Functional proteomics chemical probes

The Design of Chemical ABPP Probes for Functional Proteomics... 

Activity-based protein profiling (ABPP) is a chemical proteomic strategy in which active-site-directed covalent probes are used to profile the functional states of enzymes in complex proteomes. Activity-based probes (ABPs) can distinguish active enzymes from their inactive zymogens or inhibitor-bound forms. They contain a reactive group intended to modify enzyme active sites covalently and a reporter group (typically rhodamine or biotin) that assists in detection and identification of protein targets. 

Greenbaum D, Baruch A, Hayrapetian L, Darula Z, Burlingame A, Medzihradszky KF, Bogyo M. Chemical approaches for functionally probing the proteome. Mol Cell Proteomics 2002 1 60-68. 

The greatly increased nucleophilicity of the catalytic serine distinguishes it from all other serine residues and makes it an ideal candidate for modification via activity-based probes [58]. Of the electrophilic probe types to profile serine hydrolases, the fluorophosphonate (FP)-based probes are the most extensively used and were first introduced by Cravatt and coworkers [38, 39]. FPs have been well-known inhibitors of serine hydrolases for over 80 years and were first applied as chemical weapons as potent acetylcholine esterase inhibitors. As FPs do not resemble a peptide or ester substrate, they are nonselective towards a particular serine hydrolase, thus allowing the entire family to be profiled. FPs also show minimal cross-reactivity with other classes of hydrolases such as cysteine-, metallo-, and aspartylhydrolases [59]. Furthermore, FP-based probes react only with the active serine hydrolase, and not the inactive zymogen, allowing these probes to interact only with functional species within the proteome [59]. Extensive use of this probe family has demonstrated their remarkable selectivity for serine hydrolases and resulted in the identification of over 100 distinct serine hydrolases... 

Staub I, Sieber SA (2009) P-Lactam probes as selective chemical-proteomic tools for the identification and functional characterization of resistance associated enzymes in MRSA. J Am Chem Soc 131 6271-6276... 

Greenbaum, D., Baruch, A., Hayrapetian, L., Darula, Z., Burlingame, A., Medzihrad-szky, K.F., and Bogyo, M. (2002) Chemical approaches for functionally probing the pro-teome. Mol. Cell. Proteomics 1, 60-68. 

In chemical genomics and proteomics, tiny low molecular weight probe molecules are used to perturb the functions of individual genes and proteins. The functional consequences of that perturbation are then examined and analyzed. By using small, yet relatively complex, molecular structures to disrupt cellular events and behavior, biologists can often pick apart some of the most complex and intricate signaling processes that are operational within cells, and thus provide a biomolecular panoptic that would otherwise be unattainable by purely biological means. ... 

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