FIGURE 8.

Correlation analysis based on MD simulations (a) and a so-called dynamical coupling analysis based on an elastic network model (61) (b). The correlation maps in panel a are colored according to the amplitude of the cross correlation matrix element C(i, j) defined in the text. The matrices were calculated from 3-ns MD simulations for both the s and p states. In the s state, the average amplitude of cross correlation is ∼0.71 inside domain 1A and ∼0.68 inside domain 2A; in the p state, the average amplitude of cross correlation is ∼0.58 inside domain 1A and ∼0.63 inside domain 2A. The PcrA-DNA complexes in panel b are colored according to the dynamical coupling of residues to the fluctuations of the ATP binding pocket in both the s and p states. The dynamic coupling is probed (see (61)) through perturbation of a residue's spring constant and monitoring the ensuing effect on the vibrational fluctuation 〈δr²〉 of the ATP binding site. The protein, DNA, and ATP are shown in surface, licorice, and vdW presentations, respectively.