Proteomics

Dataset Information

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Chemical cross-linking enables drafting ClpXP proximity maps and taking snapshots of in vivo interaction networks


ABSTRACT: Protein-protein interactions within complexes and networks are often dynamic and their elucidation remains a challenging task. Here, we show on the example of the proteolytic ClpXP complex the power of combined chemical cross-linking and mass-spectrometry to capture transient binding interactions within ClpP and ClpX as well as across the enigmatic ClpX hexamer – ClpP heptamer interface. Our data suggests that a few hot spot lysine residues located in signature loops in ClpX mediate the ClpX-ClpP interaction. This study further confirms that Listeria monocytogenes ClpX solely interacts with the heterooligomeric ClpP1/2 complex via the ClpP2 apical site. Moreover, the cellular interaction network of human and bacterial proteases was elucidated via in situ chemical cross-linking followed by an antibody-based pull-down against ClpP from genetically unmodified cells. A subsequent gel-free, quantitative mass spectrometric analysis demonstrated an up to 3-fold higher coverage compared to conventional co-immunoprecipitation without cross-linker revealing unprecedented insight into intracellular ClpXP networks.

INSTRUMENT(S): Orbitrap Fusion ETD, Q Exactive

ORGANISM(S): Escherichia coli   Staphylococcus aureus   Homo sapiens  

TISSUE(S): Tissue Not Applicable To Dataset

DISEASE(S): Not Available

SUBMITTER: Anja Fux  

LAB HEAD: Stephan A. Sieber

PROVIDER: PXD009224 | Pride | 2018-11-21

REPOSITORIES: pride

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Publications

Chemical Cross-Linking Enables Drafting ClpXP Proximity Maps and Taking Snapshots of In Situ Interaction Networks.

Fux Anja A   Korotkov Vadim S VS   Schneider Markus M   Antes Iris I   Sieber Stephan A SA  

Cell chemical biology 20181108 1


Detection of dynamic protein-protein interactions within complexes and networks remains a challenging task. Here, we show by the example of the proteolytic ClpXP complex the utility of combined chemical cross-linking and mass spectrometry (XL-MS) to map interactions within ClpP and ClpX as well as across the enigmatic ClpX hexamer-ClpP heptamer interface. A few hot-spot lysines located in signature loops in ClpX were shown to be in proximity to several structural regions of ClpP providing an ini  ...[more]

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