With the growing number of crystal structures of RNA and RNA–protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA–protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes.
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We thank T. Matsui and T. Weiss at beamline 4-2 of the Stanford Synchrotron Radiation Lab (SSRL) for technical support in synchrotron small-angle X-ray scattering experiments, and members of the Herschlag, the Lilley and the Harbury labs and H. Al-Hashimi for helpful discussions and comments on the manuscript. This work was supported by US National Institutes of Health grants PO1 GM066275 (D.H.) and DP-OD000429-01 (P.B.H.) and by grants from Cancer Research UK C28/A4959 and Wellcome Trust project 092056 to D.M.J.L.
The authors declare no competing financial interests.
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Shi, X., Huang, L., Lilley, D. et al. The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nat Chem Biol 12, 146–152 (2016) doi:10.1038/nchembio.1997
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