Activity based proteomics

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File:Fp rhodamine.jpg
Fluorophosphonate-rhodamine (FP-Rhodamine) activity based probe for profiling of the serine hydrolase superfamily. In this probe the fluorophosphonate is the reactive group (RG) as it binds irreversibly to the active-site serine nucleophile of serine hydrolases and the tag is rhodamine, a fluorophore for in-gel visualization.
File:Gel-abpp eg.png
In-gel ABPP using probes with different fluorophores in the same lane to simultaneously profile differences in enzyme activities

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[1]. 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) [2].

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 [3] and metalloproteases [4]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, Matthew Bogyo at Stanford, and others.

See also

Mass spectrometry

References

  1. Berger AB, et al. Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery. American Journal of Pharmacogenomics 2004 Article
  2. 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 Article
  3. Liu Y, et al. Activity-based protein profiling: The serine hydrolases Proceedings of the National Academy of Sciences 1999 Article
  4. Saghatelian A , et al. Activity-based probes for the proteomic profiling of metalloproteases Proceedings of the National Academy of Sciences 2004 Article
Genomics topics
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