Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues
Figure 2
The covariance matrix is defined as described in Materials and Methods. Vector products representing the maximum extent of correlated motion (Å2) for each Cα pair of each hexamer are plotted. The color scale indicates the degree of correlation: red, positively correlated; blue, negatively correlated; white, uncorrelated. Each panel presents two covariance matrices fused along the diagonal to eliminate redundancy and facilitate comparison of the two simulations indicated above the panel; the simulation presented in the upper left half is indicated first, followed by a slash (/) representing the diagonal, followed by the simulation in the lower right half. The reference state for calculating the extent of Cα motion as described in Materials and Methods is the hexamer for panels A and D and the trimer composed of ABC monomers for panels B and C.