Aebersold lab: Master thesis/semester project in interactomic studies of signaling complexes


The most widely utilized mass spec(MS)-based method to determine protein-protein interaction is based on affinity purification (AP-MS). Recently, a suite of methods have been developed to determine the proximal proteome of a target protein by biotin labeling, providing information complementary to AP-MS. In this project, the student will apply a combination of AP-MS and proximity labeling to exhaustively define the full and dynamic interactome of key players in innate immunity. 

APEX is a new proteomic method for the determination of protein-protein interaction based on spatial proximity. In APEX, a 28kDa ascorbate peroxidase is fused to a protein of interest, and, by addition of biotin phenol and H2O2, it does promote the formation of phenol radicals and the labeling of proteins in the proximity of the protein of interest [1]. Proximity labeling has been shown to produce complementary results as compared to traditional affinity purification-based MS approaches [2]. The project will entail the application of both AP-MS and APEX to the three key members of the signaling complex associated with tumor necrosis factor receptor I (TNFRI), a crucial player in inflammation and autoimmune diseases [3].

The student will be jointly supervised by Dr. Rodolfo Ciuffa and Dr. Martin Mehnert. He/She will have the opportunity to learn the two most powerful interactome-determination methods in proteomics, and apply this knowledge to a key immunological problem. The project will entail a well-structured set of experiments and a subsequent statistical evaluation of the results. The outcome of the project should be the integrative and dynamic interactome map of key factors in inflammation before and after stimulation with cytokines.

The student is expected to have basic knowledge of MS, training in cell culture and a strong interest in protein signaling. He/she will learn, in the course of her/his stay, basic MS workflows and basic and advanced interactome-determination techniques.

For further information, please send a CV and a motivation statement to Dr. Rodolfo Ciuffa () and Martin Mehnert ().

[1] Hung, V., Udeshi, N. D., Lam, S. S., Loh, K. H., Cox, K. J., Pedram, K., et al. (2016). Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nature Protocols, 11(3), 456–475.

[2] Lambert, J.-P., Tucholska, M., Go, C., Knight, J. D. R., & Gingras, A.-C. (2015). Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. Journal of Proteomics, 118, 81–94.

[1] Brenner, D., Blaser, H., & Mak, T. W. (2015). Regulation of tumour necrosis factor signalling: live or let die. Nature Reviews. Immunology, 15(6), 362–374.

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