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statement as to the quality of this prediction. It is possible that the predicted structure is
closer to the holo form of matrix ADK than the holo structure of intermembrane ADK
would indicate; likewise it is possible that the prediction is actually worse than the same
comparison suggests.
MurA
We have now shown that the Conformation Explorer can predict the bound conformation
for four cases in which a large scale domain motion is required. But what if the
(presumably unknown) holo structure is similar to the known conformation that will be
used as a starting point for prediction? One such case is that of MurA, which has been
cyrstallized bound to the antibiotic T6361.[84] The peculiarity of this ligand is that it
binds to the open conformation of MurA, rather than the closed, and interferes with the
mechanism of motion rather than binding to the active site.[84] In this case if the
predicted bound conformation is correct, it should not differ significantly from the open
structure by the measure of sRMSD. The starting structure used was taken from the
complex of MurA with an analogue of its natural ligand.[108]
By the criterion of docked energy, the Conformation Explorer would have selected a
conformer significantly more closed than the actual holo (insert 5.7.e). A similar error
would have occurred by the criterion of gyration radius (inset 5.7.f). However both of
these structures have low stability and significant domain distortion. The inclusion of the
latter two terms resulted in the correct prediction of a structure (inset 5.7.g) which is
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