Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer.

Peter C Anthony, Christian F Perez, Cuauhtémoc García-García, Steven M Block

Biophysics Program, Department of Physics, Stanford University, Stanford, CA 94305, USA.

Proceedings of the National Academy of Sciences of the United States of America 2012 Jan 31

filter terms:

Riboswitches are motifs in the untranslated regions (UTRs) of RNA transcripts that sense metabolite levels and modulate the expression of the corresponding genes for metabolite import, export, synthesis, or degradation. All riboswitches contain an aptamer: an RNA structure that, upon binding ligand, folds to expose or sequester regulatory elements in the adjacent sequence through alternative nucleotide pairing. The coupling between ligand binding and aptamer folding is central to the regulatory mechanisms of thiamine pyrophosphate (TPP) riboswitches and has not been fully characterized. Here, we show that TPP aptamer folding can be decomposed into ligand-independent and -dependent steps that correspond to the formation of secondary and tertiary structures, respectively. We reconstructed the full energy landscape for folding of the wild-type (WT) aptamer and measured perturbations of this landscape arising from mutations or ligand binding. We show that TPP binding proceeds in two steps, from a weakly to a strongly bound state. Our data imply a hierarchical folding sequence, and provide a framework for understanding molecular mechanism throughout the TPP riboswitch family.

Citation

Peter C Anthony, Christian F Perez, Cuauhtémoc García-García, Steven M Block. Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. Proceedings of the National Academy of Sciences of the United States of America. 2012 Jan 31;109(5):1485-9