xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass
Thomas Walzthoeni1,2, Lukasz A Joachimiak3, George Rosenberger1,4,5
1Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
Nature Methods
|October 27, 2015
Summary
This study introduces a computational pipeline for quantitative cross-linking mass spectrometry to analyze protein complex conformational changes. The method reveals structural heterogeneity in proteins like luciferase and TRiC using limited structural data.
Area of Science:
- Biochemistry and Structural Biology
- Proteomics and Mass Spectrometry
- Computational Biology
Background:
- Chemical cross-linking coupled with mass spectrometry provides spatial restraints for amino acid pairs on protein surfaces.
- Quantifying differences in cross-linked peptides from proteins in distinct spatial states is crucial for understanding conformational dynamics.
- Existing methods may lack comprehensive pipelines for analyzing quantitative cross-linking mass spectrometry data.
Purpose of the Study:
- To develop and present a generic computational pipeline for quantitative cross-linking mass spectrometry (qXL-MS).
- To enable the quantification of differences in cross-linked peptides from protein complexes in different conformational states.
- To apply the developed method for detecting conformational changes and structural heterogeneity in model protein systems.
Main Methods:
- Utilized quantitative mass spectrometry combined with chemical cross-linking.
- Developed a computational pipeline with modules for quantitative data extraction and statistical assessment.
- Applied the qXL-MS pipeline to study conformational changes in firefly luciferase and the bovine TRiC complex.
Main Results:
- Successfully quantified differences in cross-linked peptides from protein complexes in spatially discrete states.
- Demonstrated the pipeline's ability to detect conformational changes in firefly luciferase and the bovine TRiC complex.
- The method effectively identifies and explains structural heterogeneity using sparse structural information.
Conclusions:
- The developed computational pipeline provides a robust framework for quantitative cross-linking mass spectrometry.
- This approach facilitates the study of protein complex dynamics and structural heterogeneity.
- The method offers a valuable tool for structural biology research, even with limited prior structural data.
