ArticleBiomolecules2020
Efficient Construction of Atomic-Resolution Models of Non-Sulfated Chondroitin Glycosaminoglycan Using Molecular Dynamics Data.
Article in Biomolecules, 2020. 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.
- 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
- Molecular Dynamics-Based Comparative Analysis of Chondroitin and Dermatan Sulfates.Biomolecules · 2023Article
- LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems.Biomolecules · 2023Article
- Review
- Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes.Molecules (Basel, Switzerland) · 2022Review
- In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism.Biomolecules · 2022Article
- Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins.International journal of molecular sciences · 2021Article
- Preface for the Special Issue on the Exploration of the Multifaceted Roles of Glycosaminoglycans: GAGs.Biomolecules · 2021Article
- The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans.International journal of molecular sciences · 2021Article
- Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions.ACS omega · 2021Article
- A Bittersweet Computational Journey among Glycosaminoglycans.Biomolecules · 2021Review
- Glycosaminoglycans: Carriers and Targets for Tailored Anti-Cancer Therapy.Biomolecules · 2021Review
- Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics.International journal of molecular sciences · 2020Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Glycosaminoglycans (GAGs) are linear, structurally diverse, conformationally complex carbohydrate polymers that may contain up to 200 monosaccharides. These characteristics present a challenge for studying GAG conformational thermodynamics at atomic resolution using existing experimental methods. Molecular dynamics (MD) simulations can overcome this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies all conformational parameters contributing to GAG backbone flexibility (i.e., bond lengths, bond angles, and dihedral angles) from unbiased all-atom explicit-solvent MD simulations of short GAG polymers to rapidly construct models of GAGs of arbitrary length. The algorithm was used to generate non-sulfated chondroitin 10- and 20-mer ensembles which were compared to MD-generated ensembles for internal validation. End-to-end distance distributions in constructed and MD-generated ensembles have minimal differences, suggesting that our algorithm produces conformational ensembles that mimic the backbone flexibility seen in simulation. Non-sulfated chondroitin 100- and 200-mer ensembles were constructed within a day, demonstrating the efficiency of the algorithm and reduction in time and computational cost compared to simulation.
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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.