Table 2.
Comparison of the amino acid sequence of HLA-E with sequences of five other HLA isoforms. Several peptide sequences of HLA-E are shared with the alleles of other HLA-I isoforms. Note that amino acid sequence AYDGKDY is shared with the maximum number of alleles of all isoforms of HLA-I, while sequences PRAPWMEQE and EPPKTHVT are shared with one allele of HLA-A (A*3306) and one allele of HLA-B (B*8201). The bioinformatics analysis was carried out using the Immune Epitope Database (IEDB) to predict the antigenicity rank of epitopes. The Chou and Fasman beta turn, Kolaskar and Tongaonkar antigenicity, Karplus and Schulz flexibility, and Parker hydrophilicity prediction methods in IEDB were employed. The methods predict the probability of specific sequences in HLA-E that bind to Abs being in a beta turn region, being antigenic, being flexible, or being in a hydrophilic region. Antigenicity rank is calculated by pooling the probability values.
| HLA-E Peptide Sequences | HLA Alleles | Method 1 | Method 2 | Method 3 | Method 4 | Rank of Antigenicity | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Prediction SCORES | |||||||||||
| Classical HLA-Ib | Non-Classical HLA-Ib | Specificity | Beta-Turn | Antigenicity | Flexibility | Hydrophilicity | |||||
| [total number of amino acids] | A | B | Cw | F | G | Chou & Fasman (1978) | Kolaskar & Tangaonkar (1990) | Karplus & Schulz (1985) | Parker (1986) | ||
| 47PRAPWMEQE55 [9] | 1 | 0 | 0 | 0 | 0 | A*3306 | 0.993 | 0.948 | 0.969 | 0.586/1.143/1.657 | |
| 58EYWDRETR65 [8] | 5 | 0 | 0 | 0 | 0 | A restricted | 0.993 | 0.915 | 1.024 | 3.301/2.786 | 10 |
| 90AGSHTLQW97 [8] | 1 | 10 | 48 | 0 | 0 | Polyspecific | 1.019 | 1.033 | 0.989 | 2.629/0.901 | 6 |
| 108RFLRGYE114 [7] | 24 | 0 | 0 | 0 | 0 | A restricted | 0.933 | 0.996 | 0.996 | 0.229 | 8 |
| 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 |
| 126LNEDLRSWTA135 [10] | 239 | 219 | 261 | 21 | 30 | Polyspecific | 1.046 | 0.983 | 1.039 | 2.443/2.329 | 2 |
| 137DTAAQI142 [6] | 0 | 824 | 248 | 0 | 30 | Polyspecific | 0.813 | 1.065 | 0.978 | 1.957 | 3 |
| 137DTAAQIS143 [7] | 0 | 52 | 4 | 0 | 30 | Polyspecific | 0.946 | 1.012 | 0.97 | 3.414 | 7 |
| 157RAYLED162 [6] | 0 | 1 | 0 | 0 | 0 | B*8201 | 0.929 | 0.996 | 0.969 | 2.601 | |
| 163TCVEWL168 [6] | 282 | 206 | 200 | 0 | 30 | Polyspecific | 0.841 | 1.115 | 0.929 | −0.914 | 4 |
| 183EPPKTHVT190 [8] | 0 | 0 | 19 | 0 | 0 | C restricted | 1.029 | 1.044 | 1.042 | 3.043 | 9 |
| 65RSARDTA71 [7] | 0 | 0 | 0 | 0 | 0 | E restricted | 1.011 | 0.952 | 1.038 | 4.901 | 2 |
| 143SEQKSNDASE152 [10] | 0 | 0 | 0 | 0 | 0 | E restricted | 1.231 | 0.923 | 1.222 | 7.071/6.443/6.257/6.514 | 1 |
Method 1. Predict beta turns in protein secondary structures. Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45-148. DOI: 10.1002/9780470122921.ch2. Method 2. A semi-empirical method which made use of the physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes was developed to predict antigenic determinants on proteins. Application of this method to a large number of proteins has shown that the method can predict antigenic determinants with about 75% accuracy, which is better than most of the known methods. Kolaskar AS, Tongaonkar PC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett. 1990 Dec 10;276(1-2):172-4. doi: 10.1016/0014-5793(90)80535-q. Method 3. In this method, a flexibility scale, based on the mobility of protein segments on the basis of the known temperature B factors of the a-carbons of 31 proteins of known structure, was constructed. The calculation based on a flexibility scale is similar to classical calculation, except that the center is the first amino acid of the six amino acids’ window length, and there are three scales for describing flexibility instead of a single one. Karplus PA, Schulz GE. Prediction of Chain Flexibility in Proteins—A tool for the Selection of Peptide Antigens. Naturwissenschafren 1985; 72:212-3. Method 4. In this method, a hydrophilic scale based on peptide retention times during high-performance liquid chromatography (HPLC) on a reversed-phase column was constructed. A window of seven residues was used for analyzing epitope region. The corresponding value of the scale was introduced for each of the seven residues and the arithmetical mean of the seven residue values was assigned to the fourth, (i+3), residue in the segment. Parker JM, Guo D, Hodges RS. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry. 1986 Sep 23; 25(19):5425-32.