Structural Biology by Mass Spectrometry: Mapping Protein Interaction Surfaces of Membrane Receptor Complexes with ICAT

A modification of our triphenylene ketal based receptor facilitates electrospray tandem mass spectrometry investigations. Binding affinities of eleven potential substrates, e.g. caffeine and other xanthine alkaloids, are probed in the gas phase with collision induced dissociation. The relative stabilities of the substrate-receptor complexes are rapidly determined and the findings are correlated with the corresponding results in solution.

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Chemical Cross-Linking and High-Performance Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Protein Interaction Analysis: Application to a Calmodulin/Target Peptide Complex

Analytical Chemistry ◽

10.1021/ac0487294 ◽

2005 ◽

Vol 77 (2) ◽

pp. 495-503 ◽

Cited By ~ 56

Author(s):

Stefan Kalkhof ◽

Christian Ihling ◽

Karl Mechtler ◽

Andrea Sinz

Keyword(s):

Mass Spectrometry ◽

Fourier Transform ◽

Protein Interaction ◽

Cyclotron Resonance ◽

High Performance ◽

Interaction Analysis ◽

Cross Linking ◽

Ion Cyclotron Resonance ◽

Analysis Application ◽

Chemical Cross Linking

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The Use of Mass Spectrometry in Studying Protein-Protein Interaction

Proteomics and Protein-Protein Interactions ◽

10.1007/0-387-24532-4_3 ◽

2006 ◽

pp. 33-48 ◽

Cited By ~ 1

Author(s):

Yi Wang ◽

Parvin Yazdi ◽

Jun Qin

Keyword(s):

Mass Spectrometry ◽

Protein Interaction ◽

Protein Protein Interaction

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Structural insights into Escherichia coli phosphopantothenoylcysteine synthetase by native ion mobility–mass spectrometry

Biochemical Journal ◽

10.1042/bcj20190318 ◽

2019 ◽

Vol 476 (21) ◽

pp. 3125-3139 ◽

Cited By ~ 2

Author(s):

Daniel Shiu-Hin Chan ◽

Jeannine Hess ◽

Elen Shaw ◽

Christina Spry ◽

Robert Starley ◽

...

Keyword(s):

Mass Spectrometry ◽

Escherichia Coli ◽

Structural Biology ◽

Ion Mobility ◽

Biosynthetic Pathway ◽

Screening Tool ◽

Native Mass Spectrometry ◽

Ion Mobility Mass Spectrometry ◽

E Coli ◽

Structural Insights

Abstract CoaBC, part of the vital coenzyme A biosynthetic pathway in bacteria, has recently been validated as a promising antimicrobial target. In this work, we employed native ion mobility–mass spectrometry to gain structural insights into the phosphopantothenoylcysteine synthetase domain of E. coli CoaBC. Moreover, native mass spectrometry was validated as a screening tool to identify novel inhibitors of this enzyme, highlighting the utility and versatility of this technique both for structural biology and for drug discovery.

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

10.1101/2020.12.20.423654 ◽

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.

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