Jump to main content
Jump to site search

Issue 28, 2016
Previous Article Next Article

Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations

Author affiliations

Abstract

The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence.

Graphical abstract: Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations

Back to tab navigation

Supplementary files

Publication details

The article was received on 03 May 2016, accepted on 16 Jun 2016 and first published on 16 Jun 2016


Article type: Paper
DOI: 10.1039/C6CP02970A
Citation: Phys. Chem. Chem. Phys., 2016,18, 18776-18794
  • Open access: Creative Commons BY-NC license
  •   Request permissions

    Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations

    M. Yang, T. Angles d’Ortoli, E. Säwén, M. Jana, G. Widmalm and A. D. MacKerell, Phys. Chem. Chem. Phys., 2016, 18, 18776
    DOI: 10.1039/C6CP02970A

    This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Material from this article can be used in other publications provided that the correct acknowledgement is given with the reproduced material and it is not used for commercial purposes.

    Reproduced material should be attributed as follows:

    • For reproduction of material from NJC:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the Centre National de la Recherche Scientifique (CNRS) and the RSC.
    • For reproduction of material from PCCP:
      [Original citation] - Published by the PCCP Owner Societies.
    • For reproduction of material from PPS:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the European Society for Photobiology, the European Photochemistry Association, and RSC.
    • For reproduction of material from all other RSC journals:
      [Original citation] - Published by The Royal Society of Chemistry.

    Information about reproducing material from RSC articles with different licences is available on our Permission Requests page.

Search articles by author

Spotlight

Advertisements