An algorithm for the prediction of proteasomal cleavages

Proteasomes, major proteolytic sites in eukaryotic cells, play an important part in major histocompatibility class I (MHC I) ligand generation and thus in the regulation of specific immune responses. Their cleavage specificity is of outstanding interest for this process. In order to generalize previously determined cleavage motifs of 20 S proteasomes, we developed network-based model proteasomes trained by an evolutionary algorithm with experimental cleavage data of yeast and human 20 S proteasomes. A window of ten flanking amino acid residues proved sufficient for the model proteasomes to reproduce the experimental results with 98-100% accuracy. Actual experimental data were reproduced significantly better than randomly selected cleavage sites, suggesting that our model proteasomes were able to extract rules inherent to proteasomal cleavage data. The affinity parameters of the model, which decide for or against cleavage, correspond with the cleavage motifs determined experimentally. The predictive power of the model was verified for unknown (to the program) test conditions: the prediction of cleavage numbers in proteins and the generation of MHC I ligands from short peptides. In summary, our model proteasomes reproduce and predict proteasomal cleavages with high degree of accuracy. They present a promising approach for predicting proteasomal cleavage products in future attempts and, in combination with existing algorithms for MHC I ligand prediction, will be tested to improve cytotoxic T lymphocyte epitope prediction. (C) 2000 Academic Press.