The conformational space of RNase P RNA in solution

Yun-Tzai Lee, Maximilia F. S. Degenhardt, Ilias Skeparnias, Hermann F. Degenhardt, Yuba R. Bhandari, Ping Yu, Jason R. Stagno, Lixin Fan, Jinwei Zhang and Yun-Xing Wang ()
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Yun-Tzai Lee: National Cancer Institute
Maximilia F. S. Degenhardt: National Cancer Institute
Ilias Skeparnias: National Institute of Diabetes and Digestive and Kidney Diseases
Hermann F. Degenhardt: National Cancer Institute
Yuba R. Bhandari: National Cancer Institute
Ping Yu: National Cancer Institute
Jason R. Stagno: National Cancer Institute
Lixin Fan: Inc.
Jinwei Zhang: National Institute of Diabetes and Digestive and Kidney Diseases
Yun-Xing Wang: National Cancer Institute

Nature, 2025, vol. 637, issue 8048, 1244-1251

Abstract: Abstract RNA conformational diversity has fundamental biological roles1–5, but direct visualization of its full conformational space in solution has not been possible using traditional biophysical techniques. Using solution atomic force microscopy, a deep neural network and statistical analyses, we show that the ribonuclease P (RNase P) RNA adopts heterogeneous conformations consisting of a conformationally invariant core and highly flexible peripheral structural elements that sample a broad conformational space, with amplitudes as large as 20–60 Å in a multitude of directions, with very low net energy cost. Increasing Mg2+ drives compaction and enhances enzymatic activity, probably by narrowing the conformational space. Moreover, analyses of the correlations and anticorrelations between spatial flexibility and sequence conservation suggest that the functional roles of both the structure and dynamics of key regions are embedded in the primary sequence. These findings reveal the structure–dynamics basis for the embodiment of both enzymatic precision and substrate promiscuity in the RNA component of the RNase P. Mapping the conformational space of the RNase P RNA demonstrates a new general approach to studying RNA structure and dynamics.

Date: 2025
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DOI: 10.1038/s41586-024-08336-6

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