MD simulation of ZnF-RNA complexes. (A) RMSF of each protein residue and RNA base during the simulation (average of three replicates of 50 nsec simulations) in four models (ZnF WT + GGU, ZnF WT + GGG, ZnF NRmut + GGU, ZnF NRmut + GGG). (B) Heat map of H-bond relative intensity (magnitude indicated by color bar) between the three RNA bases and the RNA-contacting residues during the simulation (average of three replicates of 50 nsec simulations). (C–E) Representative structures of ZnF-RNA complexes during the simulations. Note that the orientations in the lower panels are different from the top panels (slightly rotated). (C) The representative structure of ZnF WT + GGU (green); (D) the representative structure of ZnF NRmut + GGU (yellow); (E) the representative structure of ZnF NRmut + GGG (cyan) overlaying with the representative structure of ZnF NRmut + GGU (white). The protein residues highlighted in the top panel are Arg86/Asn86 and Trp79.
