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Mouse histocompatibility antigens were solubilized from lymphocyte membranes by limited papain degradation. Spleens from Balb/c mice (H-2d), enlarged by administration of lymphoma cells, were used for the membrane preparations. The solubilized protein components were purified by ion-exchange chromatography, gel filtration and discontinuous polyacrylamide-gel electrophoresis. A further characterization was achieved in a two-dimensional protein mapping system using disc-electrophoresis and isotachophoresis in the first and second dimension, respectively. The purification was monitored for alloantigens H-2.4(D) and H-3.21(K) (H-2D and H-2K represent two regions of the H-2 system). On Sephadex G-100 partially purified H-2-alloantigen chromatographed in a region of Mr = 35500. The pI of these substances showed a maximum at pH 5.5 and 5.3 for H-2.4 and at 5.2 for H-2.31. Free SH- and dithio-groups were determined with 5,5′-dithiobis(2-nitrobenzoic acid). 1.56 μmol SH/μmol alloantigenic material was found, but no SS-bond could be detected after alkaline cleavage. This suggests the absence of covalently linked protein subunits in papain-solubilized molecules bearing single private specificites. This was confirmed after reduction and alkylation in 4 M urea: 30-50% of the alloantigenic activity was retained and shown, in polyacrylamide-gel electrophoresis, to migrate in the original region of activity (RBPB 0.29 and 0.33 for H-2.4; about 0.33 for H-2.31, BPB = bromophenol blue). After reductive alkylation gel filtration resulted in a further purification of the alloantigenic material. Highly purified substances showed a diffuse staining pattern and a broad serological profile after electrophoresis. We assume this heterogenity to be a genuine property of H-2 antigens. Structural and genetic implications of these findings are discussed. [ABSTRACT FROM AUTHOR]