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

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).With structural glycoscience finally gaining popularity, the need for a clear way of depicting glycans and their interactions in three dimensions is more pressing than ever. Here the Glycoblocks representation is introduced, which combines a simplified bonding-network depiction with the familiar two-dimensional glycan notation brought into three-dimensions.