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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ji, T. H. (1983) Bifunctional reagents. Methods Enzymol. 91, 580–609.
Staros, J. V. and Anjaneyulu, P. S. (1989) Membrane-impermeant cross-linking reagents. Methods Enzymol. 172, 609–628.
Doms, R. W. (1990) Oligomerization and protein transport. Methods Enzymol. 191, 841–854.
Kluger, R. (1997) Chemical cross-linking and protein function, in Protein Function: A Practical Approach (Creighton, T. E., ed.), IRL Press, Oxford, p. 185.
Zimmerman, S. B. and Minton, A. P. (1993) Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu. Rev. Biophy. Biomol. Struct. 22, 27–65.
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.
Parks, R. E. J. and Agarwal, R. P. (1973) Nucleoside diphosphokinases. The Enzymes 8, 307–334.
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.
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.
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.
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.
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.
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.
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.
Taggart, A. K. and Pugh, B. F. (1996) Dimerization of TFIID when not bound to DNA. Science 272, 1331–1333.
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.
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.
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.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
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
Download citation
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