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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,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...

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Related Experiment Video

Updated: May 15, 2026

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

A conserved mammalian protein interaction network.

Åsa Pérez-Bercoff1, Corey M Hudson, Gavin C Conant

  • 1Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland.

Plos One
|January 16, 2013
PubMed
Summary
This summary is machine-generated.

Most human protein-protein interactions are ancient, originating before placental mammal radiation. These interactions show weak co-evolution and similar selective constraints, suggesting functional roles drive evolutionary pressures.

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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

Related Experiment Videos

Last Updated: May 15, 2026

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

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

Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Genomics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions like signal transduction and regulation.
  • Studying the evolutionary history of PPIs is challenging due to limited data from diverse species.
  • Phylogenomic approaches offer a way to infer the evolutionary timeline of these interactions.

Purpose of the Study:

  • To estimate the evolutionary age of human protein-protein interactions.
  • To investigate the co-evolutionary patterns and selective pressures on interacting protein pairs.
  • To analyze the distribution of selective constraints within the mammalian protein interaction network.

Main Methods:

  • Phylogenomic analysis of orthologous genes from eight mammalian species.
  • Comparative analysis of paired gene alignments for interacting proteins.
  • Network analysis to map selective constraint distribution across the PPI network.

Main Results:

  • Most human PPIs are ancient, likely originating by the radiation of placental mammals.
  • A weak but significant co-evolutionary signal was detected between genes encoding interacting proteins.
  • Interacting proteins exhibit non-random distributions of selective constraints, tending to share similar constraints.

Conclusions:

  • Mammalian protein-protein interactions are generally under selective constraint, reflecting their functional importance.
  • The evolutionary history of PPIs is shaped by functional constraints rather than strong directional selection.
  • The findings provide insights into the conservation and evolution of molecular networks.