(color online) The translocation is facilitated by an internal potential of the enzyme itself. (a) The time series of the change in position of Tyr639 relative to the PRE position (red line) and that of Arg627 relative to the position when the O helix and fingers domain are in the closed conformation (blue line) for system 7 where the DNA-RNA and αβ methylene ATP are removed, i.e., keeping only the enzyme in the insertion complex (PDB 1S76). The latter trace is offset by −0.2 nm on the y axis for clarity. (b) A snapshot of the structure produced from the trajectory shown in panel (a), where Tyr639 is in the POST position and the O helix and fingers domain are in the semi-closed conformation (yellow). Note that because there is no interaction with the DNA-RNA base pair, the side chain of Tyr639 fluctuates considerably. However, the CA atom of Tyr639 remains stable in the POST position. The structures of the enzyme shown in red and green are the same as those in Fig. 2(b). (c) The position distribution of Tyr639 for system 7, which involves 20 trajectories with simulation periods of 20 ns each. Yellow, green, and blue lines represent Gaussian fits; the cyan line represents the sum of three Gaussians. (d) The position distribution of Arg627 for system 7 with 20 trajectories with a simulation period of 20 ns each. The blue line represents the Gaussian fit. (e) The time series of the change in position of Tyr639 relative to the PRE position (red line) for system 8 where residue Arg627 is restrained in system 7. (f) A snapshot of the structure obtained from the trajectory shown in panel (e), where Tyr639 is in the POST position and the O helix and fingers domain are in the closed conformation (yellow). Note that because there is no interaction with the DNA-RNA base pair, the side chain of Tyr639 fluctuates considerably. However, the CA atom of Tyr639 remains stable in the POST position. The structures of the enzyme shown in red and green are the same as those in Fig. 2(b). (g) The position distribution of Tyr639 for system 8 with 20 trajectories with a simulation period of 20 ns each. Yellow, green, and blue lines represent Gaussian fits; the cyan line represents the sum of three Gaussians.