ArticleNucleic acids research2023
Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics.
Article in Nucleic acids research, 2023. 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, 17 citations in OpenAlex.
- Insights into the Solution Structure and Oligomeric State of Fructose-1,6-bisphosphate Aldolase and Pyruvate Kinase fromACS omega · 2026Article
- Programmed -1 ribosomal frameshifting in SARS-CoV-2: molecular mechanisms and implications for antiviral targeting.Virus genes · 2026Review
- Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot With Thermodynamics-Driven Machine Learning.Journal of computational chemistry · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- A DNA Scaffold Approach Facilitates 5' Labeling of the SARS-CoV-2 RNA Pseudoknot for Single-Molecule Förster Resonance Energy Transfer Investigation.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Identifying the interactions conferring functional mechanical rigidity on RNase-resistant RNA from Zika virus.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sarbecovirus programmed ribosome frameshift RNA element folding studied by NMR spectroscopy and comparative analyses.Nucleic acids research · 2024Article
- Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot.PLoS computational biology · 2024Article
- Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.bioRxiv : the preprint server for biology · 2023Article
- Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication.Biomolecules · 2023Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.
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Registered trials
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