ArticleNucleic acids research2016
RNA folding pathways in stop motion.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Latent thermodynamic flows: unified representation learning and generative modeling of temperature-dependent behaviors from limited data.Chemical science · 2026Article
- Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.Nucleic acids research · 2022Article
- Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field.Journal of chemical theory and computation · 2022Article
- Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.The journal of physical chemistry letters · 2022Article
- Article
- Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data.Nucleic acids research · 2020Article
- Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.Journal of structural biology · 2019Review
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.Journal of chemical theory and computation · 2019Article
- Barnaba: software for analysis of nucleic acid structures and trajectories.RNA (New York, N.Y.) · 2019Article
- Emergency Services of Viral RNAs: Repair and Remodeling.Microbiology and molecular biology reviews : MMBR · 2018Review
- Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.Science advances · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Mapping the Universe of RNA Tetraloop Folds.Biophysical journal · 2017Article
- MgBiophysical journal · 2017Article
- Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Journal of chemical theory and computation · 2017Article
- Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.RNA (New York, N.Y.) · 2017Article
- Unraveling MgRNA (New York, N.Y.) · 2017Article
- Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.RNA (New York, N.Y.) · 2017Article
- Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.Journal of chemical theory and computation · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions.
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