xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.
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.
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.|Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.
Thomas
T
Walzthoeni
Department of Biology and Genetics, Stanford University, Stanford, California, USA.
Lukasz A
LA
Joachimiak
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.|PhD Program in Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.|PhD Program in Systems Biology, University of Zurich, Zurich, Switzerland.
George
http://orcid.org/0000-0002-1655-6789
G
Rosenberger
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
Hannes L
http://orcid.org/0000-0003-0990-7488
HL
Röst
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
Lars
http://orcid.org/0000-0001-9885-9312
L
Malmström
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
Alexander
A
Leitner
Department of Biology and Genetics, Stanford University, Stanford, California, USA.
Judith
J
Frydman
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.|Faculty of Science, University of Zurich, Zurich, Switzerland.
Ruedi
R
Aebersold
D000465:Algorithms; D000818:Animals; D056404:Chaperonin Containing TCP-1 / Q000737:chemistry*; D003432:Cross-Linking Reagents / Q000737:chemistry*; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D049409:Luciferases, Firefly / Q000737:chemistry*; D013058:Mass Spectrometry / Q000379:methods*; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D011487:Protein Conformation; D012984:Software
D003432:Cross-Linking Reagents; D046912:Multiprotein Complexes; D049409:Luciferases, Firefly; D056404:Chaperonin Containing TCP-1