Discriminating self from nonself with short peptides from large proteomes

Immunogenetics

Volumn 56, Issue 5, 2004, Pages 311-320

  Burroughs, Nigel J ^a   De Boer, Rob J ^b   Keşmir, Can ^b,c  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UTRECHT UNIVERSITY   (Netherlands)

^c TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Antigen presentation; Bioinformatics; MHC class I; Self:nonself discrimination; T cell receptor specificity

Indexed keywords

AMINO ACID; HLA A ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; PROTEOME;

ALLELE; ANTIGEN PRESENTATION; ANTIGEN SPECIFICITY; ARTICLE; HUMAN; MICROORGANISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION;

EID: 4544382384     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00251-004-0691-0     Document Type: Article

References (33)

1. Baldauf SL, Roger AJ, WenkSiefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977
2. Beekman NJ, Van Veelen PA, Van Hall T, Neisig A, Sijts A, Camps M, Kloetzel PM, Neefjes JJ, Melief CJ, Ossendorp F (2000) Abrogation of CTL epitope processing by single amino acid substitution flanking the C-terminal proteasome cleavage site. J Immunol 164:1898-1905
3. Borghans JA, De Boer RJ (2002) Memorizing innate instructions requires a sufficiently specific adaptive immune system. Int Immunol 14:525-532
4. Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S (2003) Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 62:378-384
5. Engelhard VH (1994) Structure of peptides associated with class I and class II MHC molecules. Annu Rev Immunol 12:181-207
6. Germain RN, Margulies DH (1993) The biochemistry and cell biology of antigen processing and presentation. Annu Rev Immunol 11:403-450
7. Hanada K, Yewdell JW, Yang JC (2004) Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature 427:252-256
8. Holste D, Grosse I, Herzel H (2001) Statistical analysis of the DNA sequence of human chromosome 22. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 64:41917
9. Huynen MA, Van Nimwegen E (1998) The frequency distribution of gene family sizes in complete genomes. Mol Biol Evol 15:583-589
10. Janeway CA, Travers P, Walport M, Shlomchik M (2001) Immunobiology. The immune system in health and disease, 5th edn. Garland, New York
11. Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S (2002) Prediction of proteasome cleavage motifs by neural networks. Protein Eng 15:287-296
12. Kesmir C, Van Noort V, De Boer RJ, Hogeweg P (2003) Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome. Immunogenetics 55:437-449
13. Kourilsky P, Claverie JM (1986) The peptidic self model: a hypothesis on the molecular nature of the immunological self. Ann Inst Pasteur Immunol 137:3-21
14. Lucchiari-Hartz M, Van Endert PM, Lauvau G, Maier R, Meyerhans A, Mann D, Eichmann K, Niedermann G (2000) Cytotoxic T lymphocyte epitopes of HIVNef: generation of multiple definitive major histocompatibility complex class I ligands by proteasomes. J Exp Med 191:239-252
15. Mantegna RN, Buldyrev SV, Goldberger AL, Havlin S, Peng CK, Simons M, Stanley HE (1995) Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52:2939-2950
16. Matzinger P (1994) Tolerance, danger, and the extended family. Annu Rev Immunol 12:991-1045
17. Medzhitov R, Janeway Jr CA (2002) Decoding the patterns of self and nonself by the innate immune system. Science 296:298-300
18. Morel S, Levy F, BurletSchiltz O, Brasseur F, ProbstKepper M, Peitrequin AL, Monsarrat B, Van Velthoven R, Cerottini JC, Boon T, Gairin JE, Van den Eynde BJ (2000) Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells. Immunity 12:107-117
19. Nussbaum AK, Dick TP, Keilholz W, Schirle M, Stevanovic S, Dietz K, Heinemeyer W, Groll M, Wolf DH, Huber R, Rammensee HG, Schild H (1998) Cleavage motifs of the yeast 20S proteasome β subunits deduced from digests of enolase 1. Proc Natl Acad Sci USA 95:12504-12509
20. Ohno S (1992) How cytotoxic T cells manage to discriminate nonself from self at the nonapeptide level. Proc Natl Acad Sci USA 89:4643-4647
21. Parker KC, Bednarek MA, Coligan JE (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide sidechains. J Immunol 152:163-175
22. Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG (2003) Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 171:1741-1749
23. Qian J, Luscombe NM, Gerstein M (2001) Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J Mol Biol 313:673-681
24. Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50:213-219
25. Reits E, Neijssen J, Herberts C, Benckhuijsen W, Janssen L, Drijfhout JW, Neefjes J (2004) A major role for TPPII in trimming proteasomal degradation products for MHC class I antigen presentation. Immunity 20:495-506
26. Ristori G, Salvetti M, Pesole G, Attimonelli M, Buttinelli C, Martin R, Riccio P (2000) Compositional bias and mimicry toward the nonself proteome in immunodominant T-cell epitopes of self and nonself antigens. FASEB J 14:431-438
27. Ruppert J, Sidney J, Celis E, Kubo RT, Grey M, Sette A (1993) Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell 74:929-937
28. Saxova P, Buus S, Brunak S, Kesmir C (2003) Predicting proteasomal cleavage sites: a comparison of available methods. Int Immunol 15:781-787
29. Sette A, Sidney J, Livingston BD, Dzuris JL, Crimi C, Walker CM, Southwood S, Collins EJ, Hughes AL (2003) Class I molecules with similar peptide binding specificities are the result of both common ancestry and convergent evolution. Immunogenetics 54:830-841
30. Stoltze L, Schirle M, Schwarz G, Schroter C, Thompson MW, Hersh L B, Kalbacher H, Stevanovic S, Rammensee HG, Schild H (2000) Two new proteases in the MHC class I processing pathway. Nat Immunol 1:413-418
31. Vigneron N, Stroobant V, Chapiro J, Ooms A, Degiovanni G, Morel S, Van Der Bruggen P, Boon T, Van Den Eynde BJ (2004) An antigenic peptide produced by peptide splicing in the proteasome. Science 304:587-590
32. Yewdell JW, Reits E, Neefjes J (2003) Making sense of mass destruction: quantitating MHC class I antigen presentation. Nat Rev Immunol 3:952-961
33. Yusim K, Kesmir C, Gaschen B, Addo MM, Altfeld M, Brunak S, Chigaev A, Detours V, Korber BT (2002) Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV) proteins reveal imprints of immune evasion on HIV global variation. J Virol 76:8757-8768