Role of Water and Ions on the Dynamical Transition of RNA

Abstract

We have performed molecular dynamics simulations of hydrated polycrystalline powder hammerhead ribozyme at various temperatures from 50 to 300 K to determine the role of water and ions on the dynamical transition of RNA. Calculated mean-square displacement as a function of temperature is in agreement with existing neutron scattering experiments. Using this model, we were able to investigate the role of water and monovalent ion structure and dynamics on the appearance of anharmonic motions in RNA as a function of temperature. Compared to experimental and simulation results of proteins under similar environmental conditions, the amplitude of motions in RNA are smaller. While the structure and dynamics of monovalent ions interacting with RNA infer a stronger coupling than that of water, it is found that the relaxation of water from the surface of RNA is sufficient for the increase in anharmonic motions above the dynamical transition temperature. The nature and temperature dependence of fast and slow hydrogen bond dynamics between proteins and RNA were found to be similar, thus indicating that the dynamical transition of RNA and proteins are governed by relaxation of surface hydration water.