Skip to main content

Materials and Methods

  • 324 Accesses

Part of the Springer Theses book series (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).

Keywords

  • Reservoir Solution
  • Lymphocytic Choriomeningitis
  • Magnesium Acetate
  • Sterile Toothpick
  • Sodium Nitrite Solution

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-319-01556-9_3
  • Chapter length: 19 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   84.99
Price excludes VAT (USA)
  • ISBN: 978-3-319-01556-9
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   109.99
Price excludes VAT (USA)
Hardcover Book
USD   159.99
Price excludes VAT (USA)

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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  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)

    CrossRef  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

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