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Figure 4.
Figure 4. Features of the Shared Fab11F8, FabC225, and EGF
Binding Region on Domain III
(A) Molecular surface
representations of domain III of sEGFR with the contact regions
(as defined in Figure 3D) colored red for Fab11F8, yellow for
FabC225, and blue for EGF. Orientation is looking down onto the
domain III binding site.
(B) Functional features of the
domain III molecular surface. In the left panel, the surface is
colored by atom type: negative, red; positive, blue; polar
oxygen, pink; polar nitrogen, light blue; and apolar, white. The
right panel shows the electrostatic potential from −2.5 kT
(red) to +2.5 kT (blue) projected onto the surface.
Electrostatic potential calculations used the adaptive
Poisson-Boltzmann solver (APBS) implemented in PyMOL ([Baker et
al., 2001] and [DeLano, 2004]).
(C) Orthogonal views of
domain III. High-mannose chains (yellow) have been placed at
each position of glycosylation on sEGFR guided by the one or two
ordered sugar groups that are seen in the X-ray crystal
structures. For reference, the contact region of Fab11F8 is
shown (red).
(D) Three orientations of sEGFR are shown with
the electrostatic potential, as in (B), projected on the surface
and high-mannose chains shown. Both electrostatic and
carbohydrate steering might play a role in guiding Fabs or
ligands to the shared binding site on domain III.
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