The proteolytic fragments generated by vertebrate proteasomes: structural relationships to major histocompatibility complex class I binding peptides.

Proteasomes are involved in the proteolytic generation of major histocompatibility complex (MHC) class I epitopes but their exact role has not been elucidated. We used highly purified murine 20S proteasomes for digestion of synthetic 22-mer and 41/44-mer ovalbumin partial sequences encompassing either an immunodominant or a marginally immunogenic epitope. At various times, digests were analyzed by pool sequencing and by semiquantitative electrospray ionization mass spectrometry. Most dual cleavage fragments derived from 22-mer peptides were 7-10 amino acids long, with octa- and nonamers predominating. Digestion of 41/44-mer peptides initially revealed major cleavage sites spaced by two size ranges, 8 or 9 amino acids and 14 or 15 amino acids, followed by further degradation of the latter as well as of larger single cleavage fragments. The final size distribution was slightly broader than that of fragments derived from 22-mer peptides. The majority of peptide bonds were cleaved, albeit with vastly different efficiencies. This resulted in multiple overlapping proteolytic fragments including a limited number of abundant peptides. The immunodominant epitope was generated abundantly whereas only small amounts of the marginally immunogenic epitope were detected. The frequency distributions of amino acids flanking proteasomal cleavage sites are correlated to that reported for corresponding positions of MHC class I binding peptides. The results suggest that proteasomal degradation products may include fragments with structural properties similar to MHC class I binding peptides. Proteasomes may thus be involved in the final stages of proteolytic epitope generation, often without the need for downstream proteolytic events.

Immunization and affinity purification of antibodies using resin-immobilized lysine-branched synthetic peptides.

A new method has been developed to raise antibodies against synthetic peptides. A multiple antigenic peptide system (MAP) containing a branched oligolysine was synthesized on a beaded polystyrene polyoxyethylene graft copolymer resin, which acts as a synthetic hapten carrier for use in immunization. The peptides, already attached to the carrier, can be used directly after final deprotection without any further purification steps. The utility of this peptide-carrier conjugate is highlighted by its additional application for affinity purification of antibodies generated.

Role of hapten-anchoring peptides in defining hapten-epitopes for MHC-restricted cytotoxic T cells. Cross-reactive TNP-determinants on different peptides.

Synthetic hapten-peptide conjugates selectively modify cell-bound MHC class I molecules in a haplotype-specific way. We investigated the contribution of the carrier peptides to the structural specificity of T cell-antigenic TNP epitopes, using different H-2Kb-binding TNP-peptides and a collection of TNP/Kb-specific CTL clones. Adjustment of peptide sequences to the proposed Kb-specific "motif" (octamers with F or Y and L in positions 5 and 8, respectively) enhanced Kb-binding and antigenicity by many orders of magnitude. Moreover, several clones reacted to peptides, containing the "motif" and TNP-lysine in position 4 but were otherwise unrelated by sequence. TNP in other positions was not recognized by these cells, but other CTL reacted to TNP in position 7. This points to the positioning of hapten determinants within the MHC binding groove as a major role of the anchoring peptide. However, determination of the limiting amounts of TNP peptides that elicit antigenicity or inhibit other Kb-restricted CTL reactions revealed that TCR also recognize variations in the sequences of carrier peptides. This contribution is low for TNP in position 4 but high in position 7, indicating lysine in position 4 as a particularly dominant and cross-reactive hapten-anchoring site in Kb-associated peptides. This implies that cell modification with lysine-reactive TNP reagents results in immunodominant, highly repetitive TNP epitopes, which may explain the strong antigenicity and the allergenic properties of TNP, as well as the restricted TCR repertoire directed against this hapten. Our data further recommend hapten peptides for general studies of TCR-Ag interactions because in contrast to pure protein Ag, hapten epitopes tolerate substantial structural variations in the MHC-anchoring peptide, and can be located by hapten-specific antibodies.

Optimized oligonucleotide probes for DNA fingerprinting.

The three different simple repetitive oligonucleotide probes (CT)8, (CAC)5 and (TCC)5 were hybridized to a panel of human DNAs which had been digested with the restriction endonucleases Alu I, Hinf I and Mbo I. The resulting DNA fingerprints were analyzed and different parameters calculated, such as the maximal mean allele frequency and the average number of polymorphic bands per individual. The highest number of bands was obtained after hybridization of Hinf I digested DNA with (CAC)5. The probability of finding the same band pattern as in individual A in individual B is 2 x 10(-8). The DNAs of monozygous twins show indistinguishable banding patterns and the bands are inherited according to the Mendelian laws. Thus this procedure reveals informative fingerprints that can be used for individual identification, e.g. in paternity testing and in forensic applications. In most of these experiments 32P-labelled probes were employed, yet the biotinylated oligonucleotide (GACA)4 produced results which were equivalent to those obtained by hybridization with the 32P-labelled probe (GACA)4.