In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria

The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass spectrometry (CLMS) is contributing to this effort, typically through the use of mass spectrometry (MS)-cleavable cross-linkers. Here, we apply the pop...

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Bibliographic Details
Published in:Journal of proteome research Vol. 19; no. 1; p. 327
Main Authors: Ryl, Petra S J, Bohlke-Schneider, Michael, Lenz, Swantje, Fischer, Lutz, Budzinski, Lisa, Stuiver, Marchel, Mendes, Marta M L, Sinn, Ludwig, O'Reilly, Francis J, Rappsilber, Juri
Format: Journal Article
Language:English
Published: United States 03.01.2020
Subjects:
Chromatography, Gel
Cross-Linking Reagents - chemistry
Humans
K562 Cells
Mass Spectrometry - methods
Mitochondria - chemistry
Mitochondrial Proteins - analysis
Mitochondrial Proteins - chemistry
Protein Conformation
Protein Interaction Maps
Succinimides - chemistry
Workflow
noncleavable DSS cross-linker
in situ large-scale structural biology
comparative modeling
human mitochondria
cross-linking mass spectrometry
ISSN:1535-3907, 1535-3907
Online Access:Get more information
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Summary:The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass spectrometry (CLMS) is contributing to this effort, typically through the use of mass spectrometry (MS)-cleavable cross-linkers. Here, we apply the popular noncleavable cross-linker disuccinimidyl suberate (DSS) to human mitochondria and identify 5518 distance restraints between protein residues. Each distance restraint on proteins or their interactions provides structural information within mitochondria. Comparing these restraints to protein data bank (PDB)-deposited structures and comparative models reveals novel protein conformations. Our data suggest, among others, substrates and protein flexibility of mitochondrial heat shock proteins. Through this study, we bring forward two central points for the progression of CLMS towards large-scale in situ structural biology: First, clustered conflicts of cross-link data reveal in situ protein conformation states in contrast to error-rich individual conflicts. Second, noncleavable cross-linkers are compatible with proteome-wide studies.
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ISSN:1535-3907
1535-3907
DOI:10.1021/acs.jproteome.9b00541