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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: Jun 8, 2026

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation
14:44

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Published on: September 24, 2012

Mapping protein-protein interactions by quantitative proteomics.

Joern Dengjel1, Irina Kratchmarova, Blagoy Blagoev

  • 1Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.

Methods in Molecular Biology (Clifton, N.J.)
|September 15, 2010
PubMed
Summary
This summary is machine-generated.

Researchers used stable isotope labeling by amino acids in cell culture (SILAC) to study dynamic protein interactions. This method tracks how protein partnerships change with cell signaling, revealing protein function shifts.

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Last Updated: Jun 8, 2026

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation
14:44

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Published on: September 24, 2012

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Mapping Dysfunctional Protein-Protein Interactions in Disease
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Area of Science:

  • Cellular Biology
  • Proteomics
  • Biochemistry

Background:

  • Proteins function within dynamic multiprotein complexes.
  • Complex composition varies with cell state and signaling.
  • Protein function is dependent on binding partners.

Purpose of the Study:

  • To detail the use of SILAC for quantitative analysis of dynamic protein interactions.
  • To map stimulus-dependent changes in protein-protein interactions.
  • To understand how protein complex dynamics relate to cellular functions.

Main Methods:

  • Affinity purification coupled with quantitative mass spectrometry (MS).
  • Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for quantitative proteomic analysis.
  • Analysis of stimulus-dependent changes in protein interaction networks.

Main Results:

  • SILAC enables quantitative tracking of dynamic protein-protein interactions.
  • Changes in protein complex composition can be accurately measured.
  • Stimulus-induced alterations in protein interactions are elucidated.

Conclusions:

  • Quantitative MS, particularly SILAC, is a powerful tool for studying dynamic protein interactions.
  • Understanding protein complex dynamics is crucial for deciphering cellular signaling.
  • This approach facilitates the mapping of stimulus-dependent functional changes in proteins.