Introduction

Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments. We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex. Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM maps. Xlink Analyzer is available for download at http://www.beck.embl.de/XlinkAnalyzer.html.

Publications

  1. Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.
    Cite this
    Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M, 2015-03-01 - Journal of structural biology

Credits

  1. Jan Kosinski
    Developer

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Germany

  2. Alexander von Appen
    Developer

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Germany

  3. Alessandro Ori
    Developer

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Germany

  4. Kai Karius
    Developer

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Germany

  5. Christoph W Müller
    Developer

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Germany

  6. Martin Beck
    Investigator

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Germany

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Summary
AccessionBT006619
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByMartin Beck