An Unusual Carbohydrate Conformation is Evident in Moraxella catarrhalis Oligosaccharides

Abstract

Oligosaccharide structures derived from the lipooligosaccharide of M. catarrhalis show that the highly branched glucose-rich inner core of the oligosaccharide has an altered conformation compared to the most truncated tetra-glucose-Kdo lgt1/4Δ oligosaccharide structure. Addition of one residue each to the (1-4) and (1-6) chains to give the lgt2Δ oligosaccharide is the minimum requirement for this conformational change to occur. Extensive molecular modeling and NMR investigations have shown that the (1-3), (1-4), and (1-6) glycosidic linkages from the central α-D-Glcp have significantly altered conformational preferences between the two structures. For the lgt1/4Δ oligosaccharide the (1-3) and (1-4) linkage populates predominantly the syn minimum on the conformational free energy map and for the (1-6) linkage conformational flexibility is observed, which is supported by 1 H-NMR T1 measurements. For the lgt2Δ oligosaccharide the unusual "(1-4)anti-ψ(1-6)gg" conformation, which could be confirmed by long-range NOE signals, is a dominant conformation in which the oligosaccharide is very compact with the terminal α-D-GlcNAc residue folding back towards the center of the molecule leading to an extensive intra-molecular hydrophobic interaction between the terminal residues. Comparing effective H-H distances, OPEN ACCESSMolecules 2015, 20 14235 which were calculated for conformational sub-ensembles, with the NOE distances revealed that typically multiple conformations could be present without significantly violating the measured NOE restraints. For lgt2Δ the presence of more than one conformation is supported by the NOE data.

Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics

“…The msesMD simulations, as well as unbiased triplicate 1 s and 10 s MD trajectories sample the full spectrum of puckers, from 4 C 1 through skew-boat intermediates to 1 C 4 conformations, tracing similar profiles (Figure 4a). For the remaining sugar rings, the pucker free energy profiles obtained from msesMD broadly reflect those from unbiased MD albeit with some differences regarding the highest energy regions (Figure 4b-d); the greatest discrepancy is found for the high energy 4 C 1 state of Neu5Ac where biased and unbiased estimates differ by ~2.5 kcal mol -1 (Figure 4b).…”

Three-Dimensional Structures of Carbohydrates and Where to Find Them

“…Since there is no direct way to derive detailed three-dimensional representation from the observed NOE intensities, additional molecular modeling protocols are required to establish comprehensive view of conformational space at the atomic level [ 311 , 312 , 313 ]. Frank et al, demonstrated conformation filtering based on the observed NOE obtained by molecular dynamics in explicit solvent [ 314 ]. As a representative example, Figure 8 depicts 1 H- 1 H spatial contacts and conformation selection criteria illustrated by Moraxella catarrhalis lgt2Δ bacterium heptasaccharide, which adopts an unusual conformation.…”

“…( a ) Characteristic proton-proton contacts; ( b ) NOE-filtered (blue boxes) sampling of proton-proton distances from MD simulation (grey shades). Reproduced from [ 314 ], © 2020 The authors. Licensee MDPI, Basel, Switzerland.…”

Differential Dynamics at Glycosidic Linkages of an Oligosaccharide as Revealed by 13C NMR Spin Relaxation and Stochastic Modeling

“…8 The branching pattern of a sugar residue may take several forms some of which have sugars linked to it by non-adjacent residues and the conformational space of the oligosaccharide can be anticipated to be described by conformational dynamics at each of the glycosidic linkages. 9 However, depending on the absolute configuration, the anomeric configuration or the sugar residues per se that vicinally di-or multisubstitute another sugar entity significantly altered conformational preferences may result 10 represents a model for branched structures, in which the glucosyl residues vicinally substitute positions 2 and 3 of the mannosyl residue. Its conformational preferences and dynamics in solution have previously been studied by 1 H, 1 H-NOE NMR methodology 12 and 13 C NMR spin relaxation experiments at 13 C natural abundance.…”

“…8 The branching pattern of a sugar residue may take several forms, some of which have sugars linked to it by nonadjacent residues, and then the conformational space of the oligosaccharide can be anticipated to be described by conformational dynamics at each of the glycosidic linkages. 9 However, depending on the absolute configuration, the anomeric configuration or the sugar residues per se that vicinally di-or multisubstitute another sugar entity significantly altered conformational preferences may result 10 as well as the dynamics present.…”