Table 3.
Predicted binding of FVIII peptides with substitutions at M2199 to DRB1*01:01
| Substitution* | ProPred score† | IEDB consensus percentile rank‡ |
|---|---|---|
| None (WT peptide) | 1.09 | 6.87 |
| M2199L | 1.19 | 6.53 |
| M2199I | 0.79 | 14.35 |
| M2199Q | 0.39 | 13.37 |
| M2199F | 0.37 | 3.45 |
| M2199N | 0.33 | 13.67 |
| M2199A | 0.29 | 11.97 |
| M2199C | 0.29 | 15.04 |
| M2199V | 0.24 | 9.07 |
| M2199Y | <0 | 4.14 |
| M2199S | <0 | 18.03 |
| M2199T | <0 | 18.03 |
| M2199G | <0 | 12.73 |
| M2199H | <0 | 12.73 |
| M2199E | <0 | 18.03 |
| M2199W | <0 | 10.95 |
| M2199K | <0 | 18.03 |
| M2199R | <0 | 11.55 |
| M2199P | <0 | 18.03 |
| M2199D | <0 | 18.03 |
The input sequence for the ProPred and IEBD algorithms was FVIII2185-2213, which spans all possible 15-mer sequences that include the substitution site at M2199.
Predicted affinities from the ProPred algorithm.35 Possible scores range from <0 (no binding) to 6 (highest possible affinity) for DRB1*01:01. All 9 sequences with scores >0 had the same predicted binding motif, with F2196 in MHCII anchor position 1. None of the substitutions resulted in additional predicted binding modes (score >0) that would indicate creation of a potential DRB1*01:01-restricted neoepitope. Scores ≥0.14 (bolded) correspond to predicted peptide-DRB1*01:01 affinities in the top 3% of possible values. ProPred recommends a threshold of 3% for selecting potential physiologically relevant interactions.
Predicted affinities from the IEDB consensus method, which combines scores generated by 3 prediction algorithms: combinatorial library, NN-align (netMHCII-2.2), and SMM-align (netMHCII-1.1).36,37 The final scores reflect the predicted peptide affinities for DRB1*01:01. The highest predicted consensus affinity score, expressed as a percentage ranking, for each input sequence is listed. IEDB recommends a threshold of 10% for selecting potential physiologically relevant interactions (bolded). All 3 algorithms in the consensus method predicted a 9-mer MHCII-binding core for the WT sequence with F2196 in anchor position 1. The 4 modified FVIII sequences that ranked in the top 10% all had alternative predicted MHCII core sequences with either F2196 or F2200 in anchor position 1.