ArticleProceedings of the National Academy of Sciences of the United States of America2025
Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Progress toward linking single-molecule behavior and condensate material properties.Current opinion in structural biology · 2026Review
- Latent thermodynamic flows: unified representation learning and generative modeling of temperature-dependent behaviors from limited data.Chemical science · 2026Article
- Fibrillarin/Nop1 perturbs RNA folding and assembly independently of liquid-liquid phase separation.Nucleic acids research · 2026Article
- Biomolecular Condensates Dictate the Folding Landscape of Proteins.bioRxiv : the preprint server for biology · 2026Article
- All-atom simulations of biomolecular condensates.Current opinion in structural biology · 2025Review
- Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.Advances in physics: X · 2025Article
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Authors and funding
5 authors.
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Abstract
Biomolecular condensates are currently recognized to play a key role in organizing cellular space and in orchestrating biochemical processes. Despite an increasing interest in characterizing their internal organization at the molecular scale, not much is known about how the densely crowded environment within these condensates affects the structural properties of recruited macromolecules. Here, we adopted explicit-solvent all-atom simulations based on a combination of enhanced sampling approaches to investigate how the conformational ensemble of an RNA hairpin is reshaped in a highly concentrated peptide solution that mimics the interior of a biomolecular condensate. Our simulations indicate that RNA structure is greatly perturbed by this distinctive physico-chemical environment, which weakens RNA secondary structure and promotes extended nonnative conformations. The resulting high-resolution picture reveals that RNA unfolding is driven by the effective solvation of nucleobases through hydrogen bonding and stacking interactions with surrounding peptides. This solvent effect can be modulated by the amino acid composition of the model condensate as proven by the differential RNA behavior observed in the case of arginine-rich and lysine-rich peptides.
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