ArticleNucleic acids research2013
Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Integrating rna structure and protein interactions to uncover the mechanisms of viral and cellular ires function.Biology direct · 2025Article
- Pharmacophore-Based Discovery of Viral RNA Conformational Modulators.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Picornavirus translation strategies.FEBS open bio · 2022Review
- Rab1b and ARF5 are novel RNA-binding proteins involved in FMDV IRES-driven RNA localization.Life science alliance · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE.Scientific reports · 2018Article
- The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure.Nucleic acids research · 2017Article
- Insights into Structural and Mechanistic Features of Viral IRES Elements.Frontiers in microbiology · 2017Review
- Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound.RNA (New York, N.Y.) · 2016Article
- Progress and Current Challenges in Modeling Large RNAs.Journal of molecular biology · 2016Review
- Gemin5: A Multitasking RNA-Binding Protein Involved in Translation Control.Biomolecules · 2015Review
- Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation.RNA biology · 2015Article
- Magnesium-dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction.The FEBS journal · 2014Article
- Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations.Biophysical journal · 2014Article
- Using RNA inverse folding to identify IRES-like structural subdomains.RNA biology · 2013Article
- Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.The journal of physical chemistry. B · 2013Article
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2 authors.
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Abstract
The foot-and-mouth-disease virus (FMDV) utilizes non-canonical translation initiation for viral protein synthesis, by forming a specific RNA structure called internal ribosome entry site (IRES). Domain 3 in FMDV IRES is phylogenetically conserved and highly structured; it contains four-way junctions where intramolecular RNA-RNA interactions serve as a scaffold for the RNA to fold for efficient IRES activity. Although the 3D structure of domain 3 is crucial to exploring and deciphering the initiation mechanism of translation, little is known. Here, we employ a combination of various modeling approaches to propose candidate tertiary structures for the apical region of domain 3, thought to be crucial for IRES function. We begin by modeling junction topology candidates and build atomic 3D models consistent with available experimental data. We then investigate each of the four candidate 3D structures by molecular dynamics simulations to determine the most energetically favorable configurations and to analyze specific tertiary interactions. Only one model emerges as viable containing not only the specific binding site for the GNRA tetraloop but also helical arrangements which enhance the stability of domain 3. These collective findings, together with available experimental data, suggest a plausible theoretical tertiary structure of the apical region in FMDV IRES domain 3.
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