Lifetime of ground conformational state determines the activity of structured RNA

Henzler-Wildman, K. & Kern, D. Dynamic personalities of proteins. Nature 450, 964–972 (2007).

Article  CAS  PubMed  Google Scholar 

Ganser, L. R., Kelly, M. L., Herschlag, D. & Al-Hashimi, H. M. The roles of structural dynamics in the cellular functions of RNAs. Nat. Rev. Mol. Cell Biol. 20, 474–489 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alderson, T. R. & Kay, L. E. NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function. Cell 184, 577–595 (2021).

Article  CAS  PubMed  Google Scholar 

Boehr, D. D., McElheny, D., Dyson, H. J. & Wright, P. E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 1638–1642 (2006).

Article  CAS  PubMed  Google Scholar 

Fraser, J. S. et al. Hidden alternative structures of proline isomerase essential for catalysis. Nature 462, 669–673 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Neudecker, P. et al. Structure of an intermediate state in protein folding and aggregation. Science 336, 362–366 (2012).

Article  CAS  PubMed  Google Scholar 

Whittier, S. K., Hengge, A. C. & Loria, J. P. Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases. Science 341, 899–903 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xie, T., Saleh, T., Rossi, P. & Kalodimos, C. G. Conformational states dynamically populated by a kinase determine its function. Science 370, eabc2754 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nikolova, E. N. et al. Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470, 498–502 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kimsey, I. J. et al. Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature 554, 195–201 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dethoff, E. A., Petzold, K., Chugh, J., Casiano-Negroni, A. & Al-Hashimi, H. M. Visualizing transient low-populated structures of RNA. Nature 491, 724–728 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao, B., Guffy, S. L., Williams, B. & Zhang, Q. An excited state underlies gene regulation of a transcriptional riboswitch. Nat. Chem. Biol. 13, 968–974 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baronti, L. et al. Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA. Nature 583, 139–144 (2020).

Article  CAS  PubMed  Google Scholar 

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Steckelberg, A. L., Vicens, Q. & Kieft, J. S. Exoribonuclease-resistant RNAs exist within both coding and noncoding subgenomic RNAs. mBio 9, e02461–02418 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Vicens, Q. & Kieft, J. S. Shared properties and singularities of exoribonuclease-resistant RNAs in viruses. Comput. Struct. Biotechnol. J. 19, 4373–4380 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pierson, T. C. & Diamond, M. S. The continued threat of emerging flaviviruses. Nat. Microbiol. 5, 796–812 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pijlman, G. P. et al. A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity. Cell Host Microbe 4, 579–591 (2008).

Article  CAS  PubMed  Google Scholar 

Funk, A. et al. RNA structures required for production of subgenomic flavivirus RNA. J. Virol. 84, 11407–11417 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Slonchak, A. & Khromykh, A. A. Subgenomic flaviviral RNAs: what do we know after the first decade of research. Antivir. Res. 159, 13–25 (2018).

Article  CAS  PubMed  Google Scholar 

Goertz, G. P., Abbo, S. R., Fros, J. J. & Pijlman, G. P. Functional RNA during Zika virus infection. Virus Res. 254, 41–53 (2018).

Article  PubMed  Google Scholar 

Akiyama, B. M. et al. Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Science 354, 1148–1152 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chapman, E. G. et al. The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. Science 344, 307–310 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Slonchak, A. et al. Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes. Nat. Commun. 11, 2205 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Suma, A., Coronel, L., Bussi, G. & Micheletti, C. Directional translocation resistance of Zika xrRNA. Nat. Commun. 11, 3749 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pallares, H. M. et al. Zika virus subgenomic flavivirus RNA generation requires cooperativity between duplicated RNA structures that are essential for productive infection in human cells. J. Virol. 94, e00343–00320 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Niu, X. et al. Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs). Nat. Commun. 11, 5496 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Niu, X. et al. Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs. Nat. Commun. 12, 6417 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao, M. & Woodside, M. T. Mechanical strength of RNA knot in Zika virus protects against cellular defenses. Nat. Chem. Biol. 17, 975–981 (2021).

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