MOLECULAR-DYNAMICS SIMULATIONS OF 6 DIFFERENT FULLY HYDRATED MONOMERIC CONFORMERS OF ESCHERICHIA-COLI RE-LIPOPOLYSACCHARIDE IN THE PRESENCEAND ABSENCE OF CA2+

Six previously published conformational models of Escherichia coli Re lipopolysaccharide (ReLPS) were subjected to molecular dynamics simula tions using the CHARMM force field. The monomers of ReLPS were complet ely immersed in a water box. The dynamic behavior of the solvated mode ls in the presence and absence of calcium cations was compared. The st ructure of the solvent shell was analyzed in terms of radial distribut ion functions. Diffusion coefficients and mean residence times were an alyzed to characterize the dynamic behavior of the solvent. Order para meters and number of gauche defects were used for the description of t he 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 alte rs the conformation of the backbone, thus influencing the structure an d flexibility of the hydrophobic region as well. The effect of calcium on the backbone flexibility was measured in terms of glycosidic torsi on angles. The six fatty acid chains of each ReLPS monomer adopt a hig hly ordered micromembrane structure. The packing parameter indicates t hat aggregation of these ReLPS monomers will lead to lamellar structur es. Evaluation of all data enables us to present one conformation, C, which is thought to best represent the average structure of the ReLPS conformers.