Table I. Determining the peptide-binding motifs of MHC-I allotypes using PSCPL.
| Residue | Amino Acid Position in Peptide |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
| Peptide–MHC-I affinity | |||||||||
| A | 1.2 | 0.5 | 1.0 | 0.2 | 1.1 | 1.1 | 0.8 | 1.0 | 1.9 |
| C | 0.7 | 0.1 | 0.2 | 1.0 | 0.6 | 0.6 | 0.9 | 1.0 | 0.2 |
| D | 0.0 | 0.0 | 1.1 | 2.8 | 1.4 | 1.4 | 0.5 | 0.8 | 0.0 |
| E | 0.1 | 0.0 | 0.4 | 2.6 | 1.4 | 0.7 | 1.0 | 1.6 | 0.0 |
| F | 3.8 | 0.2 | 2.9 | 0.0 | 1.5 | 1.4 | 3.2 | 1.2 | 1.0 |
| G | 1.1 | 0.3 | 0.6 | 1.1 | 1.9 | 0.7 | 0.1 | 0.9 | 0.5 |
| H | 0.9 | 0.1 | 0.2 | 0.9 | 1.1 | 0.7 | 0.4 | 0.7 | 0.0 |
| I | 0.6 | 1.8 | 1.1 | 0.5 | 0.9 | 1.5 | 1.7 | 0.4 | 2.5 |
| K | 1.2 | 0.1 | 0.2 | 0.8 | 0.5 | 0.0 | 0.2 | 0.5 | 0.0 |
| L | 0.8 | 5.0 | 1.2 | 0.5 | 0.8 | 1.7 | 0.9 | 1.1 | 2.7 |
| M | 1.4 | 6.9 | 2.4 | 0.9 | 0.9 | 1.0 | 1.5 | 0.9 | 2.1 |
| N | 0.4 | 0.1 | 1.0 | 0.6 | 0.9 | 1.5 | 0.6 | 0.9 | 0.1 |
| P | 0.1 | 0.0 | 0.6 | 1.9 | 0.6 | 1.8 | 1.2 | 2.2 | 0.1 |
| Q | 0.4 | 1.8 | 1.0 | 1.2 | 0.8 | 0.5 | 1.0 | 1.3 | 0.1 |
| R | 1.4 | 0.1 | 0.2 | 0.7 | 0.8 | 0.4 | 0.3 | 0.9 | 0.1 |
| S | 1.1 | 0.1 | 1.3 | 0.6 | 0.6 | 1.2 | 0.6 | 0.7 | 0.1 |
| T | 0.7 | 1.0 | 0.9 | 1.1 | 0.8 | 0.6 | 0.9 | 1.0 | 0.1 |
| V | 1.1 | 1.6 | 0.6 | 0.8 | 1.0 | 1.2 | 0.6 | 0.6 | 8.4 |
| W | 0.6 | 0.1 | 1.2 | 0.4 | 1.4 | 0.8 | 1.7 | 0.6 | 0.0 |
| Y | 2.5 | 0.2 | 1.8 | 1.3 | 0.8 | 1.0 | 1.9 | 1.4 | 0.1 |
| Sum | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 |
| AP value | 14 | 64 | 10 | 10 | 2 | 4 | 10 | 3 | 74 |
| Peptide–MHC-I complex dissociation | |||||||||
| A | 1.01 | 0.7 | 1.7 | 1.2 | 1.1 | 1.2 | 1.5 | 1.2 | 2.2 |
| C | 0.5 | 0.5 | 1.6 | 1.1 | 0.9 | 0.7 | 1.4 | 1.2 | 0.5 |
| D | 0.0 | 0.0 | 1.3 | 2.7 | 0.8 | 0.7 | 0.4 | 0.5 | 0.0 |
| E | 0.0 | 0.0 | 0.2 | 1.9 | 0.7 | 0.8 | 0.8 | 1.7 | 0.0 |
| F | 2.3 | 0.2 | 2.5 | 0.8 | 1.3 | 0.9 | 2.7 | 1.5 | 0.4 |
| G | 0.8 | 0.2 | 0.7 | 0.0 | 1.3 | 0.5 | 0.3 | 1.0 | 0.2 |
| H | 0.7 | 0.0 | 0.7 | 1.3 | 1.2 | 1.0 | 1.3 | 0.9 | 0.0 |
| I | 0.7 | 1.9 | 0.7 | 0.3 | 0.8 | 1.6 | 0.4 | 0.4 | 2.2 |
| K | 1.8 | 0.1 | 0.1 | 0.7 | 1.0 | 0.6 | 0.1 | 0.5 | 0.1 |
| L | 1.1 | 6.4 | 1.7 | 0.2 | 0.8 | 1.4 | 0.9 | 0.5 | 4.2 |
| M | 1.5 | 5.6 | 2.7 | 0.4 | 0.8 | 1.0 | 1.5 | 0.3 | 2.4 |
| N | 0.4 | 0.1 | 1.0 | 1.1 | 0.9 | 1.6 | 0.8 | 0.5 | 0.0 |
| P | 0.0 | 0.1 | 0.4 | 1.3 | 0.6 | 1.7 | 2.3 | 2.6 | 0.1 |
| Q | 0.4 | 1.5 | 0.9 | 1.0 | 0.6 | 1.3 | 0.8 | 1.1 | 0.0 |
| R | 1.4 | 0.1 | 0.1 | 0.7 | 1.2 | 0.5 | 0.3 | 0.8 | 0.0 |
| S | 1.1 | 0.2 | 1.2 | 1.0 | 0.9 | 0.9 | 0.5 | 0.9 | 0.4 |
| T | 1.1 | 0.9 | 1.1 | 1.1 | 1.0 | 0.5 | 1.4 | 1.3 | 0.8 |
| V | 1.2 | 1.3 | 0.5 | 0.6 | 0.7 | 0.9 | 1.3 | 0.6 | 6.4 |
| W | 0.9 | 0.1 | 0.4 | 0.9 | 1.9 | 0.7 | 0.6 | 0.6 | 0.0 |
| Y | 2.9 | 0.1 | 0.7 | 1.5 | 1.5 | 1.5 | 0.7 | 1.9 | 0.0 |
| Sum | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 |
| AP value | 11 | 62 | 10 | 7 | 2 | 3 | 9 | 7 | 56 |
The peptide-binding motif of HLA-A*02:01 was determined via nonameric PSCPL analysis either by peptide–MHC-I affinity measurement or peptide–MHC-I complex dissociation. Residues with RB values larger than 2 are in terms of peptide binding considered favored (bold numbers) in the given position, residues with RB values <0.5 are considered disfavored (italic numbers), and residues with 0.5 < RB < 2.0 are accepted (numbers in regular font). Both methods capture the well-described peptide-binding motif of the HLA-A*02:01 allotype, having strong anchors in peptide positions 2 and 9 with preference for Leu/Met and Leu/Val, respectively. RB values are shown.