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

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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.

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          Most cited references 19

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          Lectins: carbohydrate-specific reagents and biological recognition molecules.

           Nathan Sharon (2007)
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            Residual dipolar couplings of freely rotating groups in small molecules. Stereochemical assignment and side-chain conformation of 8-phenylmenthol.

            A procedure for the direct use of (1)D(CH) residual dipolar couplings (RDCs) from freely rotating groups in the structural analysis of small molecules was implemented. (1)D(CH) RDCs were used to determine both the preferred conformation and the stereochemical assignment of the diastereotopic geminal methyls of 8-phenylmenthol. Furthermore, a method was also set up to fit RDC data to a set of conformations in solution on the assumption that they all have the same alignment tensor.
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              High-resolution proton NMR studies of gangliosides. 1. Use of homonuclear two-dimensional spin-echo J-correlated spectroscopy for determination of residue composition and anomeric configurations.

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                Author and article information

                Journal
                Molecules
                Molecules
                molecules
                Molecules
                MDPI
                1420-3049
                31 May 2012
                June 2012
                : 17
                : 6
                : 6658-6671
                Affiliations
                [1 ]Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Email: yzhang@ 123456ims.ac.jp (Y.Z.); sayokoy@ 123456ims.ac.jp (S.Y.); takumi@ 123456ims.ac.jp (T.Y.)
                [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
                Author notes
                [†]

                These authors contributed equally to this work.

                [* ] Author to whom correspondence should be addressed; Email: kkatonmr@ 123456ims.ac.jp ; Tel.: +81-564-59-5225; Fax: +81-564-59-5224.
                Article
                molecules-17-06658
                10.3390/molecules17066658
                6268797
                22728360
                © 2012 by the authors; licensee MDPI, Basel, Switzerland.

                This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/).

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