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f926644-25628), and the apo structure shown in Figure 6 (PDB ID 4TNC, morph ID
f960267-11022), which has calcium bound to the high affinity sites III and IV but not I
and II.
Coarse-grained geometric information was insufficient to predict the hinges of interest, as
evidenced by the failure of the hNM predictors (Figure 3, Supplementary Table 5).
Recall that the Gaussian Network Model used to implement the HNMA method uses only
alpha-carbon position information. Similarly, StoneHinge did not coincide with the HAG
hinges. The segment boundaries found by TLSMD for partitioning of the protein chain
into 2, 3, 4, or 5 segments are marked by a pair of ‘+’ symbols indicating the residues on
either side of the boundary. As can be seen, TLSMD and FO were partially successful.
This motion is particularly challenging to predict by general-purpose methods such as
those presented here, since they cannot directly treat the ion binding and release
required[83] for motion. Since the calcium ion coordinates seven ligands, including
water, backbone carbonyl and side chain oxygens in a pentagonal bipyramidal
arrangement, its neglect can be expected to strongly reduce the accuracy of the
prediction.
Interestingly, NMR studies[49, 83] indicate that that residues 83-91 are unstable (much
like the analogous region of calmodulin, residues 76-81) and tend to unwind. So
TLSMD, hNMa, StoneHinge, and (consequently) HingeMaster succeeded in finding an
experimentally characterized motion not annotated in HAG. This underscores the
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