Glycoblocks: a schematic three-dimensional representation for glycans and their interactions

Stuart Mcnicholas,Jon Agirre

doi:10.1107/s2059798316013553

Stuart Mcnicholas, Jon Agirre

Open Access

https://doi.org/10.1107/s2059798316013553

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Abstract

The close-range interactions provided by covalently linked glycans are essential for the correct folding of glycoproteins and also play a pivotal role in recognition processes. Being able to visualise protein-glycan and glycan-glycan contacts in a clear way is thus of great importance for the understanding of these biological processes. In structural terms, glycosylation sugars glue the protein together via hydrogen bonds, whereas non-covalently bound glycans frequently harness additional stacking interactions. Finding an unobscured molecular view of these multipartite scenarios is usually far from trivial; in addition to the need to show the interacting protein residues, glycans may contain many branched sugars, each composed of more than ten non-H atoms and offering more than three potential bonding partners. With structural glycoscience finally gaining popularity and steadily increasing the deposition rate of three-dimensional structures of glycoproteins, the need for a clear way of depicting these interactions is more pressing than ever. Here a schematic representation, named Glycoblocks, is introduced which combines a simplified bonding-network depiction (covering hydrogen bonds and stacking interactions) with the familiar two-dimensional glycan notation used by the glycobiology community, brought into three dimensions by the CCP4 molecular graphics project (CCP4mg).

Highlights

Unlike proteins or nucleic acids, polysaccharides are frequently branched and in addition have two alternative configurations in their glycosidic linkages
While most sequence formats provide machine-readable, univocal descriptions of glycan sequences, graphical conventions are better suited for human interaction and visualization
The graphical convention first introduced by Kornfeld et al (1978) gained widespread popularity after being standardised (Varki et al, 1999) and perfected (Varki et al, 2009, 2015) to match the needs of the glycobiology community

Summary

Introduction

Unlike proteins or nucleic acids, polysaccharides are frequently branched and in addition have two alternative configurations in their glycosidic linkages. The graphical convention first introduced by Kornfeld et al (1978) gained widespread popularity after being standardised (Varki et al, 1999) and perfected (Varki et al, 2009, 2015) to match the needs of the glycobiology community It is even possible to employ the Essentials convention to search databases, such as UniCarbKB (Campbell et al, 2014) or glycosciences.de (Loss & Lutteke, 2015), for particular glycans through the use of graphical tools such as GlycanBuilder (Damerell et al, 2012)

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