ArticleProceedings of the National Academy of Sciences of the United States of America2025
Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels.Biophysical journal · 2026Article
- Programmed -1 ribosomal frameshifting in SARS-CoV-2: molecular mechanisms and implications for antiviral targeting.Virus genes · 2026Review
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- SARS-CoV-2 Antivirals Identified from Small Molecule Modulators of Programmed -1 Ribosomal Frameshifting.ACS infectious diseases · 2026Article
- VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels.ArXiv · 2026Article
- Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.The journal of physical chemistry. B · 2026Article
- Following the Committor Flow: A Data-Driven Discovery of Transition Pathways.Journal of chemical theory and computation · 2026Article
- Covalent Probes Reveal Small-Molecule Binding Pockets in Structured RNA and Enable Bioactive Compound Design.Journal of the American Chemical Society · 2025Article
- How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.PLoS computational biology · 2025Article
- Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element.International journal of molecular sciences · 2025Article
- A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements.Biochemistry · 2025Article
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 2025Article
- Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Frameshifting is an essential mechanism employed by many viruses including coronaviruses to produce viral proteins from a compact RNA genome. It is facilitated by specific RNA folds in the frameshift element (FSE), which has emerged as an important therapeutic target. For SARS-CoV-2, a specific 3-stem pseudoknot has been identified to stimulate frameshifting. However, prior studies and our RNA-As-Graphs analysis coupled to chemical reactivity experiments revealed other folds, including a different pseudoknot. Although structural plasticity has been proposed to play a key role in frameshifting, paths between different FSE RNA folds have not been yet identified. Here, we capture atomic-level transition pathways between two key FSE pseudoknots by transition path sampling coupled to Markov State Modeling and our BOLAS free energy method. We reveal multiple transition paths within a heterogeneous, multihub conformational landscape. A shared folding mechanism involves RNA stem unpairing followed by a 5
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.