Materials and Methods

Part of the Springer Theses book series (Springer Theses)


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).


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.


  1. 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)Google Scholar
  2. 2.
    D. Hanahan, Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166, 557–580 (1983)CrossRefGoogle Scholar
  3. 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)Google Scholar
  4. 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)Google Scholar
  5. 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)CrossRefGoogle Scholar
  6. 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. 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. 8.
    Collaborative Computational Project, The CCP4 suite: programs for protein crystallography. Acta Crystallogr Sect. D - Biol. Crystallogr. 50, 760–763 (1994)CrossRefGoogle Scholar
  9. 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)CrossRefGoogle Scholar
  10. 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. 11.
    P.J. Kraulis, MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946–950 (1991)CrossRefGoogle Scholar
  12. 12.
    W.L. DeLano, The PyMOL Molecular Graphics System (DeLano Scientific, San Carlos, 2002)Google Scholar
  13. 13.
    SYBYL 8.0 Tripos International, 1699 South Hanley Rd., St. Louis, Missouri, 63144, USAGoogle Scholar
  14. 14.
    W. Kabsch, Xds. Acta Crystallogr Sect. D - Biol. Crystallogr. 66, 125–132 (2010)CrossRefGoogle Scholar
  15. 15.
    E. Krissinel, K. Henrick, Detection of protein assemblies in crystals. CompLife 2005(3695), 163–174 (2005)Google Scholar
  16. 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)CrossRefGoogle Scholar
  17. 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. 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)CrossRefGoogle Scholar
  19. 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)CrossRefGoogle Scholar
  20. 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. 21.
    F. Sanger, S. Nicklen, A.R. Coulson, DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463–5467 (1977)CrossRefGoogle Scholar
  22. 22.
    N. Gallastegui, M. Groll, Analysing properties of proteasome inhibitors using kinetic and X-ray crystallographic studies. Methods Mol. Biol. 832, 373–390 (2012)CrossRefGoogle Scholar
  23. 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)CrossRefGoogle Scholar
  24. 24.
    U.K. Laemmli, Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685 (1970)CrossRefGoogle Scholar
  25. 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)CrossRefGoogle Scholar
  26. 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)CrossRefGoogle Scholar
  27. 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. 28.
    M. Groll, R. Huber, Purification, crystallization, and X-ray analysis of the yeast 20S proteasome. Methods Enzymol. 398, 329–336 (2005)CrossRefGoogle Scholar
  29. 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. 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)CrossRefGoogle Scholar
  31. 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)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  1. 1.Chair of BiochemistryTechnische Universität MünchenGarchingGermany

Personalised recommendations