Criteria for docking
We had four criteria for acceptable docking. (1) DBD-A and DBD-B both
had to appear to make protein-DNA contacts that have been demonstrated
biochemically. The first HTH makes stronger contacts with the
DNA8 than the second HTH and had to sit properly in
the major groove. As best as possible, the second HTH also needed to be
over the major groove. (2) Each half-site had to be roughly centered on
the appropriate DBD. (3) Using the surface representation feature in
PyMol (https://pymol.org), the docked structures had to have good
surface complementarity but could not intersect each other. (4) Because
AraC has been shown experimentally to bind to direct-repeatI1-I2 ,6 we chose docked structures with the
DBDs oriented as indicated in the biochemical contact experiments in
which the second HTH is closer to RNA polymerase (see Discussion).