GD1a in phospholipid bilayer: A molecular dynamics simulation

Molecular dynamics simulation of ganglioside GD1a attached to the upper lay er of a fully hydrated lipid bilayer of dimyristoyl phosphatidyl choline (D MPC) at room temperature under periodic boundary conditions was performed. The time average conformation of GD1a reveals that the terminal sialic acid is more exposed into the solvent than the internal branched one. Many inte rresidual contacts between N-acetyl galactosamine-internal branched sialic acid; external Gal-external sialic acid; N-acetyl galactosamine-internal ga l are also observed. The conformation of the GD1-hexasaccharide is stabiliz ed by a number of intra molecular hydrogen bonds that were previously obser ved experimentally. The simulation results indicate that the presence of a single GD1a molecule has local effects on the bilayer. A local disorder in the arrangement of the acyl chains as well as the head groups is evident in the upper layer due to the presence of GD1a.