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Related Concept Videos

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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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.
Hyaluronic...
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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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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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Matrix Proteoglycans and Glycoproteins01:21

Matrix Proteoglycans and Glycoproteins

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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...
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Biosynthesis of Polysaccharides01:26

Biosynthesis of Polysaccharides

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Polysaccharides such as glycogen and starch are synthesized from nucleoside diphosphate sugars, primarily uridine diphosphate glucose (UDPG) and adenosine diphosphate glucose (ADPG). These activated glucose donors act as key intermediates in carbohydrate metabolism and biosynthesis. UDPG primarily involves glycogen synthesis in animals and many bacteria, while ADPG plays a fundamental role in starch synthesis in plants and certain bacteria.UDPG is formed when glucose-1-phosphate reacts with...
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Updated: Jul 23, 2025

Detection of Glycosaminoglycans by Polyacrylamide Gel Electrophoresis and Silver Staining
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A One-Bead-Per-Saccharide (1BPS) Model for Glycosaminoglycans.

Saber Shakibi1, Patrick R Onck1, Erik Van der Giessen1

  • 1Micromechanics of Materials, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.

Journal of Chemical Theory and Computation
|July 17, 2023
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Summary

We developed a simplified coarse-grained model for glycosaminoglycans (GAGs), specifically chondroitin sulfates and hyaluronic acid. This new model accurately simulates these large biopolymers for biological research.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Polymer Science

Background:

  • Glycosaminoglycans (GAGs) are vital polysaccharides in biological systems.
  • GAGs are crucial structural elements in cartilage and the brain's extracellular matrix.
  • Modeling large biopolymers like GAGs necessitates coarse-grained approaches.

Purpose of the Study:

  • To develop a more efficient coarse-grained model for GAGs.
  • To create a one-bead-per-saccharide model for chondroitin sulfates and hyaluronic acid.
  • To validate the new model against existing methods and experimental data.

Main Methods:

  • Developed a one-bead-per-saccharide coarse-grained model.
  • Employed iterative Boltzmann inversion (IBI) for model parameterization.
  • Incorporated a coupling potential to account for dihedral angle correlations.

Main Results:

  • The new model successfully represents chondroitin sulfates and hyaluronic acid.
  • Model predictions align with a previously established three-bead-per-saccharide model.
  • Simulated results for hyaluronic acid match experimental radius of gyration data.

Conclusions:

  • The one-bead-per-saccharide model offers an efficient coarse-graining strategy for GAGs.
  • This simplified model is suitable for large-scale simulations of GAGs.
  • The validated model can aid in understanding GAGs' biological roles.