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Molecules 2012, 17(6), 6658-6671; doi:10.3390/molecules17066658
Article

Application of Paramagnetic NMR-Validated Molecular Dynamics Simulation to the Analysis of a Conformational Ensemble of a Branched Oligosaccharide

1,2,3,†
,
1,3,†
,
1,2,3
 and
1,2,3,4,5,*
Received: 11 April 2012 / Revised: 29 May 2012 / Accepted: 29 May 2012 / Published: 31 May 2012
(This article belongs to the Special Issue Advances in Carbohydrate Chemistry)
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Abstract

Oligosaccharides of biological importance often exhibit branched covalent structures and dynamic conformational multiplicities. Here we report the application of a method that we developed, which combined molecular dynamics (MD) simulations and lanthanide-assisted paramagnetic NMR spectroscopy, to evaluate the dynamic conformational ensemble of a branched oligosaccharide. A lanthanide-chelating tag was attached to the reducing end of the branched tetrasaccharide of GM2 ganglioside to observe pseudocontact shifts as the source of long distance information for validating the conformational ensemble derived from MD simulations. By inspecting the results, the conformational space of the GM2 tetrasaccharide was compared with that of its nonbranched derivative, the GM3 trisaccharide.
Keywords: oligosaccharide; molecular dynamics; NMR spectroscopy; lanthanide; pseudocontact shift; ganglioside oligosaccharide; molecular dynamics; NMR spectroscopy; lanthanide; pseudocontact shift; ganglioside
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Zhang, Y.; Yamamoto, S.; Yamaguchi, T.; Kato, K. Application of Paramagnetic NMR-Validated Molecular Dynamics Simulation to the Analysis of a Conformational Ensemble of a Branched Oligosaccharide. Molecules 2012, 17, 6658-6671.

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