Predicting proteasomal cleavage sites: A comparison of available methods

International Immunology

Volumn 15, Issue 7, 2003, Pages 781-787

  Saxová, Patricia ^a,b   Buus, Søren ^c   Brunak, Søren ^a   Keşmir, Can ^a,d  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b P J AFÁRIK UNIVERSITY   (Slovakia)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Artificial neural network; Cleavage site prediction; MHC class I epitope; Proteasome; Protein degradation

Indexed keywords

CELL PROTEIN; EPITOPE; PEPTIDASE; PEPTIDE; PROTEASOME;

ACCURACY; AMINO TERMINAL SEQUENCE; ANTIGEN PRESENTATION; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CYTOPLASM; CYTOTOXIC T LYMPHOCYTE; ENDOPLASMIC RETICULUM; ENZYME ASSAY; ENZYME DEGRADATION; ENZYME SPECIFICITY; HUMAN; HUMAN CELL; IMMUNE RESPONSE; INTERMETHOD COMPARISON; PEPTIDE SYNTHESIS; PREDICTION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; VERTEBRATE;

EID: 0038350948     PISSN: 09538178     EISSN: None     Source Type: Journal    
DOI: 10.1093/intimm/dxg084     Document Type: Article

References (23)

1. Rock, K. L. and Goldberg, A. L. 1999. Degradation of MHC class I-presented peptides. Annu. Rev. Immunol. 17:739.
2. Rammensee, H. G., Falk, K. and Rotzschke, O. 1993. Peptides naturally presented by MHC class I molecules. Annu. Rev. Immunol. 11:213.
3. Uebel, S. and Tampe, R. 1999. Specificity of the proteasome and the TAP transporter. Curr. Opin. Immunol. 11:203.
4. Tanaka, K. and Kasahara, M. 1998. The MHC class I ligand-generating system: roles of immunoproteasomes and the interferon-γ-inducible proteasome activator PA28. Immunol. Rev. 163:161.
5. Van den Eynde, B. J. and Morel, S. 2001. Differential processing of class-I-restricted epitopes by the standard proteasome and the immunoproteasome. Curr. Opin. Immunol. 13:147.
6. Toes, R. E., Nussbaum, A. K., Degermann, S., Schirle, M., Emmerich, N. P., Kraft, M., Laplace, C., Zwinderman, A., Dick, T. P., Muller, J., Schonfisch, B., Schmid, C., Fehling, H. J., Stevanovic, S., Rammensee, H. G. and Schild, H. 2001. Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products. J. Exp. Med. 194:1.
7. Nussbaum, A. K., Kuttler, C., Hadeler, K. P., Rammensee, H. G. and Schild, H. 2001. PAProC: a prediction algorithm for proteasomal cleavages available on the WWW. Immunogenetics 53:87.
8. Kuttler, C., Nussbaum, A. K., Dick, T. P., Rammensee, H. G., Schild, H. and Hadeler, K. P. 2000. An algorithm for the prediction of proteasomal cleavages. J. Mol. Biol. 298:417.
9. Holzhutter, H. G., Frommel, C. and Kloetzel, P. M. 1999. A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome. J. Mol. Biol. 286:1251.
10. Holzhutter, H. G. and Kloetzel, P. M. 2000. A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates. Biophys. J. 79:1196.
11. Kesmir, C., Nussbaum, A. K., Schild, H. and Brunak, S. 2002. Prediction of proteasome cleavage motifs by neural networks. Protein Eng. 15:287.
12. Craiu, A., Akopian, T., Goldberg, A. and Rock, K. L. 1997. Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide. Proc. Natl Acad. Sci. USA 94:10850.
13. Stoltze, L., Dick, T. P., Deeg, M., Pommerl, B., Rammensee, H. G. and Schild, H. 1998. Generation of the vesicular stomatitis virus nucleoprotein cytotoxic T lymphocyte epitope requires proteasome-dependent and -independent proteolytic activities. Eur. J. Immunol. 28:4029.
14. Paz, P., Brouwenstijn, N., Perry, R. and Shastri, N. 1999. Discrete proteolytic intermediates in the MHC class I antigen processing pathway and MHC I-dependent peptide trimming in the ER. Immunity 11:241.
15. Mo, X. Y., Cascio, P., Lemerise, K., Goldberg, A. L. and Rock, K. 1999. Distinct proteolytic processes generate the C and N termini of MHC class I-binding peptides. J. Immunol. 163:5851.
16. Rammensee, H. G., Bachmann, J., Emmerich, N. N., Bachor, O. A. and Stevanovic, S. 1999. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50:213.
17. Bairoch, A. and Apweiler, R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28:45.
18. Pearson, W. R. and Lipman, D. J. 1988. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85:2444.
19. Hobohm, U., Scharf, M., Schneider, R. and Sander, C. 1992. Selection of representative protein data sets. Protein Sci. 1:409.
20. Lucchiari-Hartz, M., Van Endert, P. M., Lauvau, G., Maier, R., Meyerhans, A., Mann, D., Eichmann, K. and Niedermann, G. 2000. Cytotoxic T lymphocyte epitopes of HIV-1 Nef: generation of multiple definitive major histocompatibility complex class I ligands by proteasomes. J. Exp. Med. 191:239.
21. Morel, S., Levy, F., Burlet-Schiltz, O., Brasseur, F., Probst-Kepper, M., Peitrequin, A. L., Monsarrat, B., Van Velthoven, R., Cerottini, J. C., Boon, T., Gairin, J. E. and Van den Eynde, B. J. 2000. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells. Immunity 12:107.
22. Nussbaum, A. K., Dick, T. P., Keilholz, W., Schirle, M., Stevanovic, S., Dietz, K., Heinemeyer, W., Groll, M., Wolf, D. H., Huber, R., Rammensee, H. G. and Schild, H. 1998. Cleavage motifs of the yeast 20S proteasome beta subunits deduced from digests of enolase 1. Proc. Natl Acad. Sci. USA 95:12504.
23. Ayyoub, M., Stevanovic, S., Sahin, U., Guillaume, P., Servis, C., Rimoldi, D., Valmori, D., Romero, P., Cerottini, J. C., Rammensee, H. G., Pfreundschuh, M., Speiser, D. and Levy F. 2002. Proteasome-assisted identification of an SSX-2-derived epitope recognized by tumor-reactive CTL infiltrating metastatic melanoma. J. Immunol. 168:1717.