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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: May 24, 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

Combinatorial complexity and compositional drift in protein interaction networks.

Eric J Deeds1, Jean Krivine, Jérôme Feret

  • 1Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America.

Plos One
|March 14, 2012
PubMed
Summary
This summary is machine-generated.

Protein-protein interaction networks exhibit compositional drift, where initially similar simulations diverge into distinct large complexes. This uncontrolled drift may explain cellular population heterogeneity.

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

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Related Experiment Videos

Last Updated: May 24, 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

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

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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:

  • Systems Biology
  • Computational Biology
  • Biophysics

Background:

  • Molecular machine assembly occurs within complex cellular environments, not in isolation.
  • Protein-protein interaction (PPI) networks present challenges like binding site conflict and combinatorial complexity.
  • Understanding assembly dynamics in these networks is crucial for cell function.

Purpose of the Study:

  • To explore the consequences of PPI network characteristics on global dynamics using computational models.
  • To investigate the phenomenon of "compositional drift" in molecular complex formation.
  • To identify fundamental problems in controlling assembly within large biological networks.

Main Methods:

  • Utilized computational models based on curated yeast two-hybrid data.
  • Employed a rule-based approach to kinetic modeling to manage complex formation possibilities.
  • Simulated PPI network dynamics under global biophysical constraints.

Main Results:

  • Initially identical simulations rapidly diverged in molecular possibilities.
  • Simulations converged to sampling disjoint sets of large protein complexes, termed "compositional drift".
  • The study highlights limitations of current PPI data in representing cellular dynamics.

Conclusions:

  • Compositional drift is a fundamental challenge for molecular assembly in large networks.
  • Cells may require specific mechanisms to control compositional drift.
  • Uncontrolled drift could be a novel source of phenotypic heterogeneity in cell populations.