Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model

Abstract

The cell envelope of Gram-negative bacteria contains a lipopolysaccharide (LPS) rich outer membrane that acts as the first line of defense for bacterial cells in adverse physical and chemical environments. The LPS macromolecule has a negatively charged oligosaccharide domain that acts as an ionic brush, limiting the permeability of charged chemical agents through the membrane. Besides the LPS, the outer membrane has radially extending O-antigen polysaccharide chains and β-barrel membrane proteins that make the bacterial membrane physiologically unique compared to phospholipid cell membranes. Elucidating the interplay of these contributing macromolecular components and their role in the integrity of the bacterial outer membrane remains a challenge. To bridge the gap in our current understanding of the Gram-negative bacterial membrane, we have developed a coarse grained force field for outer membrane that is computationally affordable for simulating dynamical process over physiologically relevant time scales. The force field was benchmarked against available experimental and atomistic simulations data for properties such as membrane thickness, density profiles of the residues, area per lipid, gel to liquid-crystalline phase transition temperatures, and order parameters. More than 17 membrane compositions were studied with a combined simulation time of over 100 μs. A comparison of simulated structural and dynamical properties with corresponding experimental data shows that the developed force field reproduces the overall physiology of LPS rich membranes. The affordability of the developed model for long time scale simulations can be instrumental in determining the mechanistic aspects of the antimicrobial action of chemical agents as well as assist in designing antimicrobial peptides with enhanced outer membrane permeation properties.

The gram‐negative outer membrane modeler: Automated building of lipopolysaccharide‐rich bacterial outer membranes in four force fields

“…Similarly, PAL5 values (139.17–143.55 Å 2 ) are in agreement with measurements of Lipid A at the liquid crystalline state (125–142 Å 2 ) for P. aeruginosa and other related species . Finally, it should be noted that the simulation results of all Lipid A variants are in agreement with previous simulation evidence for the CHARMM36, MARTINI and GROMOS force fields. Overall, these results show that the Lipid A topologies and simulation systems offered by GNOMM are, in terms of lipid bilayer properties, valid and consistent among different levels of resolution.…”

“…These include variations of Lipid A from four different species ( E. coli , Pseudomonas aeruginosa , Helicobacter pylori and Neisseria meningitidis ) (Supporting Information Fig. S1), as well as three experimentally studied LPSs, containing Lipid A and the oligosaccharide core (Re and Ra LPS for E. coli and PAO1 LPS for P. aeruginosa ) . In addition, a number of standard lipids are also offered, representing the major categories most commonly found in bacteria .…”

“…Some glycolipid and glycan modeling tools can also be used to model LPS molecules, such as doGlycans for the AMBER/GLYCAM and OPLS force fields; however, these methods are not able to construct LPS‐containing bilayers, either homogeneous or mixed. As such, apart from CHARMM‐GUI, there are very limited options to automatically create LPS‐containing membranes with force fields or molecules outside the aforementioned systems (e.g., GROMOS, or MARTINI with LPSs from species other than E. coli ), even though valid Lipid A and LPS parameters exist . Instead, the literature shows that LPS‐containing simulation systems in such cases are, for the most part, built by hand, a process that can be time consuming and difficult, particularly for inexperienced users.…”

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale

“…Realistic modelling of the more complex outer membranes of Gram negative bacteria has required development of models for lipopolysaccharide (LPS), the major constituent of the outer leaflet of these membranes [27, 28]. Recent progress in both atomistic [29 • ] and coarse-grain [30] simulations of LPS enable studies of the interactions of a number of E. coli outer membrane proteins, for example FecA [31 •• ], OmpLA [29 • ] and OmpF [32], with this complex membrane environment.…”

Two Outer Membrane Proteins Contribute to Caulobacter crescentus Cellular Fitness by Preventing Intracellular S-Layer Protein Accumulation

“…Deletion of these OMPs causes a rearrangement to fill the voids left by the loss of these relatively abundant proteins in the outer membrane. Consequently, an increase in the amount of LPS in the outer membrane during this rearrangement could lead to a change in outer membrane permeability and increased diffusivity of nonpolar compounds, such as antibiotics, across the outer membrane (53). To test whether cells deficient in RsaF a and RsaF b exhibited altered membrane permeability, we conducted the nitrocefin hydrolysis assay developed by Misra et al (54).…”