scholarly journals EM∩IM: software for relating ion mobility mass spectrometry and electron microscopy data

The Analyst ◽  
2016 ◽  
Vol 141 (1) ◽  
pp. 70-75 ◽  
Author(s):  
Matteo T. Degiacomi ◽  
Justin L. P. Benesch
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Structural Biology ◽  
Cross Sections ◽  
Ion Mobility ◽  
Ion Mobility Mass Spectrometry ◽  
Density Maps ◽  
Transmission Electron ◽  
Microscopy Data ◽  
Means Of Transmission

EM∩IM enables the calculation of collision cross-sections from electron density maps obtained, for example, by means of transmission electron microscopy. This capability will further aid the integration of ion mobility mass spectrometry with modern structural biology.

scholarly journals The association and aggregation of the metamorphic chemokine lymphotactin with fondaparinux: from nm molecular complexes to μm molecular assemblies

2016 ◽  
Vol 52 (2) ◽  
pp. 394-397 ◽  
Author(s):  
Sophie R. Harvey ◽  
Cait E. MacPhee ◽  
Brian F. Volkman ◽  
Perdita E. Barran
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Transmission Electron Microscopy ◽  
Ion Mobility ◽  
Drift Tube ◽  
Molecular Complexes ◽  
Ion Mobility Mass Spectrometry ◽  
Molecular Assemblies ◽  
Transmission Electron

Transmission electron microscopy and drift tube ion mobility-mass spectrometry are used to study the assemblies formed by the metamorphic chemokine lymphotactin in the presence of a model glycosaminoglycan.

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 A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry

2021 ◽  
Vol 12 ◽  
Author(s):  
Kai P. Law ◽  
Wei He ◽  
Jianchang Tao ◽  
Chuanlun Zhang
Keyword(s):  
Mass Spectrometry ◽  
Cross Sections ◽  
Ion Mobility ◽  
Resolving Power ◽  
Ion Mobility Mass Spectrometry ◽  
Ion Chemistry ◽  
Lipid Species ◽  
Mobility System ◽  
Archaeal Lipids

Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.

Estimating Collision Cross Sections of Negatively Charged N-Glycans using Traveling Wave Ion Mobility-Mass Spectrometry

2014 ◽  
Vol 86 (21) ◽  
pp. 10789-10795 ◽  
Author(s):  
Johanna Hofmann ◽  
Weston B. Struwe ◽  
Charlotte A. Scarff ◽  
James H. Scrivens ◽  
David J. Harvey ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cross Sections ◽  
Ion Mobility ◽  
Traveling Wave ◽  
Ion Mobility Mass Spectrometry ◽  
Collision Cross Sections ◽  
Traveling Wave Ion Mobility

Characterisation of Calmodulin Structural Transitions by Ion Mobility Mass Spectrometry

2012 ◽  
Vol 65 (5) ◽  
pp. 504 ◽  
Author(s):  
Antonio N. Calabrese ◽  
Lauren A. Speechley ◽  
Tara L. Pukala
Keyword(s):  
Mass Spectrometry ◽  
Cross Section ◽  
Cross Sections ◽  
Ion Mobility ◽  
Collision Cross Section ◽  
Travelling Wave ◽  
Ion Mobility Mass Spectrometry ◽  
Structural Transitions ◽  
Calmodulin Binding ◽  
Negative Mode

This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.

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.

scholarly journals Distance Geometry Protocol to Generate Conformations of Natural Products to Structurally Interpret Ion Mobility-Mass Spectrometry Collision Cross Sections

2014 ◽  
Vol 118 (48) ◽  
pp. 13812-13820 ◽  
Author(s):  
Sarah M. Stow ◽  
Cody R. Goodwin ◽  
Michal Kliman ◽  
Brian O. Bachmann ◽  
John A. McLean ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Cross Sections ◽  
Ion Mobility ◽  
Distance Geometry ◽  
Ion Mobility Mass Spectrometry ◽  
Collision Cross Sections
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