We have examined the interactions of various peptides with the mouse class II major histocompatibility complex molecule I-Ak. MATERIALS AND METHODS Three sets of experiments were done. In each, peptides bound to I-Ak were examined by SDS/PAGE under reducing conditions but without boiling the immune precipitate. In the first set ofexperiments, radiolabeled peptides were incubated with purified I-Ak in detergent solution and then examined by SDS/PAGE. I-Ak was affinity-purified from CH27 B-lymphoma cells (16) by using the monoclonal antibody 10-3.6.2 (17), as reported (18). Synthetic peptides were labeled with 1251 by the chloramine-T method to a specific activity of 2-4 x 108 cpm/fug and then purified by C18 reverse-phase HPLC.Purified I-Ak was incubated with an excess of labeled peptide (30 pmol of I-Ak with 100 pmol of peptide) (19). After 72 hr, the newly formed complex was purified from unbound peptide by Sephadex G-50 chromatography (19,20). The void volume was pooled and concentrated with a Centricon 10 (Amicon). The samples were resuspended in loading buffer (12) and analyzed by SDS/10%o PAGE. The amounts of peptide bound or dissociated were then quantitated. Two regions were excised from each lane: a region at the top ofthe gel where labeled peptide bound in the intact af3 dimers was found to migrate (12, 21), and a region at the bottom of the gel where free labeled peptide migrated. The incorporated radioiodine in each excised gel fragment was determined with a standard 'y counter. The total radioactive peptide remaining bound to I-Ak after SDS/PAGE was calculated as the ratio of counts found at the top position to the total counts in each lane and is given as a percentage.In the second set of experiments, the radiolabeled peptides were incubated with an I-Ak-bearing B-lymphoma cell line, from which the complexes of peptide-I-Ak were then isolated. M12.C3.F6 B-lymphoma cells (22), 2 ml at 108 cells per ml in Dulbecco's modified Eagle's medium containing 2% fetal bovine serum and 20 mM Hepes, were incubated with 90-110 pmol of 125I-labeled peptide (-3 x 107 cpm) at 370C and 5% CO2 for 4 hr. The cells were harvested, washed, and then lysed in 5 ml of phosphate-buffered saline containing: 1% Triton X-100, 10 mM iodoacetamide, 1 mM phenylmethylsulfonyl fluoride, and 20 ;Lg of leupeptin per ml. The lysate was incubated with the monoclonal anti-I-Ak antibody 10.3.62 and the immunoprecipitates were analyzed by SDS/ PAGE as above.The third approach consisted of metabolically labeling I-Ak of B lymphoma cells with [3H]leucine and then adding nonlabeled peptide. The M12.C3.F6 cells were cultured at 107 per ml in leucine-deficient Dulbecco's modified Eagle's medium containing 10% dialyzed fetal bovine serum and, after 1 hr of incubation at 370C, were incubated in the same medium but containing [3H]leucine (800 ACi/ml; 1 ACi = 37 kBq) without or with peptide (100 AtM) or HEL (1 mg/ml).After 1 hr, nonradioactive leucine was added as a chase and the incubation continued for 4 hr. The metabolically labeled Abbr...