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 XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications

2020 ◽  
Author(s):  
Diogo Borges Lima ◽  
Ying Zhu ◽  
Fan Liu
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Large Scale ◽  
Interaction Network ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Cross Linking ◽  
Protein Interaction Data ◽  
Interaction Data ◽  
Link Type

ABSTRACTSoftware tools that allow visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a large selection of plugins for interpretation of protein interaction data. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly important source for such interaction data, but there are currently no Cytoscape tools to analyze XL-MS results. In light of the suitability of Cytoscape platform but also to expand its toolbox, here we introduce XlinkCyNET, an open-source Cytoscape Java plugin for exploring large-scale XL-MS-based protein interaction networks. XlinkCyNET offers rapid and easy visualization of intra and intermolecular cross-links and the locations of protein domains in a rectangular bar style, allowing subdomain-level interrogation of the interaction network. XlinkCyNET is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/xlinkcynet and at https://www.theliulab.com/software/xlinkcynet.

scholarly journals The Aryl-Hydrocarbon Receptor Protein Interaction Network (AHR-PIN) as Identified by Tandem Affinity Purification (TAP) and Mass Spectrometry

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Dorothy M. Tappenden ◽  
Hye Jin Hwang ◽  
Longlong Yang ◽  
Russell S. Thomas ◽  
John J. LaPres
Keyword(s):  
Mass Spectrometry ◽  
Gene Regulation ◽  
Aryl Hydrocarbon Receptor ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Affinity Purification ◽  
Interaction Network ◽  
Tandem Affinity Purification ◽  
Toxic Response ◽  
Aryl Hydrocarbon

The aryl-hydrocarbon receptor (AHR), a ligand activated PAS superfamily transcription factor, mediates most, if not all, of the toxicity induced upon exposure to various dioxins, dibenzofurans, and planar polyhalogenated biphenyls. While AHR-mediated gene regulation plays a central role in the toxic response to dioxin exposure, a comprehensive understanding of AHR biology remains elusive. AHR-mediated signaling starts in the cytoplasm, where the receptor can be found in a complex with the heat shock protein of 90 kDa (Hsp90) and the immunophilin-like protein, aryl-hydrocarbon receptor-interacting protein (AIP). The role these chaperones and other putative interactors of the AHR play in the toxic response is not known. To more comprehensively define the AHR-protein interaction network (AHR-PIN) and identify other potential pathways involved in the toxic response, a proteomic approach was undertaken. Using tandem affinity purification (TAP) and mass spectrometry we have identified several novel protein interactions with the AHR. These interactions physically link the AHR to proteins involved in the immune and cellular stress responses, gene regulation not mediated directly via the traditional AHR:ARNT heterodimer, and mitochondrial function. This new insight into the AHR signaling network identifies possible secondary signaling pathways involved in xenobiotic-induced toxicity.

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 PilMNOPQ from the Pseudomonas aeruginosa Type IV Pilus System Form a Transenvelope Protein Interaction Network That Interacts with PilA

2013 ◽  
Vol 195 (10) ◽  
pp. 2126-2135 ◽  
Author(s):  
S. Tammam ◽  
L. M. Sampaleanu ◽  
J. Koo ◽  
K. Manoharan ◽  
M. Daubaras ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Type Iv Pilus ◽  
System Form ◽  
Type Iv

scholarly journals Low throughput protocol for immunoprecipitation followed by mass spectrometry of cells stably expressing an HA-tagged protein v1

2020 ◽  
Author(s):  
Harper not provided not provided JW
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Gene Editing ◽  
Protein Complexes ◽  
Interaction Network ◽  
Epitope Tag ◽  
Powerful Approach

Analysis of protein complexes by mass spectrometry provides a powerful approach for identifying proteins that associate with other proteins. Frequently, this can be done by expressing the protein of interest with an epitope tag, such as a Hemagglutinin-A (HA) epitope, using either a stably expressed lentivirus or by gene editing the HA epitope into the gene of interest. The protocol has been used extensively to create the Bioplex protein interaction network [Huttlin et al Nature. 545:505-509 (2017); Huttlin et al Cell, 162: 425-440 (2015)].

scholarly journals Targeted Searches for Novel Peptides in Big Mass Spectrometry Data Sets

2017 ◽  
Author(s):  
Yu Gao ◽  
Jiao Ma ◽  
Alan Saghatelian ◽  
John R. Yates
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Protein Sequences ◽  
Interaction Network ◽  
Database Search ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Speed Up ◽  
Guilt By Association

We present Post-Acquisition Targeted Searches (PATS), an easy-to-use tool that allows the identification of novel peptide/protein sequences from existing big mass spectrometry data sets. PATS filters out the unrelated peptidome before the time-consuming database search to significantly speed up the identification. Using interactome data sets, PATS visualizes protein interaction network and helps to assign putative functions to the target protein based on the “guilt by association” concept.

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