l - People

Upon binding ATP, M rotates approximately 45° with respect to S. The large scale of
this change and the existence of structural domains makes BC a good test case for our
method.
We used the BC subunit of Aquifex aeolicus PC[103] as the starting or apo structure.
The ligand-free BC subunit of E. coli ACC has been crystallized (PDB ID: 1DV1), but
many residues are disordered and so the structure of the M domain is not entirely
clear.[104] No ATP-bound structure of A. aeolicus BC is available, and so we used ATP-
bound BC from E. coli ACC[104] as our holo structure. The sequence differences
between the starting and holo structures had an impact on the results as we will discuss.
FlexOracle[90] predicts a hinge at residues 86-89 and 182-185, which can be used to
choose the location of L.
The significant sequence and structural differences between the starting and holo
structures, which come from different organisms, made comparison on the basis of
sRMSD difficult. As we did for GlnBP, in figure 5.4.a we color the conformers by
sRMSD. The lowest-sRMSD conformer is indicated by the larg sphere. However that
conformer was only partially closed, and visibly different from the holo structure, shown
in inset 5.4.c. The structure that minimizes the fitness function (inset 5.4.d) bears clear
similarities to the holo in relative domain orientation. The starting structure (inset 5.4.b)
shows the extent of the Domain 3 motion involved.
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