ArticleJournal of chemical information and modeling2017
Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes.
Article in Journal of chemical information and modeling, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Trade-Offs between Stability and Activity of Glycosylated and Non-Glycosylated Polyester Hydrolases PHL7 and PHL7mut3.ACS ES&T engineering · 2025Article
- Restoring protein glycosylation with GlycoShape.Nature methods · 2024Article
- Effects of glycans and hinge on dynamics in the IgG1 Fc.Journal of biomolecular structure & dynamics · 2024Article
- Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling.Journal of chemical theory and computation · 2023Article
- Article
- Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor.eLife · 2021Article
- Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites.The EMBO journal · 2021Article
- Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.The journal of physical chemistry. A · 2021Article
- Glycan-protein interactions determine kinetics ofRSC chemical biology · 2021Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose.Proteins · 2020Article
- Molecular Conformations of Di-, Tri-, and Tetra-International journal of molecular sciences · 2019Article
- Distinct Fcα receptorThe Journal of biological chemistry · 2019Article
- Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments.Chemphyschem : a European journal of chemical physics and physical chemistry · 2019Article
- A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms.Plant signaling & behavior · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
In spite of the abundance of glycoproteins in biological processes, relatively little three-dimensional structural data is available for glycan structures. Here, we study the structure and flexibility of the vast majority of mammalian oligosaccharides appearing in N- and O-glycosylated proteins using a bottom up approach. We report the conformational free-energy landscapes of all relevant glycosidic linkages as obtained from local elevation simulations and subsequent umbrella sampling. To the best of our knowledge, this represents the first complete conformational library for the construction of N- and O-glycan structures. Next, we systematically study the effect of neighboring residues, by extensively simulating all relevant trisaccharides and one tetrasaccharide. This allows for an unprecedented comparison of disaccharide linkages in large oligosaccharides. With a small number of exceptions, the conformational preferences in the larger structures are very similar as in the disaccharides. This, finally, allows us to suggest several efficient approaches to construct complete N- and O-glycans on glycoproteins, as exemplified on two relevant examples.
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Registered trials
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