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Related Concept Videos

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

Oligosaccharide Assembly

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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.
Multiple sugar molecules that may or may...
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Proteoglycans01:05

Proteoglycans

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Glycans, a class of complex heterogeneous molecules, can be covalently attached to proteins to form glycosylated proteins that regulate various physiological and pathological processes. Glycosylated proteins or glycoproteins comprise N-linked and O-linked oligosaccharides. O-glycosylation is the most common type of protein glycosylation. Here, glycans attach to the oxygen atom of the hydroxyl groups of Serine or Threonine residues. O-linked glycosylation occurs later in protein processing,...
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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
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Glycoproteomic and glycomic databases.

Deniz Baycin Hizal1, Daniel Wolozny1, Joseph Colao1

  • 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.

Clinical Proteomics
|April 15, 2014
PubMed
Summary
This summary is machine-generated.

This study reviews 15 glycosylation databases, detailing their features for glycomic and glycoproteomic data analysis. The findings aim to guide researchers in selecting the best platforms for studying glycoproteins and glycans in various organisms.

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Area of Science:

  • Glycobiology
  • Biochemistry
  • Bioinformatics

Background:

  • Protein glycosylation is vital for cellular functions and implicated in diseases like cancer and neurological disorders.
  • Advancements in mass spectrometry (MS) have enabled high-throughput analysis of glycoproteins and glycans, leading to database development.
  • Existing glycosylation databases are not widely recognized, hindering accessibility for researchers.

Purpose of the Study:

  • To review and analyze 15 publicly available glycosylation databases.
  • To identify key features and analytical methods within these databases.
  • To guide researchers in selecting appropriate platforms for their specific analytical needs in glycobiology.

Main Methods:

  • Systematic review of 15 publicly available glycosylation databases.
  • Categorization of databases by data type (glycoproteomic, glycomic, glycan binding proteins).
  • Summary of features including enrichment techniques, analytical methods, and bioinformatics tools.

Main Results:

  • The review covers databases for glycoproteomic (7), glycomic (6), and glycan binding proteins (2) data.
  • Databases include information on experimentally identified glycans and glycopeptides from various organisms (human, rat, mouse, fly, zebrafish).
  • Unique features, analytical methods, and bioinformatics tools of each database are summarized, including newly established databases like Unipep, GlycoFly, and GlycoFish.

Conclusions:

  • This compendium serves as a valuable resource for the glycobiology community by consolidating information on analytical methods and databases.
  • It facilitates better characterization and categorization of glycoproteins and glycans for biomedical research.
  • The study represents a step towards integrating diverse glycosylation databases for enhanced research capabilities.