Outer Membrane Remodeling: The Structural Dynamics and Electrostatics of Rough Lipopolysaccharide Chemotypes

Abstract

Lipopolysaccharides (LPS) are the primary constituent of the outer membrane of Gram-negative bacteria such as Pseudomonas aeruginosa. Gram-negative bacteria can synthesize modified forms of LPS in response to environmental stimuli or due to genetic mutations, a process known as outer membrane remodeling. Chemical modifications of the LPS modulate the integrity and antibiotic susceptibility of bacterial outer membranes. It also governs microbial adhesion to tissues and artificial material surfaces. We have extended a previous model of the rough LPS to include four novel chemotypes rmlC, galU, LPS Re, and Lipid-A. Atomistic molecular dynamics (MD) simulations were performed for outer membrane models constituted of each LPS chemotypes and 1,2-dipalmitoyl-3-phosphatidylethanolamine. It is shown that the decrease in the LPS polysaccharide chain length leads to a significant increase in the diffusion coefficients for the Ca(2+) counterions, increase in acyl chain packing (decrease in membrane fluidity), and attenuation of the negative potential across the LPS surface as positive counterions becomes more exposed to the solvent. The electrostatic potential on the LPS surfaces reflects heterogeneous charge distributions with increasingly larger patches of positive and negative potentials as the polysaccharide chain length decreases. Such a pattern originates from the spatial arrangement of charged phosphate-Ca(2+) clusters in the LPS inner-core that becomes exposed in the membrane surface as monosaccharide units are lost in the shortest chemotypes LPS Re and Lipid-A. These MD-derived conformational ensembles reproduce experimental trends and provide atom-level structural information on the rough LPS chemotypes that can help to rationalize antibiotic resistance and bacterial adhesion processes.

Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes

“…MD simulations of OM with the SPC water shows slightly larger A L values compared to the SPC/E model (Figures 2a-2b). Neutron scattering measurements 51 and previous MD simulations 29,30 have shown that LPS bilayers are appreciably more hydrated than phospholipid bilayers, with water molecules penetrating deeper in the hydrophobic region. For this reason, the difference in A L for the OM in the two water models is expected to result from increased hydration by the SPC water.…”

“…In addition, the higher diffusion constant of the SPC model, and consequently higher water motional dynamics, may lead to some degree of swelling of the carbohydrate region, with increase of A L (Table 2, Figure 4). 30 Furthermore, the average carbon-deuterium order parameter S CD are higher for the SPC pair of simulations compared to the SPC/E ( Table 1). The more ordered, less fluid OM in the SPC simulations has an increased acyl chain packing, which leads to higher A L values.…”

“…The new parameter set has been further expanded to include four new chemotypes: rmlC, galU, LPS Re and Lipid-A ( Figure 1). 30,31 Furthermore, these new atomic parameters have been used to examine the effect of different cations on the stability of the LPS membranes, 32 the binding mechanism of antimicrobial peptides and proteins to LPS membranes, [33][34][35] the effect of chemical remodeling on the structural dynamics and electrostatic properties of OM, 30,31 and to validate coarsegrained parameter sets for LPS from P. aeruginosa. 36,37 Concurrently, extensions of the GROMOS force field have been developed for the penta-and hexa-acylated forms of Lipid-A, LPS Re and Lipid-A modified with 4-amino-4-deoxy-L-arabinose from P. aeruginosa 38,39 and for the Rd1 LPS from E. coli, 40 followed by an extension of the CHARMM force field for the smooth LPS from E. coli.…”

Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi

“…Previous MD simulations have shown that the rough LPS membrane maintains a lamellar aggregate structure in presence of Ca 2+ ions and water molecules without a significant conformational change in the course of 1 μs simulation time . The rough LPS chemotypes also maintain a stable bilayer arrangement in presence of Ca 2+ ions within the simulated time of 100 ns . Divalent cations bind to negatively charged groups in the LPS molecule stabilize lamellar aggregates via cross‐bridge of neighboring molecules .…”

Synergy between Active Efflux and Outer Membrane Diffusion Defines Rules of Antibiotic Permeation into Gram-Negative Bacteria

“…The different LPS aggregate into species-specific LPS-PL bilayers with various numbers of LPS molecules, thicknesses, surface charge distributions, and dynamics ( 4 ). These features, in turn, translate into differences in the permeability properties of LPS-PL bilayers ( 5 – 7 ). Most of the current knowledge on selectivity of the OM permeability barriers was determined on the basis of extensive studies of model organisms such as Escherichia coli .…”