Molecular dynamics simulation of a GM3 ganglioside bilayer

A first molecular dynamics simulation of a fully hydrated GM3 ganglioside bilayer is presented. Several properties characterizing the membrane structure and surrounding water are evaluated and compared to known data related to phospholipids. Our results are in good agreement with experimental small-angle X-ray scattering data. Overall, the simulated bilayer shows very long relaxation times such that a full equilibration is attained in about 30 ns. The long equilibration time is due to the slow relaxation of the torsional angle at the level of the galactose-sialic acid linkage. Once equilibrated, GM3 exhibits a good packing of the hydrophilic moieties, due to preferential alignment of its longitudinal axis along the bilayer normal, and a high degree of disorder in the tail region. The ionic nature of the hydrophilic heads manifests itself in a slow decay of the water orientational order parameter.