Paper Citing NAMD - Abstract
Saito, Hiroaki; Mizukami, Taku; Kawamoto, Shuhei; Miyakawa, Takeshi; Iwayama, Masashi; Takasu, Masako; Nagao, Hidemi
Molecular Dynamics Studies of Lipid Bilayer With Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:161-170, JAN 2012
The effects of gramicidin A (GA) peptide on the structure of lipid bilayer were studied by molecular dynamics (MD) simulations in the absence and presence of GA peptide. The hydrophobic match between the GA and surrounding lipid bilayer was investigated by the MD simulations of four kinds of lipid bilayer systems: 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine (diC12:0-PC), 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC, diC14:0-PC), 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (diC16:0-PC), and 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC, di18:0-PC). The observed hydrophobic thickness and order parameter increases, and the gauche conformation decreases in the presence of GA, being consistent with the experimental observations. The acyl chain structure of the DSPC membrane was sufficiently changed to match the length of GA peptide, resulting in a distortion of the membrane surface around the GA peptide. On the other hand, the minor structural changes of lipid and the small fluctuation of the GA were shown in the DMPC membrane. These results indicate that DMPC bilayer has a better hydrophobic match with the GA peptide than the other membranes. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112: 161-170, 2012
