Molecular dynamics simulations of six different fully hydrated monomeric conformers of Escherichia coli re-lipopolysaccharide in the presence and absence of Ca2+.

Six previously published conformational models of Escherichia coli Re lipopolysaccharide (ReLPS) were subjected to molecular dynamics simulations using the CHARMM force field. The monomers of ReLPS were completely immersed in a water box. The dynamic behavior of the solvated models in the presence and absence of calcium cations was compared. The structure of the solvent shell was analyzed in terms of radial distribution functions. Diffusion coefficients and mean residence times were analyzed to characterize the dynamic behavior of the solvent. Order parameters and number of gauche defects were used for the description of the dynamics of the acyl chains. The cations are preferentially located between the carboxylate and phosphate groups of the headgroup. Their presence leads to a rigidification of the headgroup structure and alters the conformation of the backbone, thus influencing the structure and flexibility of the hydrophobic region as well. The effect of calcium on the backbone flexibility was measured in terms of glycosidic torsion angles. The six fatty acid chains of each ReLPS monomer adopt a highly ordered micromembrane structure. The packing parameter indicates that aggregation of these ReLPS monomers will lead to lamellar structures. Evaluation of all data enables us to present one conformation, C, which is thought to best represent the average structure of the ReLPS conformers.