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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Related Experiment Video

Updated: May 30, 2026

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Probing small molecule-protein interactions: A new perspective for functional proteomics.

Thomas Lenz1, Jenny J Fischer, Mathias Dreger

  • 1Caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany.

Journal of Proteomics
|August 13, 2011
PubMed
Summary

This review explores small molecule probes for isolating proteins, enabling drug target discovery and functional characterization. These chemical proteomics tools advance our understanding of protein interactions and biological functions.

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Area of Science:

  • Chemical proteomics
  • Molecular interactions
  • Drug discovery

Background:

  • Proteomics is advancing through small molecule-protein interactions.
  • Small molecules can identify protein families or new protein functions.
  • Pharmaceutical compounds as probes can uncover drug targets and off-targets.

Purpose of the Study:

  • To review probe designs, workflows, and applications in chemical proteomics.
  • To highlight three dominant approaches: affinity pulldown, activity-based protein profiling, and Capture Compound Mass Spectrometry.
  • To discuss the utility of small molecule probes in drug discovery and target identification.

Main Methods:

  • Utilizing synthetic bi- or trifunctional small molecule probes.
  • Employing probes with selectivity functions (small molecule baits) and sorting functions.
  • Establishing covalent linkage via reactivity functions for robust isolation.
  • Identifying isolated proteins using mass spectrometry.

Main Results:

  • Small molecule probes enable unbiased proteomic screens.
  • Probes facilitate the discovery of drug targets and toxicity-relevant off-targets.
  • Covalent linkage enhances probe-protein conjugate isolation under denaturing conditions.

Conclusions:

  • Small molecule probes represent a powerful paradigm in proteomics.
  • These probes are crucial for identifying drug targets and understanding protein function.
  • Affinity pulldown, ABPP, and CCMS are key methodologies in this field.