CrossWork: software-assisted identification of cross-linked peptides
Morten I Rasmussen1, Jan C Refsgaard, Li Peng
1University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
Journal of Proteomics
|May 24, 2011
Summary
This study introduces a new chemical cross-linking pipeline using standard reagents and the CrossWork software to analyze large protein structures. The method successfully generated structural data for complex proteins, advancing the field of protein interaction analysis.
Area of Science:
- Biochemistry
- Structural Biology
- Proteomics
Background:
- Chemical cross-linking is vital for studying protein structure and interactions.
- Current methods struggle with large, complex proteins due to reagent availability, reactivity, and outdated or unavailable software.
Purpose of the Study:
- To present an improved method pipeline for chemical cross-linking.
- To enable structural analysis of large and complex proteins.
Main Methods:
- Utilized standard cross-linkers (BS3 and BS2G).
- Developed and employed the freely available CrossWork search program for analyzing tandem mass-spectrometric data.
- Tested the pipeline on complement factor C3 and the multi-domain ERp72 protein.
Main Results:
- The CrossWork program efficiently searches large datasets on a standard PC.
- Generated distance constraints from cross-linking data that align with established structures.
- Successfully derived structural information for large, complex proteins, including ERp72.
Conclusions:
- The presented method pipeline overcomes limitations in current chemical cross-linking approaches.
- It provides a robust and accessible tool for structural biology research.
- Enables detailed structural investigation of complex protein systems.
