A METROPOLIS MONTE-CARLO METHOD FOR ANALYZING THE ENERGETICS AND DYNAMICS OF LIPOPOLYSACCHARIDE SUPRAMOLECULAR STRUCTURE AND ORGANIZATION

A Metropolis Monte Carlo method has been developed for studying the ef fects of dielectric constant and counterion charge density and distrib ution on the energetics of formation and equilibria of the regular arr ays or domain structures formed by bacterial lipopolysaccharides. The method utilizes a regular triangular prism primitive as a reductive st ructural representation of each lipopolysaccharide anchor (lipid A mol ecule). Charges for the two phosphate groups are localized at one apex and midway along the opposite side of the regular triangular top face of each prism. The counterions are not localized but are represented as a fine cloud of charge modeled by distributing the total charge ove r a fine two-dimensional cubic lattice. The six alkyl chains of the li pid A molecule are aligned along the long axes of the prism and are co ntained by its faces. All prisms are confined to the same plane but ar e allowed to translate within the plane and to rotate about axes perpe ndicular to the plane. The potential energy function contains an elect rostatic term and a van der Waals term. A discontinuous dielectric is used to separate the aqueous and hydrophobic areas of the system. Tria l moves involve both a rotational and a translational operation. The c onfigurations predicted by this method are consistent with the crystal morphologies which have been observed for lipopolysaccharides. This a nalysis readily allows the evaluation of thermodynamic properties, suc h as heat capacity, entropy, and energy. The root mean square average separation of units was also calculated as a function of iteration num ber. (C) 1996 by John Wiley & Sons, Inc.