Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 397, Issue 5, Pages 1298-1306Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2010.02.025
Keywords
Langevin dynamics; P RNA; S-domain
Categories
Funding
- National Institutes of Health (NIH) [GM57880, GM081642, RR-08630]
- U.S. Department of Energy, Basic Energy Sciences, Office of Science [W-31-109-ENG-38]
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RNA folding occurs via a series of transitions between metastable intermediate states for Mg2+ concentrations below those needed to fold the native structure. In general, these folding intermediates are considerably less compact than their respective native states. Our previous work demonstrates that the major equilibrium intermediate of the 154-residue specificity domain (S-domain) of the Bacillus subtilis RNase P RNA is more extended than its native structure. We now investigate two models with falsifiable predictions regarding the origins of the extended intermediate structures in the S-domains of the B. subtilis and the Escherichia coli RNase P RNA that belong to different classes of P RNA and have distinct native structures. The first model explores the contribution of electrostatic repulsion, while the second model probes specific interactions in the core of the folding intermediate. Using small-angle X-ray scattering and Langevin dynamics simulations, we show that electrostatics plays only a minor role, whereas specific interactions largely account for the extended nature of the intermediate. Structural contacts in the core, including a nonnative base pair, help to stabilize the intermediate conformation. We conclude that RNA folding intermediates adopt extended conformations due to short-range, nonnative interactions rather than generic electrostatic repulsion of helical domains. These principles apply to other ribozymes and riboswitches that undergo functionally relevant conformational changes. (C) 2010 Elsevier Ltd. All rights reserved.
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