Glycoblocks: a schematic three-dimensional representation for glycans and their interactions.
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).
York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England.
Stuart
S
McNicholas
York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England.
Jon
J
Agirre
D000818:Animals; D002236:Carbohydrate Conformation; D054794:Glycomics; D006023:Glycoproteins / Q000737:chemistry / Q000378:metabolism; D006031:Glycosylation; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009005:Monosaccharides / Q000737:chemistry / Q000378:metabolism; D011134:Polysaccharides / Q000737:chemistry* / Q000378:metabolism; D012984:Software
D006023:Glycoproteins; D009005:Monosaccharides; D011134:Polysaccharides
CCP4mg; Glycoblocks; Privateer; carbohydrates; glycans; interactions; molecular graphics; three-dimensional representations