Riboswitch structure in the ligand-free state
Article first published online: 28 SEP 2011
Copyright © 2011 John Wiley & Sons, Ltd.
Wiley Interdisciplinary Reviews: RNA
Volume 3, Issue 3, pages 369–384, May/June 2012
How to Cite
Liberman, J. A. and Wedekind, J. E. (2012), Riboswitch structure in the ligand-free state. WIREs RNA, 3: 369–384. doi: 10.1002/wrna.114
- Issue published online: 19 APR 2012
- Article first published online: 28 SEP 2011
Molecular investigations of riboswitches bound to small-molecule effectors have produced a wealth of information on how these molecules achieve high affinity and specificity for a target ligand. X-ray crystal structures have been determined for the ligand-free state for representatives of the preQ1-I, S-adenosylmethionine I, lysine, and glycine aptamer classes. These structures in conjunction with complimentary techniques, such as in-line probing, NMR spectroscopy, Förster resonance energy transfer, small-angle scattering, and computational simulations, have demonstrated that riboswitches adopt multiple conformations in the absence of ligand. Despite a number of investigations that support ligand-dependent folding, mounting evidence suggests that free-state riboswitches interact with their effectors in the sub-populations of largely prefolded states as embodied by the principle of conformational selection, which has been documented extensively for protein-mediated ligand interactions. Fundamental riboswitch investigations of the bound and free states have advanced our understanding of RNA folding, ligand recognition, and how these factors culminate in communication between an aptamer and its expression platform. An understanding of these topics is essential to comprehend riboswitch gene regulation at the molecular level, which has already provided a basis to understand the mechanism of action of natural antimicrobials. WIREs RNA 2012, 3:369–384. doi: 10.1002/wrna.114.
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