Proteome-Wide Discovery of Unknown ATP-Binding Proteins and Kinase Inhibitor Target Proteins Using an ATP Probe

被引:27
作者
Adachi, Jun [1 ]
Kishida, Marina [1 ]
Watanabe, Shio [1 ]
Hashimoto, Yuuki [1 ]
Fukamizu, Kazuna [1 ]
Tomonaga, Takeshi [1 ]
机构
[1] Natl Inst Biomed Innovat, Lab Proteome Res, Osaka 5670085, Japan
关键词
Chemical proteomics; ATP-binding proteins; ATP-competitive kinase inhibitor; QUANTITATIVE PROTEOMICS; AFFINITY; KINOME; IDENTIFICATION; PHOSPHOPROTEOMICS; MECHANISMS; EXPRESSION; ENRICHMENT; SILAC; MTH1;
D O I
10.1021/pr500845u
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
ATP-binding proteins, including protein kinases, play essential roles in many biological and pathological processes and thus these proteins are attractive as drug targets. Acyl-ATP probes have been developed as efficient probes for kinase enrichment, and these probes have also been used to enrich other ATP-binding proteins. However, a robust method to identify ATP-binding proteins with systematic elimination of nonspecific binding proteins has yet to be established. Here, we describe an ATP competition assay that permitted establishment of a rigorous ATP-binding protein list with virtual elimination of nonspecific proteins. A total of 539 ATP-binding protein candidates were identified, including 178 novel candidates. In informatics analysis, ribosomal proteins were overrepresented in the list of novel candidates. We also found multiple ATP-competitive sites for several kinases, including epidermal growth factor receptor, serine/threonine-protein kinase PRP4 homologue, cyclin-dependent kinase 12, eukaryotic elongation factor 2 kinase, ribosomal protein S6 kinase alpha-1, and SRSF protein kinase 1. Using our cataloged ATP-binding protein list, a selectivity profiling method that covers the kinome and ATPome was established to identify off-target binding sites of ATP-competitive kinase inhibitors, staurosporine and crizotinib.
引用
收藏
页码:5461 / 5470
页数:10
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