What is Activity based protein profiling?

[A. Hammouda]

What is Activity based protein profiling?

This is a question for all interested members.

[Yan Zou]

Here is an answer from DeepSeek:

Activity-Based Protein Profiling (ABPP) is a chemical proteomics technique used to study the functional state of enzymes within complex biological systems. It involves the use of small molecule probes that covalently bind to the active sites of enzymes, allowing for the identification and characterization of these enzymes based on their activity rather than just their abundance.

Here’s a breakdown of how ABPP works:

1. Design of Activity-Based Probes (ABPs): These probes are typically composed of three parts:
– Reactive Group: This part of the probe covalently binds to the active site of the target enzyme. It is often designed to mimic the natural substrate of the enzyme.
– Linker: This part connects the reactive group to the reporter tag. It can vary in length and composition to optimize the binding and detection.
– Reporter Tag: This part allows for the detection and purification of the probe-enzyme complex. Common tags include fluorescent dyes for visualization or biotin for affinity purification.

2.Labeling: The ABPs are introduced to a biological sample (e.g., cell lysates, tissues, or whole organisms). The reactive group of the probe binds to the active site of the target enzymes, forming a covalent bond.

3. Detection and Analysis: After labeling, the enzymes that have bound to the probes can be detected and analyzed. If the reporter tag is a fluorescent dye, the labeled enzymes can be visualized using fluorescence microscopy or gel electrophoresis. If the tag is biotin, the labeled enzymes can be purified using streptavidin beads and subsequently identified using mass spectrometry.

ABPP has several applications, including:
– Target Identification: Identifying the targets of bioactive small molecules or drugs.
– Functional Annotation: Characterizing the activity of enzymes in different biological contexts.
– Drug Discovery: Screening for enzyme inhibitors and understanding their mechanism of action.
– Disease Biomarkers: Discovering enzyme activities that are altered in disease states, which can serve as potential biomarkers or therapeutic targets.

Overall, ABPP provides a powerful tool for understanding the functional proteome and has broad implications in biochemistry, molecular biology, and drug discovery.

[A. Diaa]

Activity-based proteomics, or activity-based protein profiling (ABPP) is a functional proteomic technology that uses chemical probes that react with mechanistically related classes of enzymes.

The basic unit of ABPP is the probe, which typically consists of two elements: a reactive group (RG, sometimes called a “warhead”) and a tag. The reactive group usually contains a specially designed electrophile that becomes covalently linked to a nucleophilic residue in the active site of an active enzyme. The tag may be a reporter such as a fluorophore or an affinity label such as biotin.

A major advantage of ABPP is the ability to monitor the availability of the enzyme active site directly, rather than being limited to protein or mRNA abundance. Furthermore, ABPP could be used to target specific proteins which were previously viewed as undruggable targets.

Activity-based proteomics – Wikipedia

 

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