Figure 3.

Root mean square deviation (rmsd; top) and radius of gyration (rgyr; bottom) with respect to the wild-type crystal structure in the closed conformation. The closed conformation (CC) and the open conformation (OC) should be viewed as reference points for the subsequent simulations of the domain movement. The simulation with position restraints (PR) shows a stepwise opening due to the position restraints and a spontaneous closing after the restraints were released. The simulation with restraints on the ϕ and ψ angles of R254 (PP) closed almost fully, but the RMSD shows that a different closed conformation is reached. The simulation with distance restraints on the two hydrogen bonds R517-Q90 and Q643-E182 (HB) shows almost a full closure of the protein.