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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.
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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Mapping protein structural changes by quantitative cross-linking.

Zdenek Kukacka¹, Michal Rosulek¹, Martin Strohalm²

¹Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic.

Methods (San Diego, Calif.)

|June 7, 2015

Summary

This summary is machine-generated.

Isotopically labeled chemical cross-linking visualizes protein structure changes. This method aids in determining protein tertiary structure under physiological conditions, especially for proteins difficult to study with other techniques.

Keywords:

Chemical cross-linking Mass spectrometry Protein structure design Proteolysis Quantification

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Area of Science:

Biochemistry
Structural Biology
Proteomics

Background:

Chemical cross-linking offers a method for protein tertiary structure determination.
It provides data at physiological conditions for proteins not amenable to X-ray, NMR, or cryo-EM.
This technique has low spatial resolution but is valuable for specific applications.

Purpose of the Study:

To demonstrate the use of isotopically labeled chemical cross-linking for visualizing protein conformation rearrangements.
To test the capabilities and limitations of this new technique using calmodulin.

Main Methods:

Proteins were chemically cross-linked in their distinct conformations (calcium-free and calcium-containing).
Cross-linked calmodulin forms were mixed, digested, and analyzed using high-resolution mass spectrometry.
Heavy/light cross-link ratios were calculated using the mMass open-source platform.

Main Results:

The study successfully visualized protein conformation rearrangements in calmodulin.
Isotopically labeled cross-linking provided insights into the structural changes between calcium-bound and unbound states.
Quantitative analysis of cross-links allowed for the assessment of conformational differences.

Conclusions:

Isotopically labeled chemical cross-linking is effective for studying protein conformational dynamics.
This technique is particularly useful for proteins with multiple conformations or those challenging for high-resolution methods.
The approach provides valuable structural information under near-native conditions.