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Related Concept Videos

Protein Networks02:26

Protein Networks

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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,...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Proteomics01:33

Proteomics

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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...
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Related Experiment Video

Updated: Apr 26, 2026

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
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Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

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Protein correlation profiling-SILAC to study protein-protein interactions.

Anders R Kristensen1, Leonard J Foster

  • 1Department of Biochemistry & Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada, V6T 1Z4.

Methods in Molecular Biology (Clifton, N.J.)
|July 26, 2014
PubMed
Summary
This summary is machine-generated.

We introduce size-exclusion chromatography with protein correlation profiling and stable isotope labeling by amino acids in cell culture (SEC-PCP-SILAC) to dynamically map protein interactions. This method quantifies protein stoichiometry and temporal interactome changes efficiently.

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Area of Science:

  • Proteomics
  • Systems Biology
  • Molecular Cell Biology

Background:

  • The cell's protein-protein interaction network, or interactome, is crucial for cellular function.
  • Current interactome mapping methods like AP-MS lack stoichiometric and temporal data.
  • Existing techniques often require protein overexpression or fusion proteins, potentially altering biological interactions.

Purpose of the Study:

  • To present a novel method for dynamic interactome analysis.
  • To enable the quantification of protein stoichiometry and temporal interactome changes.
  • To provide a time-efficient and accessible approach for studying the interactome.

Main Methods:

  • Size-exclusion chromatography (SEC) coupled with protein correlation profiling using stable isotope labeling by amino acids in cell culture (PCP-SILAC).
  • Utilizing co-elution of proteins in SEC fractions as a proxy for interaction.
  • Employing triplex SILAC for quantitative measurements of stoichiometry and temporal dynamics.

Main Results:

  • Identification of protein interactions based on co-elution profiles.
  • Quantification of protein stoichiometry within complexes.
  • Detection of dynamic changes in protein interactions over time or upon perturbation.
  • Demonstration of SEC-PCP-SILAC's efficiency, generating significantly fewer samples for analysis compared to traditional methods.

Conclusions:

  • SEC-PCP-SILAC offers a powerful, quantitative, and dynamic approach to interactome mapping.
  • The method overcomes limitations of traditional techniques by avoiding overexpression and fusion proteins.
  • SEC-PCP-SILAC is time-efficient and accessible, facilitating broader study of cellular interactomes.