Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling
By Sunhwan Jo, Hui-Sun Lee, Jeffrey Skolnick, Wonpil Im. 2013
35 citations recorded by the source corpus.
Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures.
Subfields: Molecular Biology, Organic Chemistry
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Citations in the corpus
- Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom (2023, neutral): “Predictionofglycanstructurehasapplica-tionsintherapeutics,vaccines,anddiagnostics ( 38 – 40 ).”
- CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates (2019, result): “This is also in agreement with our previous PDB glycan structure survey study (Jo et al. 2013) that the difficulties in finding the global orientation of the glycan with respect to the protein, even when the homologous N-glycan templates are present, can be significantly alleviated when a partial gl”