Background
Methods
Data retrieval and structural analysis
B-cell epitope prediction
T-cell epitope prediction
Eminent features profiling of selected T cells epitopes
Conservation analysis of selected epitopes
Structural modelling and molecular docking
Results
Structural analysis
Recognition of B-cell epitopes
Sr# | Position | Epitopes sequences | Score | Antigenicity |
---|---|---|---|---|
1 | 13 | TPTESYVDVGPDSV | 0.6484 | 0.938 |
2 | 209 | TPATDCSDGNYNRN | 0.6048 | 0.982 |
3 | 251 | LEWFGITQTAQGVH | 1.1063 | 0.845 |
4 | 566 | QLQMGFGITVQYGT | 1.5236 | 0.995 |
5 | 1287 | GNYTYYNKWPWYIW | 0.7180 | 0.884 |
6 | 1339 | RYEEYDLEPHKVHV | 1.3061 | 0.890 |
Sr# | Residues position | Residues names | Number of contacts | Propensity score | DiscoTope score |
---|---|---|---|---|---|
1 | 43 | THR | 0 | − 4.114 | − 3.641 |
2 | 159 | GLY | 2 | − 2.029 | − 2.026 |
3 | 199 | ASN | 1 | − 2.667 | − 2.591 |
4 | 215 | SER | 4 | − 2.632 | − 2.790 |
5 | 216 | ASP | 0 | − 1.426 | − 1.262 |
6 | 217 | GLY | 0 | − 0.316 | − 0.279 |
7 | 218 | ASN | 5 | − 0.626 | − 1.129 |
8 | 509 | ASP | 4 | − 3.406 | − 3.474 |
9 | 510 | ASP | 0 | − 3.963 | − 3.508 |
10 | 511 | ARG | 1 | − 3.183 | − 2.932 |
11 | 767 | PRO | 4 | − 2.719 | − 2.866 |
12 | 768 | ILE | 11 | − 2.612 | − 3.577 |
13 | 769 | GLN | 6 | − 1.481 | − 2.000 |
14 | 771 | ASP | 3 | − 1.702 | − 1.851 |
15 | 785 | ASN | 11 | − 2.269 | − 3.237 |
16 | 906 | MET | 1 | − 2.453 | − 2.286 |
17 | 907 | GLN | 1 | − 3.101 | − 2.859 |
18 | 910 | ASP | 3 | − 3.381 | − 3.337 |
19 | 914 | GLN | 7 | − 2.405 | − 2.933 |
20 | 993 | ASN | 6 | − 1.388 | − 1.918 |
21 | 1145 | ASN | 7 | − 2.245 | − 2.800 |
22 | 1146 | HIS | 13 | − 2.206 | − 3.288 |
Recognition of T-cell epitopes
Sr# | Peptides | MHC class-I alleles | Vaxijen score |
---|---|---|---|
1 | YKLQPLTFL | MHC-Db, HLA-Cw*0301, HLA-B*51, HLA-B*5401, HLA-B*5301, HLA-B*3902, HLA-B*3901, HLA-B*3701, HLA-B14, HLA-A2.1, HLA-A20 Cattle, HLA-A2, HLA-A*0201, HLA-B7 | 1.3798 |
2 | LTLLEPVSI | MHC-Kk, MHC-Kd, HLA-B*5801, HLA-B*51, HLA-B*5103, HLA-B*5301, HLA-B7 | 0.9748 |
3 | ESAALSAQL | MHC-Ld, HLA-Cw*0602, HLA-B60, HLA-B40, HLA-B*3902, HLA-A*3302, HLA-B7 | 0.7965 |
4 | IAGLVALAL | MHC-Db revised, HLA-B8, HLA-B7, HLA-B60, HLA-B*5801, HLA-B*5103, HLA-B*5102, HLA-B*5101, HLA-B*3501 | 0.7799 |
5 | AGYKVLPPL | MHC-Dd, HLA-B7, HLA-B60, HLA-B*5401, HLA-B*5201, HLA-B*5103, HLA-B*5102, HLA-B*5101, HLA-B40, HLA-B*3901, HLA-B*3701, HLA-B*2705, HLA-A*0205, HLA-B14 | 0.6416 |
6 | WPRPIDVSK | HLA-A*1101, HLA-A3, HLA-A68.1, HLA-B*5301, HLA-B*5401, HLA-B*51, HLA-B*0702, HLA-B7 | 0.6160 |
Sr# | Peptides | MHC class-II alleles | Vaxijen score |
---|---|---|---|
1 | YCILEPRSG | DRB5_0105, DRB5_0101, DRB1_1328, DRB1_1327, DRB1_1323, DRB1_1307, DRB1_1305, DRB1_1302, DRB1_1301, DRB1_1128, DRB1_1120, DRB1_1114, DRB1_1101, DRB1_0802, DRB1_0101 | 1.5044 |
2 | LYFMHVGYY | DRB1_0301, DRB1_0802, DRB1_0806, DRB1_0817, DRB1_1104, DRB1_1106, DRB1_1128, DRB1_1305, DRB1_1311, DRB1_1321 | 1.4863 |
3 | MRLASIAFN | DRB1_0301, DRB1_0306, DRB1_0307, DRB1_0308 DRB1_0311, DRB1_0405, DRB1_0410, DRB1_0423, DRB1_0801, DRB1_0802, DRB1_0804, DRB1_0806, DRB1_0817, DRB1_1101, DRB1_1102, DRB1_1104, DRB1_1106, DRB1_1107, DRB1_1114, DRB1_1120, DRB1_1121, DRB1_1128, DRB1_1301, DRB1_1302, DRB1_1304, DRB1_1305, DRB1_1307, DRB1_1311, DRB1_1321, DRB1_1322, DRB1_1323, DRB1_1327, DRB1_1328 | 1.4844 |
4 | FGITQTAQG | DRB1_1321, DRB1_1307, DRB1_1305, DRB1_1128 DRB1_1101, DRB1_0801, DRB1_0426, DRB1_0421 DRB1_0401 | 1.3764 |
5 | VRIGAAANS | DRB1_1328, DRB1_1327, DRB1_1322, DRB1_1301 DRB1_1121, DRB1_1107, DRB1_1102, DRB1_0426 DRB1_0402, DRB1_0401, DRB1_0311, DRB1_0308 DRB1_0307, DRB1_0306, DRB1_0301 | 1.1906 |
6 | VYKLQPLTF | DRB5_0101, DRB5_0105, DRB1_1327, DRB1_1328 DRB1_1128, DRB1_1301, DRB1_0102, DRB1_1101, DRB1_1104, DRB1_1106, DRB1_1305, DRB1_1311 | 1.1127 |
Eminent features profiling of selected T cells epitopes
Sr# | Peptides | Non-digesting enzymes | Mutation position | Toxicity | Allergenicity | Hydrophobicity | Hydrophilicity | Charge | PI | Mol. weight |
---|---|---|---|---|---|---|---|---|---|---|
MHC class-I binding peptides | ||||||||||
1 | YKLQPLTFL | Trypsin R, Clostripain, IodosoBenzoate, AspN, Cyanogen Bromide, Staph Protease | NM | NT | NA | 0.07 | − 0.92 | 1.00 | 8.59 | 1122.37 |
2 | LTLLEPVSI | Trypsin, Clostripain, AspN, Chymotrypsin, Cyanogen Bromide, IodosoBenzoate, Trypsin R, Trypsin K | NM | NT | NA | 0.25 | 1.80 | − 1.00 | 4.00 | 984.20 |
3 | ESAALSAQL | Clostripain, Chymotrypsin, Cyanogen Bromide, AspN Trypsin K, IodosoBenzoate, Proline Endopept, Trypsin R | NM | NT | NA | 0.05 | − 0.31 | − 1.00 | 4.00 | 888.97 |
4 | IAGLVALAL | Trypsin, Staph Protease, AspN, Chymotrypsin, Trypsin R, Clostripain, Trypsin K, CyanogenBromide, IodosoBenzoate, Proline Endopept | NM | NT | NA | 0.43 | − 1.20 | 0.00 | 5.52 | 840.72 |
5 | AGYKVLPPL | Clostripain, IodosoBenzoate, Staph Protease, AspN, Trypsin R, Cyanogen Bromide | NM | NT | NA | 0.13 | − 0.67 | 1.00 | 8.63 | 957.18 |
6 | WPRPIDVSK | Trypsin, Chymotrypsin (modified)Chymotrypsin, Cyanogen Bromide, Trypsin K, Trypsin R, Staph Protease | NM | NT | NA | − 0.26 | 0.29 | 1.00 | 8.75 | 1097.28 |
MHC class-II binding peptides | ||||||||||
1 | YCILEPRSG | Cyanogen Bromide, Trypsin K, AspN, IodosoBenzoate | NM | NT | A | − 0.11 | − 0.06 | 0.00 | 5.99 | 1037.20 |
2 | LYFMHVGYY | Trypsin, AspN, Clostripain, IodosoBenzoate, Staph Protease, Trypsin K, Trypsin R, Proline Endopept | NM | NT | NA | 0.20 | − 1.61 | 0.50 | 6.74 | 1192.40 |
3 | MRLASIAFN | IodosoBenzoate, Trypsin K, AspN, Staph Protease, Proline Endopept | NM | NT | A | − 0.07 | − 0.47 | 1.00 | 9.50 | 1022.23 |
4 | FGITQTAQG | Trypsin, AspN, Clostripain, Cyanogen Bromide, IodosoBenzoate, Trypsin R, Proline Endopept, Staph Protease, Trypsin K | NM | NT | NA | 0.02 | − 0.58 | 0.00 | 5.52 | 922.01 |
5 | VRIGAAANS | Chymotrypsin, Trypsin K, IodosoBenzoate, Proline Endopept, Staph Protease, Cyanogen Bromide, AspN | M | NT | A | − 0.07 | − 0.10 | 1.00 | 9.72 | 857.97 |
6 | VYKLQPLTF | AspN, Trypsin R, Clostripain, Staph Protease, Cyanogen Bromide, IodosoBenzoate | NM | NT | NA | 0.02 | − 0.79 | 1.00 | 8.56 | 1108.35 |
Conservation analyses of selected epitopes
Interaction study of predicted peptides with HLA alleles
Sr. | MHC class-I binding peptides | Docking score | Interacting residues |
---|---|---|---|
a | YKLQPLTFL | − 19.1695 | Tyr-9, Gln-70, Glu-76, Tyr-99 |
b | LTLLEPVSI | − 19.3901 | Arg-62, Glu-76, Arg-156 |
c | ESAALSAQL | − 19.9914 | Arg-62, Asn-63, Gln-70, Glu-152, Gln-155 |
d | IAGLVALAL | − 19.0437 | Arg-62, Glu-76, Ser-77, Arg-156 |
e | AGYKVLPPL | − 20.9793 | Asp-114, Gln-115, Lys-146, Glu-152, Arg-156 |
f | WPRPIDVSK | − 20.4007 | Arg-62, Glu-152, Glu-163, Trp-167 |