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,†email, 1,3,†email, 1,2,3email and 1,2,3,4,5,* email
1 Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan 2 Department of Functional Molecular Science, the Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan 3 Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan 4 The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan 5 GLYENCE Co., Ltd., 2-22-8 Chikusa, Chikusa-ku, Nagoya 464-0858, Japan These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 11 April 2012; in revised form: 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

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MDPI and ACS Style

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.

AMA Style

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(6):6658-6671.

Chicago/Turabian Style

Zhang, Ying; Yamamoto, Sayoko; Yamaguchi, Takumi; Kato, Koichi. 2012. "Application of Paramagnetic NMR-Validated Molecular Dynamics Simulation to the Analysis of a Conformational Ensemble of a Branched Oligosaccharide." Molecules 17, no. 6: 6658-6671.

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