TABLE 1.
8–12-mer peptides that potentially bind the most frequent HLA-A and -B haplotypes and are produced by proteasome-catalyzed digestion of the wt and/or mut gp100201–230 polypeptides
The non-spliced and spliced 8–12-mer peptides shown were produced by proteasomal processing of the wt and/or mut gp100201–230 polypeptides as such or as N-terminally extended precursors. Binding affinities of the peptides were predicted in silico by using ANN-NetMHC software version 3.4 (31). We included in the analysis the most frequent HLA-A and -B haplotypes (i.e., HLA-A*01:01, -A*02:01, -A*03:01, -A*24:02, -A*26:01, -B*07:02, -B*08:01, -B*27:05, -B*39:01, -B*40:01, -B*58:01, -B*15:01). Only 8–14-mer peptides were used for the in silico analysis, and only N-terminally extended peptides were considered as MHC class I binder precursors (i.e. the binder and the precursor peptides must have the same C terminus). Only 8–12-mer peptides with predicted IC50 values <200 nm were considered as efficient binders. In the peptide sequence the T210M is marked in bold. When both wt and mut peptides were produced by proteasome and predicted to be MHC class I binders, we reported the wt sequence and the substitution as following T(M). When both wt and mut peptides had a IC50 < 200 nm we stated whether the IC50 was affected by the T210M substitution.
| Precursors (gp100_) | Binder (gp100_) | Sequence | HLA- | IC50 influenced by T210M substitution? |
|---|---|---|---|---|
| 8–12-Mer peptide binders common to wt and mut gp100201–230-produced peptide pool | ||||
| 201–209 | 202–209 | HSSSAFTI | B*58:01 | No |
| 208–217 | 209–217 | IT(M)DQVPFSV | A*02:01 | Yes |
| 201–209 | 201–209 | AHSSSAFTI | B*39:01 | No |
| 205–215 | 207–215 | FTIT(M)DQVPF | B*15:01, B58:01 | Yes |
| 208–217 | 208–217 | TIT(M)DQVPFSV | A*02:01 | Yes |
| 207–217 | 207–217 | FTIT(M)DQVPFSV | A*02:01 | Yes |
| 205–215 | 205–215 | SAFTIT(M)DQVPF | B*15:01 | Yes |
| 8–12-Mer peptide binders unique for the wtgp100201–230-produced peptide pool | ||||
| 208–219 | 208–219 | TITDQVPFSVSV | A*02:01 | |
| 210–218/220–222 | 213–218/220–222 | VPFSVSSQL | B*07:02 | |
| 201–207/201–207 | 207/201–207 | FAHSSSAF | B*15:01 | |
| 201–207/201–207 | 206–207/201–207 | AFAHSSSAF | B*15:01 | |
| 201–207/201–207 | 205–207/201–207 | SAFAHSSSAF | B*15:01 | |
| 201–207/201–207 | 204–207/201–207 | SSAFAHSSSAF | B*15:01 | |
| 201–207/201–207 | 203–207/201–207 | SSSAFAHSSSAF | B*58:01 | |
| 210–212/214–222 | 212/214–222 | QPFSVSVSQL | B*39:01 | |
| 8–12-Mer peptide binders unique for the mutgp100201–230-produced peptide pool | ||||
| 205–215 | 208–215 | TIMDQVPF | B*15:01 | |
| 201–204/201–207 | 204/201–207 | SAHSSSAF | B*15:01 | |
| 201–204/201–207 | 203–204/201–207 | SSAHSSSAF | B*15:01 | |
| 201–204/201–207 | 202–204/201–207 | HSSAHSSSAF | B*15:01 | |