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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.
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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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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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UniCarbKB: building a knowledge platform for glycoproteomics.

Matthew P Campbell1, Robyn Peterson, Julien Mariethoz

  • 1Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland, Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva, Switzerland, Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, Japan and Section of Biology, Faculty of Sciences, University of Geneva, Switzerland.

Nucleic Acids Research
|November 16, 2013
PubMed
Summary
This summary is machine-generated.

The UniCarb KnowledgeBase (UniCarbKB) is a new, expanded glycan structure database for glycoproteins. It integrates diverse data to advance glycoscience research and improve access to glycomics and glycoproteomics information.

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Area of Science:

  • Glycoscience
  • Bioinformatics
  • Structural Biology

Background:

  • Glycosylation is crucial for protein function, but data on glycan structures and their attachment sites is fragmented.
  • Existing databases like GlycoSuiteDB provide valuable information but require updates and integration.
  • Understanding glycosylation pathways and networks is essential for advancing glycomics and glycoproteomics.

Purpose of the Study:

  • To introduce UniCarb KnowledgeBase (UniCarbKB), an enhanced public database for glycan structures of glycoproteins.
  • To integrate structural, experimental, and functional glycoscience data for a comprehensive resource.
  • To improve database searching and accessibility for researchers in glycomics and glycoproteomics.

Main Methods:

  • Consolidation and curation of glycan structure and glycoprotein data.
  • Integration of information from GlycoSuiteDB and EUROCarbDB standards.
  • Development of a refactored database with new curated collections and user interfaces.
  • Annotation of protein glycosylation sites with experimentally confirmed glycan structures.

Main Results:

  • UniCarbKB provides access to 3740 glycan structure entries and 400 glycoproteins.
  • 598 protein glycosylation sites have been annotated with confirmed glycan structures.
  • The database includes 35 new glycoproteins, 502 new structures, and 60 new publications compared to GlycoSuiteDB.
  • Enhanced user interfaces improve database searching capabilities.

Conclusions:

  • UniCarbKB represents a significant advancement in glycoscience data resources.
  • The integrated and curated data supports research in glycomics and glycoproteomics.
  • Improved accessibility and searchability of UniCarbKB will facilitate further understanding of glycosylation.