scholarly journals Ion mobility coupled to native mass spectrometry as a relevant tool to investigate extremely small ligand-induced conformational changes

The Analyst ◽  
2015 ◽  
Vol 140 (21) ◽  
pp. 7234-7245 ◽  
Author(s):  
Johann Stojko ◽  
Sonia Fieulaine ◽  
Stéphanie Petiot-Bécard ◽  
Alain Van Dorsselaer ◽  
Thierry Meinnel ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Ion Mobility ◽  
Native Mass Spectrometry ◽  
Peptide Deformylase ◽  
Ion Mobility Mass Spectrometry ◽  
Over Time

Native and ion-mobility mass spectrometry reveal the conformational evolution over time of a peptide deformylase binding different ligands, which is consistent with slow-tight inhibition of the enzyme.

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

2019 ◽  
Vol 476 (21) ◽  
pp. 3125-3139 ◽  
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.

scholarly journals Exploring the conformational landscape of a lanthipeptide synthetase using native mass spectrometry

2020 ◽  
Author(s):  
Nuwani W. Weerasinghe ◽  
Yeganeh Habibi ◽  
Kevin A. Uggowitzer ◽  
Christopher J. Thibodeaux
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Conformational Changes ◽  
Ion Mobility ◽  
Peptide Binding ◽  
Native Mass Spectrometry ◽  
Order Structure ◽  
Conformational Sampling ◽  
Precursor Peptide ◽  
Conformational Landscape

AbstractLanthipeptides are ribosomally-synthesized and post-translationally modified peptide (RiPP) natural products that are biosynthesized in a multistep maturation process by enzymes (lanthipeptide synthetases) that possess relaxed substrate specificity. Recent evidence has suggested that some lanthipeptide synthetases are structurally dynamic enzymes that are allosterically activated by precursor peptide binding, and that conformational sampling of the enzyme-peptide complex may play an important role in defining the efficiency and sequence of biosynthetic events. These “biophysical” processes, while critical for defining the activity and function of the synthetase, remain very challenging to study with existing methodologies. Herein, we show that native nanoelectrospray ionization coupled to ion mobility mass spectrometry (nanoESI-IM-MS) provides a powerful and sensitive means for investigating the conformational landscapes and intermolecular interactions of lanthipeptide synthetases. Namely, we demonstrate that the class II lanthipeptide synthetase (HalM2) and its non-covalent complex with the cognate HalA2 precursor peptide can be delivered into the gas phase in a manner that preserves native structures and intermolecular enzyme-peptide contacts. Moreover, gas phase ion mobility studies of the natively-folded ions demonstrate that peptide binding and mutations to dynamic structural elements of HalM2 alter the conformational landscape of the enzyme, and that the precursor peptide itself exhibits higher order structure in the mass spectrometer. Cumulatively, these data support previous claims that lanthipeptide synthetases are structurally dynamic enzymes that undergo functionally relevant conformational changes in response to precursor peptide binding. This work establishes nanoESI-IM-MS as a versatile approach for unraveling the relationships between protein structure and biochemical function in RiPP biosynthetic systems.

Ion mobility mass spectrometry workflows for characterizing bioactive isomer conformation, isomerization and drug–protein–liposome interaction

2018 ◽  
Vol 10 (36) ◽  
pp. 4367-4377
Author(s):  
Hui Ouyang ◽  
Tao Bo ◽  
Zhengxiang Zhang ◽  
Xinqiu Guo ◽  
Mingzhen He ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Ion Mobility ◽  
Ion Mobility Mass Spectrometry

Ion mobility mass spectrometry enhances our ability to study conformational changes of bioactive isomers and their interactions with macromolecules.

scholarly journals Native Tandem and Ion Mobility Mass Spectrometry Highlight Structural and Modular Similarities in Clustered-Regularly-Interspaced Shot-Palindromic-Repeats (CRISPR)-associated Protein Complexes From Escherichia coli and Pseudomonas aeruginosa

2012 ◽  
Vol 11 (11) ◽  
pp. 1430-1441 ◽  
Author(s):  
Esther van Duijn ◽  
Ioana M. Barbu ◽  
Arjan Barendregt ◽  
Matthijs M. Jore ◽  
Blake Wiedenheft ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Ion Mobility ◽  
Protein Complexes ◽  
Acquired Resistance ◽  
Native Mass Spectrometry ◽  
Ion Mobility Mass Spectrometry ◽  
E Coli ◽  
Ribonucleoprotein Complexes ◽  
Specific Association

The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different CRISPR/Cas subtypes. Previous studies combined mass spectrometry, electron microscopy, and small angle x-ray scattering to demonstrate that the E. coli Cascade complex (405 kDa) and the P. aeruginosa Csy-complex (350 kDa) are similar in that they share a central spiral-shaped hexameric structure, flanked by associating proteins and one CRISPR RNA. Recently, a cryo-electron microscopy structure of Cascade revealed that the CRISPR RNA molecule resides in a groove of the hexameric backbone. For both complexes we here describe the use of native mass spectrometry in combination with ion mobility mass spectrometry to assign a stable core surrounded by more loosely associated modules. Via computational modeling subcomplex structures were proposed that relate to the experimental IMMS data. Despite the absence of obvious sequence homology between several subunits, detailed analysis of sub-complexes strongly suggests analogy between subunits of the two complexes. Probing the specific association of E. coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes.

Exploring Key Parameters to Detect Subtle Ligand-Induced Protein Conformational Changes Using Traveling Wave Ion Mobility Mass Spectrometry

2012 ◽  
Vol 84 (11) ◽  
pp. 4703-4710 ◽  
Author(s):  
Cédric Atmanene ◽  
Stéphanie Petiot-Bécard ◽  
Denis Zeyer ◽  
Alain Van Dorsselaer ◽  
Valérie Vivat Hannah ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Ion Mobility ◽  
Traveling Wave ◽  
Ion Mobility Mass Spectrometry ◽  
Protein Conformational Changes ◽  
Traveling Wave Ion Mobility

Native Mass Spectrometry Approaches Using Ion Mobility-Mass Spectrometry

2015 ◽  
pp. 81-108 ◽  
Author(s):  
Frederik Lermyte ◽  
Esther Marie Martin ◽  
Albert Konijnenberg ◽  
Filip Lemière ◽  
Frank Sobott
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility ◽  
Native Mass Spectrometry ◽  
Ion Mobility Mass Spectrometry

scholarly journals Ion mobility-mass spectrometry shows stepwise protein unfolding under alkaline conditions

2021 ◽  
Author(s):  
Cagla Sahin ◽  
Nicklas Österlund ◽  
Axel Leppert ◽  
Janne Johansson ◽  
Erik Marklund ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility ◽  
Protein Unfolding ◽  
Protein Denaturation ◽  
Native Mass Spectrometry ◽  
Ion Mobility Mass Spectrometry ◽  
Alkaline Conditions

Although native mass spectrometry is widely applied to monitor chemical or thermal protein denaturation, it is not clear to what extent it can inform about alkali-induced unfolding. Here, we probe...

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