Figure 7

Calmodulin (open, calcium bound form). Morph ID: f958972-2168 PDB ID: 3cln. HAG hinges: 80,81. b. The TINKER version of the single-cut predictor gives ambiguous results for this calcium-bound protein, but good results for the calcium-free form [37]. The FoldX single-cut predictor, worked well for both calcium-bound and calcium-free forms Calmodulin. Nonetheless we recommend caution when treating metal-bound proteins, since the two-cut predictor had mixed results here. c. The 2-cut predictor results: Primary prediction: residues 30–33, 66–69. Additional predictions: 104–107;84–87. Although the primary prediction does not coincide with the annotated hinge, upon inspecting the corresponding morph (78252-5656) we observed that indeed there are hinges coinciding with the predicted location, although they result in less backbone motion than the hinge at residue 80. Similar points (residues ~36,63) are annotated hinges in the evolutionarily related Troponin C (morph 333010-30921). In the interest of maintaining the objectivity of the HAG, we did not update the hinge annotation. We further note that the third lowest-energy local minimum (84–87) is close to the HAG hinge. Thus although the first prediction did not coincide with the HAG, the results nonetheless yield significant insight into the flexibility of the protein.