scholarly journals Surface-induced dissociation of protein complexes on a cyclic ion mobility spectrometer

The Analyst ◽  
2021 ◽  
Author(s):  
Dalton T. Snyder ◽  
Benjamin J. Jones ◽  
Yu-Fu Lin ◽  
Dale A. Cooper-Shepherd ◽  
Darren Hewitt ◽  
...  
Keyword(s):  
Ion Mobility ◽  
Protein Complexes ◽  
Protein Assemblies ◽  
Ion Mobility Spectrometer ◽  
Surface Induced Dissociation ◽  
Amyloid Aggregates

Characterization of protein assemblies and amyloid aggregates by CIU, CID, SIU, and SID on a cyclic ion mobility spectrometer.

scholarly journals Development and Characterization of Ion Mobility Spectrometer

2019 ◽  
Vol 14 (0) ◽  
pp. 3406093-3406093
Author(s):  
Joey Kim T. SORIANO ◽  
Takashi TORII ◽  
Ma Camille C. LACDAN ◽  
Motoi WADA
Keyword(s):  
Ion Mobility ◽  
Ion Mobility Spectrometer

scholarly journals Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

2021 ◽  
Author(s):  
Tim Neijenhuis ◽  
Siri C. van Keulen ◽  
Alexandre M.J.J. Bonvin
Keyword(s):  
Protein Complexes ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Protein Interfaces ◽  
Density Maps ◽  
Medium Resolution ◽  
Wide Range ◽  
Multimeric Protein

A wide range of cellular processes require the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The produced density maps can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low-to-medium resolution maps. Unfortunately, the produced models frequently contain atomic clashes at the protein-protein interfaces (PPIs) as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best performing protocol, consisting of a semi-flexible simulated annealing refinement with restraints on the centroids of the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.

scholarly journals Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS

2018 ◽  
Vol 115 (6) ◽  
pp. 1268-1273 ◽  
Author(s):  
Aniruddha Sahasrabuddhe ◽  
Yang Hsia ◽  
Florian Busch ◽  
William Sheffler ◽  
Neil P. King ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Ion Mobility ◽  
Protein Complexes ◽  
Rapid Determination ◽  
Point Group ◽  
Structural Features ◽  
Group Symmetry ◽  
Protein Assemblies ◽  
Native Ms ◽  
And Topology

Computational protein design provides the tools to expand the diversity of protein complexes beyond those found in nature. Understanding the rules that drive proteins to interact with each other enables the design of protein–protein interactions to generate specific protein assemblies. In this work, we designed protein–protein interfaces between dimers and trimers to generate dodecameric protein assemblies with dihedral point group symmetry. We subsequently analyzed the designed protein complexes by native MS. We show that the use of ion mobility MS in combination with surface-induced dissociation (SID) allows for the rapid determination of the stoichiometry and topology of designed complexes. The information collected along with the speed of data acquisition and processing make SID ion mobility MS well-suited to determine key structural features of designed protein complexes, thereby circumventing the requirement for more time- and sample-consuming structural biology approaches.

Illustration of SID-IM-SID (surface-induced dissociation-ion mobility-SID) mass spectrometry: homo and hetero model protein complexes

The Analyst ◽  
2015 ◽  
Vol 140 (20) ◽  
pp. 7012-7019 ◽  
Author(s):  
Royston S. Quintyn ◽  
Sophie R. Harvey ◽  
Vicki H. Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility ◽  
Protein Complex ◽  
Protein Complexes ◽  
Second Stage ◽  
Surface Induced Dissociation ◽  
Model Protein ◽  
Complex Architecture

Surface collisions generate subcomplexes, which are then separated by ion mobility and dissociated into their individual subunitsviaa second stage of surface collisions to elucidate protein complex architecture and assembly.

scholarly journals Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry

2020 ◽  
Author(s):  
Erin Panczyk ◽  
Dalton Snyder ◽  
Mark. E. Ridgeway ◽  
Arpad Somogyi ◽  
Melvin A. Park ◽  
...  
Keyword(s):  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Protein Complexes ◽  
Small Mass ◽  
Resolving Power ◽  
Mass Selection ◽  
Trapped Ion ◽  
Surface Induced Dissociation ◽  
Trapped Ion Mobility Spectrometry ◽  
Ft Icr

<p><a>Native mass spectrometry, particularly in conjunction with gas-phase ion mobility spectrometry measurements, has proven useful as a structural biology tool for evaluating the stoichiometry, conformation, and topology of protein complexes. Here, we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer for structural analysis of protein complexes. We successfully performed SID on mobility-selected protein complexes, including streptavidin tetramer and cholera toxin B with bound ligand. Additionally, TIMS-SID was employed on a mixture of peptides bradykinin desR1 and desR9 to mobility separate and identify the individual peptides. Importantly, results show that native-like conformations can be maintained throughout the TIMS analysis. The TIMS-SID spectra are analogous to SID spectra acquired using quadrupole mass selection, indicating little measurable, if any, structural rearrangement during mobility selection. Mobility parking was used on the ion or mobility of interest and 50 to 200 SID mass spectra were averaged. High quality TIMS-SID spectra were acquired over a period of 2-10 minutes, comparable to or slightly longer than SID coupled with ion mobility on various instrument platforms in our laboratory. The ultrahigh resolving power of the 15 T FT-ICR allowed for the identification and relative quantification of overlapping SID fragments with the same nominal <i>m/z</i> based on isotope patterns and shows promise as a platform to probe small mass differences, such as protein-ligand binding or post-translational modifications. These results represent the potential of TIMS-SID-MS for the analysis of both protein complexes and peptides.</a></p>

scholarly journals Top-Down Characterization of Denatured Proteins and Native Protein Complexes Using Electron Capture Dissociation Implemented within a Modified Ion Mobility-Mass Spectrometer

2020 ◽  
Vol 92 (5) ◽  
pp. 3674-3681 ◽  
Author(s):  
Jonathan P. Williams ◽  
Lindsay J. Morrison ◽  
Jeffery M. Brown ◽  
Joseph S. Beckman ◽  
Valery G. Voinov ◽  
...  
Keyword(s):  
Electron Capture ◽  
Mass Spectrometer ◽  
Electron Capture Dissociation ◽  
Ion Mobility ◽  
Protein Complexes ◽  
Native Protein ◽  
Top Down ◽  
Denatured Proteins

Characterization of Tear Gas Residues by Ion Mobility Spectrometry

1997 ◽  
Vol 51 (12) ◽  
pp. 1880-1889 ◽  
Author(s):  
Graeme Allinson ◽  
Cameron W. McLeod
Keyword(s):  
Ambient Temperature ◽  
Ion Mobility ◽  
Degradation Products ◽  
Negative Ion ◽  
Ion Mobility Spectrometer ◽  
Relative Standard ◽  
Acquisition Mode ◽  
Tear Gas ◽  
Negative Ion Mode

In this study a hand-held ion mobility spectrometer was used to characterize the vapors produced by α-chloroacetophenone (CN) and 2-chlorobenzylidenemalononitrile (CS), their isomers, and then-degradation products at ambient temperature and 50 °C, and in both the positive- and negative-ion acquisition modes. Minimum determinable residues were as follows: in the negative-ion acquisition mode at ambient temperature, CN 0.5 μg, CS 10 mg; at 50 °C, CN 0.5 μg, CS 16 μg; and in the positive-ion acquisition mode at ambient temperature, CN 0.5 μg, CS not detected; at 50 °C, CN 0.1 μg, CS not detected. The steady-state reproducibility was found to be independent of ion acquisition mode but dependent on signal intensity and background noise [relative standard deviation (RSD) 3–17%]—the smaller the signal, the greater the variation. The day-to-day variation in positive- and negative-mode signal intensities showed the same trends (RSD 3–33%). By comparing positive- and negative-ion mode spectra, it was possible to differentiate not only between CN and CS but also between their isomers and breakdown products.

scholarly journals Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry

2020 ◽  
Author(s):  
Erin Panczyk ◽  
Dalton Snyder ◽  
Mark. E. Ridgeway ◽  
Arpad Somogyi ◽  
Melvin A. Park ◽  
...  
Keyword(s):  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Protein Complexes ◽  
Small Mass ◽  
Resolving Power ◽  
Mass Selection ◽  
Trapped Ion ◽  
Surface Induced Dissociation ◽  
Trapped Ion Mobility Spectrometry ◽  
Ft Icr

<p><a>Native mass spectrometry, particularly in conjunction with gas-phase ion mobility spectrometry measurements, has proven useful as a structural biology tool for evaluating the stoichiometry, conformation, and topology of protein complexes. Here, we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer for structural analysis of protein complexes. We successfully performed SID on mobility-selected protein complexes, including streptavidin tetramer and cholera toxin B with bound ligand. Additionally, TIMS-SID was employed on a mixture of peptides bradykinin desR1 and desR9 to mobility separate and identify the individual peptides. Importantly, results show that native-like conformations can be maintained throughout the TIMS analysis. The TIMS-SID spectra are analogous to SID spectra acquired using quadrupole mass selection, indicating little measurable, if any, structural rearrangement during mobility selection. Mobility parking was used on the ion or mobility of interest and 50 to 200 SID mass spectra were averaged. High quality TIMS-SID spectra were acquired over a period of 2-10 minutes, comparable to or slightly longer than SID coupled with ion mobility on various instrument platforms in our laboratory. The ultrahigh resolving power of the 15 T FT-ICR allowed for the identification and relative quantification of overlapping SID fragments with the same nominal <i>m/z</i> based on isotope patterns and shows promise as a platform to probe small mass differences, such as protein-ligand binding or post-translational modifications. These results represent the potential of TIMS-SID-MS for the analysis of both protein complexes and peptides.</a></p>

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