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PDBsum entry 1yt6

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De novo protein PDB id
1yt6
Jmol
Contents
Ligands
ALA-CYS-LEU-PRO-
TRP-SER-ASP-GLY-
PRO-CYS
PDB id:
1yt6
Name: De novo protein
Title: Nmr structure of peptide sd
Structure: Peptide sd. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized
NMR struc: 50 models
Authors: T.Murata,H.Hemmi,S.Nakamura,K.Shimizu,Y.Suzuki,I.Yamaguchi
Key ref:
T.Murata et al. (2005). Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand. FEBS J, 272, 4938-4948. PubMed id: 16176267 DOI: 10.1111/j.1742-4658.2005.04902.x
Date:
10-Feb-05     Release date:   27-Sep-05    
 Headers
 References

 

 
DOI no: 10.1111/j.1742-4658.2005.04902.x FEBS J 272:4938-4948 (2005)
PubMed id: 16176267  
 
 
Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand.
T.Murata, H.Hemmi, S.Nakamura, K.Shimizu, Y.Suzuki, I.Yamaguchi.
 
  ABSTRACT  
 
Using NMR spectroscopy and simulated annealing calculations, we determined the solution structure of the disulfide-linked cyclized decapeptide ACLPWSDGPC (SD), which is bound to an anti-(gibberellin A(4)) mAb 4-B8(8)/E9 and was found to be the first peptidyl mimotope for a hydrophobic ligand. The resulting structure of the peptide showed a beta-turn-like conformation in residues three to seven and the region converges well (average rmsd 0.54 A). The binding activity and the epitopes of the peptide to the antibody were assessed using saturation transfer difference (STD)-NMR experiments. We also conducted docking simulations between the peptide and the mAb to determine how the peptide is bound to the mAb. Resonances around the beta-turn-like conformation of peptide SD (residues 3-5) showed strong STD enhancement, which agreed well with results from docking simulation between peptide SD and the mAb. Together with the commonality of amino acid residues of the mAb involved in interactions with gibberellin A(4) (GA(4)) and peptide SD, we concluded that peptide SD is bound to the antigen-binding site of mAb 4-B8(8)/E9 as a GA(4) mimic, confirming evidence for the existence of peptide mimics even for hydrophobic ligands.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structures of gibberellin A[4] and cyclized decapeptide ACLPWSDGPC (SD).
Figure 3.
Fig. 3. Superimposition of 50 structures (A) and ribbon diagram of the lowest energy structure of the major conformer of peptide SD (B). One disulfide bridge (Cys2–Cys10) and side chains of all residues are ball-and-stick representations. This figure was generated using MOLMOL[31].
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2005, 272, 4938-4948) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20957656 Y.Xia, Q.Zhu, K.Y.Jun, J.Wang, and X.Gao (2010).
Clean STD-NMR spectrum for improved detection of ligand-protein interactions at low concentration of protein.
  Magn Reson Chem, 48, 918-924.  
16880593 H.Sekimoto, S.H.Park, M.Nakajima, I.Yamaguchi, and Y.Suzuki (2006).
Identification of a peptide mimic of bioactive gibberellins with affinity to GA 2-oxidase.
  Biosci Biotechnol Biochem, 70, 2004-2006.  
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