A semi-empirical method for prediction of antigenic determinants on protein antigens(1)
Identification of epitopes on proteins would be useful for diagnostic purposes and also in the development of peptide vaccines. The factors, hydrophilicity, accessibility and flexibility, can be used to predict B cell epitopes using a composite plot.
Frequency of occurrence of each type of amino acid in antigenic determinants (fAg) was calculated. Residues on the surface of protein were predicted using the following procedure. HydrophiIicity (Pi,), accessibility (Pa) and flexibility (Pf) values.
Algorithm to predict antigenic determinants. This algorithm was used to predict antigenic determinants on 34 proteins for which some experimental results are available. The com- puter program is available for PC compatible systems.
Step 1: The average antigenic propensity values for each of the overlapping heptapeptides from N-terminal to C-terminal of the protein were calculated. These average values were assigned to the fourth, (i+3), residue in the segment.
Step 2: the average antigenic propensity (Ap) value for the protein was determined.
Step 3: if Ap >1.0 then those residues having > 1.0 were termed as potential antigenic residues. If Ap < 1.0 then those residues having APp were termed as potential antigenic residues.
Step 4: to pick up antigenic determinants a condition was set that six consecutive residues must satisfy step 3.
Ser, Lys, Thr, Glu and Ala occur with relatively high frequency in antigenic determinants. A, values are very large for Cys, Val and Leu which are hydrophobic amino acids. Thus, whenever these residues occur on the surface, they are likely to be a part of antigenic determinants.