A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome

Journal of Molecular Biology

Volumn 286, Issue 4, 1999, Pages 1251-1265

  Holzhütter, Hermann Georg ^a   Frömmel, Cornelius ^a   Kloetzel, Peter Michael ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

Kinetics; Pattern recognition; Proteasome; Proteolytic cleavage site; Regression analysis

Indexed keywords

PROTEASOME;

AMINO ACID SEQUENCE; ARTICLE; COVALENT BOND; PRIORITY JOURNAL; PROTEIN DEGRADATION;

EID: 0345291184     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2530     Document Type: Article

References (31)

1. Arendt C. S., Hochstrasser M. Identification of the yeast 20S proteasome catalytic centres and subunit interactions required for active-site formation. Proc. Natl Acad. Sci. USA. 94:1997;7156-7161.
2. Brannigan J. A., Dodson G., Duggleby H. J., Moody P. C. E., Smith J. L., Tomchick D. R., Murzin A. G. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature. 378:1995;416-419.
3. Dick L. R., Aldrich C., Jameson S. C., Moomaw C. R., Pramanik B. C., Doyle C. K., DeMartino G. N., Bevan M. J., Forman J. M., Slaughter C. A. Proteolytic processing of ovalbumin and β-galctosidase by the proteasome to yield antigenic peptides. Immunology. 152:1994;3884-3894.
4. Djaballah H., Harness J. A., Savory P. J., Rivett A. J. Use of serine-protease inhibitors as probes for the different proteolytic activities of the rat liver multicatalytic proteinase complex. Eur. J. Biochem. 209:1992;629-634.
5. Eggers M., Boes-Fabian B., Ruppert T., Kloetzel P.-M., Koszinowski U. H. The cleavage preference of the proteasome governs the yield of antigenic peptides. J. Exp. Med. 182:1995;1865-1870.
6. Ehring B., Meyer T., Eckerkorn Ch., Lottspeich F., Tampé R. Effects of major-histocompatibility-complex-encoded subunits on the peptidase and proteolytic activities of human 20 S proteasomes. Eur. J. Biochem. 235:1995;404-415.
7. Enenkel C., Lehmann H., Kipper J., Guckel R., Hilt W., Wolf D. H. PRE3, highly homologous to the human major histocompatibility complex-linked LMP2 (RING12) gene codes for a yeast proteasome subunit necessary for the peptidylglutamyl-peptide hydrolyzing activity. FEBS Letters. 341:1994;193-196.
8. Fontana A. Limited proteolysis of globular proteins occurs at exposed and flexible loops. Kotyk, Skoda J., Paces V., Kostka V. Highlights of Modern Biochemistry. 1989;1711-1726 VSP International Science Publishers, Zeist.
9. Frömmel C. The apolar surface area of amino acids and it's empirical correlation with hydrophobic free energy. J. Theor. Biol. 111:1984;247-260.
10. Goldberg A., Gaczynska M., Grant E., Michalek M., Rock K. L. Functions of the proteasome in antigen presentation. Cold Spring Harbor Symp. Quant. Biol. 60:1995;479-490.
11. Groll M., Ditzel L., Löwe J., Stock D., Bochtler M., Bartunik H. D., Huber R. Structure of 20 S proteasome from yeast at 2.4 A resolution. Nature. 386:1997;463-471.
12. Heinemeyer W., Gruhler A., Mohrle V., Mahe Y., Wold D. H. PRE2, highly homologous to the human major histocompatibility complex-linked RING10 gene, codes for a yeast proteasome subunit necessary for chymotryptic activity and degradation of ubiquitinated proteins. J. Biol. Chem. 268:1993;5115-5120.
13. Hochstrasser M. Ubiquitin, proteasomes & the regulation of intracellular protein degradation. Curr. Opin. Cell Biol. 7:1995;215-223.
14. Hubbard S. J., Eisenmenger F., Thornton J. M. Modeling studies of the change in conformation required for cleavage of limited proteolytic sites. Protein Sci. 3:1994;757-768.
15. Jentsch S., Schenker S. Selective protein degradation: a journey's end within the proteasome. Cell. 82:1995;881-884.
16. Kramer A., Keitel T., Winkler K., Stöcklein W., Höhne W., Schneider-Mergner J. Molecular basis for the binding promiscuity of an anti-p24 (HIV-1) monoclonal antibody. Cell. 91:1998;799-809.
17. Kuckelkorn U., Frentzel S., Kraft R., Kostka S., Groettrup M., Kloetzel P. M. Incorporation of major histocompatibility complex - encoded subunits LMP2 and LMP7 changes the quality of the 20S proteasome polypeptide processing products independent of interferon-γ Eur. J. Immunol. 252:1995;605-611.
18. Lehner P. J., Cresswell P. Processing and delivery of peptides presented by MHC class I molecules. Curr. Opin. Immunol. 8:1996;59-67.
19. Löwe J., Stock D., Jap B., Zwickl P., Baumeister W., Huber R. Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. Science. 268:1995;533-539.
20. Motoc I., Marshall G. R. Van der Waals volume fragmental constants. Chem. Phys. Letters. 116:1985;415-419.
21. Niedermann G., King G., Butz S., Ihlenfeldt H. G., Grimm R., Lucciari M., Hoschützky H., Jung G., Maier B., Eichmann K. Contribution of proteasome-mediated proteolysis to the hierarchy of epitopes presented by major histocompatibility complex class I molecules. Immunity. 2:1995;289-299.
22. Niedermann G., King G., Butz S., Birsner U., Grimm R., Shabanowitz J., Hunt D. F., Eichmann K. The proteolytic fragments generated by vertebrate proteasomes: structural relationships to major histocompatibility complex I binding peptides. Proc. Nat. Acad. Sci. USA. 93:1996;8572-8577.
23. Orlowski M., Michaud C. Pituitary multicatalytic proteinase complex. Specificity of components and aspects of proteolytic activity. Biochemistry. 28:1989;9270-9278.
24. Orlowski M., Cardozo C., Michaud C. Evidence for the presence of five distinct proteolytic components in the pituitary multicatalytic proteinase complex. Properties of two components cleaving bonds on the carboxyl side of branched chain and small neutral amino acids. Biochemistry. 32:1993;1563-1572.
25. Ossendorp F., Eggers M., Neisig A., Ruppert T., Groettrup M., Sijts A., Mengedé E., Kloetzel P., Neefjes J., Koszinowski U., Melief C. A single residue exchange within a viral CTL epitope alters proteasome-mediated degradation resulting in lack of antigen presentation. Immunity. 5:1996;115-124.
26. Schechter I., Berger A. On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. 27:1992;157-162.
27. Schneider G., Rohlk S., Wrede P. Analysis of cleavage-site patterns in protein precursor sequences with a perceptron-type neural network. Biochem. Biophys. Res. Commun. 124:1993;951-959.
28. Seemüller E., Lupas A., Stock D., Baumeister W. Autocatalytic processing of the 20S proteasome. Nature. 382:1996;468-470.
29. Shimbara N., Nakajima H., Tanahashi N., Ogawa K., Niwa S., Uenaka A., Tanaka K. Double-cleavage production of the CTL epitope by proteasomes and PA28: role of the flanking region. Genes Cells. 2:1997;785-800.
30. Theobald M., Ruppert T., Kuckelkorn U., Hernandez J., Häußler A., Ferreira E. A., Liewer U., Biggs J., Levine A. J., Huber C., Koszinowski U., Kloetzel P. M., Shermann L. A. The sequence alteration associated with a mutational hotspot in p53 protects cells from lysis by cytotoxic T lymphocytes specific for a flanking peptide epitope. J. Exp. Med. 188:1998;1017-1028.
31. Wenzel T., Eckerkorn Ch., Lottspeich F., Baumeister W. Existence of a molecular ruler in proteasomes suggested by analysis of degradation products. FEBS Letters. 349:1994;205-209.