ArticleInternational journal of molecular sciences2021
Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins.
Article in International journal of molecular sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 24 citations in OpenAlex.
- Resolving Conformational Preferences of Monosaccharides fromJournal of chemical information and modeling · 2026Article
- Advances in understanding the dual roles of testicular immune responses: From immune privilege to inflammation.Seminars in immunopathology · 2026Review
- Article
- Iduronate Ring Puckering Effects on Preferred Glycosidic Linkage Conformations in Heparin/Heparan Sulfate and Dermatan Sulfate Disaccharides.Molecules (Basel, Switzerland) · 2026Article
- Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?Journal of chemical information and modeling · 2025Review
- Elucidating the Mechanism of Recognition and Binding of Heparin to Amyloid Fibrils of Serum Amyloid A.Biochemistry · 2025Article
- Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.Journal of chemical theory and computation · 2024Article
- Thrombin-derived C-terminal peptides bind and form aggregates with sulfated glycosaminoglycans.Heliyon · 2024Article
- Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes.Molecules (Basel, Switzerland) · 2022Review
- Assortment of Frontiers in Protein Science.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between
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