Molecular modelling of the three-dimensional structure and conformational flexibility of bacterial lipopolysaccharide

Abstract

Molecular modelling techniques have been applied to calculate the three-dimensional architecture and the conformational flexibility of a complete bacterial S-form lipopolysaccharide (LPS) consisting of a hexaacyl lipid A identical to Escherichia coli lipid A, a complete Salmonella typhimurium core oligosaccharide portion, and four repeating units of the Salmonella serogroup B O-specific chain. X-ray powder diffraction experiments on dried samples of LPS were carried out to obtain information on the dimensions of the various LPS partial structures. Up to the Ra-LPS structure, the calculated model dimensions were in good agreement with experimental data and were 2.4 nm for lipid A, 2.8 nm for Re-LPS, 3.5 nm for Rd-LPS, and 4.4 nm for Ra-LPS. The maximum length of a stretched S-form LPS model bearing four repeating units was evaluated to be 9.6 nm; however, energetically favored LPS conformations showed the O-specific chain bent with respect to the Ra-LPS portion and significantly smaller dimensions (about 5.0 to 5.5 nm). According to the calculations, the Ra-LPS moiety has an approximately cylindrical shape and is conformationally well defined, in contrast to the O-specific chain, which was found to be the most flexible portion within the molecule.

Ultrastructural examination of the lipopolysaccharides of Pseudomonas aeruginosa strains and their isogenic rough mutants by freeze-substitution

“…Strains AK1401, rd7513, and rd7513(pFV3), which express the core-plus-one 0-antigen repeat, had outer leaflet staining regions that were 1.4-to 1.7-fold wider those of the A-Bcore-deficient mutants, AK1012 and R5. The slight variation observed in the outer leaflet widths among the core-plus-one 0-antigen strains is in accordance with the findings of Kastowsky et al (18), who suggested that the 0-antigen components should be flexible. Thus it is not surprising to expect that even one 0 repeat in the various core-plus-one 0-antigen-containing strains may present numerous conformational states in situ, although specific orientations may be preferred by individual strains.…”

“…In addition, the 0-specific sugars in their study are uncharged saccharides. The S-form LPS of P. aeruginosa used in our study is obviously highly charged and much larger in dimension (30 to 50 0 repeats were observed in SDS-PAGE (18). Both quantitative and qualitative differences in the appearance of the LPS layer between serotype 05 and 06 P. aeruginosa cells were observed by EM.…”

“…More recently, Kastowsky et al (18) used data from X-ray diffraction of dried LPS, information on the defined chemical structures, minimal energy conformational requirements, and computer analysis to come up with several molecular models to explain the conformation of Salmonella LPS.…”

The Role of Lipopolysaccharide Binding Protein in Resistance to Salmonella Infections in Mice

“…One of the signature molecules that activate innate immune responses is the lipid A portion of LPS, the principal constituent of the outer membrane of Gram-negative bacteria. The fatty acid-substituted disaccharide structure of the lipid A is largely conserved (3), and lipid A is a potent stimulus for many mammalian cells. The binding of LPS to cell surfaces is complex and has not been completely determined, but it involves mCD14 (a glycerophosphoinositol-linked membrane protein) (4), a transmembrane protein (Toll-like receptor 4 (TLR4)…”

Lipopolysaccharide as a target for brucellosis vaccine design

“…Although purified lipid A has a potent endotoxic activity by itself, the innermost part of the core oligosaccharide is also part of the LPS PAMP. Molecular modeling and X-ray diffraction show that it forms a compact entity with an unusually high partial density [27]. This tight packing and the dense negative charge created by the 2-keto, 3-deoxyoctulosonic residues (Kdo) and phosphates ( Figure 1) make the inner core a unique structure targeted by polycationic bactericidal peptides and the C1q complement component of innate immunity [24].…”