The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes

Ben‐Nissan, Gili; Sharon, Michal

doi:10.1016/j.cbpa.2017.10.026

Cited by 118 publications

(138 citation statements)

References 67 publications

(81 reference statements)

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“…Native IM-MS measurements enable us to separate ions not only based on their mass-to-charge ratio, but also by their shape, yielding rotationally averaged CCS values that depict the overall shapes and conformational dynamics of the various proteasome particles [36][37][38][39] . We therefore continued by calculating the CCS values, using the centroid of each peak, for each of the proteasomes ( proteasomes, respectively.…”

Section: Figure 1 Native Im-ms Characterization Reveals Differencesmentioning

confidence: 99%

Comparative structural analysis of 20S proteasome ortholog protein complexes by native mass spectrometry

Vimer¹,

Nissan²,

Morgenstern³

et al. 2020

Preprint

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Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multi-level experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the T. acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast (S. cerevisiae) and mammals (rat - R. norvegicus, rabbit - O. cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native Ms structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution three-dimensional structures, highly resembled that of the human complex. Using cryo-electron microscopy single-particle analysis we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size, and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the <a></a><a>PSMA7 </a>subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.

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Section: Figure 1 Native Im-ms Characterization Reveals Differencesmentioning

confidence: 99%

Comparative structural analysis of 20S proteasome ortholog protein complexes by native mass spectrometry

Vimer¹,

Nissan²,

Morgenstern³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Ion mobility measurements can hence serve a two‐fold purpose; they can add a separation dimension that is partly orthogonal to mass spectrometry, and can be used for structural elucidation. Structural inferences based on comparing experimental CCS values with those calculated from 3D models have become increasingly prominent in structural biology (Politis et al, ; Konijnenberg, Butterer, & Sobott, ; Thalassinos et al, ; Marklund et al, ; Ben‐Nissan & Sharon, ), structural chemistry (Ujma et al, ; Surman et al, ) and physical chemistry (Wyttenbach et al, ). For these reasons, we devoted special attention to define K 0 and IM‐derived CCS values, and to clarify what influences these quantities.…”

Section: Introductionmentioning

confidence: 99%

Recommendations for reporting ion mobility Mass Spectrometry measurements

Gabelica

Shvartsburg

Afonso

et al. 2019

Mass Spectrometry Reviews

361

477

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Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values ( K 0 ) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E / N ; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method‐dependent results) only if the gas nature, temperature or E / N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

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“…This enables us to determine the masses and abundances of intact complexes, or their individual components following dissociation inside the mass spectrometer . In combination with ion mobility (IM) measurements, the approach can provide information about their overall structure and connectivity . Since MS has been used to monitor pH and concentration effects on the assembly light‐harvesting complexes, we expect IM‐MS to be able to unravel the architectures of native phycobiliprotein assemblies.…”

Section: Introductionmentioning

confidence: 99%

A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes

et al. 2019

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Biotechnological applications of protein complexes require detailed information about their structure and composition, which can be challenging to obtain for proteins from natural sources. Prominent examples are the ring‐shaped phycoerythrin (PE) and phycocyanin (PC) complexes isolated from the light‐harvesting antennae of red algae and cyanobacteria. Despite their widespread use as fluorescent probes in biotechnology and medicine, the structures and interactions of their noncrystallizable central subunits are largely unknown. Here, we employ ion mobility mass spectrometry to reveal varying stabilities of the PC and PE complexes and identify their closest architectural homologues among all protein assemblies in the Protein Data Bank (PDB). Our results suggest that the central subunits of PC and PE complexes, although absent from the crystal structures, may be crucial for their stability, and thus of unexpected importance for their biotechnological applications.

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The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes

Cited by 118 publications

References 67 publications

Comparative structural analysis of 20S proteasome ortholog protein complexes by native mass spectrometry

Comparative structural analysis of 20S proteasome ortholog protein complexes by native mass spectrometry

Recommendations for reporting ion mobility Mass Spectrometry measurements

A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes

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