Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops
Figure 4
Hub residues and their location on the 3D structure of ARID domains.
The connectivity degree for each PSN hub of DriFREE (A) and DriDNA (B) simulations are shown as a function of the protein residue in the left panels. Since in a PSN a hub is defined as a residue connected by at least three edges, all the residues with node degree lower than three are set at zero. Black triangles indicate the position of the residues experimentally known to impair DNA-binding [9], whereas a gray triangle indicates Q101/Q111 position. The right panels show the location of these hubs on a reference 3D structure of the corresponding target protein. The structure is depicted as ribbon with rainbow shade of colors according to the node degree. The corresponding figures for ARID3AFREE and 1 µs DriFREE simulations are shown in Figure S4. The residue numbering is referred to Dri in the figure where P47, W78, F96, Q101 and Y109 correspond to P57, W88, F106, Q111 and Y119 in ARID3A.