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Figure 2.
Fig. 2. Superposition of the structures of the germline Fab
without hapten (light blue) and the germline Fab-hapten complex
(light purple), illustrating the structural changes that occur
on hapten binding to the germline Fab. In all figures, the
aliphatic linker of the hapten has been omitted for clarity.
Gray dotted lines denote hydrogen bonds in the structure of the
germline Fab without hapten, while black dotted lines denote
hydrogen bonds in the^ germline Fab-hapten complex. (A) CDR3 of
the heavy chain is reorganized on hapten binding. To make room
for the hapten, the side chain of TyrH99 moves 6 Å away
from the hapten. The side chain of TyrH98 moves 8.3 Å and
inserts between TyrH99 and TyrH33, and TyrH33 moves toward the
phosphonate group. These movements establish a  -cation
interaction between the side chains of ArgL46 and TyrH99, a - interaction
between the aryl groups of TyrH99 and TyrH98, and a T-stack
interaction between the aryl rings of TyrH98 and TyrH33 (yellow
dotted lines). In addition, the ArgL46 side chain is stabilized
by salt bridges to the AspL55 carboxylate group and to the
TyrH99 main chain carbonyl group. (B) The interactions between
residues in CDR1, CDR2, and CDR3 of the heavy chain in the
germline^ Fab structures. The side chain of ArgH50 forms
hydrogen bonds to the hydroxyl groups of TyrH33 and TyrL94 upon
hapten binding. The guanidinium group of ArgH50 is positioned by
a hydrogen bond with AsnH56. Although TyrH33 forms one hydrogen
bond to ArgH50, it does not interact directly with either TyrL94
or the bound hapten, nor does LysH58 interact with residue H56
(cf. Fig. 3B). (C) Closeup of^ the combining site showing the
orientations of the residues directly involved in hapten binding
in the germline-hapten complex HisH35, TyrH33, and ArgL96. All
four hydrogen bonds are directed to the oxygens (red) of^ the
phosphonate group (phosphorus-yellow). TyrH33 moves 2.2 Å
toward the phosphonate group, which is a key binding determinant
in the hapten and is located in approximately the^ same position
in the combining sites of the germline and affinity-matured^
Fab-hapten complexes.
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