ArticlePhysical chemistry chemical physics : PCCP2016
Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.
Article in Physical chemistry chemical physics : PCCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 35 citations in OpenAlex.
- Synthesis, conformational analysis and biological activity of xylopyranosyl sulfur-containing glycosides: dependence of sulfur atom configuration.RSC advances · 2025Article
- Rapid Stereochemical Analysis of Glycosylations in Flow by Ion Mobility Spectrometry.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides.Journal of chemical information and modeling · 2023Article
- Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields.Physical chemistry chemical physics : PCCP · 2023Article
- Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins.International journal of molecular sciences · 2021Article
- Insights into substrate recognition and specificity for IgG by Endoglycosidase S2.PLoS computational biology · 2021Article
- A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.Glycobiology · 2021Article
- Glycans in Virus-Host Interactions: A Structural Perspective.Frontiers in molecular biosciences · 2021Review
- Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.PLoS computational biology · 2020Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Advancing Solutions to the Carbohydrate Sequencing Challenge.Journal of the American Chemical Society · 2019Review
- Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design.Carbohydrate research · 2019Article
- Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H.Antonie van Leeuwenhoek · 2017Article
- Conformational Heterogeneity of the HIV Envelope Glycan Shield.Scientific reports · 2017Article
- Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4.The journal of physical chemistry. B · 2017Article
- Development of a glycoconjugate vaccine to prevent invasive Salmonella Typhimurium infections in sub-Saharan Africa.PLoS neglected tropical diseases · 2017Article
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.