Molecular Dynamics Simulation Studies of Membrane Bilayers of Lipid a from Various Gram-Negative Bacteria

Abstract

Lipid A is a lipid component of a lipopolysaccharide (LPS) in the outer leaflet of the outer membrane of gram-negative bacteria. Lipid A plays an important role as an LPS anchor to the outer membrane using its several acyl chains, and its structure is also important to bacterial pathogenesis and membrane integrity. Thus, the considerable efforts have been made to identify structural features of lipid A from various gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains which are directly linked to the two sugars. Depending on the bacterial species, acyl chain varies in length and number. Also, some bacterium can have multiple lipid A types and further be substituted by residues such as L-Ara4N or peptide. In this work, homogeneous lipid bilayers using 23 distinctive lipid A types from 15 bacterial species are modeled and simulated to investigate the differences and similarities of the membrane properties. In addition, the models at different ion type are built to examine the ion's influence on the membrane properties.