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J Struct Biol. 2015 Mar;189(3):177-83. doi: 10.1016/j.jsb.2015.01.014. Epub 2015 Feb 7.

Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.

Author information

1
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
2
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany. Electronic address: martin.beck@embl.de.

Abstract

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.

KEYWORDS:

Analysis; Cross-linking; Integrative modeling; Mass spectrometry; Visualization; XL-MS

PMID:
25661704
PMCID:
PMC4359615
DOI:
10.1016/j.jsb.2015.01.014
[Indexed for MEDLINE]
Free PMC Article

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