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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 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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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...

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Related Experiment Video

Updated: Jun 26, 2026

Detecting and Characterizing Protein Self-Assembly In Vivo by Flow Cytometry
05:58

Detecting and Characterizing Protein Self-Assembly In Vivo by Flow Cytometry

Published on: July 17, 2019

Exploiting genomic patterns to discover new supramolecular protein assemblies.

Morgan Beeby1, Thomas A Bobik, Todd O Yeates

  • 1UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California 90095, USA.

Protein Science : a Publication of the Protein Society
|January 30, 2009
PubMed
Summary

Researchers discovered that genes for proteins assembling into large structures are often grouped together in bacterial DNA. This genomic pattern helps identify new protein assemblies, like bacterial microcompartments, gas vesicles, and pili.

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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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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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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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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 and Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Bacterial microcompartments are protein-based organelles that sequester enzymes and metabolic intermediates.
  • Their outer shells are built from multiple paralogous proteins, often encoded together in bacterial genomes.
  • This co-transcription suggests a conserved assembly mechanism across different supramolecular structures.

Purpose of the Study:

  • To determine if the genomic pattern of co-transcribed paralogs is a general feature of supramolecular assemblies.
  • To identify novel protein families exhibiting this pattern for further investigation.
  • To explore the utility of this genomic signature for discovering new biological structures.

Main Methods:

  • Comparative genomics approach to identify protein families with clustered, paralogous genes.
  • Analysis of genomic data to find patterns similar to those of known bacterial microcompartments.
  • Experimental characterization of selected protein families to confirm supramolecular assembly behavior.

Main Results:

  • Identified diverse supramolecular assemblies, including bacterial gas vesicles, pili, and small heat-shock protein complexes, exhibiting the co-transcribed paralog pattern.
  • Discovered several widely distributed protein families of unknown function that fit the genomic signature.
  • Experimental validation confirmed supramolecular assembly behavior in proteins from one of the newly identified families.

Conclusions:

  • Co-transcribed paralogs are a common characteristic of various large supramolecular assemblies in bacteria.
  • This genomic pattern serves as a powerful signature for discovering novel protein assemblies.
  • The findings expand our understanding of bacterial organelle biogenesis and protein complex formation.