Building and rebuilding N-glycans in protein structure models.
N-Glycosylation is one of the most common post-translational modifications and is implicated in, for example, protein folding and interaction with ligands and receptors. N-Glycosylation trees are complex structures of linked carbohydrate residues attached to asparagine residues. While carbohydrates are typically modeled in protein structures, they are often incomplete or have the wrong chemistry. Here, new tools are presented to automatically rebuild existing glycosylation trees, to extend them where possible, and to add new glycosylation trees if they are missing from the model. The method has been incorporated in the PDB-REDO pipeline and has been applied to build or rebuild 16 452 carbohydrate residues in 11 651 glycosylation trees in 4498 structure models, and is also available from the PDB-REDO web server. With better modeling of N-glycosylation, the biological function of this important modification can be better and more easily understood.
['van Beusekom|Bart|B|0000-0002-2183-2901', 'Wezel|Natasja|N|', 'Hekkelman|Maarten L|ML|0000-0002-9081-4707', 'Perrakis|Anastassis|A|0000-0002-1151-6227', 'Emsley|Paul|P|', 'Joosten|Robbie P|RP|0000-0002-2323-2686']
D002236:Carbohydrate Conformation D002240:Carbohydrate Sequence D018360:Crystallography, X-Ray D030562:Databases, Protein D006023:Glycoproteins D006801:Humans D008958:Models, Molecular D011134:Polysaccharides D011487:Protein Conformation
N-glycans carbohydrates PDB-REDO Coot crystallography model building validation