Computational Study of Unfolding and Regulation Mechanism of preQ₁ Riboswitches

Riboswitches are novel RNA regulatory elements. Each riboswitch molecule consists of two domains: aptamer and express platform. The three-dimensional (3D) structure of the aptamer domain, depending on ligand binding or not, controls that of the express platform, which then switches on or off transcriptional or translational process. Here we study the two types of preQ1 riboswitch aptamers from T. Tengcongensis (denoted as Tte preQ1 riboswitch for short below) and Bacillus subtilis (denoted as Bsu preQ1 riboswitch for short below), respectively. The free-state 3D structure of the Tte preQ1 riboswitch is the same as its bound state but the Bsu preQ1 riboswitch is not. Therefore, it is very interesting to investigate how these riboswitches realize their different regulation functions. We simulated the unfolding of these two aptamers through all-atom molecular dynamic simulation and found that they have similar unfolding or folding pathways and ligand-binding processes. The main difference between them is the folding intermediate states. The similarity and difference of their unfolding or folding dynamics may suggest their similar regulation mechanisms and account for their different functions, respectively. These results are also useful to understand the regulation mechanism of other riboswitches with free-state 3D structures similar to their bound states.