Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile

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. © 2012 Wiley Periodicals, Inc. Gramicidin is a peptide that forms ion channels specific for monovalent cations in biological membranes. The effect of gramicidin on the structure and lateral pressure profile of lipid bilayers is studied by molecular dynamics simulations. Due to the hydrophobic mismatch between gramicidin and the lipid bilayer, the membrane surface is largely distorted. The lateral pressure in the hydrophobic region of the membrane is found to decrease the pore size around the ion channel entrance.