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Fig. 6.4
The 1TR8 homodimer.
Red spheres
in the A chain indicate residues which correspond to
local
Δ
H
profile maxima (local hydrophobicity deficiencies). In line with theoretical predictions,
these residues are actually involved in complexation
Reviewing the 3D representation of the homodimer reveals that residues which
correspond to local
Δ
H
profile maxima form a docking cavity, anchoring the part-
ner molecule (Fig.
6.4
).
The 1YGA homodimer provides an example of complexation mediated by sur-
face residues with excess hydrophobicity. Contact between both monomers enables
their surface-bound hydrophobic residues to shield one another from water, resulting
in the formation of a stable complex. This phenomenon is illustrated in Fig.
6.5
.
Figure
6.6
presents a 3D view of the 1YGA homodimer, indicating which
residues correspond to
Δ
H
profile minima and are actually involved in complex-
ation. Such residues, when present on the surface of the molecule, hint at a potential
complexation site (Fig.
6.6
).
An interesting phenomenon occurs in the 1SD6 homodimer (Safo et al.
2005
). Here,
one monomer exposes residues with low hydrophobicity, which, in turn, interact with
areas of excess hydrophobicity on the surface of its partner. This homodimer ranks near
the top of the F-measure list, both for
Δ
H
<0. As it turns out, 1SD6 mono-
mers are capable of mutually compensating their deviations from the idealized hydro-
phobicity distribution, by forming a “lock-and-key-like” configuration (Fig.
6.7
).
The list of 51 nonbonding interactions between 1SD6 monomers includes 24
“lock-key” pairs (i.e. pairs where one residue has a positive
Δ
H
>0 and
Δ
H
value while the
other one corresponds to a negative value of the same profile). We can therefore
conclude that, in the case of 1SD6, complexation is dominated by mutual compen-
sation of deviations from the idealized profile. Figure
6.8
further illustrates this
situation and in 3-D presentation (Fig.
6.9
) .
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