Table 3.
The difference between peptides 115QFAYDGKDY123 and 117AYDGKDY123 clarified by the bioinformatics analysis done with the Immune Epitope Database (IEDB) to predict antigenicity rank of epitopes. Chou and Fasman beta turn, Kolaskar and Tongaonkar antigenicity, Karplus and Schulz flexibility and Parker hydrophilicity prediction methods in IEDB were employed to predict the immunogenic rank of the two sequences. Note the striking difference in antigenicity, flexibility and hydrophilicity between 115QFAYDGKDY123 and 117AYDGKDY123 due to presence are absence of the two amino acids Q and F. This finding stresses the importance of the role of each amino acids in promoting antigenicity as well as immunogenicity.
| Peptide Sequence Exposed in the Absence of β2-Microglobuin | Number of Positive HLA-I Alleles |
Prediction SCORES | Immunogenicity Rank | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Classical HLA-Ia |
Non-Classical HLA-Ib | Specificity | Beta-Turn | Antigencity | Flexibility | Hydro Philicity | |||||
| [Total Number of Amino Acids] | A | B | Cw | F | G | Chou & Fasman (1978) | Kolaskar & Tangaonkar (1990) | Karplus & Schulz (1985) | Parker (1986) | ||
| 115QFAYDGKDY123 [9] | 1 | 104 | 75 | 0 | 0 | Polyspecific | 1.059 | 1.001 | 0.993 | 2.629/3.201 | 5 |
| 117AYDGKDY123 [7] | 491 | 831 | 271 | 21 | 30 | Polyspecific | 1.204 | 0.989 | 1.061 | 4.243 | 1 |