Diffuse ions coordinate dynamics in a ribonucleoprotein assembly

Proper ionic concentrations are required for the functional dynamics of RNA and ribonucleoprotein (RNP) assemblies. While experimental and computational techniques have provided many insights into the properties of chelated ions, less is known about the structural/energetic contributions of diffuse ions. To address this, we present a model that is designed to identify the influence of diffuse ions on the dynamics of biomolecular assemblies. This model employs all-atom (non-H) resolution and explicit ions (monovalent and divalent), where effective potentials account for hydration effects. To benchmark the model, we show that it accurately predicts the number of excess Mg2+ ions for prototypical RNA systems. We then apply it to a bacterial ribosome and find that diffuse ions control the position of the extended L1 stalk region. The simulations also illustrate how diffuse ions facilitate long-range attraction between tRNA and the stalk region. Together, this analysis reveals the direct impact of diffuse ions on the dynamics of an RNP assembly.