SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition

Angewandte Chemie
Bin ChenT Kwaku Dayie

Abstract

Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From (13) C and (1) H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1',C1') chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg(2+) will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.

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Citations

Mar 2, 2017·PLoS Computational Biology·Susmita RoyKarissa Y Sanbonmatsu
Apr 20, 2016·Methods : a Companion to Methods in Enzymology·Andrew P LonghiniT Kwaku Dayie
Jun 14, 2017·Nucleic Acids Research·Mary C ClayHashim M Al-Hashimi
Nov 21, 2017·Chemical Communications : Chem Comm·J KremserC Kreutz
Apr 19, 2019·Chembiochem : a European Journal of Chemical Biology·Maja MarušičKatja Petzold
Aug 18, 2016·Angewandte Chemie·Michael Andreas JuenChristoph Kreutz
Jun 3, 2018·Journal of Biomolecular NMR·Regan M LeBlancT Kwaku Dayie
Jul 18, 2018·Proceedings of the National Academy of Sciences of the United States of America·Jorjethe RocaAnjum Ansari
Oct 27, 2020·Nucleic Acids Research·Hala Abou AssiHashim M Al-Hashimi
Jul 27, 2017·Biophysical Journal·Susmita RoyKarissa Y Sanbonmatsu
Dec 6, 2019·Journal of the American Chemical Society·Alex PlumridgeLois Pollack

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