Related Experiment Video
Updated: Aug 13, 2025
11:21
Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
Published on: January 20, 2022
3.5K
Building, Visualizing, and Analyzing Glycosaminoglycan-Protein Interaction Networks
1ICBMS, UMR 5246 University Lyon 1, CNRS, Institute of Molecular and Supramolecular Chemistry and Biochemistry, Villeurbanne Cedex, France. sylvie.ricard-blum@univ-lyon1.fr.
Methods in Molecular Biology (Clifton, N.J.)
|January 20, 2023
Summary
This chapter details a protocol for analyzing glycosaminoglycan (GAG) interaction networks. It covers data collection, visualization, and computational analysis to understand GAG functions and identify therapeutic targets.
Area of Science:
- Biochemistry
- Bioinformatics
- Molecular Biology
Background:
- Glycosaminoglycans (GAGs) are crucial linear polyanionic polysaccharides.
- GAGs are primarily found on cell surfaces and in the extracellular matrix.
- Understanding GAG interactions is vital for deciphering their biological roles.
Purpose of the Study:
- To provide a comprehensive protocol for generating and analyzing GAG interaction networks.
- To enable the identification of overrepresented features within GAG networks.
- To facilitate the discovery of GAG-protein interactions for therapeutic applications.
Main Methods:
- Collection of GAG-mediated interaction data.
- Visualization of GAG interaction networks.
- Computational enrichment analyses of networks against a reference proteome.
Main Results:
- Identification of overrepresented protein domains, locations, molecular functions, and biological pathways.
- Interpretation of GAG interactomic datasets.
- Deciphering GAG specificities and functions.
Conclusions:
- The described protocol is essential for interpreting GAG interaction data.
- This approach aids in understanding GAG functions and specificities.
- The method can identify GAG-protein interactions for therapeutic targeting.
Related Concept Videos
02:26Protein Networks
4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K
02:04Protein-protein Interfaces
12.6K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.6K
01:05Proteoglycans
4.0K
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,...
4.0K
01:23Glycosaminoglycans
4.9K
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.
Hyaluronic...
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.
Hyaluronic...
4.9K
01:25Protein Glycosylation
7.1K
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...
Glycosylation occurs in...
7.1K
01:21Matrix Proteoglycans and Glycoproteins
4.0K
Proteoglycans are extensively glycosylated proteins, commonly found in the extracellular matrix, interwoven with collagen fibers. Hyaline cartilage, the most common type of cartilage in the body, consists of short and dispersed collagen fibers associated with large amounts of proteoglycans. These proteoglycans have long negative charges that attract cations, which in turn attract water molecules. This influx of ions and water molecules swells up the proteoglycan like a water-soaked gel that can...
4.0K