Molecular modelling of bacterial deep rough mutant lipopolysaccharide of Escherichia coli

Abstract

Molecular modelling techniques have been applied to compute the conformations accessible to bacterial deep rough lipopolysaccharide of Escherichia coli (Re-LPS). Analyses of the results showed that the models typically exhibit a tilt of the diglucosamine backbone with respect to the membrane normal of 53 7" while both the glucosamine ring planes are orientated approximately parallel to the membrane normal. Different models were found to show compact and elongated types of acyl chain arrangements, both producing anisotropic lateral dimensions of the models of 1.0-1.1 nm and 1.7-2.0 nm for the shorter and the longer side, respectively. The conformationally allowed range of the isolated dOclA(a-2-4)dOclA disaccharide (dOclA = 3-deoxy-~-mannooctulosonic acid) was found to be extremely limited. It appeared that the dOclA disaccharide (dOclA)2 is centred at the top of the Re-LPS molecule preferring two orientations stabilized by hydrogen bonds involving only one phosphate group of the lipid A moiety at a time.The effect of charges on the Re-LPS conformations has been studied in separate calculations. From these calculations it was obvious that charges have no significant effects on the conformations of the isolated lipid A and (dOclA)2 moieties. However, it was found that the orientation of (dOclA), with respect to the lipid A part is highly sensitive to charges, i. e. in the charged models the proximity of phosphate and carboxyl groups is prevented by strong electrostatic repulsion between these negatively charged groups.In order to rationalize the acyl chain packing of the models, a simple geometrical model which correlates the tilt of the diglucosamine backbone with the energetically favoured close packing of the acyl chains is proposed. Furthermore, the possibility of a chelate-like complexation of divalent cations and its contribution to head group mobility is discussed.Lipopolysaccharides (LPS) are the main constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. As LPS are of special significance to bacterial viability and to interactions of bacteria with host organisms, many studies have been focused on the elucidation of their structure and function [l -51. Chemically, LPS consists of a lipid A and a polysaccharide component, of which the latter is usually subdivided into two regions [6], i.e. the 0-specific chain and the core oligosaccharide. Re-LPS is the smallest LPS found in viable Escherichia coli bacteria [2, 71. It consists of the lipid A part and a partial core built up by a dimer of the rare saccharide 3-deoxy-~-manno-octu~osonic acid (dOclA). Recent work has shown that LPS endotoxic activity is determined by structural components as they are present in E. coli lipid A, i.e. a 8-1-6 interlinked diglucosamine, two phosphoryl groups and at least five, but not more than six, fatty acids including one or two 3-acyloxyacyl groups [S]. However, as itCorrespondence to

Comparison of X‐ray powder‐diffraction data of various bacterial lipopolysaccharide structures with theoretical model conformations

“…3). It was also instructive that the electron-density profile calculated froin a three-dimensional model of a lipid-A bilayer was in excellent agreement with X-ray measurements [31] (Fig. 6).…”

“…Molecular models of the LPS lipid-A portion were built from Re-LPS models [14]. Using the MEMBRANE program, a reasonable head-head and tail-tail packing was simulated resulting in a bilayer model.…”

Disruption of lipid homeostasis in the Gram-negative cell envelope activates a novel cell death pathway

“…Unlike Mg 2+ (41), intracellular Ca 2+ levels are low (42), but extracellular Ca 2+ is known to stabilize the OM (43). The effects of CaCl 2 on death suppression in mlaA* cells were nearly identical to those of Mg 2+ : 1 mM and 5 mM CaCl 2 partially and fully suppressed death, respectively (Fig.…”

Molecular Basis of Bacterial Outer Membrane Permeability Revisited

“…The quasi-crystalline, ordered arrangement of hydrocarbon chains was also confirmed by using synthetic lipid A with the correct structure, whereas the synthetic compounds representing the earlier, incorrect structure showed a liquid crystalline, disordered structure (364). The modeling was extended to hexa-acylated lipid A from E. coli, and the prediction was similar in that the six hydrocarbon chains were optimally located in the nodes of a hexagonal lattice (326,439) (Fig. 11).…”

“…(The conformation of the polysaccharide chain of LPS was also estimated by energy minimization, with the result that O chains were predicted to be bent strongly against the membrane normal [325].) The energy minimization approach predicted several different conformers of Re LPS (326), and molecular dynamics simulation of single LPS molecules preserved the initial conformation (469). The next important step, the simulation of the LPS aggregate, an effort that required 3 months of computer time, was performed by Kotra et al (350).…”