Properties of Lipid a Bilayers Analyzed by Molecular Dynamics Simulations

Abstract

Lipopolysaccharide (LPS), responsible for the toxicity of Gram-negative bacteria, is made up of three regions: the O antigen, the core, and the innermost lipid A. Lipid A is the lipid component whose hydrophobic nature allows LPS to anchor to the bacteria outer membrane. Utilizing the latest C36 CHARMM lipid and carbohydrate force field, we have constructed a lipid A molecule of E. coli. Various bilayer systems were then constructed six different conditions: 1) CaCl2 at 80% water and at 303K or 323K, 2) KCl at 80% water at 303K or 323K, and 3) KCl at 40% water at 303K or 323K. We are currently running molecular dynamics simulations of these systems. The simulation results will be discussed in terms of how different temperatures, ratios of water molecules to lipids, and charged ions affects the lipid A bilayer properties such as surface area, ion location, chain order, bilayer thickness and shape, and the carbohydrate conformations. The results from these simulations will be also compared with available experimental data. This work will be the basis of the future simulations of the complex glycolipid simulations such as LPS, and membrane protein simulations in more native bilayer environments.