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Protein Networks

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 Interfaces

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...

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Related Experiment Video

Updated: Mar 3, 2026

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling.

Mercedes Pardo¹, Daniel Bode², Lu Yu²

¹Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute; mp3@sanger.ac.uk.

Journal of Visualized Experiments : Jove

|April 28, 2017

Summary

This study introduces a new method to map protein interactions and their complexes. It resolves protein assemblies before mass spectrometry analysis, providing better insights into biological functions.

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Last Updated: Mar 3, 2026

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Multimer-PAGE: A Method for Capturing and Resolving Protein Complexes in Biological Samples

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Published on: May 5, 2017

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

Published on: December 9, 2016

Area of Science:

Proteomics
Molecular Biology
Biochemistry

Background:

Proteins function in complexes, necessitating the study of these units for biological understanding.
Affinity purification coupled to mass spectrometry (AP-MS) identifies protein-protein interactions but loses organizational data.
Existing methods struggle to resolve protein complexes with similar molecular weights.

Purpose of the Study:

To develop a strategy for unraveling distinct functional protein assemblies.
To resolve affinity-purified protein complexes before mass spectrometry characterization.
To obtain protein complex topological information alongside interaction identification.

Main Methods:

Developed a strategy combining affinity purification with blue native electrophoresis and quantitative mass spectrometry.
Used epitope-tagged bait proteins and competitive elution for complex isolation.
Separated complexes via blue native electrophoresis and analyzed migration profiles using correlation profiling.

Main Results:

Successfully resolved distinct functional protein assemblies.
Assigned interacting proteins to specific molecular entities by comparing migration profiles.
Demonstrated the ability to resolve complexes with close molecular weights, outperforming traditional chromatography.
Achieved topological information with minimal additional effort compared to conventional AP-geLC-MS/MS.

Conclusions:

The developed strategy effectively resolves protein complexes and identifies interactions.
This method provides crucial topological information about protein assemblies.
It offers a valuable advancement for understanding protein complex organization and function.