title: Large scale mass spectrometric profiling of peptides eluted from HLA molecules reveals N-terminal-extended peptide motifs.
abstract: 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.
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Hernando
authors.initials: H
authors.lastname: Escobar
authors.forename: David K
authors.initials: DK
authors.lastname: Crockett
authors.forename: Eduardo
authors.initials: E
authors.lastname: Reyes-Vargas
authors.forename: Andres
authors.initials: A
authors.lastname: Baena
authors.forename: Alan L
authors.initials: AL
authors.lastname: Rockwood
authors.forename: Peter E
authors.initials: PE
authors.lastname: Jensen
authors.forename: Julio C
authors.initials: JC
authors.lastname: Delgado
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D002460:Cell Line; D002461:Cell Line, Transformed; D015797:HLA-B35 Antigen / Q000737:chemistry / Q000378:metabolism; D015395:Histocompatibility Antigens Class I / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D020014:K562 Cells; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D040081:Protein Array Analysis; D011485:Protein Binding / Q000276:immunology; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D053719:Tandem Mass Spectrometry
chemical_list: D015797:HLA-B35 Antigen; D015395:Histocompatibility Antigens Class I; D010446:Peptide Fragments