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In Vivo Protein Cross-Linking

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Protein-Protein Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 261))

Abstract

In the cell, homo- and heteroassociations of polypeptide chains evolve and take place within subcellular compartments that are crowded with many other cellular macromolecules. In vivo chemical cross-linking of proteins is a powerful method to examine changes in protein oligomerization and protein-protein interactions upon cellular events such as signal transduction. This chapter is intended to provide a guide to the selection of the cell-membrane-permeable cross-linkers, the optimization of in vivo cross-linking conditions, and the identification of specific cross-links in a cellular context where the frequency of random collisions is high. By combining the chemoselectivity of the homo-bifunctional cross-linker and the length of its spacer arm with knowledge on the protein structure, we show that selective cross-links can be introduced specifically on either the dimer or the hexamer form of the same polypeptide in vitro as well as in vivo, using the human type B nucleoside diphosphate kinase as a protein model.

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References

  1. Ji, T. H. (1983) Bifunctional reagents. Methods Enzymol. 91, 580–609.

    Article  PubMed  CAS  Google Scholar 

  2. Staros, J. V. and Anjaneyulu, P. S. (1989) Membrane-impermeant cross-linking reagents. Methods Enzymol. 172, 609–628.

    Article  PubMed  CAS  Google Scholar 

  3. Doms, R. W. (1990) Oligomerization and protein transport. Methods Enzymol. 191, 841–854.

    Article  PubMed  CAS  Google Scholar 

  4. Kluger, R. (1997) Chemical cross-linking and protein function, in Protein Function: A Practical Approach (Creighton, T. E., ed.), IRL Press, Oxford, p. 185.

    Google Scholar 

  5. Zimmerman, S. B. and Minton, A. P. (1993) Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu. Rev. Biophy. Biomol. Struct. 22, 27–65.

    Article  CAS  Google Scholar 

  6. Wang, K. and Richards, F. M. (1975) Reaction of dimethyl-3,3′-dithiobispropionimidate with intact human erythrocytes. Cross-linking of membrane proteins and hemoglobin. J. Biol. Chem. 250, 6622–6626.

    PubMed  CAS  Google Scholar 

  7. Parks, R. E. J. and Agarwal, R. P. (1973) Nucleoside diphosphokinases. The Enzymes 8, 307–334.

    Article  CAS  Google Scholar 

  8. Lacombe, M.-L., Wallet, V., Troll, H., and Veron, M. (1990) Functional cloning of a nucleoside diphosphate kinase from Dictyostelium discoideum. J. Biol. Chem. 265, 10,012–10,018.

    PubMed  CAS  Google Scholar 

  9. Postel, E. H., Berberich, S. J., Flint, S. J., and Ferrone, C. A. (1993) Human c-myc transcription factor PuF identified as nm23-H2 nucleoside diphosphate kinase, a candidate suppressor of tumor metastasis. Science 261, 478–480.

    Article  PubMed  CAS  Google Scholar 

  10. Mesnildrey, S., Agou, F., Karlsson, A., Deville-Bonne, D., and Veron, M. (1998) Coupling between catalysis and oligomeric structure in NDP kinase. J. Biol. Chem. 273, 4436–4442.

    Article  PubMed  CAS  Google Scholar 

  11. Karlsson, A., Mesnildrey, S., Xu, Y., Morera, S., Janin, J., and Veron, M. (1996) Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography. J. Biol. Chem. 271, 19,928–19,934.

    Article  PubMed  CAS  Google Scholar 

  12. Mesnildrey, S., Agou, F., and Veron, M. (1997) The in vitro DNA-binding properties of NDP kinase are related to its oligomeric state. FEBS Lett. 418, 53–57.

    Article  PubMed  CAS  Google Scholar 

  13. Agou, F., Raveh, S., Mesnildrey, S., and Veron, M. (1999) Single strand DNA specificity analysis of human nucleoside diphosphate kinase B. J. Biol. Chem. 274, 19,630–19,638.

    Article  PubMed  CAS  Google Scholar 

  14. Pogulis, R. J., Vallejo, A. N., and Pease, L. R. (1996) In vitro recombination and mutagenesis by overlap extension PCR. Meth. Mol. Biol. 57, 167–176.

    CAS  Google Scholar 

  15. Taggart, A. K. and Pugh, B. F. (1996) Dimerization of TFIID when not bound to DNA. Science 272, 1331–1333.

    Article  PubMed  CAS  Google Scholar 

  16. Jackson-Fisher, A. J., Chitikila, C., Mitra, M., and Pugh, B. F. (1999) A role for TBP dimerization in preventing unregulated gene expression. Molecular Cell 3, 717–727.

    Article  PubMed  CAS  Google Scholar 

  17. Morera, S., Lacombe, M.-L., Xu, Y., LeBras, G., and Janin, J. (1995) X-ray structure of nm23 human nucleoside diphophate kinase B complexed with GDP at 2 Å resolution. Structure 3, 1307–1314.

    Article  PubMed  CAS  Google Scholar 

  18. Agou, F., Ye, F., Goffinont, S., et al. (2002) NEMO trimerizes through its coiled-coil C-terminal domain. J. Biol. Chem. 277, 17,464–17,475.

    Article  PubMed  CAS  Google Scholar 

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© 2004 Humana Press Inc., Totowa, NJ

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Agou, F., Ye, F., Véron, M. (2004). In Vivo Protein Cross-Linking. In: Fu, H. (eds) Protein-Protein Interactions. Methods in Molecular Biology, vol 261. Humana Press. https://doi.org/10.1385/1-59259-762-9:427

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  • DOI: https://doi.org/10.1385/1-59259-762-9:427

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-120-2

  • Online ISBN: 978-1-59259-762-8

  • eBook Packages: Springer Protocols

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