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. Author manuscript; available in PMC: 2012 Apr 12.
Published in final edited form as: Structure. 2010 Jan 13;18(1):83–93. doi: 10.1016/j.str.2009.10.014

Figure 4.

Figure 4

Effect of PPi. Top- Fluctuations obtained from equilibrium/equilibration trajectories for the closed conformation of pol-I-DNA complex with and without PPi in the parameter space of θ (degrees) vs. δ (Å). θ fluctuations are suppressed in the presence of the pyrophosphate indicating that the closed conformation is more stable in the presence of the pyrophosphate. Fluctuations for the open conformation are also given for comparison. Bottom- The time evolution of the order parameter θ during RP-TMD simulations of pol-I-DNA complex with and without PPi using the same perturbation. Fluctuations obtained from equilibration trajectories for the closed and open conformations are shown for reference (with time scaled to fit the range of the plot).