ArticlePLoS computational biology2017
A magnesium-induced triplex pre-organizes the SAM-II riboswitch.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Critical Role of MgThe journal of physical chemistry. B · 2025Article
- Modeling riboswitches: The impact of concentration of MgBiophysical journal · 2025Article
- Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.Nucleic acids research · 2025Article
- Understanding the Thermodynamics of Magnesium Binding to RNA Structural Motifs.Life (Basel, Switzerland) · 2024Article
- Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch.Nature communications · 2023Article
- Structural insights into translation regulation by the THF-II riboswitch.Nucleic acids research · 2023Article
- Review
- Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.Journal of molecular biology · 2022Article
- Getting to the bottom of lncRNA mechanism: structure-function relationships.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance.RNA biology · 2022Article
- Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.The journal of physical chemistry. B · 2021Article
- Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection.Frontiers in molecular biosciences · 2021Article
- Unraveling the structure and biological functions of RNA triple helices.Wiley interdisciplinary reviews. RNA · 2020Review
- Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch.Nucleic acids research · 2019Article
- Structure and ligand binding of the SAM-V riboswitch.Nucleic acids research · 2018Article
- Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.Biophysical journal · 2017Article
- Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance RProgress in nuclear magnetic resonance spectroscopyReview
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function.
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Registered trials
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 OpenQuestion graph.