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Related Concept Videos

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 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...
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...
Protein Complexes with Interchangeable Parts01:57

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 to...
Protein Complexes with Interchangeable Parts01:57

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 to...

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Related Experiment Video

Updated: Jun 25, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

How perfect can protein interactomes be?

Emmanuel D Levy1, Christian R Landry, Stephen W Michnick

  • 1Université de Montréal, Montreal, Quebec, Canada.

Science Signaling
|March 6, 2009
PubMed
Summary
This summary is machine-generated.

Biological systems, unlike engineered devices, can accumulate nonfunctional elements. This study proposes that noisy, nonselected protein-protein interactions (PPIs) exist in interactomes, explaining their characteristics.

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Area of Science:

  • Evolutionary biology
  • Systems biology
  • Bioinformatics

Background:

  • Engineered devices require optimization, avoiding nonfunctional components.
  • Evolutionary theory permits non-optimized biological systems that may accumulate nonfunctional elements.
  • Eukaryotic genomes and transcriptional networks contain nonfunctional elements like 'junk' DNA.

Purpose of the Study:

  • To investigate whether protein interactomes contain nonselected, nonfunctional protein-protein interactions (PPIs), termed 'noisy' interactions.
  • To propose a model predicting the fraction of noisy PPIs based on evolutionary parameters.
  • To explain observed characteristics of PPIs using the concept of evolutionary noise.

Main Methods:

  • Developing a theoretical relationship between the fraction of noisy interactions and key parameters.
  • Analyzing the number of mutations for interaction creation/deletion, proteome size, and fitness cost of noisy interactions.
  • Proposing experimental strategies for estimating evolutionary noise in PPI networks.

Main Results:

  • The proposed model suggests that noisy PPIs are expected to exist in biological systems.
  • The fraction of noisy interactions is influenced by mutation rates, proteome size, and the fitness cost associated with these interactions.
  • The existence of noisy PPIs provides a potential explanation for several observed phenomena in protein interaction networks.

Conclusions:

  • Noisy protein-protein interactions are a likely feature of biological interactomes, driven by evolutionary processes.
  • The prevalence of noisy PPIs can account for the lack of functional coherence in experimentally determined PPIs, poor cross-species conservation, and the vastness of the PPI space.
  • Further experimental work is needed to quantify the extent of evolutionary noise within specific PPI networks.