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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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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: Jul 7, 2025

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Multidimensional Cross-Linking and Real-Time Informatics for Multiprotein Interaction Studies.

Jared P Mohr1, Arianne Caudal2,3, Rong Tian2,3

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States.

Journal of Proteome Research
|December 26, 2023
PubMed
Summary
This summary is machine-generated.

A novel tetrameric cross-linker enables simultaneous covalent bonding of up to four proteins, advancing the study of complex protein structures. This method aids in identifying higher-order cross-links for improved structural modeling and analysis of protein assemblies.

Keywords:
adaptive instrument controlcross-linkingintelligent data acquisitionmitochondriaprotein modelingprotein−protein interactions

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Proteomics

Background:

  • Chemical cross-linking coupled with mass spectrometry is vital for protein structure and complex identification.
  • Traditional cross-linkers identify only pairs of interacting residues, limiting higher-order structure analysis.
  • Existing methods often require prior knowledge of complex composition for modeling.

Purpose of the Study:

  • To introduce a novel tetrameric cross-linker with four amine-reactive groups for simultaneous cross-linking of multiple proteins.
  • To develop a real-time instrument method for identifying these higher-order cross-links.
  • To demonstrate the utility of higher-dimensional cross-linking in characterizing complex protein interfaces and assemblies.

Main Methods:

  • Development and application of a new tetrameric cross-linker.
  • Utilizing a real-time instrument method for tetrameric cross-link identification.
  • Applying the technique to isolated mitochondria, focusing on OXPHOS complexes and ATP synthase.

Main Results:

  • Successful identification of higher-order cross-links in mitochondrial OXPHOS complexes and ATP synthase.
  • Demonstrated the capability of the new cross-linker to link up to four proteins simultaneously.
  • Showcased the utility of higher-order cross-links in filtering models of large protein assemblies generated by AlphaFold.

Conclusions:

  • The tetrameric cross-linker and associated method provide a powerful new tool for higher-dimensional cross-linking.
  • This approach effectively characterizes multiple protein interfaces within complex biological samples like intact mitochondria.
  • Higher-dimensional cross-linking offers new possibilities for understanding the architecture of large protein assemblies.