SugarBindDB, a resource of glycan-mediated host-pathogen interactions.

Julien Mariethoz,Khaled Khatib,Frederique Lisacek,Nicolle H Packer,Niclas G Karlsson,Davide Alocci,Davide Alocci,Matthew P Campbell,Elaine H Mullen

doi:10.1093/nar/gkv1247

Abstract

The SugarBind Database (SugarBindDB) covers knowledge of glycan binding of human pathogen lectins and adhesins. It is a curated database; each glycan–protein binding pair is associated with at least one published reference. The core data element of SugarBindDB is a set of three inseparable components: the pathogenic agent, a lectin/adhesin and a glycan ligand. Each entity (agent, lectin or ligand) is described by a range of properties that are summarized in an entity-dedicated page. Several search, navigation and visualisation tools are implemented to investigate the functional role of glycans in pathogen binding. The database is cross-linked to protein and glycan-relaled resources such as UniProtKB and UniCarbKB. It is tightly bound to the latter via a substructure search tool that maps each ligand to full structures where it occurs. Thus, a glycan–lectin binding pair of SugarBindDB can lead to the identification of a glycan-mediated protein–protein interaction, that is, a lectin–glycoprotein interaction, via substructure search and the knowledge of site-specific glycosylation stored in UniCarbKB. SugarBindDB is accessible at: http://sugarbind.expasy.org.

Highlights

Glycosylation is the addition of glycan/carbohydrate/oligos accharide/sugar molecules to proteins and/or lipids
Glycans modify proteins or lipids overlaying the surface of cells, but they offer numerous binding opportunities influencing cell–cell interactions. Information on these binding events is crucial to feed our understanding of intercellular communication
Even in cases such as host–pathogen interactions, which have been extensively studied over decades, information that is recorded across diverse resources (e.g. 2,3), does not cover details of the recognition of host glycans by the pathogen proteins, known as lectins

Summary

Introduction

Glycosylation is the addition of glycan/carbohydrate/oligos accharide/sugar molecules to proteins and/or lipids. Even in cases such as host–pathogen interactions, which have been extensively studied over decades, information that is recorded across diverse resources (e.g. 2,3), does not cover details of the recognition of host glycans by the pathogen proteins, known as lectins (or adhesins if the binding partner is unknown). The core data element of SugarBindDB is a set of three inseparable components: the pathogenic agent, a lectin adhesin and a glycan ligand.

Results

Conclusion