ArticlePloS one2015
Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Structural and Thermodynamic Properties of RNA Molecules Using a Knowledge-Based Model.Journal of chemical theory and computation · 2026Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- What is the best reference state for building statistical potentials in RNA 3D structure evaluation?RNA (New York, N.Y.) · 2019Article
- Coarse-grained dynamic RNA titration simulations.Interface focus · 2019Article
- Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism.International journal of molecular sciences · 2018Article
- Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions.Biophysical journal · 2018Article
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.PLoS computational biology · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- A profound computational study to prioritize the disease-causing mutations in PRPS1 gene.Metabolic brain disease · 2018Article
- Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot.Nucleic acids research · 2017Article
- Article
- Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.Biophysical journal · 2015Article
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Authors and funding
5 authors.
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Abstract
How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA.
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