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Formation of Ubiquitin Dimers via Azide–Alkyne Click Reaction

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Ubiquitin Family Modifiers and the Proteasome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 832))

Abstract

The conjugation of poly-ubiquitin chains is a widespread post-translational modification of proteins that plays a role in many different cellular processes. Notably, the biological function of the attached ubiquitin chain depends on which lysine residue is used for chain formation. Here, we report a method for the modular synthesis of site-specifically linked ubiquitin dimers, which is based on click reaction between two artificial amino acids. In this way, it is possible to synthesize all seven naturally occurring ubiquitin connectivities, thus giving access to all ubiquitin dimers. Furthermore, this method can be generally applied to link ubiquitin to any substrate protein or even to link any two proteins site specifically.

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References

  1. Hershko A, Ciechanover A (1998) The ubiquitin system. Annu. Rev. Biochem. 67:425–479.

    Article  PubMed  CAS  Google Scholar 

  2. Hicke L, Dunn R (2003) Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. Annu. Rev. Cell. Dev. Biol. 19:141–172.

    Article  PubMed  CAS  Google Scholar 

  3. Pickart CM (2001) Mechanisms underlying ubiquitylation. Annu. Rev. Biochem. 70:503–533.

    Article  PubMed  CAS  Google Scholar 

  4. Kerscher O, Felberbaum R, Hochstrasser M (2006) Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell. Dev. Biol. 222:159–180.

    Article  Google Scholar 

  5. Peng J, Schwartz D, Elias JE et al (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21:921–926.

    Article  PubMed  CAS  Google Scholar 

  6. Li W, Ye Y (2008) Polyubiquitin chains: function, structures and mechanisms, Birkäuser Verlag, Basel.

    Google Scholar 

  7. Hershko A, Ciechanover A (1992) The ubiquitin system for protein degradation. Annu. Rev. Biochem. 61:761–807.

    Article  PubMed  CAS  Google Scholar 

  8. Williamson A, Wickliffe KE, Mellone BG et al (2009) Identification of a physiological E2 module for the human anaphase-promoting complex. PNAS 106:18213–18218.

    Article  PubMed  CAS  Google Scholar 

  9. Al-Hakim AK, Zagorska A, Chapman L et al (2008) Control of AMPK-related kinases by USP9X and atypical Lys29/Lys33-linked polyubiquitin chains. Journal of Biochemistry 411:249–260.

    Article  CAS  Google Scholar 

  10. Budisa N (2004) Prolegomena to future experimental efforts on genetic code engineering by expanding its amino acid repertoire. Angewandte Chemie International Edition 43:6426–6463.

    Article  CAS  Google Scholar 

  11. Young TS, Schultz PG (2010) Beyond the Canonical 20 Amino Acids: Expanding the Genetic Lexicon. J. Biol. Chem. 285:11039–11044.

    Article  PubMed  CAS  Google Scholar 

  12. Kiick KL, Saxon E, Tirrell DA et al (2002) Incorporation of azides into revombinant proteins for chemosolective modification by the Staudinger ligation. PNAS 99:19–24.

    Article  PubMed  CAS  Google Scholar 

  13. Kasteren SIv, Kramer HB, Jensen HH et al (2007) Expanding the diversity of chemical protein modification allows post-translational mimicry. Nature 446:1105–1109.

    Google Scholar 

  14. Shanmugham A, Fish A, Luna-Vargas MPA et al (2010) Nonhydrolyzable ubiquitin-isopeptide isosteres as deubiquitinating enzyme probes. J. Am. Chem. Soc. 132:8834–8835.

    Article  PubMed  CAS  Google Scholar 

  15. Kaya E, Gutsmiedl K, Vrabel M et al (2009) Synthesis of Threefold Glycosylated Proteins using Click Chemistry and Genetically Encoded Unnatural Amino Acids. ChemBioChem 10:2858–2861.

    Article  PubMed  CAS  Google Scholar 

  16. Nguyen DP, Lusic H, Neumann H et al (2009) Genetic Encoding and Labeling of Aliphatic Azides and Alkynes in Recombinant Proteins via a Pyrrolysyl-tRNA Synthetase/tRNACUA Pair and Click Chemistry. Journal of the American Chemical Society 131:8720–8721.

    Article  PubMed  CAS  Google Scholar 

  17. Fekner T, Li X, Lee MM et al (2009) A Pyrrolysine Analogue for Protein Click Chemistry. Angew. Chem. Int. Ed. 48:1633 –1635.

    Article  CAS  Google Scholar 

  18. Masson J-M, Miller JH (1986) Expression of synthetic suppressor tRNA genes under the control of a synthetic promoter. Gene 47:179–183.

    Article  PubMed  CAS  Google Scholar 

  19. Young RA (1979) Transcription Termination in the Escherichia coli Ribosomal RNA Operon rrnC. THE JOURNAL OF BIOLOGICAL CHEMISTRY 254:12725–12731.

    PubMed  CAS  Google Scholar 

  20. Huisgen R (1963) 1,3-Dipolar Cycloadditions. Past and Future. Angew. Chem. Int. Ed. 2:565–598.

    Article  Google Scholar 

  21. Rostovtsev VV, Green LG, Fokin VV et al (2002) A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective Ligation of Azides and Terminal Alkynes. Angew. Chem. Int. Ed. 41:2596–2599.

    Article  CAS  Google Scholar 

  22. Tornoe CW, Christensen C, Meldal M (2002) Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(i)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67:3057–3064.

    Article  PubMed  CAS  Google Scholar 

  23. Link AJ, Vink MKS, Tirrell DA (2007) Preparation of the functionoalized methionine surrogate azidohomoalanine via copper-catalyzed diazo transfer. Nature Protocols 2:1879–1883.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

We gratefully acknowledge funding by the Boehringer Ingelheim Fonds (S.E.), the EU-network of excellence RUBICON (M.S.) and the DFG (M.S., A.M.).

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Correspondence to Marina Rubini .

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Eger, S., Scheffner, M., Marx, A., Rubini, M. (2012). Formation of Ubiquitin Dimers via Azide–Alkyne Click Reaction. In: Dohmen, R., Scheffner, M. (eds) Ubiquitin Family Modifiers and the Proteasome. Methods in Molecular Biology, vol 832. Humana Press. https://doi.org/10.1007/978-1-61779-474-2_41

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  • DOI: https://doi.org/10.1007/978-1-61779-474-2_41

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-473-5

  • Online ISBN: 978-1-61779-474-2

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