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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 Networks

Protein Networks

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

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Related Experiment Video

Updated: Apr 15, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Module organization and variance in protein-protein interaction networks.

Chun-Yu Lin¹, Tsai-Ling Lee¹, Yi-Yuan Chiu¹

¹Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.

Scientific Reports

|March 24, 2015

Summary

Protein modules, groups of interacting proteins, have core and ring components. Core components are essential, conserved across species, and form dynamic network hubs crucial for biological functions.

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Last Updated: Apr 15, 2026

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

Systems Biology
Computational Biology
Genomics

Background:

Protein modules are groups of interacting proteins performing specific biological functions.
Understanding the organization and evolutionary variance of these modules is crucial but remains unclear.

Purpose of the Study:

To infer module families and protein-protein interaction (PPI) families from genomic data.
To analyze the evolutionary conservation and functional roles of module components.

Main Methods:

Collected module templates to infer module and PPI families across 1,678 species.
Derived PPI evolution and interface evolution scores to characterize core and ring components.
Analyzed gene essentiality, module variance, and gene co-expression.

Main Results:

Identified 58,041 homologous modules and numerous PPI families.
Core components are highly conserved across species and essential, correlating with essential gene functions.
Core components form dynamic network hubs, playing key roles in biological functions.

Conclusions:

Protein modules comprise conserved core components and variable ring components.
Core components are essential for major biological functions and network stability.
Module organization and variance are shaped by the conserved nature of core components.