ArticleMolecular bioSystems2016
Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network.
Article in Molecular bioSystems, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed, 8 citations in OpenAlex.
- The protection of UCK2 protein stability by GART maintains pyrimidine salvage synthesis for HCC growth under glucose limitation.Oncogene · 2025Article
- Dynamical important residue network (DIRN): network inference via conformational change.Bioinformatics (Oxford, England) · 2019Article
- Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch.Nucleic acids research · 2019Article
- Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB.The Journal of chemical physics · 2018Article
- Synergistic regulation mechanism of iperoxo and LY2119620 for muscarinic acetylcholine M2 receptor.RSC advances · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Riboswitches are cis-acting genetic control elements. Due to their fundamental importance in bacteria gene regulation, they have been proposed as antibacterial drug targets. Tetrahydrofolate (THF) is an essential cofactor of one-carbon transfer reactions and downregulates the expression of downstream genes. However, information on how to transfer from the binding site of THF to the expression platform is still unavailable. Herein, a nucleotide/nucleotide dynamics correlation network based on an all-atom molecular dynamic simulation was used to reveal the regulation mechanism of a THF-sensing riboswitch. Shortest pathway analysis based on the network illustrates that there is an allosteric pathway through the P2 helix to the pseudoknot, then to the P1 helix in the THF-riboswitch. Thus the hypothesis of "THF-binding induced allosteric switching" was proposed and evaluated using THF and pseudoknot weakened experiments. Furthermore, a possible allosteric pathway of C30-C31-G33-A34-G35-G36-G37-A38-G48-G47-U46-A90-U91-C92-G93-C94-G95-C96 was identified and confirmed through the perturbation of the network. The proposed allosteric mechanism and the underlying allosteric pathway provide fundamental insights for the regulation of THF sensing riboswitches.
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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.