Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics

Abstract

We compare the performance of five magnesium (Mg(2+)) ion models in simulations of an RNA stem loop which has an experimentally determined divalent ion dependent conformational shift. We show that despite their differences in parametrization and resulting van der Waals terms, including differences in the functional form of the nonbonded potential, when the RNA adopts its folded conformation, all models behave similarly across ten independent microsecond length simulations with each ion model. However, when the entire structure ensemble is accounted for, chelation of Mg(2+) to RNA is seen in three of the five models, most egregiously and likely artifactual in simulations using a 12-6-4 model for the Lennard-Jones potential. Despite the simple nature of the fixed point-charge and van der Waals sphere models employed, and with the exception of the likely oversampled directed chelation of the 12-6-4 potential models, RNA-Mg(2+) interactions via first shell water molecules are surprisingly well described by modern parameters, allowing us to observe the spontaneous conformational shift from Mg(2+) free RNA to Mg(2+) associated RNA structure in unrestrained molecular dynamics simulations.