ArticleScientific reports2016
Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR.Journal of the American Chemical Society · 2024Article
- Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR.bioRxiv : the preprint server for biology · 2023Article
- Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.Nature communications · 2022Article
- How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs.International journal of molecular sciences · 2020Review
- Dynamical important residue network (DIRN): network inference via conformational change.Bioinformatics (Oxford, England) · 2019Article
- Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies.RNA (New York, N.Y.) · 2019Article
- Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana.Scientific reports · 2019Article
- Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation.International journal of molecular sciences · 2018Article
- Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB.The Journal of chemical physics · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Synergistic regulation mechanism of iperoxo and LY2119620 for muscarinic acetylcholine M2 receptor.RSC advances · 2018Article
- Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with theRSC advances · 2017Article
- Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network.Molecular bioSystems · 2016Article
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Authors and funding
6 authors.
Funding
Abstract
Riboswitches are a class of metabolism control elements mostly found in bacteria. Due to their fundamental importance in bacteria gene regulation, riboswitches have been proposed as antibacterial drug targets. Prequeuosine (preQ1) is the last free precursor in the biosynthetic pathway of queuosine that is crucial for translation efficiency and fidelity. However, the regulation mechanism for the preQ1 riboswitch remains unclear. Here we constructed fluctuation correlation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism. The results suggest that the correlation network in the bound riboswitch is distinctly different from that in the apo riboswitch. The community network indicates that the information freely transfers from the binding site of preQ1 to the expression platform of the P3 helix in the bound riboswitch and the P3 helix is a bottleneck in the apo riboswitch. Thus, a hypothesis of "preQ1-binding induced allosteric switching" is proposed to link riboswitch and translation regulation. The community networks of mutants support this hypothesis. Finally, a possible allosteric pathway of A50-A51-A52-U10-A11-G12-G56 was also identified based on the shortest path algorithm and confirmed by mutations and network perturbation. The novel fluctuation network analysis method can be used as a general strategy in studies of riboswitch structure-function relationship.
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