Fig. 2
From: Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations
Analysis of sodium (Na⁺) and chloride (Cl⁻) ion interactions with the MS2 capsid. (a) Density of sodium across the entire capsid in the MS2_MP system. (b) Sodium occupancy in a CP trimer of dimers. (c) CP trimer of dimers interface with sodium binding sites (Y129, S2, F4). (d) Density of chloride ions on the capsid interior surface. (e) Chloride occupancy in CP trimeric dimers. (f) CP dimer unit showing basic residue side chains that interact with chlorides. Experimental structures are shown of: (g) RNA – dimer capsid complex highlighting all protein basic residues involved in this interaction; and (h) MP – RNA complex with depicted protein basic residue side chains involved in this interaction. (i) Per-residue chloride occupancy fraction is shown for MP with interacting basic residues highlighted. Protein is shown in cartoon representation in all panels. RNA is shown in licorice representation in (g) and cartoon representation in (h). In (a), (c) and (d) CP is coloured according to asymmetric (blue/red) and symmetric dimers (grey/grey)
