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 an d physiology of proteins, The prediction of epitopes by molecular mode lling has been used successfully for the papilloma virus, and valuable antibodies have been raised [Muller ct al, (1990) J, Gen, Virol., 71, 2709-2717], We have improved the modelling approach to allow us to pr edict epitopes from the primary sequences of the cystic fibrosis trans membrane conductance regulator, The procedure involves searching for f ragments of primary sequences likely to make amphipathic secondary str uctures, which are hydrophilic enough to be at the surface of the fold ed 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 algori thm of Eisenberg, Tertiary structures were calculated using 'FOLDING', a software developed by R,Brasseur for the prediction of small protei n structures [Brasseur (1995) J, Mol. Graphics, in press], We selected sequences that folded as turns with at least five protruding polar re sidues, One important property of antibodies is selectivity, To optimi ze the selectivity of the raised antibodies, each sequence was screene d for similarity (FASTA) to the protein sequences from several databan ks, Ubiquitous sequences were discarded, This approach led to the iden tification of 13 potential epitopes in the cystic fibrosis transmembra ne conductance regulator: seven helices and six loops.