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Related Concept Videos

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...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
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,...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...

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Related Experiment Video

Updated: May 9, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Shared protein complex subunits contribute to explaining disrupted co-occurrence.

Adrian Schneider1, Michael F Seidl, Berend Snel

  • 1Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.

Plos Computational Biology
|July 23, 2013
PubMed
Summary
This summary is machine-generated.

Gene presence and absence patterns, called phylogenetic profiles, usually indicate functional relationships. This study explains how multi-functional proteins disrupt these profiles, impacting our understanding of protein interactions.

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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

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Related Experiment Videos

Last Updated: May 9, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment
09:02

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment

Published on: April 20, 2018

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Gene composition varies across genomes due to evolutionary history.
  • Phylogenetic profiles (gene presence/absence patterns) often correlate with protein function.
  • A significant number of interacting proteins lack matching phylogenetic profiles.

Purpose of the Study:

  • Investigate why interacting proteins sometimes lack similar phylogenetic profiles.
  • Analyze the impact of multi-functional proteins on gene co-occurrence patterns.
  • Explain discrepancies in phylogenetic profiles of interacting proteins.

Main Methods:

  • Analysis of gene distributions across diverse genomes.
  • Comparison of phylogenetic profiles for gene families.
  • Modeling the effect of multi-functional proteins on profile similarity.

Main Results:

  • Multi-functional proteins, acting as shared subunits, can distort phylogenetic profiles.
  • Considering protein triplets involving multi-functional proteins resolves many disturbed co-occurrence patterns.
  • This explains a large fraction of observed profile dissimilarities between interacting proteins.

Conclusions:

  • Multi-functional proteins are a key factor in understanding gene co-occurrence patterns.
  • Phylogenetic profile analysis needs to account for protein multifunctionality.
  • This research refines methods for inferring protein function and interactions from genomic data.