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Related Concept Videos

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.
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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.
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Proteoglycans01:05

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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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Protocol for constructing glycan biosynthetic networks using glycowork.

Jon Lundstrøm1, Luc Thomès2, Daniel Bojar1

  • 1Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 41390 Gothenburg, Sweden.

STAR Protocols
|April 17, 2024
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Summary

This study introduces a computational protocol using the Python package glycowork to build biosynthetic networks from observed glycans. This method aids in analyzing complex carbohydrate structures and their biological pathways.

Keywords:
BioinformaticsEvolutionary biologySequence analysis

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Area of Science:

  • Carbohydrate Chemistry
  • Systems Biology
  • Bioinformatics

Background:

  • Glycans are essential biomolecules found in all life forms, characterized by complex, branched structures of monosaccharides.
  • Understanding glycan biosynthesis is crucial for various biological processes and disease mechanisms.
  • Computational tools are increasingly vital for analyzing complex biological data, including glycan structures.

Purpose of the Study:

  • To present a standardized in silico protocol for constructing glycan biosynthetic networks.
  • To enable the analysis of observed glycan data through network modeling.
  • To provide a reproducible computational framework for glycomics research.

Main Methods:

  • Development of a Python-based protocol utilizing the glycowork package.
  • Implementation of steps for data preparation, network construction, and feature analysis.
  • Demonstration with example data, adaptable for custom glycan datasets.

Main Results:

  • A functional protocol for generating glycan biosynthetic networks from observed glycan lists.
  • The protocol facilitates systematic analysis of glycan features within a network context.
  • Exportable data formats for further downstream analysis and visualization.

Conclusions:

  • The presented in silico protocol offers a robust method for glycan network construction and analysis.
  • This computational approach can advance the study of glycan biosynthesis and function.
  • The protocol is a valuable resource for researchers in glycomics and systems biology.