ArticleNucleic acids research2005
Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.
Article in Nucleic acids research, 2005. 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.
- RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.Biophysical journal · 2022Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Identification of compound heterozygous variants in the noncoding RNU4ATAC gene in a Chinese family with two successive foetuses with severe microcephaly.Human genomics · 2018Article
- Spatial code recognition in neuronal RNA targeting: role of RNA-hnRNP A2 interactions.The Journal of cell biology · 2011Article
- Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.Journal of biophysics (Hindawi Publishing Corporation : Online) · 2011Article
- Structure of the K-turn U4 RNA: a combined NMR and SANS study.Nucleic acids research · 2010Article
- A structural database for k-turn motifs in RNA.RNA (New York, N.Y.) · 2010Article
- An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.Journal of chemical theory and computation · 2010Article
- Ion-induced folding of a kink turn that departs from the conventional sequence.Nucleic acids research · 2009Article
- Review
- The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA.RNA (New York, N.Y.) · 2007Article
- Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.Nucleic acids research · 2007Article
- Molecular dynamics simulations of sarcin-ricin rRNA motif.Nucleic acids research · 2006Article
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3 authors.
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Abstract
Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.
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