Simulating the Melting of the Salmonella 4-U RNA Thermometer Using Replica Exchange Molecular Dynamics to Assess Force-Field Accuracy

Abstract

We have developed a coarse-grained structure based model to investigate the excess ion atmosphere around an irregular RNA structure in aqueous solution containing MgCl 2 and KCl under physiological ionic strength. The structure based model captures the dynamics of outer sphere Mg 2þ population. Condensation of K þ and Clis described implicitly, while Mg 2þ ions are treated explicitly. The implicit model takes into account electrostatic heterogeneity of phosphates, electrostatic and mixing free energy of the screening ions, and enforces ion accessibility near the RNA. We couple the electrostatics to the structure based coarse-grained model and probe fluctuations by molecular dynamics simulations. KCl condensation dynamically responds to conformational fluctuations of the RNA. The RNAs investigated are 58-mer from the large subunit ribosomal RNA and a 26 nucleotide pseudoknot from Beet Western Yellow Virus RNA. We predict the excess ion atmosphere of the native and mimics of intermediate state conformations of the RNAs. We determine the effects of chelated ions (Mg 2þ and K þ) on the excess ion atmosphere and the Mg 2þ-RNA interaction free energy. We show the that excess ion atmosphere is sensitive to small native basin fluctuations, i.e., RNA dynamics must be included for a quantitative description of the full conformational ensemble. For both RNAs, we compare our predictions against fluorescence titration data of Draper and coworkers. Work done in collaboration with A. Wang, S. Roy, R. Hayes, K. Streu, and J. N. Onuchic. Work supported by John Simon Guggenheim Memorial Foundation Fellowship (UM).