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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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Structure of PeptidoglycanPeptidoglycan is a vital structural component of the bacterial cell wall, providing mechanical strength and shape to the cell. It consists of repeating units of two sugars—N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)—linked by β-1,4 glycosidic bonds. These sugar chains are cross-linked by short peptide chains, forming a mesh-like polymer that surrounds the bacterial plasma membrane.Cytoplasmic Phase – Precursor SynthesisPeptidoglycan...
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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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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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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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GS-align for glycan structure alignment and similarity measurement.

Hui Sun Lee1, Sunhwan Jo1, Srayanta Mukherjee2

  • 1Department of Molecular Biosciences and Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA.

Bioinformatics (Oxford, England)
|April 11, 2015
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Summary

A new computational method, GS-align, enables size-independent comparison of glycan structures. This tool aligns and measures similarity between glycans, advancing structural biology research.

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Area of Science:

  • Carbohydrate Chemistry
  • Structural Biology
  • Computational Biology

Background:

  • Glycans are crucial for biological processes, with structural diversity enabling specific protein-glycan interactions.
  • Existing computational tools primarily focus on protein structures, lacking methods for glycan structure comparison.
  • There is a need for tools that can compare glycan structures independently of sequence order and size.

Purpose of the Study:

  • To develop a novel computational method for aligning and measuring the similarity of glycan structures.
  • To provide a tool that allows for size-independent comparison of complex carbohydrate structures.

Main Methods:

  • Developed GS-align, a novel method for glycan structure alignment and similarity measurement.
  • Employed iterative maximum clique search and fragment superposition to generate potential glycan alignments.
  • Utilized a size-independent structural similarity score (GS-score) to determine optimal alignment.

Main Results:

  • GS-align effectively aligns glycan structures and quantifies their similarity.
  • Benchmark tests using the Protein Data Bank (PDB) N-linked glycan library and N-glycoprotein sets validated GS-align's robustness.
  • Demonstrated utility in template-based glycan structure prediction and monosaccharide substitution matrix generation.

Conclusions:

  • GS-align is a robust computational tool for glycan structure alignment and similarity assessment.
  • The method facilitates a deeper understanding of glycan structure-function relationships.
  • GS-align has potential applications in glycan-related fields, including prediction and database development.