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Figure 2.
Fig. 2. (A) Cross-correlation matrix plot of the
distances between  -carbons i
and j of each DNA-bound structure, and roll angle of the DNA at
the center TA step. Shown is the upper right quadrant of the
full matrix. Residues 1-245 of subunit I are on the horizontal
axis, and residues 1-245 of subunit II are on the vertical axis.
A gray point is placed for -carbon
atom pairs having |r| > 0.90 (i.e., the distance between these
atoms is significantly correlated with roll angle for the five
structures I-IV and NS). Shading of points from gray to black
indicates values of |r| ranging from 0.9 to 1.0. Colored
segments 1 through 5 (Upper and Left) are assigned by inspection
of this plot. Residues 184-187 in segment 4 and 221-228 in
segment 5 are not included in the calculation because they are
disordered in the nonspecific complex; these residues appear as
stripes with discrete borders. Similar plots were calculated
with each of the other two measures of DNA-bending angle (Table
3) as well as with random values for the bend angle. The total
number of points (i, j) having |r| > 0.90 are: using center-step
bend of the DNA, 28,251; using roll angle at the center step,
34,681; using overall bend of the DNA, 10,465; using random
values for bend angles, 1,893. Segments 1 through 5 appear in
the three plots using experimental DNA-bending angles but not in
the plot using random bend angles. Inspection of other quadrants
of the matrix plot shows no significant correlations for
interatomic distances within either subunit. Analysis of
cross-correlation coefficients has also been used to assess
correlated atomic displacements in molecular dynamics
simulations of proteins (32). (B) Ribbon diagram of the specific
complex in crystal form IV color coded by segments defined by
the plot in A. (C) Schematic drawing of the protein
conformational changes occurring with DNA bending. The white and
black models represent complexes containing DNA which is bent to
a lesser and greater degree, respectively. As the DNA bends, the
B helices translate apart and rotate up into the DNA-binding
site, and the DNA-binding domains rotate about the axes
indicated.
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