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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 23, 2026

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

Identifying hubs in protein interaction networks.

Ravishankar R Vallabhajosyula1, Deboki Chakravarti, Samina Lutfeali

  • 1Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA.

Plos One
|April 29, 2009
PubMed
Summary

Defining hub proteins in protein interaction networks (PINs) is crucial. Objective methods show good agreement for reliable PINs, validating the hub concept in systems with balanced interactions.

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Last Updated: Jun 23, 2026

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Area of Science:

  • Systems Biology
  • Network Science
  • Bioinformatics

Background:

  • Protein interaction networks (PINs) exhibit scale-free degree distributions.
  • Ad hoc degree scales for defining "hub" proteins may limit robustness of functional significance conclusions.

Purpose of the Study:

  • To present objective methods for defining hub proteins in PINs.
  • To assess agreement among different hub definition methods.
  • To explore implications for network construction.

Main Methods:

  • Developed three objective methods: one topological, two based on gene expression and function.
  • Applied methods to four distinct protein interaction networks.
  • Examined agreement between topological, expression, and functional methods.

Main Results:

  • Found good agreement among methods for networks with balanced error-free and unbiased interactions.
  • The definition of hub proteins is meaningful in such balanced networks.
  • Results inform network construction strategies.

Conclusions:

  • Objective methods provide a robust framework for identifying hub proteins.
  • The hub concept is validated in protein interaction networks with reliable data.
  • Findings support more accurate functional predictions based on network topology.