Diffuse Ions Coordinate Dynamics in a Ribonucleoprotein Assembly

Abstract

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 energetic contributions of diffuse ions to large-scale conformational rearrangements. To address this, we present a model that is designed to quantify the influence of diffuse monovalent and divalent ions on the dynamics of biomolecular assemblies. This model employs all-atom (non-H) resolution and explicit ions, where effective potentials account for hydration effects. We first show that the model accurately predicts the number of excess Mg 2+ ions for prototypical RNA systems, at a level comparable to modern coarse-grained models. We then apply the model to a complete ribosome and show how the balance between diffuse Mg 2+ and K + ions can control the dynamics of tRNA molecules during translation. The model predicts differential effects of diffuse ions on the free-energy barrier associated with tRNA entry and the energy of tRNA binding to the ribosome. Together, this analysis reveals the direct impact of diffuse ions on the dynamics of an RNP assembly.

Identifying Strategies to Experimentally Probe Multidimensional Dynamics in the Ribosome

“…To address this, a SMOG model variant was recently presented that includes explicit electrostatics and diffuse ions. 70 In that specific study, the process of aa-tRNA accommodation was simulated, where the tRNA molecule spontaneously associates and dissociates with the ribosomal A site. Those calculations showed that, even though the free-energy barrier was very sensitive to the ionic composition, the overall mechanistic/structural properties were robust.…”

Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome

“…42 While it is common for all-atom SMOG models to use homogeneous atom sizes, 42 the current study applies a heterogeneous approach that is based on comparison with the nonbonded parameters in AMBER. Specifically, we used the excluded volume model developed by Wang et al, 37 which is available in the SMOG 2 template repository (force field ID: AA_12−18_cutoff_Wang22.v1). Here, excluded volume interactions between atom pairs are defined by a 12−18 potential, where the values of C 12 and C 18 were obtained by fitting to the corresponding vdW parameters in the AMBER99sb-ildn force field.…”

“…Since the PTC imposes a highly confined environment on the tRNA molecule (Figure 1g), we used a recently released model that has a refined representation of atomic-level steric interactions. 37 With this model, we examine the behavior of the 3′-CCA tail during aa-tRNA accommodation and describe the sterically defined pathways by which the tail can enter the PTC. We find a pronounced, sterically induced barrier for accommodation of the 3′-CCA tail.…”

“…For this, we constructed a simplified energetic model of the ribosome, which was inspired by the energy landscape principles developed by Onuchic, Wolynes and colleagues. − Specifically, we applied an all-atom “structure-based” (Go-like) model to perform molecular dynamics simulations (over 1000 independent tail accommodation events). Since the PTC imposes a highly confined environment on the tRNA molecule (Figure g), we used a recently released model that has a refined representation of atomic-level steric interactions . With this model, we examine the behavior of the 3′-CCA tail during aa-tRNA accommodation and describe the sterically defined pathways by which the tail can enter the PTC.…”

Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts

“…Analyses of RNA structures and simulations have shown that cations bind to discrete sites on RNA rather than nonspecifically (18)(19)(20)(21)(22)(23)(24). Optical melting experiments, small-angle x-ray scattering (SAXS), nuclear magnetic resonance, and gel electrophoretic studies suggest that there is a complicated interplay between RNA conformations and charge density (25)(26)(27)(28)(29)(30)(31)(32)(33).…”