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Figure 4.4: Glutamine Binding Protein (open)
Morph ID: f205132-23662 PDB ID: 1GGG
HAG hinges (residues 85-86,176-177)
Above, (a) and (b) illustrate the procedure for generating CDBI and ERI predictions.
First, the α-carbon correlation matrix (plotted in a.) is obtained using GNM. In this case,
residues ranging from 85 to 180 check have highly correlated motion. To a somewhat
lesser degree, residues 1 to 80 are also correlated (dotted turquoise box). A second
matrix is obtained the elements i,j of which contain the average correlation for a
submatrix of the correlation matrix spanning residues i to j. This is then weighted by
multiplying each element by -|i-j|. The resulting matrix is plotted in (b). The minima of
this matrix correspond to the boundaries of structural domains which are continuous in
sequence. The most significant of these (in absolute value) is i,j = 84,180. A secondary
minimum also exists at i,j = 1,80. hNMb therefore reports residues 84,85,180,181 as the
predicted hinge location. hNMd works by excluding residues in continuous domains and
reporting the remaining ones as possible hinges. Therefore, ERI reports residues 85-88
and 181-217 as hinges.
In (c.) we show the two-cut FlexOracle (FoldX) graph,. The minimum at 83,179 is
visible.
In (d) we show the protein colored by HingeMaster score.
In (e) we show the output of the FO1, hNMa, HingeSeq, and HingeMaster predictors.
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