Unravelling Mg$^{2+}$-RNA binding with atomistic molecular dynamics

TL;DR

This study uses advanced molecular dynamics simulations to map Mg$^{2+}$ binding sites on RNA, revealing how ion competition, RNA flexibility, and hybridization influence binding affinities with high accuracy.

Contribution

It introduces a modified bias-exchange metadynamics method for accurate, comprehensive mapping of Mg$^{2+}$-RNA interactions, including both direct and indirect binding modes.

Findings

Mg$^{2+}$ binding affinities are accurately reproduced and match crystallographic data.

Ion competition decreases Mg$^{2+}$ affinity, while hybridization increases it.

RNA flexibility affects Mg$^{2+}$ binding in a site-dependent manner.

Abstract

Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases. Based on this, we simulate a carefully chosen set of models that allows us to quantify the effects of competition with monovalent cations, RNA flexibility, and RNA hybridization. Our simulations reproduce the decrease and increase of Mg$^{2+}$ affinity due to ion competition and hybridization respectively, and predict that RNA flexibility has a site dependent effect. This suggests a non trivial interplay between RNA conformational entropy and divalent cation binding.