Table 1.
Prediction of H-2 b binding peptides from NS1 and binding assays
| |
|
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|
Predictive algorithm scores |
|
||
|---|---|---|---|---|---|---|---|
| Position | Name | Sequence | Predicted allele binding | SYFPEITHI score (D b /K b ) | NetMHC predicted affinity nM (D b /K b ) | BIMAS proPred-I score (D b /K b ) | Binding assay* (D b /K b ) |
| 14 |
NS1(14) |
YANATRTFL |
Db |
16 |
341 |
17.892 |
+ |
| 125 |
NS1(125) |
SALVNSERV |
Db |
28 |
10 |
138.526 |
+++ |
| 152 |
NS1(152) |
GQIVNPTFI |
Db |
28 |
5 |
1502.928 |
+++ |
| 222 |
NS1(222) |
IQLINFLRM |
Db/Kb |
22/17 |
239/201 |
226.359/11.000 |
++/++ |
| 403 |
NS1(403) |
NCYTGAEAL |
Db/Kb |
14/11 |
21953/18590 |
3.982/6.000 |
+/- |
| 141 |
NS1(141) |
AMPYIYVPI |
Kb |
22 |
137 |
19.800 |
+ |
| 166 |
NS1(166) Cl I |
IAYYFYNPD |
Kb |
19 |
30 |
1.320 |
+++ |
| 235 |
NS1(235) |
KHFNRYASM |
Kb |
17 |
22 |
40.000 |
+++ |
| 166 |
NS1(166) Cl II |
IAYYFYNPDAADDWI |
I-Ab |
NA |
194.8 |
NA |
NA |
| 402 |
NS1(402) |
TNCYTGAEALITTAI |
I-Ab |
NA |
87.3 |
NA |
NA |
| 522 | NS1(522) | KVHFAGFAAPACESG | I-Ab | NA | 59.1 | NA | NA |
NA: Not available.
*Peptides were ranked relative to the binding of the control peptide gp33-41 from LCMV to Db and Kb molecules on RMA-s cells (fluorescence ratio between NS1 peptide and gp33-41 peptide) (Rojas et al. [21]). +++: strong binder where ratio > 0.9; ++: moderate binder where ratio > 0.7 and < 0.9; +: weak binder where ratio > 0.5 and < 0.7; and -: no binder where ratio < 0.5.