Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Summary

This protocol illustrates how to explore, compare, and interpret human protein glycomes with online resources.

Abstract

The Glyco@Expasy initiative was launched as a collection of interdependent databases and tools spanning several aspects of knowledge in glycobiology. In particular, it aims at highlighting interactions between glycoproteins (such as cell surface receptors) and carbohydrate-binding proteins mediated by glycans. Here, major resources of the collection are introduced through two illustrative examples centered on the N-glycome of the human Prostate Specific Antigen (PSA) and the O-glycome of human serum proteins. Through different database queries and with the help of visualization tools, this article shows how to explore and compare content in a continuum to gather and correlate otherwise scattered pieces of information. Collected data are destined to feed more elaborate scenarios of glycan function. Glycoinformatics introduced here is, therefore, proposed as a means to either strengthen, shape, or refute assumptions on the specificity of a protein glycome in a given context.

Introduction

Glycans, proteins to which they are attached (glycoproteins) and proteins to which they bind (lectins or carbohydrate-binding proteins) are the main molecular actors at the cell surface¹. Despite this central role in cell-cell communication, large-scale studies, including glycomics, glycoproteomics, or glycan-interactomics data are still scarce compared to their counterpart in genomics and proteomics.

Until recently, methods for characterizing the branching structures of complex carbohydrates while still being conjugated to the carrier protein had not been developed. The biosynthesis of glycoproteins is a non-templat....

Protocol

NOTE: A device with an Internet connection (larger screen preferred) and an up-to-date Web browser such as Chrome or Firefox is required. Using Safari or Edge may not be as reliable.

1. From a protein N-glycome in GlyConnect to a lectin of UniLectin

1. Accessing resources from Glyco@Expasy
   NOTE: The procedure described here is to access GlyConnect but can be applied to accessing any resource recorded in the platform.
   1. Go to https://g.......

Discussion

GlyConnect Octopus as a tool for revealing unexpected correlations
GlyConnect Octopus was originally designed to query the database with a loose definition of glycans. Indeed, the literature often reports the main characteristics of glycans in a glycome such as being fucosylated or sialylated, being made of two or more antennae, etc. Furthermore, glycans whether N- or O-linked are classified in cores, as detailed in the reference manual Essentials of Glycobiology¹, that are .......

Materials

Name	Company	Catalog Number	Comments
internet connection	user's choice
recent version of web browser	user's choice