RNA catalysis emerges from dynamic structural ensembles

Draper, D. E., Grilley, D. & Soto, A. M. Ions and RNA folding. Annu. Rev. Biophys. Biomol. Struct. 34, 221–243 https://doi.org/10.1146/annurev.biophys.34.040204.144511 (2005).Article 
CAS 
PubMed 

Google Scholar 
Bowman, J. C., Lenz, T. K., Hud, N. V. & Williams, L. D. Cations in charge: magnesium ions in RNA folding and catalysis. Curr. Opin. Struct. Biol. 22, 262–272 https://doi.org/10.1016/j.sbi.2012.04.006 (2012).Article 
CAS 
PubMed 

Google Scholar 
Hayes, R. L. et al. Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J. Am. Chem. Soc. 134, 12043–12053 https://doi.org/10.1021/ja301454u (2012).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zheng, H., Shabalin, I. G., Handing, K. B., Bujnicki, J. M. & Minor, W. Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection. Nucleic Acids Res. 43, 3789–3801 https://doi.org/10.1093/nar/gkv225 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Al-Hashimi, H. M. & Walter, N. G. RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, 321–329 https://doi.org/10.1016/j.sbi.2008.04.004 (2008).Article 
CAS 
PubMed 
PubMed Central 

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 https://doi.org/10.1038/s41580-019-0136-0 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bothe, J. R. et al. Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nat. Methods 8, 919–931 https://doi.org/10.1038/nmeth.1735 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bottaro, S., Bussi, G., Kennedy, S. D., Turner, D. H. & Lindorff-Larsen, K. Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. Sci. Adv. 4, eaar8521 https://doi.org/10.1126/sciadv.aar8521 (2018).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sponer, J. et al. RNA structural dynamics as captured by molecular simulations: a comprehensive overview. Chem. Rev. 118, 4177–4338 https://doi.org/10.1021/acs.chemrev.7b00427 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Degenhardt, M. F. S. et al. Determining structures of RNA conformers using AFM and deep neural networks. Nature 637, 1234–1243 https://doi.org/10.1038/s41586-024-07559-x (2025).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Lee, Y. T. et al. The conformational space of RNase P RNA in solution. Nature 637, 1244–1251 https://doi.org/10.1038/s41586-024-08336-6 (2025).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290 https://doi.org/10.1038/Nmeth.4169 (2017).Article 
CAS 
PubMed 

Google Scholar 
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 https://doi.org/10.1016/j.jsb.2012.09.006 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lyumkis, D., Brilot, A. F., Theobald, D. L. & Grigorieff, N. Likelihood-based classification of cryo-EM images using FREALIGN. J. Struct. Biol. 183, 377–388 https://doi.org/10.1016/j.jsb.2013.07.005 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. eLife https://doi.org/10.7554/eLife.35383 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18, 176–185 https://doi.org/10.1038/s41592-020-01049-4 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Punjani, A. & Fleet, D. J. 3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J. Struct. Biol. 213, 107702 https://doi.org/10.1016/j.jsb.2021.107702 (2021).Article 
CAS 
PubMed 

Google Scholar 
Degenhardt, H. F. EMCrafter: large-scale cryo-EM simulation toolkit driven by experimental data profiles [computer software]. Zenodo https://doi.org/10.5281/zenodo.16366716 (2025).Zhang, J. & Ferre, D. A. R. Trying on tRNA for size: RNase P and the T-box riboswitch as molecular rulers. Biomolecules https://doi.org/10.3390/biom6020018 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849–857 https://doi.org/10.1016/0092-8674(83)90117-4 (1983).Article 
CAS 
PubMed 

Google Scholar 
Niranjanakumari, S., Stams, T., Crary, S. M., Christianson, D. W. & Fierke, C. A. Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA. Proc. Natl Acad. Sci. U.S.A. 95, 15212–15217 https://doi.org/10.1073/pnas.95.26.15212 (1998).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Klemm, B. P. et al. The diversity of ribonuclease P: protein and RNA catalysts with analogous biological functions. Biomolecules https://doi.org/10.3390/biom6020027 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Riziotis, I. G., Ribeiro, A. J. M., Borkakoti, N. & Thornton, J. M. Conformational variation in enzyme catalysis: a structural study on catalytic residues. J. Mol. Biol. 434, 167517 https://doi.org/10.1016/j.jmb.2022.167517 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sengupta, R. N. et al. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. RNA 22, 32–48 https://doi.org/10.1261/rna.053710.115 (2016).Article 
CAS 
PubMed 

Google Scholar 
Giarimoglou, N., Kouvela, A., Zhang, J., Stamatopoulou, V. & Stathopoulos, C. Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria. RNA 30, 1328–1344 https://doi.org/10.1261/rna.080071.124 (2024).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wu, J. et al. Cryo-EM structure of the human ribonuclease P holoenzyme. Cell 175, 1393–1404.e1311 https://doi.org/10.1016/j.cell.2018.10.003 (2018).Article 
CAS 
PubMed 

Google Scholar 
Wan, F. et al. Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme. Nat. Commun. 10, 2617 https://doi.org/10.1038/s41467-019-10496-3 (2019).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Torres-Larios, A., Swinger, K. K., Krasilnikov, A. S., Pan, T. & Mondragon, A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437, 584–587 https://doi.org/10.1038/nature04074 (2005).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Wang, J., Liu, Z., Frank, J. & Moore, P. B. Identification of ions in experimental electrostatic potential maps. IUCrJ 5, 375–381 https://doi.org/10.1107/S2052252518006292 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Leonarski, F., D’Ascenzo, L. & Auffinger, P. Mg2+ ions: do they bind to nucleobase nitrogens?. Nucleic Acids Res. 45, 987–1004 https://doi.org/10.1093/nar/gkw1175 (2017).Article 
CAS 
PubMed 

Google Scholar 
Kretsch, R. C. et al. Complex water networks visualized by cryogenic electron microscopy of RNA. Nature 642, 250–259 https://doi.org/10.1038/s41586-025-08855-w (2025).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Leonarski, F., Henning-Knechtel, A., Kirmizialtin, S., Ennifar, E. & Auffinger, P. Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – part I: Mg2+. Nucleic Acids Res. https://doi.org/10.1093/nar/gkae1148 (2025).Article 
PubMed 
PubMed Central 

Google Scholar 
Alonso, D. & Mondragon, A. Mechanisms of catalytic RNA molecules. Biochem. Soc. Trans. 49, 1529–1535 https://doi.org/10.1042/BST20200465 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Walter, N. G. Ribozyme catalysis revisited: is water involved?. Mol. Cell 28, 923–929 https://doi.org/10.1016/j.molcel.2007.12.001 (2007).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Masquida, B. & Westhof, E. RNase P: at last, the key finds its lock. RNA 17, 1615–1618 https://doi.org/10.1261/rna.2841511 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Auffinger, P., Louisemay, S. & Westhof, E. Multiple molecular-dynamics simulations of the anticodon loop of tRNAAsp in aqueous-solution with counterions. J. Am. Chem. Soc. 117, 6720–6726 https://doi.org/10.1021/ja00130a011 (1995).Article 
ADS 
CAS 

Google Scholar 
Misra, V. K. & Draper, D. E. The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317, 507–521 https://doi.org/10.1006/jmbi.2002.5422 (2002).Article 
CAS 
PubMed 

Google Scholar 
Guth-Metzler, R. et al. Goldilocks and RNA: where Mg2+ concentration is just right. Nucleic Acids Res. 51, 3529–3539 https://doi.org/10.1093/nar/gkad124 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kumawat, A. & Chakrabarty, S. Hidden electrostatic basis of dynamic allostery in a PDZ domain. Proc. Natl Acad. Sci. U.S.A. 114, E5825–E5834 https://doi.org/10.1073/pnas.1705311114 (2017).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Nussinov, R., Ma, B. & Tsai, C. J. Multiple conformational selection and induced fit events take place in allosteric propagation. Biophys. Chem. 186, 22–30 https://doi.org/10.1016/j.bpc.2013.10.002 (2014).Article 
CAS 
PubMed 

Google Scholar 
Kar, G., Keskin, O., Gursoy, A. & Nussinov, R. Allostery and population shift in drug discovery. Curr. Opin. Pharmacol. 10, 715–722 https://doi.org/10.1016/j.coph.2010.09.002 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chakraborty, A. et al. RNA’s dynamic conformational selection and entropic allosteric mechanism in controlling cascade protein binding events. J. Phys. Chem. Lett. 15, 6115–6125 https://doi.org/10.1021/acs.jpclett.4c00740 (2024).Article 
CAS 
PubMed 

Google Scholar 
Misra, V. K. & Draper, D. E. On the role of magnesium ions in RNA stability. Biopolymers 48, 113–135 (1998).Article 
CAS 
PubMed 

Google Scholar 
Cate, J. H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678–1685 https://doi.org/10.1126/science.273.5282.1678 (1996).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Manning, G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11, 179–246 https://doi.org/10.1017/s0033583500002031 (1978).Article 
CAS 
PubMed 

Google Scholar 
Cunha, R. A. & Bussi, G. Unraveling Mg2+-RNA binding with atomistic molecular dynamics. RNA 23, 628–638 https://doi.org/10.1261/rna.060079.116 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Degenhardt, H. F. CMM Web Submitter: scripted web interface for parallel file submission and result retrieval from CheckMyMetal (CMM) [computer software]. Zenodo https://doi.org/10.5281/zenodo.16367407 (2025).Degenhardt, M. F. d. S. RNAIonScan: ion binding mode classifier for RNA [computer software]. Zenodo https://doi.org/10.5281/zenodo.17832303 (2025).