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Studies on the conformational flexibility of alpha-L-rhamnose-containing oligosaccharides using C-13-site-specific labeling, NMR spectroscopy and molecular simulations: implications for the three-dimensional structure of bacterial rhamnan polysaccharides
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Stockholm University, Faculty of Science, Department of Organic Chemistry.
2012 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 10, no 12, 2453-2463 p.Article in journal (Refereed) Published
Abstract [en]

Bacterial polysaccharides are comprised of a variety of monosaccharides, L-rhamnose (6-deoxy-L-mannose) being one of them. This sugar is often part of alpha-(1 -> 2)- and/or alpha-(1 -> 3)-linkages and we have therefore studied the disaccharide alpha-L-Rhap-(1 -> 2)-alpha-L-Rhap-OMe to obtain information on conformational preferences at this glycosidic linkage. The target disaccharide was synthesized with C-13 site-specific labeling at C1' and at C2', i.e., in the terminal group. 2D H-1, C-13-HSQC-HECADE and H-1, C-13-J-HMBC NMR experiments, 1D C-13 and H-1 NMR spectra together with total line-shape analysis were used to extract conformationally dependent hetero- and homonuclear spin-spin coupling constants. This resulted in the determination of (2)JC(2',H1'), (3)J(C1',C1), (3)J(C1',C3), (3)J(C2',C2), (2)J(C1',C2), (1)JC(1',C2'), and (1)J(C1',H1'). These data together with previously determined J(CH) and H-1, H-1 NOEs result in fourteen conformationally dependent NMR parameters that are available for analysis of glycosidic linkage flexibility and conformational preferences. A 100 ns molecular dynamics (MD) simulation of the disaccharide with explicit water molecules as solvent showed a major conformational state at phi(H) approximate to 40 degrees and psi(H) approximate to -35 degrees, consistent with experimental NMR data. In addition, MD simulations were carried out also for alpha-L-Rhap-(1 -> 3)-alpha-L-Rhap-OMe and a rhamnan hexasaccharide. The gathered information on the oligosaccharides was used to address conformational preferences for a larger structure, a 2- and 3-linked nonasaccharide, with implications for the 3D structure of rhamnan polysaccharides, which should be regarded as flexible polymers.

Place, publisher, year, edition, pages
2012. Vol. 10, no 12, 2453-2463 p.
National Category
Organic Chemistry
URN: urn:nbn:se:su:diva-76739DOI: 10.1039/c2ob06924eISI: 000301058100018OAI: diva2:527327
Swedish Research CouncilKnut and Alice Wallenberg Foundation
3Available from: 2012-05-19 Created: 2012-05-16 Last updated: 2012-07-13Bibliographically approved

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Widmalm, Göran
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