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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,...

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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

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Published on: November 17, 2019

Quantitative fragmentomics allow affinity mapping of interactomes.

Gergo Gogl¹, Boglarka Zambo², Camille Kostmann³

¹Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404, Illkirch, France. goglg@igbmc.fr.

Nature Communications

|September 17, 2022

Summary

This study quantifies 65,000 human protein interactions, revealing binding affinities crucial for understanding protein networks and their functions in disease. This advances quantitative interactomics and disease research.

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Area of Science:

Proteomics
Systems Biology
Structural Biology

Background:

Human protein networks are extensively studied, but quantitative binding affinities are largely unknown.
This knowledge gap hinders in-depth analysis of protein interactions and their functional consequences.
Quantifiable affinities are essential for understanding complex biological systems.

Purpose of the Study:

To measure the binding affinities of a large set of human protein interactions.
To investigate the role of these interactions in viral infection and cancer.
To develop a quantitative approach for comprehensive interactome analysis.

Main Methods:

Measured affinities for 65,000 interactions involving PDZ domains and PDZ-binding motifs (PBMs).
Utilized mass spectrometry on cell extracts and literature surveys.
Employed crystallographic studies to explain specific binding interactions.

Main Results:

Generated binding profiles and specificity logos for PDZ domain interactions.
Identified key interaction 'hot spots' relevant to viral interference.
Demonstrated that quantitative fragmentomics complements traditional interactomics by providing affinity data.
Showcased how viral PBMs hijack host interactomes, impacting cellular proteomes beyond direct binders.

Conclusions:

Quantitative fragmentomics provides crucial affinity data, enabling a comprehensive human interactome affinity survey.
Understanding these affinities is key to deciphering complex system-wide relationships between interactome and cellular function.
This approach offers insights into disease mechanisms, particularly viral interference and cancer.