High-resolution AFM-imaging and mechanistic analysis of the 20 S proteasome

Journal of Molecular Biology

Volumn 288, Issue 5, 1999, Pages 1027-1036

  Dorn, Ingmar T ^a,b   Eschrich, Rainer ^a   Seemüller, Erika ^a   Guckenberger, Reinhard ^a   Tampé, Robert ^a,b  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Antigen processing; Enzyme; Interface; Membrane; Multicatalytic proteinase

Indexed keywords

HISTIDINE; PROTEASOME; PROTEIN SUBUNIT;

ARTICLE; ATOMIC FORCE MICROSCOPY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; IMAGING; LIPID MEMBRANE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN DEGRADATION; PROTEIN STRUCTURE; SURFACE PLASMON RESONANCE; THERMOPLASMA ACIDOPHILUM;

THERMOPLASMA ACIDOPHILUM;

EID: 0033591349     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2714     Document Type: Article

References (40)

1. Akopian T., Kisselev A., Goldberg A. Processive degradation of proteins and other catalytic properties of the proteasome from Thermoplasma acidophilum. J. Biol. Chem. 272:1997;1791-1798.
2. Barklis E., McDermott J., Wilkens S., Schabtach E., Schmid M. F., Fuller S., Karanjia S., Love Z., Jones R., Rui Y., Zhao X., Thompson D. Structural analysis of membrane-bound retrovirus capsid proteins. EMBO J. 16:1997;1199-1213.
3. Baumeister W., Dahlmann B., Hegerl R., Kopp F., Kuehn L., Pfeifer G. Electron microscopy and image analysis of the multicatalytic proteinase. FEBS Letters. 241:1988;239-245.
4. Baumeister W., Walz J., Zühl F., Seemüller E. The proteasome: paradigm of a self-compartmentalizing protease. Cell. 92:1998;367-380.
5. Bischler N., Balavoine F., Milkereit P., Tschochner H., Mioskowski C., Schultz P. Specific interaction and two-dimensional crystallization of histidine-tagged yeast RNA polymerase I on nickel-chelating lipids. Biophys. J. 74:1998;1522-1532.
6. Brannigan J., Dodson G., Duggleby H., Moody P., Smith J., Tomchick D., Murzin A. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature. 378:1995;416-419.
7. Dietrich C., Schmitt L., Tampé R. Molecular organization of histidine-tagged biomolecules at self-assembled lipid interfaces using a novel class of chelator lipids. Proc. Natl Acad. Sci. USA. 92:1995;9014-9018.
8. Dietrich C., Boscheinen O., Scharf K. D., Schmitt L., Tampé R. Functional immobilization of a DNA-binding protein at a membrane interface via histidine tag and synthetic chelator lipids. Biochemistry. 35:1996;1100-1105.
9. Dorn I. T., Hofmann U. G., Peltonen J., Tampé R. Diacetylene chelator lipids as supports for immobilization and imaging of proteins by atomic force microscopy. Langmuir. 14:1998a;4836-4842.
10. Dorn I. T., Neumaier K. R., Tampé R. Molecular recognition of histidine-tagged molecules by metal-chelating lipids monitored by fluorescence energy transfer and correlation spectroscopy. J. Am. Chem. Soc. 121:1998b;2753-2763.
11. Dorn I. T., Pawlitschko K., Pettinger S. C., Tampé R. Orientation and two-dimensional organization of proteins at chelator lipid interfaces. Biol. Chem. 379:1998c;1151-1159.
12. Ehring B., Meyer T. H., Eckerskorn C., 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. 235:1996;404-415.
13. Engel A., Schoenenberger C.-A., Müller D. J. High-resolution imaging of native biological sample surfaces with scanning probe microscopy. Curr. Opin. Struct. Biol. 7:1997;279-284.
14. Florin E.-L., Moy V., Gaub H. Adhesion forces between individual ligand-receptor pairs. Science. 264:1994;415-417.
15. Frazier R., Davies M., Matthijs G., Roberts C., Schacht E., Tendler S., Williams P. In situ surface plasmon resonance analysis of dextran monolayer degradation by dextranase. Langmuir. 13:1997;7115-7120.
16. Frey W., Schief W. R., Pack D. W., Chen C. T., Chilkoti A., Stayton P., Vogel V., Arnold F. H. 2-Dimensional protein crystallization via metal-ion coordination by naturally-occurring surface histidines. Proc. Natl Acad. Sci. USA. 93:1996;4937-4941.
17. Gritsch S., Neumaier K., Schmitt L., Tampé R. Engineered fusion molecules at chelator lipid interfaces imaged by reflection interference contrast microscopy (RICM). Biosens. Bioelect. 10:1995;805-812.
18. Haruki M., Noguchi E., Kanaya S., Crouch R. Kinetic and stochiometric analysis for the binding of Escherichia coli ribonuclease HI to RNA-DNA hybrids using surface plasmon resonance. J. Biol. Chem. 272:1997;22015-22022.
19. Khilko S., Jelonek M., Corr M., Boyd L., Bothwell A., Margulies D. Measuring interactions of MHC class I molecules using surface plasmon resonance. J. Immunol. Methods. 183:1995;77-94.
20. Kisselev A. F., Akopian T. N., Goldberg A. L. Range of sizes of peptide products generated during degradation of different proteins by archaeal proteasomes. J. Biol. Chem. 273:1998;1982-1989.
21. Kubalek E. W., Le Grice F. J., Brown P. O. Two-dimensional crystallization of histidine-tagged HIV-1 reverse transcriptase promoted by a novel nickel-chelating lipid. J. Struct. Biol. 113:1994;117-123.
22. Levitskaya J., Sharipo A., Leonchiks A., Ciechanover A., Masucci M. G. Inhibition of ubiquitin/proteasome-dependent protein degradation by the Gly-Ala repeat domain of the Epstein-Barr virus nuclear antigen 1. Proc. Natl Acad. Sci. USA. 94:1997;12616-12621.
23. Löwe J., Stock D., Jap B., Zwickl P., Baumeister W., Huber R. Crystal structure of the 20 S proteasome from the archaeon Thermoplasma acidophilum at 3.4 Å resolution. Science. 268:1995;533-539.
24. Müller D., Baumeister W., Engel A. Conformational change of the hexagonally packed intermediate layer of Deinococcus radiodurans monitored by atomic force microscopy. J. Bacteriol. 178:1996;3025-3030.
25. Müller D., Amrein M., Engel A. Adsorption of biological molecules to a solid support for scanning probe microscopy. J. Struct. Biol. 119:1997;172-188.
26. Nettikadan S., Tokumasu F., Takeyasu K. Quantitative analysis of the transcription factor AP2 binding to DNA by atomic force microscopy. Biochem. Biophys. Res. Commun. 226:1996;645-649.
27. O'Shannessy D. J., Brigham-Burke M., Soneson K. K., Hensley P., Brooks I. Determination of rate and equilibrium binding constants for macromolecular interaction using surface plasmon resonance: use of nonlinear least squares analysis methods. Anal. Biochem. 212:1993;457-468.
28. Ohnishi S., Hara M., Furuno T., Sasabe H. Imaging two-dimensional crystals of catalase by atomic force microscopy. Jpn. J. Appl. Phys. 35:1996;6233-6238.
29. Radmacher M., Fritz M., Hansma H., Hansma P. Direct observation of enzyme activity with the atomic force microscope. Science. 265:1994;1577-1579.
30. Reviakine I., Bergsma-Schutter W., Brisson A. Growth of protein 2-D crystals on supported planar lipid bilayers imaged in situ by AFM. J. Struct. Biol. 121:1998;356-361.
31. Schmid E. L., Tairi A. P., Hovius R., Vogel H. Screening ligands for membrane-protein receptors by total internal-reflection fluorescence - the 5HT3 serotonin receptor. Anal. Chem. 70:1998;1331-1338.
32. Schmitt L., Dietrich C., Tampé R. Synthesis and characterization of chelator lipids for reversible immobilization of engineered proteins at self-assembled lipid interfaces. J. Am. Chem. Soc. 116:1994;8485-8491.
33. Seemüller E., Lupas A., Stock D., Löwe J., Huber R., Baumeister W. Proteasome from Thermoplasma acidophilum: a threonine protease. Science. 268:1995;579-582.
34. Shao Z., Mou J., Czajkowsky D., Yang J., Yuan J. Biological atomic force microscopy - What is achieved and what is needed. Advan. Phys. 45:1996;1-86.
35. Shnek D. R., Pack D. W., Sasaki D. Y., Arnold F. H. Specific protein attachment to artificial membranes via coordination to lipid-bound copper(II). Langmuir. 10:1994;2382-2388.
36. Vinckier A., Gervasoni P., Zaugg F., Ziegler U., Lindner P., Groscurth P., Plückthun A., Semenza G. Atomic force microscopy detects changes in the interaction forces between GroEL and substrate proteins. Biophys. J. 74:1998;3256-3263.
37. Wagner P., Hegner M., Kernen P., Zaugg F., Semenza G. Covalent immobilization of native biomolecules onto Au(111) via N-hydroxysuccinimide ester functionalized self-assembled monolayers for scanning probe microscopy. Biophys. J. 70:1996;2052-2066.
38. Weisenhorn A., Drake B., Prater C., Gould A., Hansma P., Ohnesorge F., Egger M., Heyn S., Gaub H. Immobilized proteins in buffer imaged at molecular resolution by atomic force microscopy. Biophys. J. 58:1990;1251-1258.
39. Wenzel T., Eckerskorn C., Lottspeich F., Baumeister B. Existence of a molecular ruler in proteasomes suggested by analysis of degradation products. FEBS Letters. 349:1994;205-209.
40. York I., Rock K. Antigen processing and presentation by the class I major histocompatibility complex. Annu. Rev. Immunol. 14:1996;369-396.