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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,...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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...
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 7, 2026

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Coupling protein complex analysis to peptide based proteomics.

Qiang Gao1, Ashraf G Madian, Xiuping Liu

  • 1Department of Chemistry, Purdue Univeristy, West Lafayette, IN 47907, USA.

Journal of Chromatography. A
|November 2, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a new proteomics method using size exclusion chromatography (SEC) before digestion to preserve protein complex structures. This approach successfully identifies proteins within complexes and their interaction partners, including crucial hub proteins.

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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
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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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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Area of Science:

  • Proteomics
  • Biochemistry
  • Molecular Biology

Background:

  • Proteolysis in proteomics often leads to loss of protein structural information.
  • Understanding protein complexes and their interactions is crucial for biological insights.

Purpose of the Study:

  • To develop a proteomics method that preserves native protein structures and identifies protein complexes.
  • To identify hub proteins and their interaction partners within the yeast proteome.

Main Methods:

  • Fractionation of the native yeast proteome using size exclusion chromatography (SEC).
  • Trypsin digestion of SEC fractions followed by reversed-phase chromatography-mass spectral analysis (RPC-MS/MS).
  • Optimization of cell lysis and sample storage conditions to maintain protein complex integrity.

Main Results:

  • Successful identification of proteins within high molecular mass complexes.
  • Identification of hub proteins and their associated interaction partners.
  • Optimal cell lysis conditions identified (French press/bead-beater, pH 8, 200 mM NaCl) and storage at -20°C favored complex recovery.

Conclusions:

  • Initial fractionation by SEC prior to proteolysis and RPC-MS/MS enables recognition and identification of proteins within native complexes.
  • This method enhances the study of protein-protein interactions and complex structures.
  • Preserving native structure during lysis and storage is critical for successful complex analysis.