Functional proteomics activity-based probes

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. 

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... 

Tully SE, Cravatt BF (2010) Activity-based probes that target functional subclasses of phospholipases in proteomes. J Am Chem Soc 132 3264-3265... 

The benefit of addressing the proteome at the level of distinct enzyme classes, as well as the versatility of ABPP reagents, is highlighted in a third example of comparative ABPP profiling. In this study, carried out by Greenbaum and colleagues, activity-based probes were applied to characterize the functional role of the papain subclass of cysteine proteases in the Plasmodium falciparum life cycle [47]. While cysteine proteases are known to be essential for the... 

Fonovic, M. and Bogyo, M. (2008) Activity-based probes as a tool for functional proteomic analysis of proteases. Expert Rev. Proteomics, 5 (5), 721-730. 

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