SOACS index: an easy NMR-based query for glycan retrieval

Maës, Emmanuel; Bonachéra, Fanny; Strecker, Gérard; Guérardel, Yann

doi:10.1016/j.carres.2008.11.001

Cited by 24 publications

(14 citation statements)

References 30 publications

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“…Accordingly, Neu5Ac(α2,3) and Neu5Ac(α2,6) were identified owing to their different H3 ax /H3 eq 1 H parameters at δ 1.801/2.774 and 1.692/2.728, respectively (Table ). Finally, the calculated SOACS/SOACS-ol indexes of OG1 at 6.165/10.544 ppm and OG2 at 8.034/12.413 ppm perfectly matched with the oligosaccharides 9 and 85 reported by Kamerling and Vliegenthart. , Altogether, NMR and MS analyses established that the two major O -glycans OG1 and OG2 synthesized by ZFL cells are Gal(β1,3)[Neu5Ac(α2,6)]GalNAc-ol and Neu5Ac(α2,3)Gal(β1,3)[Neu5Ac(α2,6)]GalNAc-ol.…”

Section: Resultsmentioning

confidence: 99%

Mapping the Expressed Glycome and Glycosyltransferases of Zebrafish Liver Cells as a Relevant Model System for Glycosylation Studies

et al. 2012

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The emergence of zebrafish as a model organism for human diseases was accompanied by the development of cellular model systems that extended the possibilities for in vitro manipulation and in vivo studies after cell implantation. The exploitation of zebrafish cell systems is, however, still hampered by the lack of genomic and biochemical data. Here, we lay a path toward the efficient use of ZFL, a zebrafish liver-derived cell system, as a platform for studying glycosylation. To achieve this, we established the glycomic profile of ZFL by a combination of mass spectrometry and NMR. We demonstrated that glycoproteins were substituted by highly sialylated multiantennary N-glycans, some of them comprising the unusual zebrafish epitope Galβ1-4[Neu5Ac(α2,3)]Galβ1-4[Fuc(α1,3)]GlcNAc, and core 1 multisialylated O-glycans. Similarly, these analyses established that glycolipids were dominated by sialylated gangliosides. In parallel, analyzing the expression patterns of all putative sialyl- and fucosyltransferases, we directly correlated the identified structures to the set of enzymes involved in ZFL glycome. Finally, we demonstrated that this cell system was amenable to metabolic labeling using functionalized monosaccharides that permit in vivo imaging of glycosylation processes. Altogether, glycomics, genomics, and functional studies established ZFL as a relevant cellular model for the study of glycosylation.

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Section: Resultsmentioning

confidence: 99%

Mapping the Expressed Glycome and Glycosyltransferases of Zebrafish Liver Cells as a Relevant Model System for Glycosylation Studies

et al. 2012

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“…1 H NMR spectroscopy. 11 This may also be the modification of choice when anomeric mixtures of the reducing end of an oligosaccharide are to be avoided. 20 Two of the monosaccharides were methyl glycosides (5 and 6) and three (7 -9) were carrying substituents.…”

Section: Compound Selectionmentioning

confidence: 99%

“…9 The complexity of these problems has led to the development of computerized approaches. [10][11][12][13] The CASPER program and its database have been continuously improved since the introduction in the late 1980s. 8,[13][14][15][16] We here report improvements of 1 H and 13 C NMR chemical shift predictions made by CASPER based on chemical shift assignments of 30 mono-, di-, and trisaccharides and present the results for NMR chemical shift predictions of three O-antigen polysaccharides.…”

Section: Introductionmentioning

confidence: 99%

Complete 1H and 13C NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligosaccharides using the computer program CASPER

Rönnols

Pendrill

Fontana

et al. 2013

Carbohydrate Research

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(1)H and (13)C NMR chemical shift data are used by the computer program CASPER to predict chemical shifts of oligo- and polysaccharides. Three types of data are used, namely, those from monosaccharides, disaccharides, and trisaccharides. To improve the accuracy of these predictions we have assigned the (1)H and (13)C NMR chemical shifts of eleven monosaccharides, eleven disaccharides, twenty trisaccharides, and one tetrasaccharide; in total 43 compounds. Five of the oligosaccharides gave two distinct sets of NMR resonances due to the α- and β-anomeric forms resulting in 48 (1)H and (13)C NMR chemical shift data sets. In addition, the pyranose ring forms of Neu5Ac were assigned at two temperatures, due to chemical shift displacements as a function of temperature. The (1)H NMR chemical shifts were refined using total line-shape analysis with the PERCH NMR software. (1)H and (13)C NMR chemical shift predictions were subsequently carried out by the CASPER program (http://www.casper.organ.su.se/casper/) for three branched oligosaccharides having different functional groups at their reducing ends, namely, a mannose-containing pentasaccharide, and two fucose-containing heptasaccharides having N-acetyllactosamine residues in the backbone of their structures. Good to excellent agreement was observed between predicted and experimental (1)H and (13)C NMR chemical shifts showing the utility of the method for structural determination or confirmation of synthesized oligosaccharides.

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“…In addition most of these databases store only experiments generated by the research group or consortium providing the database. Example databases storing experimental data are EUROCarbDB (MS, NMR, HPLC), GlycoBase in Dublin, Ireland [34] (HPLC), GlycoBase in Lille, France [35] (NMR) and the CFG database (MS profile, Glycan Array). As mass spectrometry (MS) has now become the most common method for solving glycan structures and identifying glycopeptides, there is now an increasing range of software tools that are available for analysing MS data produced in glycomics [36].…”

Section: Methodsmentioning

confidence: 99%

Toolboxes for a standardised and systematic study of glycans

et al. 2014

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BackgroundRecent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists.MethodsFollowing our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software.ResultsVarious solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented.ConclusionsDespite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.

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SOACS index: an easy NMR-based query for glycan retrieval

Cited by 24 publications

References 30 publications

Mapping the Expressed Glycome and Glycosyltransferases of Zebrafish Liver Cells as a Relevant Model System for Glycosylation Studies

Mapping the Expressed Glycome and Glycosyltransferases of Zebrafish Liver Cells as a Relevant Model System for Glycosylation Studies

Complete 1H and 13C NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligosaccharides using the computer program CASPER

Toolboxes for a standardised and systematic study of glycans

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