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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 polypeptide...

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Related Experiment Video

Updated: Jun 8, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

High-quality binary interactome mapping.

Matija Dreze¹, Dario Monachello, Claire Lurin

¹Center for Cancer Systems Biology (CCSB), Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

Methods in Enzymology

|October 16, 2010

Summary

This summary is machine-generated.

High-throughput methods can generate high-quality protein-protein interaction maps, advancing our understanding of the cellular interactome. This study details a pipeline for creating reliable, large-scale protein interaction data.

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Area of Science:

Molecular Biology
Systems Biology
Biochemistry

Background:

Protein interactions form the basis of cellular functions, creating complex macromolecular networks.
Systematic mapping of these interactions (protein-protein, DNA, RNA, metabolite) is crucial for understanding cellular systems.
High-throughput methods for interactome mapping have advanced rapidly, producing numerous interaction maps.

Purpose of the Study:

To describe a high-quality, high-throughput pipeline for mapping binary protein-protein interactions.
To demonstrate that proteome-scale interactome datasets can achieve high quality comparable to or exceeding curated datasets.
To emphasize the importance of rigorous experimental controls, verification, and orthogonal validation for reliable interactome maps.

Main Methods:

Development of a high-throughput pipeline for binary protein-protein interaction assays.
Implementation of thorough experimental steps, including necessary controls and quality standards.
Inclusion of careful verification of interacting pairs and validation using independent, orthogonal assays.

Main Results:

Demonstrated that proteome-scale interactome datasets can be generated with high quality.
Showed that high-throughput methods can yield data quality equal to or superior to literature-curated datasets.
Established a reliable pipeline for producing high-quality interactome maps.

Conclusions:

High-quality, high-throughput interactome mapping is achievable.
Rigorous validation and quality control are essential for reliable interactome data.
The described pipeline facilitates advancements in understanding cellular functions and systems properties through comprehensive interactome analysis.