ArticleThe journal of physical chemistry. B2025
Benchmark of Available Explicit Solvent Models in CHARMM36m to Characterize Glycosaminoglycans.
Article in The journal of physical chemistry. B, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.Journal of biological physics · 2026Review
- Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.Journal of chemical information and modeling · 2026Article
- Solvent Models and Charge Scaling: Benchmarks for Molecular Dynamics of Glycosaminoglycans.The journal of physical chemistry. B · 2026Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Heparin is a highly sulfated glycosaminoglycan (GAG) with essential roles in anticoagulation, angiogenesis, cell signaling, and host-pathogen interactions, mediated largely through electrostatic binding to diverse protein targets. While the TIP3P water model is commonly used in molecular simulations of GAGs, the influence of solvent representation on HP structure within the CHARMM36m force field remains poorly understood. Here, we report 5 μs molecular dynamics simulations of an HP dodecamer in five explicit solvent models: TIP3P, TIP4P, TIP5P, SPC/E, and OPC. TIP3P and SPC/E yield stable HP conformations, whereas TIP4P, TIP5P, and OPC introduce greater structural variability. Comparison with GLYCAM06 reveals that CHARMM36m preserves global HP architecture but differs in sampling specific glycosidic linkages. These findings highlight the critical impact of water model choice on GAG conformational dynamics and offer practical guidance for the accurate simulation of sulfated carbohydrates.
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