Protein profiling, activity-based

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. 

Until recently, irreversible chemistries have not been applied to the systematic discovery of novel ligands. Instead, such methods have proven to be more useful for ligand-directed protein discovery, in which ligands specific to a certain protein or class of proteins are used to identify related proteins from a crude cell extract.14 511 Irreversible site-directed ligand discovery forms a continuum with affinity labeling and activity-based protein profiling, in which a reactive (often substrate-like) molecule binds covalently to a protein of interest.152 531 These techniques are typically used to probe enzyme mechanism or function or to identify a specific protein or class of proteins from a complicated mixture such as... 

Cravatt BF, Wright AT, Kozarich JW (2008) Activity-based protein profiling from enzyme chemistry to proteomic chemistry. Annu Rev Biochem 77 383-414... 

Barglow KT, Cravatt BF (2007) Activity-based protein profiling for the functional annotation of enzymes. Nat Methods 4 822-827... 

Speers AE, Adam GC, Cravatt BF (2003) Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-alkyne [3+2] cycloaddition. J Am Chem Soc 125 4686-4687... 

Liu Y, Patricelli MP, Cravatt BF (1999) Activity-based protein profiling the serine hydrolases. Proc Natl Acad Sci USA 96 14694—14699... 

Overkleeft HS et al. (2012) Photoaffinity labeling in activity-based protein profiling. Topics in Current Chemistry. Springer, Berlin, Heidelberg, doi 10.1007/128 2011 XXX... 

Slack JL, Causey CP, Luo Y et al (2011) Development and use of clickable activity based protein profiling agents for protein arginine deiminase 4. ACS Chem Biol 6 466-476... 

Luo Y, Knuckley B, Bhatia M et al (2006) Activity-based protein profiling reagents for protein arginine deiminase 4 (PAD4) synthesis and in vitro evaluation of a fluorescently labeled probe. J Am Chem Soc 128 14468-14469... 

Jessani N, Young JA, Diaz SL et al (2005) Class assignment of sequence-unrelated members of enzyme superfamilies by activity-based protein profiling. Angew Chem Int Ed Engl 44 2400-2403... 

Activity-Based Protein Profiling for Natural Product Target Discovery... 

Keywords Activity-based protein profiling Chemical biology Molecular probes Natural products Target profiling... 

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