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Related Concept Videos

Protein Networks02:26

Protein Networks

4.4K
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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Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
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Isobaric Quantitative Protein Interaction Reporter Technology for Comparative Interactome Studies.

Juan D Chavez1, Andrew Keller1, Jared P Mohr1

  • 1Department of Genome Sciences, University of Washington, Seattle 98195, Washington, United States.

Analytical Chemistry
|September 24, 2020
PubMed
Summary
This summary is machine-generated.

Isobaric quantitative protein interaction reporter (iqPIR) technology offers enhanced protein structure and interaction analysis. This new method improves quantitative cross-linking mass spectrometry (qXL-MS) by simplifying data analysis and increasing confidence in results.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Structural Biology

Background:

  • Chemical cross-linking with mass spectrometry (XL-MS) is vital for studying protein structures and interactions in complex biological samples.
  • Quantitative XL-MS (qXL-MS) reveals protein conformational and interaction changes under various conditions.
  • Previous qXL-MS methods relied on deuterium incorporation or SILAC labeling for quantitation.

Purpose of the Study:

  • To introduce a novel isobaric quantitative protein interaction reporter (iqPIR) technology for enhanced qXL-MS.
  • To enable more accurate and confident quantitation of cross-linked peptides from proteome-wide samples.
  • To provide additional information on protein abundance and lysine site modifications within a single experiment.

Main Methods:

  • Development of iqPIR technology utilizing stable isotopes incorporated into the cross-linker design.
  • Application of iqPIR to enable isobaric cross-linked peptide pairs from different samples to have distinct isotope signatures.
  • Analysis of reduced complexity tandem mass spectra for improved quantitation compared to MS1 spectra.

Main Results:

  • iqPIR technology allows for improved quantitation of cross-linked peptide levels due to simplified tandem mass spectra.
  • Isotope incorporation in iqPIR reporters enhances quantitative assessment confidence through multiple fragmentation spectrum opportunities.
  • Dead-end iqPIR cross-linked products provide data on protein abundance and lysine site modification levels.

Conclusions:

  • iqPIR technology represents a significant advancement in quantitative cross-linking mass spectrometry.
  • This method offers improved accuracy, confidence, and data richness for studying protein interactions and structures.
  • iqPIR facilitates comprehensive analysis of protein dynamics and modifications from a single in vivo experiment.