Supplementary material for Horton and Perona, Proc. Natl. Acad. Sci. USA, 10.1073/pnas.090370797
Results
The 12 difference distance plots provided are for the following pairs of structures:
While these do not provide exhaustive coverage of all pairwise comparisons among the seven structures, they are representative of all the significant combinations (i.e., the plots between Unliganded A or B vs. the other DNA-bound forms are very similar to plots 1 and 2, etc).
For each plot the interatomic distances are subtracted in the order of the second-named structure minus the first-named structure. The contours from -3 to +3 Å are color-coded from red to blue as indicated on each plot. Numbering of the two monomers of the dimer is found across the top and down the left side; the numbering begins again at 1 at the start of the second monomer. Sharply lined regions of dark red or dark blue represent disordered segments of protein missing in one or both of the structures.
A summary of these data follows. The difference-distance matrix plot between form I and unliganded structures (A or B; plots 1 or 2) shows many large differences, particularly between monomers (or subunits) in the dimer. The dimerization domain (20-32, 150-161) and DNA binding domains (2-17, 37-141, 165-190) move in opposite directions. The loops binding DNA (Q: 68-73, R: 184-187, 100s: 97-103) also move differently than the regions around them do. The difference-distance matrix plot between nonspecific and forms I-IV (plots 3-6) shows that the specific complexes have shorter distances between the two monomers in the dimer at residues 37-92, 97-127, and 160-240. In addition to those segments, others move in opposing directions and include the dimerization domain (20-32, 150-161), the 100s loop (97-103), and the R loop (184-187). The difference-distance matrix plot between forms I-IV (plots 7-9) indicates that the regions getting closer are very similar to those identified on comparing the nonspecific and specific (I-IV) structures. The remaining part of the structure moves in a different way. Comparing forms II-IV (plots 10-12) to each other shows far fewer differences than between form I and forms II-IV. Segments 42-66 and 94-99 of one subunit move closer to the other subunit in II relative to III, but also in IV relative to III. The residues of the dimerization domain (20-32, 150-161) and C-terminal domain (210-245) also show changes in orientation. In summary, the largest differences in conformation between all structures occur between the two monomers of the dimer. However, the conformational changes are not simple, and contain regions moving independently of each other.