Activity based proteomics

Activity based proteomics, or activity based protein profiling (ABPP) is a functional proteomic technology that uses specially designed chemical probes that react with mechanistically-related classes of enzymes [Berger AB, et al. "Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery." American Journal of Pharmacogenomics 2004 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed Article] ] . The basic unit of ABPP is the probe which typically consists of two elements: a reactive group (RG) and a tag. Additionally, some probes may contain a binding group which enhances selectivity. The reactive group usually contains an electrophile that gets covalently-linked to a nucleophilic residue in the active site of an active enzyme. An enzyme that is inhibited by enzyme inhibitors or post-translational modifications will not react with an activity-based probe. The tag may be either a reporter such as a fluorophore or a "handle" such as biotin or an alkyne or azide for use with the Huisgen 1,3-dipolar cycloaddition (also known as click chemistry) [Speers AE, et al. "Activity-Based Protein Profiling in Vivo Using a Copper(I)-Cataqlyzed Azide-Alkyne [3+2] Cycloaddition" Journal of the American Chemical Society 2003 [http://www.scripps.edu/cb/cravatt/pdf/Speersetal2003.pdf Article] ] .

A major advantage of ABPP is the ability to monitor enzyme "activity" directly, rather than being limited to protein or mRNA abundance. With classes of enzymes such as the serine proteases [ Liu Y, et al. "Activity-based protein profiling: The serine hydrolases" Proceedings of the National Academy of Sciences 1999 [http://www.pnas.org/cgi/content/abstract/96/26/14694 Article] ] and metalloproteases [ Saghatelian A , et al. "Activity-based probes for the proteomic profiling of metalloproteases" Proceedings of the National Academy of Sciences 2004 [http://www.pnas.org/cgi/content/abstract/101/27/10000 Article] ] that often interact with endogenous inhibitors or that exist as inactive zymogens, this technique offers a valuable advantage over traditional techniques that rely on abundance rather than activity.

Finally, in recent years ABPP has been combined with tandem mass spectrometry enabling the identification of hundreds of active enzymes from a single sample. This technique, known as "ABPP-MudPIT" is especially useful for profiling inhibitor selectivity as the potency of an inhibitor can be tested against hundreds of targets simultaneously.

ABPP was developed by in the late 1990s and early 2000s by Benjamin Cravatt at The Scripps Research Institute, [http://bogyolab.stanford.edu/ Matthew Bogyo] at Stanford, and others.

ee also

* Mass spectrometry
* Proteomics
* Related inhibitors MAFP and DIFP

References