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A systems chemoproteomic analysis of acyl-CoA/protein interaction networks

By Michaella J Levy, David C Montgomery, Mihaela E. Sardiu, Sarah E Bergholtz, Kellie D Nance, Jose Montano, Abigail L Thorpe, Stephen D Fox, Qishan Lin, Thorkell Andresson, Laurence Florens, Michael P Washburn, Jordan L. Meier

Posted 10 Jun 2019
bioRxiv DOI: 10.1101/665281 (published DOI: 10.1016/j.chembiol.2019.11.011)

Acyl-CoA/protein interactions are required for many functions essential to life including membrane synthesis, oxidative metabolism, and macromolecular acetylation. However, despite their importance, the global scope and selectivity of these protein-metabolite interactions remains undefined. Here we describe the development of CATNIP (CoA/AcetylTraNsferase Interaction Profiling), a chemoproteomic platform for the high-throughput analysis of acyl-CoA/protein interactions in endogenous proteomes. First, we apply CATNIP to identify acetyl-CoA-binding proteins through unbiased clustering of competitive dose-response data. Next, we use this method to profile diverse protein-CoA metabolite interactions, identifying biological processes susceptible to altered acetyl-CoA levels. Finally, we apply systems-level analyses to assess the features of novel protein networks that may interact with acyl-CoAs, and demonstrate a strategy for high-confidence proteomic annotation of acetyl-CoA binding proteins. Overall our studies illustrate the power of integrating chemoproteomics and systems biology, and provide a resource for understanding the roles of acyl-CoA metabolites in biology and disease.

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