Large Scale Mass Spectrometric Profiling of Peptides Eluted from HLA Molecules Reveals N-Terminal-Extended Peptide Motifs

• Published in: The Journal of immunology (1950) Vol. 181; no. 7; pp. 4874 - 4882
• Main Authors: Escobar, Hernando, Crockett, David K, Reyes-Vargas, Eduardo, Baena, Andres, Rockwood, Alan L, Jensen, Peter E, Delgado, Julio C
• Format: Journal Article
• Language: English
• Published: United States Am Assoc Immnol 01.10.2008
• Subjects: Amino Acid Motifs; Amino Acid Sequence; Cell Line; Cell Line, Transformed; Histocompatibility Antigens Class I - biosynthesis; Histocompatibility Antigens Class I - chemistry; Histocompatibility Antigens Class I - genetics; Histocompatibility Antigens Class I - metabolism; HLA-B35 Antigen - chemistry; HLA-B35 Antigen - metabolism; Humans; K562 Cells; Molecular Sequence Data; Peptide Fragments - chemistry; Peptide Fragments - metabolism; Protein Array Analysis; Protein Binding - immunology; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Tandem Mass Spectrometry
• ISSN: 0022-1767; 1550-6606
• DOI: 10.4049/jimmunol.181.7.4874

The majority of >2000 HLA class I molecules can be clustered according to overlapping peptide binding specificities or motifs recognized by CD8(+) T cells. HLA class I motifs are classified based on the specificity of residues located in the P2 and the C-terminal positions of the peptide. However, it has been suggested that other positions might be relevant for peptide binding to HLA class I molecules and therefore be used for further characterization of HLA class I motifs. In this study we performed large-scale sequencing of endogenous peptides eluted from K562 cells (HLA class I null) made to express a single HLA molecule from HLA-B*3501, -B*3502, -B*3503, -B*3504, -B*3506, or -B*3508. Using sequence data from >1,000 peptides, we characterized novel peptide motifs that include dominant anchor residues extending to all positions in the peptide. The length distribution of HLA-B35-bound peptides included peptides of up to 15 residues. Remarkably, we determined that some peptides longer than 11 residues represented N-terminal-extended peptides containing an appropriate HLA-B35 peptide motif. These results provide evidence for the occurrence of endogenous N-terminal-extended peptide-HLA class I configurations. In addition, these results expand the knowledge about the identity of anchor positions in HLA class I-associated peptides that can be used for characterization of HLA class I motifs.