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 Waa

SUBMITTER: Bergonzo C 

PROVIDER: S-EPMC4944181 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature