ArticleInternational journal of molecular sciences2020
Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 19 citations in OpenAlex.
- Iduronate Ring Puckering Effects on Preferred Glycosidic Linkage Conformations in Heparin/Heparan Sulfate and Dermatan Sulfate Disaccharides.Molecules (Basel, Switzerland) · 2026Article
- The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties.Journal of chemical theory and computation · 2024Article
- Glycosaminoglycans: What Remains To Be Deciphered?JACS Au · 2023Review
- Molecular Dynamics-Based Comparative Analysis of Chondroitin and Dermatan Sulfates.Biomolecules · 2023Article
- Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes.Molecules (Basel, Switzerland) · 2022Review
- Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins.International journal of molecular sciences · 2021Article
- Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications.International journal of molecular sciences · 2021Article
- The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans.International journal of molecular sciences · 2021Article
- A Bittersweet Computational Journey among Glycosaminoglycans.Biomolecules · 2021Review
- NMR Characterization of the Interactions Between Glycosaminoglycans and Proteins.Frontiers in molecular biosciences · 2021Review
- GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans.Biomolecules · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) and are key mediators in the bioactivity of PGs in animal tissue. GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharide units. These complexities make studying GAG conformation a challenge for existing experimental and computational methods. We previously described an algorithm we developed that applies conformational parameters (i.e., all bond lengths, bond angles, and dihedral angles) from molecular dynamics (MD) simulations of nonsulfated chondroitin GAG 20-mers to construct 3-D atomic-resolution models of nonsulfated chondroitin GAGs of arbitrary length. In the current study, we applied our algorithm to other GAGs, including hyaluronan and nonsulfated forms of dermatan, keratan, and heparan and expanded our database of MD-generated GAG conformations. Here, we show that individual glycosidic linkages and monosaccharide rings in 10- and 20-mers of hyaluronan and nonsulfated dermatan, keratan, and heparan behave randomly and independently in MD simulation and, therefore, using a database of MD-generated 20-mer conformations, that our algorithm can construct conformational ensembles of 10- and 20-mers of various GAG types that accurately represent the backbone flexibility seen in MD simulations. Furthermore, our algorithm efficiently constructs conformational ensembles of GAG 200-mers that we would reasonably expect from MD simulations.
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