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PDBsum entry 1e4x
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Immune system
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PDB id
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1e4x
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Cross-Reactive binding of cyclic peptides to an anti-Tgfalpha antibody FAB fragment: an X-Ray structural and thermodynamic analysis.
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Authors
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M.Hahn,
D.Winkler,
K.Welfle,
R.Misselwitz,
H.Welfle,
H.Wessner,
G.Zahn,
C.Scholz,
M.Seifert,
R.Harkins,
J.Schneider-Mergener,
W.Höhne.
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Ref.
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J Mol Biol, 2001,
314,
293-309.
[DOI no: ]
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PubMed id
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Abstract
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The monoclonal antibody tAb2 binds the N-terminal sequence of transforming
growth factor alpha, VVSHFND. With the help of combinatorial peptide libraries
it is possible to find homologous peptides that bind tAb2 with an affinity
similar to that of the epitope. The conformational flexibility of short peptides
can be constrained by cyclization in order to improve their affinity to the
antibody and their stability towards proteolysis. Two cyclic peptides which are
cross-reactive binders for tAb2 were selected earlier using combinatorial
peptide libraries. One is cyclized by an amide bond between the N-alpha group
and the side-chain of the last residue (cyclo-SHFNEYE), and the other by a
disulfide bridge (cyclo-CSHFNDYC). The complex structures of tAb2 with the
linear epitope peptide VVSHFND and with cyclo-SHFNEYE were determined by X-ray
diffraction. Both peptides show a similar conformation and binding pattern in
the complex. The linear peptide SHFNEYE does not bind tAb2, but cyclo-SHFNEYE is
stabilized in a loop conformation suitable for binding. Hence the cyclization
counteracts the exchange of aspartate in the epitope sequence to glutamate.
Isothermal titration calorimetry was used to characterize the binding energetics
of tAb2 with the two cyclic peptides and the epitope peptide. The binding
reactions are enthalpically driven with an unfavorable entropic contribution
under all measured conditions. The association reactions are characterized by
negative DeltaC(p) changes and by the uptake of one proton per binding site. A
putative candidate for proton uptake during binding is the histidine residue in
each of the peptides. Hydrogen bonds and the putative formation of an
electrostatic pair between the protonated histidine and a carboxy group may
contribute markedly to the favorable enthalpy of complex formation.Implications
to cyclization of peptides for stabilization are discussed.
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Figure 3.
Figure 3. Stereo view of the tAb2 binding site accomodating
the peptides (a) e-pep (in yellow) or (b) h[c]-pep2 (in orange).
Two conserved water molecules (in red) are involved. The solvent
accessible surface is shown for the antibody with the CDRs L1 in
light green, L2 in medium green, L3 in dark green, H1 in light
blue, H2 in medium blue, and H3 in dark blue. The Figure was
created by WebLab ViewerPro 3.7 (Molecular Simulations Inc., San
Diego, CA).
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Figure 4.
Figure 4. Stereo view of peptide h[c]-pep2 with its binding
partners in the binding groove of Fab fragment tAb2. h[c]-pep2
is drawn in red, light chain residues in light blue and heavy
chain residues in dark blue. h[c]-pep2 and two conserved water
molecules (no. 9, no. 204) are shown with their 2F[o] -F[c]
electron density, contoured at 1.5 s. Hydrogen bonds between
h[c]-pep2 and tAb2 are indicated by dotted lines in purple.
Figure 4 and Figure 5 Enlarge Image- [0?wchp=dGLzVlz-zSkzS]
(51K)
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
314,
293-309)
copyright 2001.
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