Conformational Dynamics of the Single Lipopolysaccharide O‐Antigen in Solution

Abstract

The O-antigen is the most variable and highly immunogenic part of the lipopolysaccharide molecule that covers the surface of Gram-negative bacteria and makes up the first line of cellular defense. To provide insight into the details of the O-antigen arrangement on the membrane surface, we simulated its behavior in solution by molecular dynamics. We developed the energetically favorable O-antigen conformation by analyzing free-energy distributions for its disaccharide fragments. Starting from this conformation, we simulated the behavior of the O-antigen chain on long timescales. Depending on the force field and temperature, the single molecule can undergo reversible or irreversible coil-to-globule transitions. The mechanism of these transitions is related either to the rotation of the carbohydrate residues around O-glycosidic bonds or to flips of the pyranose rings. We found that the presence of rhamnose in the O-antigen chain crucially increases its conformational mobility.

Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by Nuclear Magnetic Resonance Spectroscopy and Molecular Simulations

“…21,22 The conformation can be assessed by molecular modeling techniques, 23 preferably in combination with NMR spectroscopy that gives atomicresolution information, 24,25 and further insights to their conformational behavior can be gained by carrying out molecular dynamics (MD) simulations. 26,27,28,29 We herein carry out NMR-based nuclear Overhauser effect (NOE) experiments on the 13 C-isotope labeled O-antigen from E. coli O91 in isotropic water solution. In this way resolved NMR spectra can be obtained alleviating severe overlap present in homonuclear 1 H-based NMR spectra of natural abundance material.…”

Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide

“…In particular, molecular dynamics (MD) simulations are especially well suited to the characterization of the structure and dynamics of glycans and glycoconjugates (10). Indeed, MD simulations are increasingly used for conformational prediction of bacterial polysaccharide structures (20,21). MD has been used to probe the interaction modes of oligosaccharides with molecules such as proteins (22,23), but, to date, there have been few MD studies targeted at other molecular classes, such as lipids or hydrocarbons.…”

Increasing the Affinity of an O‐Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein

“…The S. flexneri Y octasaccharide contains α‐ l ‐rhamnosyl residues to a large extent, like for any of the O‐antigens from various S. flexneri serotypes. The methyl groups at C6 of l ‐rhamnosyl residues thus enable an increased flexibility of the glycans compared to contributions of other, fully hydroxylated monosaccharide building blocks . In the 2D 1 H, 1 H‐trNOESY NMR analysis, the methyl groups at C6 facilitate a unique conformational landscape to be revealed, where correlation times between fast‐spinning methyl groups and methine protons are significantly shorter than for the methine‐methine interactions in the oligosaccharide (Figure S4); this is the basis for using different correlation times in the analysis of the experimental NMR data.…”