Figure 5.

Effects of the dinucleotide substitution on the structural dynamics of psi. Ψ^CES models without or with indicated substitution were subjected to MD simulations using the Amber 16 program package [19]. Structural changes during 0–500 ns of MD simulations were monitored with the root mean square deviations (RMSDs) between the initial model structure and the structures at given time points of MD simulation using the cpptraj module in AmberTools 16 as described previously [20,21,22,23,24]. (A) and (B) Changes in RMSDs during MD simulations. Ψ^CES RNAs without or with indicated substitution (A). Structural units of Ψ^CES RNAs without or the 226/227 dinucleotide substitution (B). (C) Means of RMSDs of indicated structural units of Ψ^CES RNA. Structural units of Ψ^CES were extracted from Ψ^CESs at 460, 470, 480, 490, and 500ns after MD simulations, superposed, and used for calculating RMSDs between NL4-3 and mutants. White, gray, black bars indicate RMSDs between NL4-3 Ψ^CES and Ψ^CESs with a G226A substitution, an A227C substitution, and a G226A/A227C dinucleotide substitution, respectively. Mean values and standard deviation with the five time points are shown.