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Nat Methods. 2015 Dec;12(12):1185-90. doi: 10.1038/nmeth.3631. Epub 2015 Oct 26.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

Author information

1
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
2
Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.
3
Department of Biology and Genetics, Stanford University, Stanford, California, USA.
4
PhD Program in Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
5
PhD Program in Systems Biology, University of Zurich, Zurich, Switzerland.
6
Faculty of Science, University of Zurich, Zurich, Switzerland.

Abstract

Chemical cross-linking in combination with mass spectrometry generates distance restraints of amino acid pairs in close proximity on the surface of native proteins and protein complexes. In this study we used quantitative mass spectrometry and chemical cross-linking to quantify differences in cross-linked peptides obtained from complexes in spatially discrete states. We describe a generic computational pipeline for quantitative cross-linking mass spectrometry consisting of modules for quantitative data extraction and statistical assessment of the obtained results. We used the method to detect conformational changes in two model systems: firefly luciferase and the bovine TRiC complex. Our method discovers and explains the structural heterogeneity of protein complexes using only sparse structural information.

PMID:
26501516
PMCID:
PMC4927332
DOI:
10.1038/nmeth.3631
[Indexed for MEDLINE]
Free PMC Article

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