Proteomic discovery of chemical probes that perturb protein complexes in human cells Journal Article
| Authors: | Lazear, M. R.; Remsberg, J. R.; Jaeger, M. G.; Rothamel, K.; Her, H. L.; DeMeester, K. E.; Njomen, E.; Hogg, S. J.; Rahman, J.; Whitby, L. R.; Won, S. J.; Schafroth, M. A.; Ogasawara, D.; Yokoyama, M.; Lindsey, G. L.; Li, H.; Germain, J.; Barbas, S.; Vaughan, J.; Hanigan, T. W.; Vartabedian, V. F.; Reinhardt, C. J.; Dix, M. M.; Koo, S. J.; Heo, I.; Teijaro, J. R.; Simon, G. M.; Ghosh, B.; Abdel-Wahab, O.; Ahn, K.; Saghatelian, A.; Melillo, B.; Schreiber, S. L.; Yeo, G. W.; Cravatt, B. F. |
| Article Title: | Proteomic discovery of chemical probes that perturb protein complexes in human cells |
| Abstract: | Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such “binding-first” assays affect protein function, nonetheless, often remains unclear. Here, we describe a “function-first” proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells. © 2023 Elsevier Inc. |
| Keywords: | metabolism; proteasome; transcription factor; proteomics; transcription factors; ligand; ligands; spliceosome; cysteine; procedures; covalent; protein complexes; humans; human; size-exclusion chromatography; chemical probe; activity-based protein profiling |
| Journal Title: | Molecular Cell |
| Volume: | 83 |
| Issue: | 10 |
| ISSN: | 1097-2765 |
| Publisher: | Cell Press |
| Date Published: | 2023-05-18 |
| Start Page: | 1725 |
| End Page: | 1742.e12 |
| Language: | English |
| DOI: | 10.1016/j.molcel.2023.03.026 |
| PUBMED: | 37084731 |
| PROVIDER: | scopus |
| PMCID: | PMC10198961 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 June 2023 -- Source: Scopus |
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