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emoving ligands from the structure should increase accuracy over the alternative. In fact
the single-cut predictions are roughly as accurate for the closed conformer as for the open
(molmovdb.org/FO). The two-cut predictor did not work well for either the open or
closed conformer of this protein. When one considers that results were also poor for
Troponin C (see Figure 3.2) it is clear that the two-cut predictor is not very good at
detecting triple-stranded hinges.
Ribose binding protein (RBP) (open)
RBP belongs to a sizeable family of soluble gram-negative bacterial periplasmic binding
proteins with diverse ligands and functions. They are abundant and bind their substrates
with high affinity and specificity, and thus easily sequester nutrients appearing in
sporadically in the environment.[70] The open conformation is predominant in the
uncomplexed form. Upon ligand binding, the two separated domains close down around
the ligand by virtue of a 30° rotation in the hinge that connects them.
Results for the apo form are shown in Figure 3.7. The single-cut predictor had a strong
minimum at residue 103, and a weak one at residue 235, corresponding to HAG hinges at
those locations. It incorrectly suggests flexible points around residues 208 and 50. The
two-cut predictor worked perfectly for both open and closed conformers.
Calmodulin (CaM) (open, calcium-bound form)
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