Aebersold lab: Master thesis/semester project in Structural Proteomics
We are looking for motivated semester/master students to join our structural proteomics team at ETH to work at the interface between proteomics and structural biology.
Background
Protein complexes are the functional machines of the cell, solving their structure is essential to understand how they work.
A new structural technique called cross-linking mass spectrometry (XL-MS) takes advantage of simple linking chemistry and a mass-spectrometer to determine what aminoacidic residues are close in 3D space in a protein complex.
Our group is one of the world leaders in XL-MS having developed innovative experimental (1) and computational workflows (2).
In the past we have applied XL-MS to key protein complexes such as the ribosome, chromatin remodellers and proteasomes (3,4).
Goals
The next challenge in XL-MS is to determine more accurate distances in 3D.
We call this Ruler-XL. We showed that accurate distance restraints will greatly improve 3D structural models of complexes including XL-MS data.
We are in a unique position for such development as we recently developed a key software package.
You will learn
Basic proteomics workflows, protein cross-linking, mass-spectrometer operation, data analysis and scripting. Your direct supervisor has a background in structural biology (5), cross-linking MS and computational modeling. You will also have a chance to join ongoing projects and contribute to research publications.
We are looking for
A motivated student with interest in protein biochemistry and structures, willing to learn basic computational tools. You will join our team working at the interface between proteomics and structural biology.
For any questions and details please contact Marco Faini at
Literature
1) Leitner, A., Walzthoeni, T., & Aebersold, R. (2014). Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nature Protocols, 9(1), 120–137. external page http://www.ncbi.nlm.nih.gov/pubmed/24356771
2) Walzthoeni, T., Claassen, M., Leitner, A., Herzog, F., Bohn, S., Förster, F., et al. (2012). False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nature Methods. external page http://www.ncbi.nlm.nih.gov/pubmed/22772729
3) Greber, B. J., Boehringer, D., Leibundgut, M., Bieri, P., Leitner, A., Schmitz, N., et al. (2014). The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature, 515(7526), 283–286. external page http://www.ncbi.nlm.nih.gov/pubmed/25271403
4) Nguyen, V. Q., Ranjan, A., Stengel, F., Wei, D., Aebersold, R., Wu, C., & Leschziner, A. E. (2013). Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell, 154(6), 1220–1231. external page http://www.ncbi.nlm.nih.gov/pubmed/24034246
5) Faini, M., Prinz, S., Beck, R., Schorb, M., Riches, J. D., Bacia, K., et al. (2012). The Structures of COPI-Coated Vesicles Reveal Alternate Coatomer Conformations and Interactions. Science, 336, 1451(2012). external page http://www.ncbi.nlm.nih.gov/pubmed/?term=22628556