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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: Jul 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Specificity and evolvability in eukaryotic protein interaction networks.

Pedro Beltrao1, Luis Serrano

  • 1European Molecular Biology Laboratory, Structures and Computational Biology Program, Heidelberg, Germany. beltrao@embl.de

Plos Computational Biology
|February 20, 2007
PubMed
Summary

Eukaryotic protein interaction networks evolve rapidly, with changes in binding specificity driving rewiring. This molecular divergence significantly impacts network organization and biological functions, explaining network structure.

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
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Related Experiment Videos

Last Updated: Jul 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

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

Published on: March 3, 2015

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
07:57

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

  • * Molecular Biology
  • * Systems Biology
  • * Evolutionary Biology

Background:

  • * Understanding the organizational principles of protein interaction networks is crucial.
  • * Few studies have investigated the evolutionary impact of protein network changes on species differences.
  • * Protein interaction networks are fundamental to cellular function and organismal complexity.

Purpose of the Study:

  • * To investigate the rate and principles of eukaryotic protein interaction network evolution.
  • * To determine how protein binding specificity influences interaction network dynamics.
  • * To explore the evolutionary pressures on protein interactions in different biological processes.

Main Methods:

  • * Comparative genomics analysis.
  • * Utilizing structural information of protein interactions.
  • * Analyzing evolutionary rates and interaction turnover across eukaryotic species.

Main Results:

  • * Eukaryotic interactomes rewire at a high rate (approx. 10^-5 interactions per protein pair per million years).
  • * Protein binding specificity is a key determinant of interaction turnover.
  • * Immune response, transport, and localization proteins show positive selection for interaction changes.

Conclusions:

  • * Rapid interactome rewiring occurs even with limited molecular divergence.
  • * Binding specificity influences network dynamics and may explain power-law distributions in protein interaction networks.
  • * Evolutionary changes in protein interactions contribute to physiological differences between species.