Thermodynamic and kinetic folding of riboswitches

Methods in Enzymology
Stefan BadeltIvo L Hofacker

Abstract

Riboswitches are structured RNA regulatory elements located in the 5'-UTRs of mRNAs. Ligand-binding induces a structural rearrangement in these RNA elements, effecting events in downstream located coding sequences. Since they do not require proteins for their functions, they are ideally suited for computational analysis using the toolbox of RNA structure prediction methods. By their very definition riboswitch function depends on structural change. Methods that consider only the thermodynamic equilibrium of an RNA are therefore of limited use. Instead, one needs to employ computationally more expensive methods that consider the energy landscape and the folding dynamics on that landscape. Moreover, for the important class of kinetic riboswitches, the mechanism of riboswitch function can only be understood in the context of co-transcriptional folding. We present a computational approach to simulate the dynamic behavior of riboswitches during co-transcriptional folding in the presence and absence of a ligand. Our investigations show that the abstraction level of RNA secondary structure in combination with a dynamic folding landscape approach is expressive enough to understand how riboswitches perform their function. We apply our ap...Continue Reading

Citations

Aug 31, 2016·Nucleic Acids Research·Adi MillmanRotem Sorek
Jan 31, 2017·Journal of the American Chemical Society·Christina HelmlingHarald Schwalbe
Feb 17, 2017·Biochemistry·Maja Etzel, Mario Mörl
Sep 9, 2017·Bioinformatics·Juraj MichálikYann Ponty
Nov 18, 2017·International Journal of Molecular Sciences·Sha GongWenbing Zhang
Oct 9, 2020·Nature Communications·Nicolaas M Angenent-MariJames J Collins
Nov 14, 2017·Emerging Topics in Life Sciences·Bernhard C ThielIvo L Hofacker

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