PDBsum entry 1e4x

Immune system

PDB id: 1e4x

Contents

Protein chains

216 a.a. *

214 a.a. *

Ligands

VAL-VAL-SER-HIS-PHE-ASN-ASP ×2

Waters ×407

* Residue conservation analysis

PDB id:

1e4x

Name:

Immune system

Title:

Crossreactive binding of a circularized peptide to an anti-tgfalpha antibody fab-fragment

Structure:

Tab2. Chain: h. Fragment: ig kappa heavy chain. Other_details: murine fab-fragment. Tab2. Chain: i. Fragment: ig kappa heavy chain. Other_details: murine fab-fragment. Tab2.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: mouse hybridoma. Organ: spleen. Strain: balb/c. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Biol. unit:

Trimer (from PQS)

Resolution:

1.90Å R-factor: 0.245 R-free: 0.311

Authors:

M.Hahn,D.Winkler,R.Misselwitz,H.Wessner,K.Welfle,G.Zahn,J.Schneider- Mergener,W.Hoehne

Key ref:

M.Hahn et al. (2001). Cross-reactive binding of cyclic peptides to an anti-TGFalpha antibody Fab fragment: an X-ray structural and thermodynamic analysis. J Mol Biol, 314, 293-309. PubMed id: 11718562 DOI: 10.1006/jmbi.2001.5135

Date:

12-Jul-00 Release date: 12-Jul-01

Protein chains

No UniProt id for this chain

Struc: 216 a.a.

Protein chains

P01837  (IGKC_MOUSE) -  Immunoglobulin kappa constant from Mus musculus

Seq: 107 a.a.

Struc: 214 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1006/jmbi.2001.5135

J Mol Biol 314:293-309 (2001)

PubMed id: 11718562

Cross-reactive binding of cyclic peptides to an anti-TGFalpha antibody Fab fragment: an X-ray structural and thermodynamic analysis.

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.

ABSTRACT

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.

Selected figure(s)

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).

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)

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 293-309) copyright 2001.

Figures were selected by an automated process.