General NMR Spectroscopy of Carbohydrates and Conformational Analysis in Solution

Widmalm, Göran

doi:10.1016/b978-0-12-819475-1.00001-8

Cited by 11 publications

(5 citation statements)

References 316 publications

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“…The 1 H and 13 C NMR chemical shifts of disaccharide 3 were previously assigned at 343 K, [28] though for the H6 protons only approximate chemical shifts were obtained due to small chemical shift differences within each hydroxymethyl group. A series of 1 H NMR spectra were acqired in the temperature range 300 K–330 K (Figure 6), as well as a 13 C NMR spectrum at 300 K, and assigned by NMR experiments suitable for carbohydrates [83] . Refinement of 1 H NMR chemical shifts and n J HH coupling constants at 300 K and 330 K (Table 4) were subsequently carried out using NMR spin‐simulation [30,31] .…”

Section: Resultsmentioning

confidence: 99%

“…A series of 1 H NMR spectra were acqired in the temperature range 300 K-330 K (Figure 6), as well as a 13 C NMR spectrum at 300 K, and assigned by NMR experiments suitable for carbohydrates. [83] Refinement of 1 H NMR chemical shifts and n J HH coupling constants at 300 K and 330 K (Table 4) were subsequently carried out using NMR spin-simulation. [30,31] In non-substituted hydroxymethyl groups of methyl glycopryanosides having the gluco-or galacto-configuration 3 J H5,H6pro-R > 3 J H5,H6pro-S , [84,85] which was used to assign H6 resonances of compound 3 resulting in that δ H6pro-R > δ H6pro-S in both sugar residues at 300 K. The 3 J H5,H6 coupling constants differ somewhat to those of the monosaccharides and the rotamer distributions from experimental coupling constant data show that for ω' the major rotamer has the gg conformation whereas for ω the major rotamer has the gt conformation (Table 3).…”

Section: Disaccharidementioning

confidence: 99%

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Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations: Comparison to Crystal Structures

Dorst,

Widmalm

2024

Chemistry A European J

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Glycans are central to information content and regulation in biological systems. These carbohydrate molecules are active either as oligo‐ or polysaccharides, often as glycoconjugates. The conformational preferences and population distributions at the glycosidic torsion angles ϕ and ψ have been investigated for O‐methyl glycosides of three disaccharides where the substitution takes place at a secondary alcohol. Stereochemical differences at or adjacent to the glycosidic linkage were explored by solution state NMR spectroscopy using one‐dimensional 1H,1H‐NOESY NMR experiments to obtain transglycosidic proton‐proton distances and one‐ and two‐dimensional heteronuclear NMR experiments to obtain 3JCH transglycosidic coupling constants related to torsion angles ϕ and ψ. Computed effective proton‐proton distances from molecular dynamics (MD) simulations showed excellent agreement to experimentally derived distances for the α‐(1→3)‐linked disaccharides and revealed that for the bimodal distribution at the ψ torsion angle for the α‐(1→4)‐linked disaccharide experiment and simulation were at variance with each other, calling for further force field developments. The MD simulations disclosed a highly intricate inter‐residue hydrogen bonding pattern for the α‐(1→4)‐linked disaccharide, including a nonconventional hydrogen bond between H5' in the glucosyl residue and O3 in the galactosyl residue, supported by a large downfield 1H NMR chemical shift displacement compared to α‐d‐Glcp‐OMe.

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Section: Resultsmentioning

confidence: 99%

Section: Disaccharidementioning

confidence: 99%

Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations: Comparison to Crystal Structures

Dorst,

Widmalm

2024

Chemistry A European J

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“…1989 ). NMR experiments suitable for resonance assignments of carbohydrates ( Widmalm 2021 ) were recorded essentially as previously described ( Furevi et al. 2020 ); specific additional experimental conditions are given below.…”

Section: Methodsmentioning

confidence: 99%

Elucidation of the O-antigen structure of Escherichia coli O93 and characterization of its biosynthetic genes

et al. 2022

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The structure of the O-antigen from the international reference strain Escherichia coli O93:−:H16 has been determined. A nonrandom modal chain-length distribution was observed for the lipopolysaccharide, a pattern which is typical when long O-specific polysaccharides are expressed. By a combination of (i) bioinformatics information on the gene cluster related to O-antigen synthesis including putative function on glycosyl transferases, (ii) the magnitude of NMR coupling constants of anomeric protons and (iii) unassigned 2D 1H,13C-HSQC and 1H,1H-TOCSY NMR spectra it was possible to efficiently elucidate the structure of the carbohydrate polymer in an automated fashion using the computer program CASPER. The polysaccharide also carries O-acetyl groups and their locations were determined by 2D NMR experiments showing that ~½ of the population was 2,6-di-O-acetylated, ~¼ was 2-O-acetylated, whereas ~¼ did not carry O-acetyl group(s) in the 3-O-substituted mannosyl residue of the repeating unit. The structure of the tetrasaccharide repeating unit of the O-antigen is given by: →2)-β-d-Manp-(1 → 3)-β-d-Manp2Ac6Ac-(1 → 4)-β-d-GlcpA-(1 → 3)-α-d-GlcpNAc-(1→, which should also be the biological repeating unit and it shares structural elements with capsular polysaccharides from E. coli K84 and K50. The structure of the acidic O-specific polysaccharide from Cellulophaga baltica strain NN015840T differs to that of the O-antigen from E. coli O93 by lacking the O-acetyl group at O6 of the O-acetylated mannosyl residue.

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“…The 2D 1 H, 13 C-HSQC NMR spectrum revealed, inter alia, a characteristic cross-peak at δ H /δ C 5.06/98.27 originating from the anomeric atoms of the α-(1→2)-linked glucosyl group as a side-chain. A 31 P NMR spectrum of the WT SCC showed a resonance at 1.1 ppm, indicative of a phosphodiester linkage 36 . This was also the case for the ΔsccP and ΔsccQ SCCs, whereas 31 P NMR signals were absent in spectra from the ΔsccM, ΔsccN and ΔsccMΔsccQ SCCs.…”

Section: Grop Is Linked To Position 6 On α-Glc Located At Position 2 ...mentioning

confidence: 99%

“…SCCs isolated from WT and the various mutant strains were dissolved in D 2 O. NMR experiments were conducted in 5 mm outer diameter NMR tubes on Bruker NMR spectrometers operating at 1 H frequencies of 400 or 700 MHz at temperatures of 23 °C or 50 °C, respectively, using experiments suitable for resonance assignments of glycans 36,44 . 1 H NMR chemical shifts were referenced to internal sodium 3-trimethylsilyl-(2,2,3,3-2 H 4 )-propanoate (δ H 0.0), 13 C chemical shifts were referenced to external dioxane in D 2 O (δ C 67.4) and 31 P chemical shifts were referenced to external 2% H 3 PO 4 in D 2 O (δ P 0.0).…”

Section: Nmr Spectroscopymentioning

confidence: 99%

Structure and mechanism of biosynthesis ofStreptococcus mutanscell wall polysaccharide

Rush,

Zamakhaeva,

Murner

et al. 2024

Preprint

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Streptococcus mutans, the causative agent of human dental caries, expresses a cell wall attached Serotype c-specific Carbohydrate (SCC) that is critical for cell viability. SCC consists of a repeating →3)α-Rha(1→2)α-Rha(1→ polyrhamnose backbone, with glucose (Glc) side-chains and glycerol phosphate (GroP) decorations. This study reveals that SCC has one major and two minor Glc modifications. The major Glc modification, @[alpha]-Glc, attached to position 2 of 3-rhamnose, is installed by SccN and SccM glycosyltransferases and is the site of the GroP addition. The minor Glc modifications are @[beta]-Glc linked to position 4 of 3-rhamnose installed by SccP and SccQ glycosyltransferases, and @[alpha]-Glc attached to position 4 of 2- rhamnose installed by SccN working in tandem with an unknown enzyme. Both the major and the minor @[beta]-Glc modifications control bacterial morphology, but only the GroP and major Glc modifications are critical for biofilm formation.

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General NMR Spectroscopy of Carbohydrates and Conformational Analysis in Solution

Cited by 11 publications

References 316 publications

Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations: Comparison to Crystal Structures

Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations: Comparison to Crystal Structures

Elucidation of the O-antigen structure of Escherichia coli O93 and characterization of its biosynthetic genes

Structure and mechanism of biosynthesis ofStreptococcus mutanscell wall polysaccharide

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