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Protein Sci. 2019 Mar;28(3):654-662. doi: 10.1002/pro.3570. Epub 2019 Jan 31.

Chemically reprogramming the phospho-transfer reaction to crosslink protein kinases to their substrates.

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Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California.
Department of Pathology, University of California San Francisco, San Francisco, California.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.
Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California.


The proteomic mapping of enzyme-substrate interactions is challenged by their transient nature. A method to capture interacting protein kinases in complexes with a single substrate of interest would provide a new tool for mapping kinase signaling networks. Here, we describe a nucleotide-based substrate analog capable of reprogramming the wild-type phosphoryl-transfer reaction to produce a kinase-acrylamide-based thioether crosslink to mutant substrates with a cysteine nucleophile substituted at the native phosphorylation site. A previously reported ATP-based methacrylate crosslinker (ATP-MA) was capable of mediating kinase crosslinking to short peptides but not protein substrates. Exploration of structural variants of ATP-MA to enable crosslinking of protein substrates to kinases led to the discovery that an ADP-based methacrylate (ADP-MA) crosslinker was superior to the ATP scaffold at crosslinking in vitro. The improved efficiency of ADP-MA over ATP-MA is due to reduced inhibition of the second step of the kinase-substrate crosslinking reaction by the product of the first step of the reaction. The new probe, ADP-MA, demonstrated enhanced in vitro crosslinking between the Src tyrosine kinase and its substrate Cortactin in a phosphorylation site-specific manner. The kinase-substrate crosslinking reaction can be carried out in a complex mammalian cell lysate setting, although the low abundance of endogenous kinases remains a significant challenge for efficient capture.


chemical genetics; kinase-substrate interactions; mass spectrometry; phosphorylation; protein kinases; signaling networks

[Available on 2020-03-01]

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