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Visualizing spatially correlated dynamics that directs RNA conformational transitions

Nature volume 450, pages 1263–1267 (2007)Cite this article

Abstract

RNAs fold into three-dimensional (3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals1,2,3. RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways4,5. However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using ‘relativistic’ sets of residual dipolar couplings (RDCs)6,7. Using this approach, we uncovered super-large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 53° and 110° in a highly correlated manner (R = 0.97) while simultaneously (R = 0.81–0.92) bending by about 94°. Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand-bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand-induced transitions along specific predefined conformational pathways.

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Figure 1: Measurement of RNA helix motions in 3D using helix-anchored frames and RDCs.
Figure 2: Helix motions from model-free order-tensor analysis of RDCs.
Figure 3: Visualizing TAR inter-helical motions in 3D.
Figure 4: Correlated TAR dynamics steer ligand-induced transitions.

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Acknowledgements

We thank A. Kurochkin for NMR expertise. We acknowledge the Michigan Economic Development Cooperation and the Michigan Technology Tri-Corridor for the support of the purchase of a 600 MHz spectrometer, and the W. F. Keck Foundation, National Science Foundation (NSF) and National Institutes of Health (NIH) for funds for the purchase of an 800 MHz spectrometer. Supported by an NIH and NSF grant.

Author Contributions H.M.A. conceived the technique, Q.Z. and H.M.A. analysed the data and wrote the paper. Q.Z., C.K.F. and H.M.A. analysed the HIV-2 TAR data. Q.Z., A.C.S. and C.K.F. prepared the samples and performed the NMR experiments.

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Authors and Affiliations

  1. Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA,

    Qi Zhang, Andrew C. Stelzer, Charles K. Fisher & Hashim M. Al-Hashimi

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  1. Qi Zhang
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  4. Hashim M. Al-Hashimi
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Corresponding author

Correspondence to Hashim M. Al-Hashimi.

Additional information

Supplementary Movies are hosted at the publicly accessible Database of Macromolecular Movements (http://www.molmovdb.org/).

Supplementary information

Supplementary Information

This file contains Supplementary Discussion; Supplementary Tables S1-S4; Supplementary Figures S1-S5 with Legends; Legends to Supplementary Movies 1-2; and additional references. (PDF 3655 kb)

Supplementary Movie 1

This file contains Supplementary Movie 1 showing the TAR inter-helix motional trajectory. Shown are transitions 1→2, 2→3, and 3→1 between conformers in ensemble A via the linear conformational pathway in 3D inter-helix Euler space (see green lines in Fig. 4a of the main manuscript). HI and HII are shown in black and orange and are elongated in gray for clarity. (MOV 2411 kb)

Supplementary Movie 2

This file contains Supplementary Movie 2 showing how the TAR inter-helix motional trajectory encapsulates ligand-bound conformations. The TAR inter-helical motional trajectory is shown (in green) together with the ligand bound TAR conformations (in gray). Helix HI was used to superimpose all structures, which are represented using idealized A-form helices. (MOV 10611 kb)

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Zhang, Q., Stelzer, A., Fisher, C. et al. Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450, 1263–1267 (2007). https://doi.org/10.1038/nature06389

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