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Protein Glycosylation01:25

Protein Glycosylation

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Glycosylation, the most common post-translational modification for proteins, serves diverse functions. Adding sugars to proteins makes the proteins more resistant to proteolytic digestion. Glycosylated proteins can act as markers and receptors to promote cell-cell adhesion. Additionally, they have many essential quality control functions in the cell, such as correct protein folding and facilitating transport of misfolded proteins to the cytosol, which can be degraded.
Glycosylation occurs in...
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Oligosaccharide Assembly01:24

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Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
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Glycocalyx and its Functions01:14

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The glycocalyx is a carbohydrate-rich, fuzzy-appearing layer on the outer surface of the cell membrane. It is highly hydrophilic, because of this it attracts large amounts of water to the cell's surface. This aids the cell's interaction with the watery environment and also helps it to obtain substances dissolved in the water. It is also important for cell identification, self/non-self determination, and embryonic development and is used in cell-to-cell attachments to form tissues.
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Glycosaminoglycans01:23

Glycosaminoglycans

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Glycosaminoglycans (GAGs), also known as mucopolysaccharides, are long and linear polymers comprising of specific repeating disaccharides - the amino sugar that can be N-acetylglucosamine or N-acetylgalactosamine, and a uronic acid that is usually glucuronic acid or iduronic acid.
GAGS are found in the extracellular matrix of vertebrates, invertebrates, and bacteria. Due to their polar nature they attract water, and serve as excellent lubricants or shock absorbers in an animal body.
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Glucose Absorption Into the Small Intestine01:26

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Complex carbohydrates consumed cannot be absorbed into the small intestine in their original form. First, they must be hydrolyzed to a monosaccharide form such as glucose or galactose. These monosaccharides are then transported across the intestinal membrane and into the blood via transcellular transport. The intestinal epithelial cells allow the movement of these monosaccharides with a defined 'entry' through membrane transporter proteins present on their apical membrane and...
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Glucose Transporters01:27

Glucose Transporters

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Glucose transporters facilitate the transport of glucose across the cell membrane. In addition to glucose, some glucose transporters can also aid the movement of other hexoses such as fructose, mannose, and galactose.
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Resources for screening the literature for glycan-related terms using PubAnnotation in GlyCosmos.

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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

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Introducing glycomics data into the Semantic Web.

Kiyoko F Aoki-Kinoshita, Jerven Bolleman, Matthew P Campbell

  • 1Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba Central-2, Umezono 1-1-1, Tsukuba 305-8568, Japan. h.narimatsu@aist.go.jp.

Journal of Biomedical Semantics
|November 28, 2013
PubMed
Summary
This summary is machine-generated.

Glycoscience researchers can now link diverse databases using Semantic Web technologies. This enables flexible querying across glycomics, proteomics, and other life science data, enhancing research capabilities.

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Area of Science:

  • Glycoscience
  • Bioinformatics
  • Computational Biology

Background:

  • Glycoscience studies complex carbohydrates (glycans) crucial for biological functions.
  • Advancements in glycomics technologies have led to numerous public databases.
  • Existing glycomics databases lack integration with other life science databases.

Purpose of the Study:

  • To establish a standardized method for representing glycan data for Semantic Web integration.
  • To demonstrate the utility of Semantic Web technologies in cross-database querying for glycoscience.

Main Methods:

  • Developed a minimal standard for glycan structure and annotation using Resource Description Framework (RDF).
  • Converted major glycomics database data into RDF format.
  • Utilized a Virtuoso triple store and SPARQL queries for data integration and retrieval.

Main Results:

  • Successfully linked UniCarbKB, GlycomeDB, and JCGGDB using SPARQL queries.
  • Demonstrated cross-domain querying by linking proteomics (UniProt) with glycomics (GlycoEpitope) and lectin data (GlycomeDB) with protein structures (PDB).

Conclusions:

  • Semantic Web technologies enable successful integration and flexible querying of disparate glycomics and other life science datasets.
  • This integration facilitates linking proteomics and glycomics data, opening new avenues for research.