Towards Mimetic Membrane Systems in Molecular Dynamics: Characteristics of E. Coli Membrane System.

Plenty of research is focused on the analysis of the interactions between bacteria membrane and antimicrobial compounds or proteins. The hypothesis of the research is formed according to the results from the numerical models such as molecular docking or molecular dynamics. However, simulated membrane models often vary significantly from the real ones. This may lead to inaccurate conclusions. In this paper, we employed molecular dynamic simulations to create a mimetic Escherichia coli full membrane model and to evaluate how the membrane complexity may influence the structural, mechanical and dynamical mainstream parameters. The impact of the O-antigen region presence in the outer membrane was also assessed. In the analysis, we calculated membrane thickness, area per lipid, order parameter, lateral diffusion coefficient, interdigitation of acyl chains, mechanical parameters such as bending rigidity and area compressibility, and also lateral pressure profiles. We demonstrated that outer membrane characteristics strongly depend on the structure of lipopolysaccharides, changing their properties dramatically in each of the investigated parameters. Furthermore, we showed that the presence of the inner membrane during simulations, as it exists in a full shell of E. coli, significantly changed the measured properties of the outer membrane.