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Related Concept Videos

Protein Networks02:26

Protein Networks

3.9K
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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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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...
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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
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Related Experiment Video

Updated: Jun 13, 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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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

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Modelling protein complexes with crosslinking mass spectrometry and deep learning.

Kolja Stahl1, Robert Warneke2, Lorenz Demann2

  • 1Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany.

Nature Communications
|September 9, 2024
PubMed
Summary

Integrating crosslinking mass spectrometry (MS) data into protein structure modeling significantly enhances accuracy for complex targets. This approach enables detailed structural investigations, such as mapping iron homeostasis in Bacillus subtilis.

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Analyzing Large Protein Complexes by Structural Mass Spectrometry
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Analyzing Large Protein Complexes by Structural Mass Spectrometry
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Analyzing Large Protein Complexes by Structural Mass Spectrometry

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Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • Deep learning models for protein complex structure prediction face limitations due to scarce structural and evolutionary data.
  • Accurate protein complex structures are crucial for understanding cellular mechanisms.

Purpose of the Study:

  • To enhance deep learning-based protein complex structure modeling by integrating experimental data.
  • To improve the accuracy and reliability of AlphaFold-Multimer predictions for challenging protein complexes.

Main Methods:

  • Extended AlphaLink to incorporate distance restraints from crosslinking mass spectrometry (MS) into AlphaFold-Multimer.
  • Applied the integrated approach to model protein complexes, including those with limited prior structural information.

Main Results:

  • Integration of crosslinking MS data substantially improved modeling performance for challenging protein complex targets.
  • The method effectively identified protein interfaces, focused computational sampling, and enhanced model selection.
  • Demonstrated the utility of single crosslinks from whole-cell MS for structural investigations.

Conclusions:

  • Crosslinking MS data integration is a powerful strategy to overcome limitations in deep learning-based protein complex modeling.
  • This approach enables high-resolution structural investigations of cellular processes, exemplified by elucidating iron homeostasis in Bacillus subtilis.