ArticleThe journal of physical chemistry. B2015
Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.
Article in The journal of physical chemistry. B, 2015. 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.
- Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops.International journal of molecular sciences · 2020Article
- Data-driven analysis of the number of Lennard-Jones types needed in a force field.Communications chemistry · 2020Article
- Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2).Communications chemistry · 2020Article
- Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.Journal of structural biology · 2019Review
- Structural insights into DNA-stabilized silver clusters.Soft matter · 2019Article
- Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.Journal of biomolecular NMR · 2019Article
- Predicting RNA-Metal Ion Binding with Ion Dehydration Effects.Biophysical journal · 2019Article
- An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Hexahydrated MgBiophysical journal · 2018Article
- Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.Wiley interdisciplinary reviews. RNA · 2017Review
- MgBiophysical journal · 2017Article
- NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.The journal of physical chemistry letters · 2016Article
- Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.Journal of chemical theory and computation · 2016Article
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Authors and funding
3 authors.
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Abstract
The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5'-rUGACU loop of the isolated SLV has been shown to adopt a Mg(2+)-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg(2+) ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure. We propose this structure is a "gatekeeper" or precursor to Mg(2+) binding when those ions are present.
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