ArticlePloS one2012
Computational study of unfolding and regulation mechanism of preQ1 riboswitches.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- The effect of mutation in the stem of the MicroROSE thermometer on its thermosensing ability: insights from molecular dynamics simulation studies.RSC advances · 2022Article
- Recent advances and future trends of riboswitches: attractive regulatory tools.World journal of microbiology & biotechnology · 2018Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Structure and function of preQBiochimica et biophysica acta · 2014Review
- Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction.Advanced pharmaceutical bulletin · 2014Article
- Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations.PloS one · 2014Article
- Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are novel RNA regulatory elements. Each riboswitch molecule consists of two domains: aptamer and express platform. The three-dimensional (3D) structure of the aptamer domain, depending on ligand binding or not, controls that of the express platform, which then switches on or off transcriptional or translational process. Here we study the two types of preQ(1) riboswitch aptamers from T. Tengcongensis (denoted as Tte preQ(1) riboswitch for short below) and Bacillus subtilis (denoted as Bsu preQ(1) riboswitch for short below), respectively. The free-state 3D structure of the Tte preQ(1) riboswitch is the same as its bound state but the Bsu preQ(1) riboswitch is not. Therefore, it is very interesting to investigate how these riboswitches realize their different regulation functions. We simulated the unfolding of these two aptamers through all-atom molecular dynamic simulation and found that they have similar unfolding or folding pathways and ligand-binding processes. The main difference between them is the folding intermediate states. The similarity and difference of their unfolding or folding dynamics may suggest their similar regulation mechanisms and account for their different functions, respectively. These results are also useful to understand the regulation mechanism of other riboswitches with free-state 3D structures similar to their bound states.
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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.