Definition of the peptide binding motif within DRB1*1401 restricted epitopes by peptide competition and structural modeling

Abstract

This study identified the peptide-binding motif of HLA-DRB1*1401 (DR1401). First, peptides containing DR1401 restricted epitopes were identified using tetramer guided epitope mapping. Among these, an influenza B peptide was selected for the motif study. After confirming the binding register for this peptide using a set of arginine substitutions, binding affinities were determined for 33 peptides derived from this influenza B sequence with single amino acid substitutions. The DR1401 peptide binding motif was deduced from the relative binding affinities of these peptides and confirmed by structural modeling. Pocket 1 demonstrated a preference for aliphatic anchor residues and methionine. Pocket 4 accommodated methionine and aliphatic residues, but also allowed some polar and charged amino acids. Pocket 6 preferred basic residues but also allowed some polar and aliphatic amino acids. Pocket 9 preferred aliphatic and aromatic amino acids and tolerated some polar residues but excluded all charged residues. Together these preferences define a distinct set of peptides that can be presented by DR1401. The resulting motif was used to verify T cell epitopes within the novel antigenic peptides identified by tetramer guided epitope mapping and within peptides from published reports that contain putative DR1401 epitopes.

The Binding of Antigenic Peptides to HLA-DR Is Influenced by Interactions between Pocket 6 and Pocket 9

“…Proline anchoring in these positions would cost at least one hydrogen bond in antigenic peptide-polar side chain interaction (27). Preference for proline at pocket 6 has also recently been observed for HLA-DRB1*1401 (28). It is also interesting that in HLA-DRB1*0901 pocket 6 shows almost as wide an acceptance of amino acids as pocket 7, which usually is the pocket most accommodating of bulky aromatic residues.…”

Immunodominant CD4+T-Cell Responses to Influenza A Virus in Healthy Individuals Focus on Matrix 1 and Nucleoprotein

“…We also noticed that immunodominant epitopes seemed to have been subjected to greater selective pressure than subdominant ones, if the number of such variants is a direct indication. For three of the PR8-derived immunodominant epitopes, M1 209-221 , NP [404][405][406][407][408][409][410][411][412][413][414][415][416] , and especially NP 463-475 , a perfect sequence match can rarely be found in the IAV strains that have emerged in the last decade in Australia, while the subdominant epitopes, such as M1 [43][44][45][46][47][48][49][50][51][52][53][54][55] and M1 101-113 , showed higher levels of conservation. Although IAV infections are resolved quickly in each infected individual, it is entirely possible that such epitope variants can be generated due to both the immune pressure and the lack of an error-proof nature of the IAV polymerase.…”

“…After that, ex vivo assessments of these epitope-specific memory CD4 ϩ T cell precursor frequencies were conducted to confirm the immunodominance hierarchy (ranking). Using the same approach described above, three subdominant epitopes-M1 [43][44][45][46][47][48][49][50][51][52][53][54][55] , restricted to HLA-DRB1*0701 (Fig. 7A); M1 101-113 , restricted to HLA-DRB1*0404 (Fig.…”

Papillomavirus-Specific CD4+ T Cells Exhibit Reduced STAT-5 Signaling and Altered Cytokine Profiles in Patients with Recurrent Respiratory Papillomatosis

“…Various concentrations of each test peptide were incubated in competition with 0.01 mM biotinylated reference peptide – HA 306-318 (PKYVKQNTLKLAT) for DR0102 and myo 137-148 (LFRKDIAAKYKE) for DR0301 – in wells coated with DR0102 or DR0301 protein as previously described (21). After washing, the residual biotin-peptide was labeled using europium-conjugated streptavidin (Perkin Elmer) and quantified using a Victor2 D time resolved fluorometer (Perkin Elmer).…”