ArticleJournal of molecular biology2013
The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A high-throughput search for intracellular factors that affect RNA folding identifiesRNA biology · 2024Article
- Topological crossing in the misfoldedProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA.Science advances · 2022Article
- Measurement of ATP utilization in RNA unwinding and RNA chaperone activities by DEAD-box helicase proteins.Methods in enzymology · 2022Article
- Article
- Single-nucleotide control of tRNA folding cooperativity under near-cellular conditions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The Story of RNA Folding, as Told in Epochs.Cold Spring Harbor perspectives in biology · 2018Review
- Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs.Biochemical Society transactions · 2017Review
- Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.Biochemistry · 2017Article
- Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.Nucleic acids research · 2017Article
- Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.Scientific reports · 2017Article
- Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.Journal of molecular biology · 2016Article
- Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Bridging the gap between in vitro and in vivo RNA folding.Quarterly reviews of biophysics · 2016Article
- Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence.Nucleic acids research · 2015Article
- DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Folding pathways of the Tetrahymena ribozyme.Journal of molecular biology · 2014Article
- ATP utilization by a DEAD-box protein during refolding of a misfolded group I intron ribozyme.The Journal of biological chemistryArticle
- Sisyphus observed: Unraveling the high ATP usage of an RNA chaperone.The Journal of biological chemistryArticle
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5 authors.
Funding
Abstract
RNAs are prone to misfolding, but how misfolded structures are formed and resolved remains incompletely understood. The Tetrahymena group I intron ribozyme folds in vitro to a long-lived misfolded conformation (M) that includes extensive native structure but is proposed to differ in topology from the native state (N). A leading model predicts that exchange of the topologies requires unwinding of the long-range, core helix P3, despite the presence of P3 in both conformations. To test this model, we constructed 16 mutations to strengthen or weaken P3. Catalytic activity and in-line probing showed that nearly all of the mutants form the M state before folding to N. The P3-weakening mutations accelerated refolding from M (3- to 30-fold) and the P3-strengthening mutations slowed refolding (6- to 1400-fold), suggesting that P3 indeed unwinds transiently. Upon depletion of Mg(2+), the mutations had analogous effects on unfolding from N to intermediates that subsequently fold to M. The magnitudes for the P3-weakening mutations were larger than in refolding from M, and small-angle X-ray scattering showed that the ribozyme expands rapidly to intermediates from which P3 is disrupted subsequently. These results are consistent with previous results indicating unfolding of native peripheral structure during refolding from M, which probably permits rearrangement of the core. Together, our results demonstrate that exchange of the native and misfolded conformations requires loss of a core helix in addition to peripheral structure. Further, the results strongly suggest that misfolding arises from a topological error within the ribozyme core, and a specific topology is proposed.
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