GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research

Background: Anti-polysialic acid monoclonal antibody mAb735 preferentially binds longer polysialic acid chains. Results: Crystal structure of the single chain Fv fragment was determined in complex with octasialic acid. Conclusion: Two linked units of three consecutive sialic acid residues interact with two antibody fragments in extended conformation. Significance: An immunological strategy for preference of longer polysialic acid polymers is revealed conflicting with the conformational epitope hypothesis.

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“…The structural superposition was performed with SUPERPOSE (32). Dihedral angles of glycosidic linkages were calculated with CARP (33).…”

Section: Methodsmentioning

confidence: 99%

“…Dihedral angles of ␣2-8 glycosidic linkages between two sialic acid residues. The data were extracted from the PDB, and the dihedral angles and were plotted using glycoscience.de on-site tool (33).…”

Section: Dihedralmentioning

confidence: 99%

Crystal Structure of Anti-polysialic Acid Antibody Single Chain Fv Fragment Complexed with Octasialic Acid

Nagae

Ikeda

Hane

et al. 2013

Journal of Biological Chemistry

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“…Structural data can be imported into the drawing panel from various encoding formats in use by existing databases initiatives, such as: LINUCS 26 used by the Glycosciences.de 27 portal, the format devised by GlycoMinds Ltd 28 used by the Consortium for Functional Glycomics 29 and Glyco-CT 30 developed by the EUROCarbDB initiative 17 . In this way structures that are already defined and stored in a database can be easily tested against the acquired spectra.…”

Section: Input and Display Of Structuresmentioning

confidence: 99%

GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans

et al. 2008

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Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-throughput glycomics projects, and robust solutions to this problem are of critical importance. However, all the approaches currently available have inherent restrictions to the type of glycans they can identify and none of them has proved to be a definitive tool for glycomics.GlycoWorkbench is a software tool developed by the EUROCarbDB initiative to assist the manual interpretation of MS data. The main task of GlycoWorkbench is to evaluate a set of structures proposed by the user by matching the corresponding theoretical list of fragment masses against the list of peaks derived from the spectrum. The tool provides an easy to use graphical interface, a comprehensive and increasing set of structural constituents, an exhaustive collection of fragmentation types, and a broad list of annotation options. The aim of GlycoWorkbench is to offer complete support for the routine interpretation of MS data. The software is available for download from: http://www.eurocarbdb.org/applications/ms-tools.

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“…Based on the results from Western Blot, we deduced the molecular weight of a carbohydrate chain which is about 3,000 Da, and hypothesized the stucture of carbohydrate chain (LinucsID 3961) from glycosciences.de (http://glycosciences.de, a web databases and bioinformatics tools for glycobiology and glycomics). 31 The full model of b2 subunit was then constructed by connecting the predicted extracellular b2 loop, 2 transmembrane helices, N-terminal 32 (PDB ID: 1JO6) and the carbohydrate chains. The full models of BK channels were built as previous.…”

Section: Patch Clamp Recordingmentioning

confidence: 99%

The glycosylation of the extracellular loop ofβ2 subunits diversifies functional phenotypes of BK Channels

et al. 2016

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Large-conductance Ca 2C -and voltage-activated potassium (MaxiK or BK) channels are composed of a pore-forming a subunit (Slo) and 4 types of auxiliary b subunits or just a pore-forming a subunit. Although multiple N-linked glycosylation sites in the extracellular loop of b subunits have been identified, very little is known about how glycosylation influences the structure and function of BK channels. Using a combination of site-directed mutagenesis, western blot and patch-clamp recordings, we demonstrated that 3 sites in the extracellular loop of b2 subunit are N-glycosylated (N-X-T/S at N88, N96 and N119). Glycosylation of these sites strongly and differentially regulate gating kinetics, outward rectification, toxin sensitivity and physical association between the a and b2 subunits. We constructed a model and used molecular dynamics (MD) to simulate how the glycosylation facilitates the association of a/b2 subunits and modulates the dimension of the extracellular cavum above the pore of the channel, ultimately to modify biophysical and pharmacological properties of BK channels. Our results suggest that N-glycosylation of b2 subunits plays crucial roles in imparting functional heterogeneity of BK channels, and is potentially involved in the pathological phenotypes of carbohydrate metabolic diseases.

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GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research

Cited by 240 publications

References 31 publications

Crystal Structure of Anti-polysialic Acid Antibody Single Chain Fv Fragment Complexed with Octasialic Acid

Crystal Structure of Anti-polysialic Acid Antibody Single Chain Fv Fragment Complexed with Octasialic Acid

GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans

The glycosylation of the extracellular loop ofβ2 subunits diversifies functional phenotypes of BK Channels

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