Petrone, Paula, Whitehead, Lewis, Dewhurst, Janetta, Tommasi, Ruben and Pomerantz, Andrea (2011) Atomic-Scale Characterization of Conformational Changes in the PreQ1 Riboswitch Aptamer upon Ligand Binding. Journal of Molecular Graphics and Modeling. ISSN 1093-3296

Abstract

Riboswitches are mRNA structural elements that act as intracellular sensors of small-molecule metabolites. By undergoing conformational changes capable of modulating translation or terminating transcription, riboswitches are able to play a role in regulating the concentration of essential metabolites in the cell. Computer-guided fluorescence experiments were carried out to interrogate molecular dynamics and conformational changes in the minimal riboswitch aptamer that binds 7-aminomethyl-7-deazaguanine (preQ1). Our combined experimental results and computational analysis suggest that the preQ1 riboswitch apo form is structured but shows no evidence of a ligand-binding pocket. Simulations of the apo and bound forms indicate a large conformational change is triggered by the breaking of the Watson-Crick base pairing of nucleotides G11 and C31 upon preQ1 removal, followed by collapse of the pocket due to interfering π-stacking. Computational predictions of local aptamer dynamics were validated by fluorescence experiments employing 2-aminopurine substitutions. In-line probing reactions confirmed that fluorophore-labeled riboswitches retain similar higher-order structural features as the unlabeled aptamer upon ligand binding, although their affinity for the ligand is reduced by the introduction of the fluorescent reporter.

Item Type:	Article
Related URLs:	Organisation
Related URLs:	Organisation
Date Deposited:	13 Oct 2015 13:15
Last Modified:	13 Oct 2015 13:15
URI:	https://oak.novartis.com/id/eprint/3564