Impact of TMAO on the preQ1 RNA Riboswitch Studied using Molecular Dynamics Simulations

Abstract

Trimethylamine N-oxide (TMAO) is an osmolyte that accumulates in response to cellular osmotic stress. TMAO is traditionally known for its role as a protein stabilizer but it has not been clear if it also stabilizes RNA structure. Here, we perform multiple molecular dynamics (MD) simulations to determine the effect of TMAO on RNA using the preQ1 riboswitch as a model system. To investigate osmolyte stabilization, several systems were run using the riboswitch solvated in different TMAO concentrations, including TMAO in its fully neutral state and with a fraction of TMAO in its protonated state.