Dynamics of metal ions around an RNA molecule

Noncoding RNA molecules take part in many biological processes, while metal ions play crucial roles in helping RNAs to perform their functions. However, the statics and dynamics of these metal ions around RNA molecules are still not well understood. In this work, we report a detailed molecular dynamics study of the type-I $\mathrm{pre}{\mathrm{Q}}_{1}\text{\ensuremath{-}}\mathrm{bound}$ riboswitch aptamer domain (PRAD) at different ionic conditions (${\mathrm{K}}^{+}$, $\mathrm{N}{\mathrm{a}}^{+}$, and $\mathrm{M}{\mathrm{g}}^{2+}$). The results show that the structural properties and flexibility of the PRAD molecule greatly influence the distributions and dynamics of metal ions around it. Simultaneously, $\mathrm{N}{\mathrm{a}}^{+}$ ions show a stronger competitiveness with $\mathrm{M}{\mathrm{g}}^{2+}$ ions than ${\mathrm{K}}^{+}$ ions, and the three types of metal ions have different modes of interaction with the RNA molecule. Furthermore, we have also investigated specific binding sites of metal ions on the PRAD molecule and found that the dynamics and hydration structures of metal ions located at the ion-binding sites were obviously affected by the RNA structure near these ion-binding sites. These results may be useful to understand the role of the metal ions in noncoding RNA functions.