ArticleNucleic acids research2021
An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 15 citations in OpenAlex.
- Structural basis and affinity improvement for an ATP-binding DNA aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- The translational repressor Glorund uses interchangeable RNA recognition domains to recognize Drosophila nanos.Nucleic acids research · 2023Article
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats.Nucleic acids research · 2022Article
- NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin.Nucleic acids research · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
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