Because the effective concentration of

Crizotinib manufacturer HLA (1–3 nm) used in these assays is below the equilibrium dissociation constant (KD) of most high-affinity peptide–HLA interactions, the peptide concentration leading to half-saturation of the HLA is a reasonable approximation of the affinity of the interaction. Affinity measurements of peptides to recombinant HLA-DRB1*0101, -DRB1*0301, -DRB1*0302, -DRB1*0401, -DRB3*0301, -DRB5*0101 and DPA1*0103/DPB1*0401 molecules were performed according to previous work.32 Briefly, peptides including reference peptides known to bind the used HLA-II alleles [DR-binding peptide HA 306–318 (sequence: YKYVKQNTLKLAT) and DP-binding peptide, Plasm. Falciparum 239–253 (3D7)33 (sequence: YILLKKILSSRFNQM)] were dissolved and titrated in 25% glycerol, 0·1% pluriol (F68) and 150 mm NaCl. An HLA-II stock solution consisting of bacterially expressed and urea-denatured α- and β-chains, at appropriate concentrations

were diluted into refolding buffer: 100 mm Tris/Citrate, 25% glycerol, 0·01% Pluriol F68 containing protease inhibitors (TPCK and Pepstatin both 3·3 μg/ml) at pH 6 (DRB1*0101. DRB5*0101) or pH 7 (remaining HLA-II alleles). The diluted HLA-II stock was subsequently mixed 1 : 1 with peptide titrations and incubated at 18° for 48 hr. Formed HLA-II complexes were detected PARP inhibitor using a homogeneous proximity assay (Alpha Screen; Perkin Elmer, Waltham, MA, USA); briefly, streptavidin-coated donor click here beads and L243 (murine monoclonal anti-DR) coupled acceptor beads, both 5 mg/ml, were diluted 500 times into PBS 0·1% Pluriol (F68). Ten microlitres of bead mix was mixed with 10 μl HLA-II/peptide samples in 384 Optiplates (Perkin Elmer). Following 18 hr of incubation at 18° they were read on an Envision Reader (Perkin Elmer) and analysed accordingly.32 The CD4+ T cells were positively depleted from PBMC according to the manufacturer’s instruction using monoclonal anti-CD4-coated Dynabeads from Dynal Biotech ASA (Oslo, Norway). The PBMC were effectively (>98%) depleted of CD4+ T cells as verified by flow cytometry. The PBMC

were thawed, washed and then used for CD4+ or CD8+ T-cell depletion or cultured directly in RPMI-1640 supplemented with 5% heat-inactivated AB serum (Valley Biomedical, Winchester, VA), 2 mm l-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin. The PBMC (4 × 106 to 6 × 106) or depleted PBMC were cultured in 1 ml culture medium in 24-well plates (Nunc, Roskilde, Denmark) in the presence of individual peptides with a final concentration of 10 μg/ml per well, and incubated for 10 days at 37°, 5% CO2 in humidified air. Recombinant human interleukin-2 (rhIL-2; Proleukin; Chiron, Amsterdam, the Netherlands) 20 U/ml was added on day 1. Cells were harvested on day 10, washed twice in RPMI-1640 and resuspended in complete medium to a final concentration of 1 × 106 to 2 × 106 cells/ml.