Prediction Of The Antigenic Sites Of The Cystic-Fibrosis Transmembrane Conductance Regulator Protein By Molecular Modeling

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
hydrophobic-hydrophilic 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 sequence 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.