title: Amino acid 95 causes strong alteration of peptide position Pomega in HLA-B*41 variants.
abstract: There have been several attempts over the years to identify positions in the peptide-binding region (PBR) of human leukocyte antigens (HLA) that influence the specificity of bound amino acids (AAs) at each position in the peptide. Originally, six pockets (A-F) were defined by calculating the surface area of the PBR on the crystal structure of HLA-A2 molecules. More recent crystallographic analyses of a variety of HLA alleles have led to broader pocket definitions. In this study, we examined the peptide-binding specificity of HLA-B*41 alleles and compared our results with the available pocket definitions. By generating recombinant HLA-B molecules and studying the eluted peptides by mass spectrometry and pool sequencing, we detected two different POmega peptide motifs within the B*41 group: Leu vs Val/Pro. Specificity was dependent on the presence of Leu (B*4102, B*4103, and B*4104) vs Trp (B*4101, B*4105, and B*4106) at AA position 95 in the HLA molecule, whose impact on POmega has been a subject of controversy in current pocket definitions. In contrast, the Arg97Ser mutation did not affect pocket F binding specificity in B*41 subtypes although residue 97 was previously identified as a modulator of peptide binding for several HLA class I alleles. According to most pocket definitions, this study shows that the Asn80Lys substitution in B*4105 impels the peptide's POmega anchor toward more promiscuity. Our sequencing results of peptides eluted from HLA-B*41 variants demonstrate the limitations of current pocket definitions and underline the need for an extended peptide motif database for improved understanding of peptide-major histocompatibility complex interactions.
authors.affiliation: Institute for Transfusion Medicine, Hanover Medical School, Hanover, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Bade-Doeding
authors.forename: David S
authors.initials: DS
authors.lastname: DeLuca
authors.forename: Axel
authors.initials: A
authors.lastname: Seltsam
authors.forename: Rainer
authors.initials: R
authors.lastname: Blasczyk
authors.forename: Britta
authors.initials: B
authors.lastname: Eiz-Vesper
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D000596:Amino Acids / Q000737:chemistry* / Q000235:genetics; D015235:HLA-B Antigens / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D011487:Protein Conformation
chemical_list: D000596:Amino Acids; D015235:HLA-B Antigens; C425025:HLA-B*41:04 antigen; C056322:HLA-B41 antigen; D010455:Peptides