title: Databases of Conformations and NMR Structures of Glycan Determinants.
abstract: The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr.
authors.affiliation: Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France.
authors.forename: Anita
authors.initials: A
authors.lastname: Sarkar
authors.affiliation: Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Drouillard
authors.affiliation: Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Rivet
authors.affiliation: Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France Département de Pharmacochimie Moléculaire, UMR5063 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France spsergeperez@gmail.com.
authors.forename: Serge
authors.initials: S
authors.lastname: Perez
mesh_terms: D002236:Carbohydrate Conformation; D019992:Databases as Topic; D006028:Glycosphingolipids / Q000737:chemistry*; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D011134:Polysaccharides / Q000737:chemistry*
chemical_list: D006028:Glycosphingolipids; D011134:Polysaccharides
keywords: NMR spectroscopy; disaccharides; molecular mechanics; oligosaccharides