Skip to main content
SpringerLink
Log in
Book cover

Structural and Functional Characterization of the Immunoproteasome pp 21–39Cite as

Materials and Methods

  • Chapter
  • First Online:

  • 344 Accesses

Part of the book series: Springer Theses ((Springer Theses))

Abstract

All chemicals were obtained from the following companies: AppliChem (Darmstadt, DE), Biomol (Hamburg, DE), Fluka (Neu-Ulm, DE), Merck (Darmstadt, DE), Sigma-Aldrich (Steinheim, DE), Serva (Heidelberg, DE), Roth (Karlsruhe, DE) and VWR (Darmstadt, DE).

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. W.O. Bullock, J.M. Fernandez, J.M. Short, XL1-Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta-galactosidase selection. Biotechniques 5, 376–379 (1987)

    CAS  Google Scholar 

  2. D. Hanahan, Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166, 557–580 (1983)

    Article  CAS  Google Scholar 

  3. W. Heinemeyer, A. Gruhler, V. Mohrle, Y. Mahe, D.H. Wolf, PRE2, highly homologous to the human major histocompatibility complex-linked RING10 gene, codes for a yeast proteasome subunit necessary for chrymotryptic activity and degradation of ubiquitinated proteins. J. Biol. Chem. 268, 5115–5120 (1993)

    CAS  Google Scholar 

  4. W. Heinemeyer, J.A. Kleinschmidt, J. Saidowsky, C. Escher, D.H. Wolf, Proteinase yscE, the yeast proteasome/multicatalytic-multifunctional proteinase: mutants unravel its function in stress induced proteolysis and uncover its necessity for cell survival. EMBO J. 10, 555–562 (1991)

    CAS  Google Scholar 

  5. W. Heinemeyer, M. Fischer, T. Krimmer, U. Stachon, D.H. Wolf, The active sites of the eukaryotic 20 S proteasome and their involvement in subunit precursor processing. J. Biol. Chem. 272, 25200–25209 (1997)

    Article  CAS  Google Scholar 

  6. R.J.C. Estiveira,The active subunits of the 20S proteasome in Saccharomyces cerevisiae—Mutational analysis of their specificities and a C-terminal extension, PhD thesis, Universität Stuttgart (2008)

    Google Scholar 

  7. R.M. Esnouf, An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model. 15(132–134), 112–133 (1997)

    Google Scholar 

  8. Collaborative Computational Project, The CCP4 suite: programs for protein crystallography. Acta Crystallogr Sect. D - Biol. Crystallogr. 50, 760–763 (1994)

    Article  Google Scholar 

  9. P. Emsley, B. Lohkamp, W.G. Scott, K. Cowtan, Features and development of coot, acta crystallogr. Sect. D - Biol. Crystallogr. 66, 486–501 (2010)

    Article  CAS  Google Scholar 

  10. D. Turk, Improvement of a programme for molecular graphics and manipulation of electron densities and its application for protein structure determination, PhD thesis, Technische Universität München (1992)

    Google Scholar 

  11. P.J. Kraulis, MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946–950 (1991)

    Article  Google Scholar 

  12. W.L. DeLano, The PyMOL Molecular Graphics System (DeLano Scientific, San Carlos, 2002)

    Google Scholar 

  13. SYBYL 8.0 Tripos International, 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA

    Google Scholar 

  14. W. Kabsch, Xds. Acta Crystallogr Sect. D - Biol. Crystallogr. 66, 125–132 (2010)

    Article  CAS  Google Scholar 

  15. E. Krissinel, K. Henrick, Detection of protein assemblies in crystals. CompLife 2005(3695), 163–174 (2005)

    Google Scholar 

  16. K. Mullis, F. Faloona, S. Scharf, R. Saiki, G. Horn, H. Erlich, Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51(Pt 1), 263–273 (1986)

    Article  CAS  Google Scholar 

  17. C. Papworth, J.C. Bauer, J. Braman, D.A. Wright, Site-directed mutagenesis in one day with >80 % efficiency. Strategies 9, 3–4 (1996)

    Google Scholar 

  18. W.J. Dower, J.F. Miller, C.W. Ragsdale, High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 16, 6127–6145 (1988)

    Article  CAS  Google Scholar 

  19. R.D. Gietz, R.A. Woods, Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 350, 87–96 (2002)

    Article  CAS  Google Scholar 

  20. R.S. Sikorski, J.D. Boeke, In vitro mutagenesis and plasmid shuffling from cloned gene to mutant yeast. Academic Press Inc, San Diego 194 302–318 (1991)

    Google Scholar 

  21. F. Sanger, S. Nicklen, A.R. Coulson, DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463–5467 (1977)

    Article  CAS  Google Scholar 

  22. N. Gallastegui, M. Groll, Analysing properties of proteasome inhibitors using kinetic and X-ray crystallographic studies. Methods Mol. Biol. 832, 373–390 (2012)

    Article  CAS  Google Scholar 

  23. G. Schmidtke, S. Emch, M. Groettrup, H.G. Holzhutter, Evidence for the existence of a non-catalytic modifier site of peptide hydrolysis by the 20S proteasome. J. Biol. Chem. 275, 22056–22063 (2000)

    Article  CAS  Google Scholar 

  24. U.K. Laemmli, Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685 (1970)

    Article  CAS  Google Scholar 

  25. W. Kabsch, Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800 (1993)

    Article  CAS  Google Scholar 

  26. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, R.J. Read, Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  27. M. Groll, L. Ditzel, J. Löwe, D. Stock, M. Bochtler, H.D. Bartunik, R. Huber, Structure of 20S proteasome from yeast at 2.4 Å resolution. Nature 386, 463–471 (1997)

    Google Scholar 

  28. M. Groll, R. Huber, Purification, crystallization, and X-ray analysis of the yeast 20S proteasome. Methods Enzymol. 398, 329–336 (2005)

    Article  CAS  Google Scholar 

  29. M. Unno, T. Mizushima, Y. Morimoto, Y. Tomisugi, K. Tanaka, N. Yasuoka, T. Tsukihara The structure of the mammalian 20S proteasome at 2.75 Å resolution. Structure 10 609-618 (2002)

    Google Scholar 

  30. A.A. Vagin, R.A. Steiner, A.A. Lebedev, L. Potterton, S. McNicholas, F. Long, G.N. Murshudov, REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr Sect. D - Biol. Crystallogr. 60, 2184–2195 (2004)

    Article  Google Scholar 

  31. A. Nicholls, K.A. Sharp, B. Honig, Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991)

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Chair of Biochemistry, Technische Universität München, Lichtenbergstr 4, 85747, Garching, Germany

    Eva Maria Huber

Authors
  1. Eva Maria Huber
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eva Maria Huber .

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Huber, E.M. (2013). Materials and Methods. In: Structural and Functional Characterization of the Immunoproteasome. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-319-01556-9_3

Download citation

Publish with us

Policies and ethics

Search

Navigation