Mg2+ Shifts Ligand-Mediated Folding of a Riboswitch from Induced-Fit to Conformational Selection

• Published in: Journal of the American Chemical Society Vol. 137; no. 44; pp. 14075 - 14083
• Main Authors: Suddala, Krishna C, Wang, Jiarui, Hou, Qian, Walter, Nils G
• Format: Journal Article
• Language: English
• Published: American Chemical Society 11.11.2015
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/jacs.5b09740

Bacterial riboswitches couple small-molecule ligand binding to RNA conformational changes that widely regulate gene expression, rendering them potential targets for antibiotic intervention. Despite structural insights, the ligand-mediated folding mechanisms of riboswitches are still poorly understood. Using single-molecule fluorescence resonance energy transfer (smFRET), we have investigated the folding mechanism of an H-type pseudoknotted preQ1 riboswitch in dependence of Mg2+ and three ligands of distinct affinities. We show that, in the absence of Mg2+, both weakly and strongly bound ligands promote pseudoknot docking through an induced-fit mechanism. By contrast, addition of as low as 10 μM Mg2+ generally shifts docking toward conformational selection by stabilizing a folded-like conformation prior to ligand binding. Supporting evidence from transition-state analysis further highlights the particular importance of stacking interactions during induced-fit and of specific hydrogen bonds during conformational selection. Our mechanistic dissection provides unprecedented insights into the intricate synergy between ligand- and Mg2+-mediated RNA folding.