Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops
Figure 5
Long-range paths are promoted by DNA interaction in Dri simulations.
Left panel) Distribution of the shortest paths of communication identified by the PSN-LMI approach in the different simulations employed in this study. Average values from the different replicates of the same system are shown. Right panel) Differences among the paths of length higher than 8 residues (starting and final residues included) in DriDNA and DriFREE simulations. The paths that are present only in DriDNA or DriFREE simulations are shown as red and blue cylinders, respectively. Nodes of the paths are shown as spheres centered on the Cα atom. The nodes belonging to the paths from K113 to both L56 at the base of L1 (K113→Y109→L32→L106→F28→L56) and L87-I91-P88 in L2 (K113→Y109→L32→L106→L59→L98→L87→I91→P88, Dri numbering) are highlighted by different shades of colors from red to blue/black. K113, L56 and P88 are shown as sticks.