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Protein Engineering vol. 8 no. 8 pp. 829-834, 1995
© 1995 Oxford University Press

RESEARCH-ARTICLE

Prediction of the antigenic sites of the cystic fibrosis transmembrane conductance regulator protein by molecular modelling

Xavier Gallet1, Nora Benhabiles, Miguel Lewin, Robert Brasseur2 and Annick Thomas-Soumarmon

INSERM U10, Hopital Bichat-Claude Bernard, 170 Boulevard Ney, 75018 Paris, France 2Laboratoire de Biophysiquc Moleculaire Numirique, Faculty Universitaire Gembloux, Belgium

1To whom correspondence should be addressed

Antibodies are powerful tools for studying the in situ localization and physiology of proteins. The prediction of epitopes by molecular modelling has been used successfully for the papilloma virus, and valuable antibodies have been raised [Muller et aL (1990) J. Gen. Virol, 71, 2709–2717]. We have improved the modelling approach to allow us to predict epitopes from the primary sequences of the cystic fibrosis transmembrane conductance regulator. The procedure involves searching for fragments of primary sequences likely to make amphipathic secondary structures, which are hydrophilic enough to be at the surface of the folded protein and thus accessible to antibodies. Amphipathic helices were predicted using the methods of Berzofsky, Eisenberg and Jahnig. Their hydrophobichydrophilic interface was calculated and drawn, and used to predict the orientation of the helices at the surface of the native protein. Amino acids involved in turns were selected using the algorithm of Eisenberg. Tertiary structures were calculated using ‘FOLDING’, a software developed by R.Brasseur for the prediction of small protein structures [Brasseur (1995) J. MoL Graphics, in press]. We selected sequences that folded as turns with at least five protruding polar residues. One important property of antibodies is selectivity. To optimize the selectivity of the raised antibodies, each sequence was screened for similarity (FASTA) to the protein sequences from several databanks. Ubiquitous sequences were discarded. This approach led to the identification of 13 potential epitopes in the cystic fibrosis transmembrane conductance regulator: seven helices and six loops.

Keywords: antibody/cystic fibrosis transmembrane conductance/regulator/epitope/molecular modelling

Received March 16, 1995; revised June 21, 1995; accepted July 3, 1995.


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