Carbon Nanoparticles and Their Differential Association with the Membranes of E. coli: A Coarse-Grained Molecular Dynamics Simulation Study

Abstract

Lipopolysaccharide (LPS), is a large molecule that is the primary component of the outer membrane of Gram-negative bacteria. LPS is composed of three key sections: a repetitive glycan polymer, a core domain of oligosaccharides, and lipid A, which anchors LPS molecules into the outer membrane of Gram-negative bacteria. The molecule acts as the first line of defense in bacteria, and confers resistance against both chemical and biological attack. Therefore to understand e.g. how resistance to antibiotics develops, it is imperative to have a detailed knowledge of the biophysical properties of LPS-containing membranes. Molecular dynamics simulations provide an ideal route to doing this. Here we present our coarse-grained model of the E. coli outer membrane, which is compatible with the MARTINI force field. A total of 10 microseconds of simulation are benchmarked against atomistic simulation and experimental data. Our simulations show the dramatic effects of the asymmetry of the bacterial outer membrane, in the context of solute permeation. A case study provides insights into the association of C60 fullerenes and carbon nanotubes with both membranes of E. coli. We show that the association is strongly dependent on the membrane type, this finding has profound implications for future antibiotic design.