University of Dundee

Dr Satpal Virdee

Chemical Biology Approaches for Studying The Ubiquitin System
Position: 
Programme Leader in Protein Ubiquitylation
Address: 
College of Life Sciences, University of Dundee, Dundee
Full Telephone: 
+44 (0) 1382 388738, int ext 88738
Email: 

Research

Protein ubiquitylation is a versatile post-translational modification that regulates most aspects of eukaryotic biology. Classically, it was assumed to simply be a mechanism for targeting misfolded proteins for degradation but we now know that the regulated degradation of functional proteins is critical for important cellular processes such as gene activation. In addition, it is apparent that ubiquitin regulates processes other than degradation such as DNA repair, kinase activation and endocytosis. Defects in these regulatory mechanisms are the cause of a number of diseases such as autoimmune and neurodegenerative disorders. Using a multidisciplinary approach composed of synthetic, biochemical, structural and chemical genetic methods we study the various polyubiquitin topologies and how they are decoded. We also have an interest in the mechanism of the ubiquitin conjugation machinery.

Complexity of the ubiquitin signal

Ubiquitin can be conjugated to numerous lysine residues within a substrate protein and can also be conjugated to any of the 7 lysine residues, or N-terminus, of another ubiquitin molecule. This gives rise to 8 different polyubiquitin chains all of which have been shown to exist in cells. It is emerging that the various cellular roles mediated by ubiquitin may be encoded in the distinct properties of the different ubiquitin chains. There are several challenges in studying these complex ubiquitin signals as the enzymes responsible for their assembly and their site-specific attachment to substrates are not known. Our laboratory has pioneered the application of genetic code expansion methods for genetically directing the site-specific chemical conjugation of ubiquitin. This grants us with precise control over the topology of the polyubiquitin signal and where it is attached.

Figure 1 The genetically-directed, chemical conjugation of ubiquitin involves the incorporation of a designed, unnatural amino acid (UAA) into a recombinant protein
This is achieved by reengineering of the cells protein translation machinery to allow it to incorporate unnatural amino acids in response to an amber stop codon. The designed amino acid can undergo specific chemistry with a ubiquitin molecule that has a complementary chemical group appended to its C-terminus. Using various designed unnatural amino acids and modified ubiquitin molecules we can conjugate ubiquitin via its natural isopeptide bond, or, via a stable mimic.

Figure 2 Genetically directed, chemical ubiquitylation has enabled us to prepare K6-linked ubiquitin and determine its crystal structure
Using the diubiquitin structure and modelling we can predict what an extended K6-linked polyubiquitin chain may look like as shown above. K6 polyubiquitin chains have been implicated in DNA repair processes with genetic links to cancer.

Recognition of the ubiquitin signals

We are interested in identifying which proteins recognize the various ubiquitin chains. Identification of these decoding modules will provide valuable insight into the cellular roles of the various ubiquitin linkages. Using our chemical ubiquitylation technology we have used synthesized ubiquitin chains to identify deubiquitylating enzymes (DUBS) which demonstrate preference for distinct topologies. We have shown that the deubuitylating enzyme TRABID has strong preference for the poorly characterised K29-linked ubiquitin chain

Figure 3 Quantifying deubiquitylase (DUB) specificity against newly synthesized atypical ubiquitin linkages.
This allowed the rapid identification of a DUB which is highly active against the atypical K29 ubiquitin linkage.

Ubiquitin ligases

The enzymes responsible for ubiquitin attachment are known as E3 ubiquitin ligases and it is these enzymes that confer substrate specificity in ubiquitin attachment [3]. The are several E3 ligase sub-families including RING, HECT and RING-in-between-RING ligases. We still did not fully understand the mechanistic aspects of how E3 ligases catalyse ubiquitin conjugation and how they specifically recruit substrates. Understanding substrate selection is particularly pressing as therapeutic targeting of this process has great potential. It has not been possible to determine the structures of key intermediates of Ub transfer owing to the transient nature of the process. Such structures should enlighten our understanding of ubiquitin transfer to substrates and how RING E3 and E2 activating enzymes work together. We wish to develop chemical approaches to isolate these key intermediates in stable forms which would be amenable to structure determination and could even be used to search for unknown substrates or E3 ligases.

References

  1. Virdee, S., Ye, Y., Nguyen, D.P., Komander, D. and Chin, J.W. (2010). Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase. Nat. Chem. Biol. 6, 750-757
  2. Virdee, S, Kapadnis, P. B., Elliott, T., Lang, K., Madrzak, J., Nguyen, D. P., et al. (2011). Traceless and Site-Specific Ubiquitination of Recombinant Proteins. J Am Chem Soc, 133, 10708–10711
  3. Deshaies, R.J. and Joazeiro, C.A.P. (2009). RING domain E3 ubiquitin ligases. Ann. Rev. Biochem. 78, 399-434
  4. Davis, L., & Chin, J. W. (2012). Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol, 13, 168–182
 
 

Publications

Selected Publications

Virdee, S., Ye, Y., Nguyen, D. P., Komander, D. and Chin, J. W. (2010).
Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase.
Nat Chem Biol 6, 750-757

Virdee, S., Kapadnis, P. B., Elliott, T., Lang, K., Madrzak, J., Nguyen, D. P., Riechmann, L. and Chin, J. W. (2011).
Traceless and site-specific ubiquitination of recombinant proteins.
J Am Chem Soc 133, 10708-10711

Licchesi, J. D., Mieszczanek, J., Mevissen, T. E., Rutherford, T. J., Akutsu, M., Virdee, S., El Oualid, F., Chin, J. W., Ovaa, H., Bienz, M. and Komander, D. (2012).
An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.
Nat Struct Mol Biol 19, 62-71

Akutsu, M., Ye, Y., Virdee, S., Chin, J. W. and Komander, D. (2011).
Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains.
Proc Natl Acad Sci U S A 108, 2228-2233

Virdee, S., Macmillan, D. and Waksman, G. (2010).
Semisynthetic Src SH2 domains demonstrate altered phosphopeptide specificity induced by incorporation of unnatural lysine derivatives.
Chem Biol 17, pp. 274-284

Nguyen, D. P., Garcia Alai, M. M., Virdee, S. and Chin, J. W. (2010).
Genetically directing varepsilon-N, N-dimethyl-L-lysine in recombinant histones.
Chem Biol 17, 1072-1076

Geroult, S., Hooda, M., Virdee, S. and Waksman, G. (2007).
Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations.
Chem Biol Drug Des 70, 87-99

Geroult, S., Virdee, S. and Waksman, G. (2006).
The role of water in computational and experimental derivation of binding thermodynamics in SH2 domains.
Chem Biol Drug Des 67, 38-45

Impact

Commercial Impact:

In collaboration with the pharmaceutical industry via the Division of Signal Transduction Therapy collaboration with AstraZeneca, Boehringer Ingelheim, GlaxoSmithKline, Janssen Pharmaceutica, Merck Serono and Pfizer the research ouptuts from my group contribute to accelerating the development of company drug development programmes through access to research data and reagents. Reagents are also commercialised to provide access to the wider scientific community via license arrangements with companies such as Millipore, AbCam and Ubiquigent.