ArticlePloS one2014
Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- In Vitro, In Silico, and In Vivo Studies ofACS omega · 2023Article
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana.Scientific reports · 2019Article
- Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation.International journal of molecular sciences · 2018Article
- Recent advances and future trends of riboswitches: attractive regulatory tools.World journal of microbiology & biotechnology · 2018Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated.Journal of the American Chemical Society · 2016Article
- DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.Journal of computational chemistry · 2016Article
- Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.RNA (New York, N.Y.) · 2015Article
- Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.Nucleic acids research · 2015Article
- Probing and perturbing riboswitch folding using a fluorescent base analogue.Photochemistry and photobiologyArticle
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Authors and funding
5 authors.
Funding
Abstract
Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer domain from Bacillus subtilis is studied by overall 1.5 μs all-atom molecular dynamics simulations We found that the ligand-free aptamer has a stable state with a folded P1-L3 and open binding pocket. The latter forms a cytosine-rich pool in which the nucleotide C19 oscillates between close and open positions, making it a potential conformation for preQ1 entrance. The dynamic picture further suggests that the specific recognition of preQ1 by the aptamer domain is not only facilitated by the key nucleotide C19 but also aided and enhanced by other cytosines around the binding pocket. These results should help to understand the details of preQ1 binding.
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