scholarly journals Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry

2015 ◽  
Vol 8 (11) ◽  
Author(s):  
Boris Zybailov ◽  
Kuppan Gokulan ◽  
Jadon Wiese
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Mitochondrial Proteins ◽  
Cross Linking ◽  
Protein Protein Interaction ◽  
Interaction Interface ◽  
Chemical Cross Linking

scholarly journals Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry

Structure ◽  
2015 ◽  
Vol 23 (4) ◽  
pp. 762-773 ◽  
Author(s):  
Arti T. Navare ◽  
Juan D. Chavez ◽  
Chunxiang Zheng ◽  
Chad R. Weisbrod ◽  
Jimmy K. Eng ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Pseudomonas Aeruginosa ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Cross Linking ◽  
Chemical Cross Linking

scholarly journals Mitochondrial protein interaction landscape of SS-31

2019 ◽  
Author(s):  
Juan D. Chavez ◽  
Xiaoting Tang ◽  
Matthew D. Campbell ◽  
Gustavo Reyes ◽  
Philip A. Kramer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Mitochondrial Function ◽  
Mitochondrial Membrane ◽  
Cross Linking ◽  
Pharmacological Effects ◽  
Inner Mitochondrial Membrane ◽  
Atp Production ◽  
Mechanistic Insight ◽  
Chemical Cross Linking

AbstractMitochondrial dysfunction underlies the etiology of a broad spectrum of diseases including heart disease, cancer, neurodegenerative diseases, and the general aging process. Therapeutics that restore healthy mitochondrial function hold promise for treatment of these conditions. The synthetic tetrapeptide, elamipretide (SS-31), improves mitochondrial function, but mechanistic details of its pharmacological effects are unknown. Reportedly, SS-31 primarily interacts with the phospholipid cardiolipin in the inner mitochondrial membrane. Here we utilize chemical cross-linking with mass spectrometry to identify protein interactors of SS-31 in mitochondria. The SS-31-interacting proteins, all known cardiolipin binders, fall into two groups, those involved in ATP production through the oxidative phosphorylation pathway and those involved in 2-oxoglutarate metabolic processes. Residues cross-linked with SS-31 reveal binding regions that in many cases, are proximal to cardiolipin-protein interacting regions. These results offer the first glimpse of the protein interaction landscape of SS-31 and provide new mechanistic insight relevant to SS-31 mitochondrial therapy.Significance StatementSS-31 is a synthetic peptide that improves mitochondrial function and is currently undergoing clinical trials for treatments of heart failure, primary mitochondrial myopathy, and other mitochondrial diseases. SS-31 interacts with cardiolipin which is abundant in the inner mitochondrial membrane, but mechanistic details of its pharmacological effects are unknown. Here we apply a novel chemical cross-linking/mass spectrometry method to provide the first direct evidence for specific interactions between SS-31 and mitochondrial proteins. The identified SS-31 interactors are functional components in ATP production and 2-oxoglutarate metabolism and signaling, consistent with improved mitochondrial function resultant from SS-31 treatment. These results offer the first glimpse of the protein interaction landscape of SS-31 and provide new mechanistic insight relevant to SS-31 mitochondrial therapy.

scholarly journals A Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions

2019 ◽  
Author(s):  
Michael Götze ◽  
Claudio Iacobucci ◽  
Christian Ihling ◽  
Andrea Sinz
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Cross Linking ◽  
Protein Protein Interaction ◽  
Cellular Environment ◽  
Protein Protein Interaction Networks

ABSTRACTWe present a cross-linking/mass spectrometry (XLMS) workflow for performing proteome-wide cross-linking analyses within one week. The workflow is based on the commercially available MS-cleavable cross-linker disuccinimidyl dibutyric urea (DSBU) and can be employed by every lab having access to a mass spectrometer with tandem MS capabilities. We provide an updated version 2.0 of the freeware software tool MeroX, available at www.StavroX.com, that allows conducting fully automated and reliable studies delivering insights into protein-protein interaction networks and protein conformations at the proteome level. We exemplify our optimized workflow for mapping protein-protein interaction networks in Drosophila melanogaster embryos on a system-wide level. From cross-linked Drosophila embryo extracts, we detected 18,037 cross-link spectrum matches corresponding to 5,129 unique cross-linked residues in biological triplicate experiments at 5% FDR (3,098 at 1% FDR). Among these, 1,237 interprotein cross-linking sites were identified that contain valuable information on protein-protein interactions. The remaining 3,892 intra-protein cross-links yield information on conformational changes of proteins in their cellular environment.

scholarly journals Probing the interaction interface of the GADD45β/MKK7 and MKK7/DTP3 complexes by chemical cross-linking mass spectrometry

2018 ◽  
Vol 114 ◽  
pp. 114-123 ◽  
Author(s):  
Camilla Rega ◽  
Rosita Russo ◽  
Annalia Focà ◽  
Annamaria Sandomenico ◽  
Emanuela Iaccarino ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cross Linking ◽  
Interaction Interface ◽  
Chemical Cross Linking
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