Conformational study of a peptide epitope shows large preferences for beta-turn conformations.
The conformational preferences of the 7-residue peptide Glu-Val-Val-Pro-His-Lys-Lys was investigated using a global search algorithm, namely the Electrostatically Driven Monte Carlo (EDMC) method, and the ECEPP/2 potential energy function. This particular sequence corresponds to the N-terminal portion of a 19-residue peptide antigen whose three dimensional structure, when complexed to a cognate antibody, was reported recently. As a result of this study a series of low-energy conformations were identified showing a common folding pattern with residues Val-3, Pro-4, His-5 and Lys-6 forming a beta turn. A comparison of the computed conformations with the one determined by X-ray crystallography in the antibody-antigen complex reveals marked similarities. In most of the cases rms deviations smaller than 1.1 A were found for the backbone atoms of the four residues forming the turn. These results suggest that the recognition process is accomplished in this case through the interaction of the antibody with relatively stable conformers of the antigenic peptide.
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Biotechnology Research Institute, National Research Council of Canada, Montreal.
D000595:Amino Acid Sequence; D000939:Epitopes / Q000737:chemistry*; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry* / Q000276:immunology; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D000939:Epitopes; D009842:Oligopeptides