TABLE 1.
Binding affinities (IC50 in nm) for the recombinant DR1-B0101 MHC II of the selected peptides eluted from human MHC II (DR1-B0101) and from human lymph in the absence (−) or presence (+) of DM
The reported data sets were used to generate the graphs and statistical analyses in Fig. 6. Shown are the average ± S.D. and number of replicates (in parentheses). *, these peptides were reported as part of human the lymph peptidome sequenced at low resolution using the nanoLC-MS/MS on LTQ-ion trap (27).
| Peptide source | Peptide identified | Peptide synthesized | IC50 − DM | IC50 + DM | Protein ID |
|---|---|---|---|---|---|
| nm | nm | ||||
| DC | ALDFEQEMATAASSS | ALDFEQEMATAASSS | 116 ± 47 (3) | 112 ± 18 (3) | P60710 |
| DC | RDALNIETAVKTKG | RDALNIETAVKTKG | 283 ± 119 (3) | 274 ± 39 (3) | P07356 |
| DC | TGKLISLSAQNLVD | TGKLISLSAQNLVD | 18 ± 1 (3) | 14 ± 5 (3) | O70370 |
| DC | KGGSFQLLQGGQALE | GGSFQLLQGGQALE | 42 ± 8 (3) | 28 ± 9 (3) | P04186 |
| DC | SEKMFLSEESERSTDD | KMFLSEESERSTD | 896 ± 735 (3) | 721 ± 49 (3) | Q504P2 |
| DC | DENQFVAVTSTNAAK | NQFVAVTSTNAAK | 48 ± 9 (3) | 41 ± 6 (3) | O08553 |
| DC | GEFIKASSIEARQ | GEFIKASSIEARQ | 158 ± 52 (3) | 93 ± 18 (3) | P57759 |
| DC | NSNQFQTEVGKQLIS | NQFQTEVGKQLIS | 96 ± 21 (3) | 250 ± 90 (3) | P11835 |
| DC | SPNIVIALAGNKAD | NIVIALAGNKAD | 123 ± 34 (3) | 99 ± 34 (3) | P35278 |
| DC | VDKVIQAQTAYSANPA | KVIQAQTAYSANP | 53 ± 27 (3) | 87 ± 28 (3) | O08992 |
| DC | EAFQAMPPEELNK | EAFQAMPPEELNK | 292 ± 38 (3) | 452 ± 76 (3) | P82198 |
| DC | EEFGRFASFEAQGALA | EEFGRFASFEAQGALA | 50 ± 9 (2) | 120 ± 13 (2) | P01903.1 |
| DC | IPMYSIITPNVLRLESE | IPMYSIITPNVLRLESEET | 17 ± 1 (2) | 17 ± 3 (2) | P01027 |
| Lymph | ASFEAQGALANIAVDKA | ASFEAQGALANIAVDKA | 740 ± 109 (3) | 4142 ± 567 (3) | P01903 |
| Lymph | SSKITHRIHWESASLLR | SSKITHRIHWESASLLR | 53 ± 4 (3) | 110 ± 9 (3) | P01024 |
| Lymph | AGFKGEQGPKGEP | AGFKGEQGPKGEP | 4399 ± 243 (2) | 12641 ± 2897 (2) | P02458 |
| Lymph | MLHLLALFLH* | MLHLLALFLH | 7558 ± 3617 (2) | 19244 ± 1002 (2) | Q96CW9 |
| Lymph | PGALLGAPPPLVPAP* | PGALLGAPPPLVPAP | 2121 ± 152 (2) | 6809 ± 177 (2) | Q9HAH7 |
| Lymph | AWLDLEFISTVLGAP* | AWLDLEFISTVLGAP | 141 ± 7 (2) | 426 ± 48 (2) | P43026 |
| Lymph | RNMTLFSDLVAEKFI* | RNMTLFSDLVAEKFI | 2542 ± 203 (2) | 7413 ± 1225 (2) | P12110 |
| Lymph | EDTFAHLTPTPT* | EDTFAHLTPTPT | 221 ± 9 (2) | 783 ± 19 (2) | Q9NR99 |
| Lymph | KNFASVQGVSLESG* | KNFASVQGVSLESG | 242 ± 55 (2) | 341 ± 68 (2) | Q99715 |
| DM-resistant control | PKYVKQNTLKLAT | 63 ± 11 (4) | 88 ± 17 (4) | P03438 | |
| DM-susceptible control | VSKMRMATPLLMQ | 60 ± 12 (3) | 179 ± 28 (3) | P04233 |