The solution structural ensembles of RNA kink-turn motifs and their protein complexes

Abstract

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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Figure 1: RNA kink-turns and Au-conjugated constructs.
Figure 2: The salt dependence of the KtA (Kt7) kinking equilibrium.
Figure 3: The ensemble of the kinked state of KtA (Kt7) and its salt dependence.
Figure 4: The KtA and KtB kink-turn conformational states without and with L7Ae.
Figure 5: The KtA•L7Ae and KtB•L7Ae ensemble and their salt dependence.
Figure 6: The distribution of N1- and N3-type kink-turn conformations.

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Acknowledgements

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.

Author information

X.S. designed the research, performed the experiments and analyzed and interpreted the data, with input from all authors. L.H. and D.M.J.L. provided the L7Ae protein. All authors contributed to writing of the paper.

Correspondence to Xuesong Shi or Pehr B Harbury or Daniel Herschlag.

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Supplementary Results, Supplementary Tables 1 and 2 and Supplementary Figures 1–11. (PDF 2028 kb)

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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). https://doi.org/10.1038/nchembio.1997

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