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Protein Glycosylation

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...

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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Published on: January 20, 2022

Databases and Associated Tools for Glycomics and Glycoproteomics.

Frederique Lisacek¹, Julien Mariethoz¹, Davide Alocci¹

¹Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.

Methods in Molecular Biology (Clifton, N.J.)

|October 16, 2016

Summary

This chapter explores essential biodatabases for glycobiology research, covering glycan structures, experimental data, and associations with disease and proteins. It provides practical search protocols for glycomics and glycoproteomics data analysis.

Keywords:

Databases Glycobioinformatics HPLC Mass spectrometry NMR Oligosaccharide Omics

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A Quantitative Glycomics and Proteomics Combined Purification Strategy

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A Quantitative Glycomics and Proteomics Combined Purification Strategy

A Quantitative Glycomics and Proteomics Combined Purification Strategy

Published on: March 8, 2016

Area of Science:

Glycobiology
Bioinformatics
Computational Biology

Background:

Glycobiology research relies heavily on access to comprehensive biodatabases.
Existing databases cover various aspects of glycans and glycorelated proteins, but integration and accessibility can be challenging.

Purpose of the Study:

To present a comprehensive overview of available biodatabases for glycobiology research.
To detail specific search protocols for utilizing these databases in glycobioinformatics.
To guide researchers in converting experimental data into structural and functional glycan information.

Main Methods:

Database Curation: Compiling information on oligosaccharide sequence, experimental, and 3D structure databases.
Protocol Development: Providing specific search strategies for tools like GlycoBase, GlycoWorkbench, UniCarb-DB, GlycoDigest, CASPER, UniCarbKB, and SugarBind.
Data Integration: Demonstrating methods to link glycan structural information with protein associations and disease relevance.

Main Results:

A curated list of diverse glycobioinformatics databases is presented.
Practical protocols are provided for analyzing glycoanalytical data from U/HPLC, MS, and NMR.
Methods are outlined for querying databases to understand glycan-protein interactions and pathogen associations.

Conclusions:

Effective utilization of specialized biodatabases is crucial for advancing glycobiology.
The chapter equips researchers with tools and protocols for enhanced glycomics and glycoproteomics data analysis.
Improved access and searchability of glycan information facilitate deeper insights into biological roles and disease mechanisms.