Dataset Information

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans.

ABSTRACT: Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG and GAG-protein complexes determined by X-ray single-crystal diffraction methods, X-ray fiber diffractometry, solution NMR spectroscopy, and scattering data often associated with molecular modeling. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to the description of the bound glycan ligands using simple graphical representation and numerical format for cross-referencing to other databases in glycoscience and functional data. GAG-DB provides detailed information on GAGs, their bound protein ligands, and features their interactions using several open access applications. Binding covers interactions between monosaccharides and protein monosaccharide units and the evaluation of quaternary structure. GAG-DB is freely available.

SUBMITTER: Perez S

PROVIDER: S-EPMC7763844 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans.

Pérez Serge S Bonnardel François F Lisacek Frédérique F Imberty Anne A Ricard Blum Sylvie S Makshakova Olga O

Biomolecules 20201211 12

Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG and GAG-protein complexes determined by X-ray single-crystal diffraction methods, X-ray fiber diffractometry, solution NMR spectroscopy, and scattering ...[more]

PMID: 33322545

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Project description:Histological analysis is considered to be the gold standard method of evaluating osseointegration around a bone-implant. However, this method requires invasive specimen preparation and is capable of representing only one plane. By comparison, micro-computed tomography (μCT) is a fast and convenient method that offers three-dimensional information but is hampered by problems related to resolution and artifacts, making it a supplementary method for osseointegration analysis. To verify the reliability of μCT for osseointegration evaluation, this animal model study compared bone-to-implant contact (BIC) ratios obtained by the gold standard histomorphometric method with those obtained by the μCT method, using a rabbit tibia implant model. A sandblasted, large-grit, acid-etched (SLA) implant and a machined surface implant were inserted into each tibia of two rabbits (giving eight implants in total). Bone-implant specimens were analyzed using μCT with a spiral scan technique (SkyScan 1275) and histological sections were prepared thereafter. Three-dimensional (3D) reconstructed μCT data and four two-dimensional (2D) μCT sections, including one section corresponding to the histologic section and three additional sections rotated 45°, 90°, and 135°, were used to calculate the BIC ratio. The Pearson's test was used for correlation analysis at a significance level of 0.05. The histomorphometric BIC and the 2D-μCT BIC showed strong correlation (r = 0.762, P = 0.046), whereas the histomorphometric BIC and 3D-μCT BIC did not (r = -0.375, P = 0.385). However, the mean BIC value of three or four 2D-μCT sections showed a strong correlation with the 3D-μCT BIC (three sections: r = 0.781, P = 0.038; four sections: r = 0.804, P = 0.029). The results of this animal model study indicate that μCT can be used to complement the histomorphometric method in bone-implant interface analyses. With the limitations of this study, 3D-μCT analysis may even have a superior aspect in that it eliminates random variables that arise as a consequence of the selected cutting direction.

Dataset Information

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans.

Publications

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans.

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