Glycan determinants, also called glycoepitopes, have been collected by different authors and recorded in different ways in a few unrelated databases or simply printed in tables of articles. In all cases, glycoepitopes are listed as independent entities despite their compositional similarity and the common set of enzymes required to synthesise them.
We designed Glydin’ (Glycan Dynamics) to (1) merge the distinct sources describing glycoepitopes in different formats and (2) map the similarity between these entities in an interactive network. Glydin’ is as a result, a tool to visualise and explore the relationships between glycoepitopes based on either their shared monosaccharide composition or the glycosyltransferase needed to get one from the other.
Glydin’ displays glycoepitopes as nodes in a network. Two networks are mapped to emphasise two different types of shared properties:
In the “Substructure Based Map”, two nodes are connected if one glycoepitope is a substructure of the other.
In the “Enzyme Base Map”, two nodes are connected as the result of a glycosyltransferase adding a monosaccharide to the other.
In the “Substructure Based Map”, the network is one large connected component whereas in the “Enzyme Base Map” it is a collection of connected components each stemming from a single monosaccharide.
As a result, the “Substructure Based Map” shows connections between a trimer and a pentamer if the former is part of the latter while the “Enzyme Base Map” only connects structures differing of one or possibly two monosaccharides when two identical monosaccharides are added with the same linkage. This the case for example, of core 4 (GlcNAc(b1-3)[GlcNAc(b1-6)]GalNAc(a-) that becomes 3,6-(LacNAc)2Tn (Gal(b1-4)GlcNAc(b1-3)[Gal(b1-4)GlcNAc(b1-6)]GalNAc(a-) through the action of β4Gal-T4 that adds 2 galactoses with a beta4 linkage on each branch of the core 4 structure.
Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes. Alocci D. et al, Glycobiology. 2018. (PubMed Id: 29518231)