ArticleThe journal of physical chemistry. B2014
Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 54 citations in OpenAlex.
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- Extraction and Optimization of Fucoidan From Sargassum muticum Using Acidic Eutectic Solvents and Evaluation of Their Effects on Fibroblast Cell Lines.ChemistryOpen · 2026Article
- 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
- The importance of side branches of glycosylphosphatidylinositol anchors: a molecular dynamics perspective.Glycobiology · 2022Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Influence of Carbohydrate Additives on the Growth Rate of Microalgae Biomass with an Increased Carbohydrate Content.Marine drugs · 2021Article
- 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
- Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations.International journal of molecular sciences · 2020Article
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- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
- CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.Journal of chemical theory and computation · 2018Article
- Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes.Journal of chemical information and modeling · 2017Article
- NMR and Molecular Recognition of N-Glycans: Remote Modifications of the Saccharide Chain Modulate Binding Features.ACS chemical biology · 2017Article
- Conformational Populations of β-(1→4) O-Glycosidic Linkages Using Redundant NMR J-Couplings and Circular Statistics.The journal of physical chemistry. B · 2017Article
- Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.Physical chemistry chemical physics : PCCP · 2016Article
- Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies.Glycobiology · 2016Article
- Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins.Glycobiology · 2016Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Conformational sampling for a set of 10 α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e., within ∼0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6···HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored.
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