TMAO Osmoprotectant Interactions with E.coli 16S Ribosomal RNA using Molecular Dynamics

Trimethylamine N-Oxide (TMAO) is an osmolyte that has been extensively characterized through experiments and computational studies for its role in stabilizing proteins under osmotic stress. However, its effects on RNA, while experimentally demonstrated and recently computationally characterized to a limited extent, are poorly understood. Previous studies have primarily examined TMAO-RNA interactions with single nucleotides or simple hairpin structures. In this study, we conducted all-atom molecular dynamics (MD) simulations to explore TMAO-RNA interactions of the folded E.coli 16S rRNA, focusing on both canonical nucleotides and post-transcriptional modifications. We aim to investigate emergent phenomena and possibly pave the road to understanding the role of TMAO in the stability and function of RNA and the ribosome. We generated three independent 500 ns MD simulation trajectories in TMAO solution and three 500 ns controls in a water box with the 16s rRNA. We found interactions between the TMAO oxygen atom and hydrogen bond donors in canonical and modified nucleotide bases, similar to what was observed for hairpins. Differences in unfolding behavior were observed. We also report TMAO interactions with the hydroxyl groups of specific chemically modified nucleotides.