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Related Concept Videos

Protein Glycosylation01:25

Protein Glycosylation

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...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Oligosaccharide Assembly01:24

Oligosaccharide Assembly

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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Proteoglycans01:05

Proteoglycans

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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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
11:21

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Published on: January 20, 2022

Data mining the PDB for glyco-related data.

Thomas Lütteke1, Claus W von der Lieth

  • 1German Cancer Research Center (DKFZ), Central Spectroscopic Department (B090), Heidelberg, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|March 12, 2009
PubMed
Summary
This summary is machine-generated.

Researchers can now easily find and analyze carbohydrate structures in the Protein Data Bank (PDB) using the GLYCOSCIENCES.de portal. This tool simplifies the identification and consistency checks of protein-carbohydrate complexes for glycobiologists.

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A Quantitative Glycomics and Proteomics Combined Purification Strategy
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A Quantitative Glycomics and Proteomics Combined Purification Strategy

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A Quantitative Glycomics and Proteomics Combined Purification Strategy
11:38

A Quantitative Glycomics and Proteomics Combined Purification Strategy

Published on: March 8, 2016

Area of Science:

  • Structural biology
  • Glycobiology
  • Bioinformatics

Background:

  • The Protein Data Bank (PDB) contains valuable 3D structural data for glycoproteins and protein-carbohydrate complexes.
  • Identifying and analyzing carbohydrate components within these PDB structures is challenging with existing PDB tools.

Purpose of the Study:

  • To introduce the GLYCOSCIENCES.de internet portal as a resource for glycobiologists.
  • To describe methods for locating specific carbohydrate structures within PDB entries.
  • To explain how to analyze carbohydrate residue consistency and surrounding amino acid properties in 3D structures.

Main Methods:

  • Utilizing the GLYCOSCIENCES.de portal to search for PDB entries containing specific carbohydrate structures.
  • Developing methods to identify and verify carbohydrate residues within 3D structural files.
  • Implementing statistical analyses for torsion angles and amino acid distribution near glycosylation sites and non-covalently bound carbohydrates.

Main Results:

  • The GLYCOSCIENCES.de portal provides effective tools for finding and analyzing carbohydrate-related structures in the PDB.
  • Methods for locating and checking the consistency of carbohydrate residues are detailed.
  • Statistical insights into the local environment of glycosylation sites and non-covalent carbohydrate interactions are obtainable.

Conclusions:

  • The GLYCOSCIENCES.de portal significantly enhances the ability of glycobiologists to explore and analyze carbohydrate structures in the PDB.
  • This resource facilitates a deeper understanding of protein-carbohydrate interactions through structural and statistical analysis.