Figure 5.

Dynamics in dimer during 150-ns simulation. (A and B) C^α-RMSF of dimer is shown for subunits A and B, respectively, calculated using two different superposition schemes. In one scheme, all dimer structures in the simulation were superimposed using C^α-atom best fits for subunit A (green), and in the other scheme, for subunit B (purple). In segments indicated by arrows corresponding to helices α2 (residues 36–46) and α11 (residues 262–272), C^α-RMSF was smaller in the case of superimposition on the other subunit than on its own subunit. (C) Rigid part of subunit (blue) and two helices α2 and α11 of other subunit (cyan) form a rigid core (rigid core RCA for subunit A, and RCB for subunit B). (D) C^α-RMSD from DNA-free crystal structure in 150-ns simulation is shown for RCA (green), RCB (purple), and a combined residue group of RCA and RCB (black).