Mechanisms determining TAP-independent HLA-B surface expression.

<p>The TAP1 dependencies (A) and TAP2 dependencies (B) of HLA-B allotypes are partly correlated with their tapasin dependencies. The MFI ratios of HLA-B allotypes (derived from <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007171#ppat.1007171.g001" target="_blank">Fig 1A</a> or <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007171#ppat.1007171.g001" target="_blank">1B</a>) were used as indexes of TAP1 and TAP2 dependencies and MFI ratios of HLA-B allotypes (derived from Fig 1A of Ref. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007171#ppat.1007171.ref022" target="_blank">22</a>) were used as index of tapasin dependencies. HLA-B supertypes are color-coded, B7, blue; B44, pink; B62, green; B58, orange. (C and D) The anchor residue preferences at P₂ based on peptide sequences mined from two recent mass spectrometric studies (Ref. 42 and 43 respectively). In A-D, alleles belonging to the same supertype are color-coded. (E) Frequencies of indicated amino acids at the N-termini (excluding the last 6 residues at the C-terminus which cannot be P₂ for any epitope) of known human signal peptide sequences obtained from <a href="http://www.signalpeptide.de/" target="_blank">www.signalpeptide.de</a>. (F) Signal peptide sequences were used to predict potential 9-mer epitopes for the indicated HLA-B, using NetMHC 4.0. For each allele, the number of peptides with predicted IC₅₀ values < 500 nM and 50 nM are shown. (G and H) Similar to E and F, but using human transmembrane domain sequences obtained from <a target="_blank">ftp://ftp.ncbi.nih.gov/repository/TMbase/</a>, to estimate the frequencies of occurrence of indicated amino acids, excluding the last 6 residues at the C-terminus (G) and the predicted number of epitopes for each indicated HLA-B (H).