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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.
Multiple sugar molecules that may or may...
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Glycocalyx and its Functions01:14

Glycocalyx and its Functions

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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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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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Related Experiment Video

Updated: Feb 22, 2026

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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GLYDE-II: The GLYcan data exchange format.

Rene Ranzinger1, Krys J Kochut2, John A Miller2

  • 1Complex Carbohydrate Research Center, University of Georgia, USA.

Perspectives in Science
|September 29, 2017
PubMed
Summary

The GLYcan Data Exchange (GLYDE) standard provides a universal XML format for representing complex carbohydrate structures. This enables unambiguous data sharing and computational analysis across diverse glycoinformatics tools.

Keywords:
BioinformaticsGlycanRepresentationStructureXML

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Area of Science:

  • Glycoinformatics
  • Computational Chemistry
  • Structural Biology

Background:

  • Standardized representation of carbohydrate structures is crucial for data sharing and analysis in glycoinformatics.
  • Existing methods often lack the flexibility to represent novel or complex glycans.
  • The need for a robust, unambiguous format for monosaccharides, glycans, and glycoconjugates is evident.

Purpose of the Study:

  • To describe the GLYcan Data Exchange (GLYDE) standard for representing chemical structures of carbohydrates.
  • To detail the philosophical and technical foundations of GLYDE-II.
  • To present recent implementations and enhanced features of the GLYDE-II standard.

Main Methods:

  • Development of an XML-formatted connection table formalism for structural representation.
  • Implementation of a partonomy model based on human language for consistent representations.
  • Establishment of a namespace for specifying monosaccharides and rules for structural consistency.

Main Results:

  • GLYDE enables unambiguous representation and sharing of diverse carbohydrate structures, including novel ones.
  • The partonomy model and namespace facilitate software reuse at various levels of granularity.
  • GLYDE-II has been successfully integrated into several glycoinformatics tools.

Conclusions:

  • The GLYDE standard offers a powerful and flexible solution for carbohydrate structure representation.
  • GLYDE-II enhances interoperability and data processing capabilities in glycoinformatics.
  • The described features and underpinnings support the broader adoption and application of GLYDE in the field.