Gene Regulation by Riboswitches: From Folding Landscape to System Level Description

Riboswitches are RNA elements located in the untranslated regions of mRNAs that regulate gene expression by sensing and binding target cellular metabolites. In bacteria, they bind specific metabolites with a conserved aptamer domain, resulting in a change of the folding patterns of downstream expression platform that controls transcription termination or translation initiation. Purine riboswitches, which are among the simplest, display remarkable ligand selectivity and carry out entirely different functions despite the structural similarity of the aptamers. In this talk I will describe coarse-grained to map the folding landscape of purine riboswitches.  The folding landscapes provide insights into the differences between two purine riboswitches.  The results of the simulations are used as guide to develop a kinetic network model at the system level.