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Figure 2.
Fig. 2. Structural features of GA modules. Panel A,
stereo representation of 30 G148-GA3 NMR solution structures
superimposed onto their unminimized average coordinates by
minimizing the r.m.s. deviations for the backbone atoms of
helices. Panel B, ribbon representation of the structure closest
to the mean of the 30 structures representing G148-GA3. Panel C,
ribbon representation of the structure closest to the mean of
the 20 structures (the atomic coordinates are available in the
Research Collaboratory for Structural Bioinformatics Protein
Data Bank under PDB 1GAB (13)). The whole protein fragment of
ALB8-GA (53 residues) is shown, and the corresponding residues
of G148-GA3 are shown in panel B, although not all residues
belong to the intact protein G sequence. Panel D, tube
representation of ALB8-GA (light gray) and G148-GA3 (dark gray)
with backbone atoms of helical regions superimposed. Residue
Thr-18 in ALB8-GA is indicated with an arrow, and at the
corresponding position in G148-GA3 there is a deletion.
Structures (all oriented with their N terminus upward) in panels
A-D were visualized using MOLMOL (40). Panel E, graphical DDM
comparing the two GA modules in this study. The average distance
differences between C^  and C^
in the
30 conformers of G148-GA3 and the 20 structures of ALB8-GA (PDB
1GAB (13) were calculated to generate the DDM (29). Only
residues belonging to the defined GA module sequence were
analyzed. Residue Thr-18 in ALB8-GA was excluded because there
is a deletion at the corresponding position in the G148-GA3
sequence, and these locations are marked by arrows. The lower
right half of the matrix shows the average distance differences
for all residue pairs; the upper left part shows only the
average distance differences that are larger than 2 S.D. The
distance differences are coded using a gradient from white to
black with gray representing interatomic distances that are the
same in both ensembles. Interatomic distances that become larger
in G148-GA3 tend toward white, whereas distances that become
smaller tend toward black.
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