes the reduction of pore radius around the GA channel entrance, suggesting the decrease of ion accessibility to the GA channel entrance. (C) 2012 Wiley Periodicals, Inc.
