Our biological proteomics team is working on the global mapping and localization of posttranslational modifications (PTMs), in particular phosphorylation and ubiquitination (in collaboration with Brenda Schulman’s lab at our institute) to better understand the signaling networks that regulate essentially all of the biology of cells and organisms in normal and disease states.
Using MS-based phosphoproteomics, we discovered that the Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases (Steger et al., Elife, 2016, Steger et al., Elife, 2017 ). Based on these findings, we further investigate how LRRK2-mediated phosphorylation influences their function and downstream signaling pathways. We are also actively working on the development of clinical methods for the analysis of Rab phosphorylations to measure LRRK2 activity. This work is funded partly by the Michael J. Fox Foundation for Parkinson research (www.michaeljfox.org)
Furthermore, to provide fundamental information on the regulation and structure of biological systems, we investigate protein-protein interactions (PPIs). We have established workflows for affinity purification coupled to MS as a major tool for the mapping of PPIs in several organisms. For instance, we have successfully connected 5,400 proteins with more than 28,500 interactions in human systems without overexpression in 'three quantitative dimensions' (Hein et al., Cell, 2015). Based on recent MS improvements in speed and sensitivity as well as the establishment of affinity enrichment coupled to MS (Keilhauer et al., MCP, 2014) we are now developing highly reproducible workflows for the large-scale identification of PPIs with very high completeness and quantitative accuracy (Hosp et al., MCP, 2015).
Another area of interaction proteomics focusses on chromatin proteomics (Wierer and Mann, Hum Mol Gen, 2016). Here, we develop and apply purification methods aimed to characterize chromatin bound transcription factor complexes, which are involved in mammalian development as well as human disease states.
To study protein PTMs in different species, we developed PHOSIDA (www.phosida.com) (Gnad et al., Nucleic Acids Res., 2011 ). PHOSIDA provides rich information about PTM sites identified in our lab, including evolutionary conservation, matching kinase motifs, predicted structure information, and details about the associated MS identification.
We are planning to upload future PTM datasets to PhosphoSitePlus (www.phosphosite.org). PhosphoSitePlus is the most comprehensive resource for the study of PTM sites, containing more than 450,000 PTM sites from over 22,000 articles and thousands of MS datasets (Hornbeck et al., Nucleic Acids Res., 2018). PhosphoSitePlus also integrates somatic cancer mutations and germline mutations associated with inherited diseases, allowing the users to investigate the worlds of PTMs and disease mutations. Our collaboration with PhosphoSitePlus will help the scientific community by enabling further exploration of our datasets using the rich content provided by this web resource.