Cryo-EM of soft-landed<i>β</i>-galactosidase: Gas-phase and native structures are remarkably similar

Esser, Tim K.; Böhning, Jan; Önür, Alpcan; Chinthapalli, Dinesh K.; Eriksson, Lukas; Grabarics, Marko; Fremdling, Paul; Konijnenberg, Albert; Makarov, Alexander; Botman, Aurelien; Peter, Christine; Benesch, Justin L. P.; Robinson, Carol V.; Gault, Joseph; Baker, Lindsay; Bharat, Tanmay A. M.; Rauschenbach, Stephan

doi:10.1101/2023.08.17.553673

Cited by 10 publications

(9 citation statements)

References 68 publications

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“…We believe the future work outlined above will provide a path for continued improvements that ultimately allow for the direct coupling of MS with cryo-EM. Finally, we note that while this manuscript was under peer review, a preprint describing a similar cryogenic ion landing apparatus has been released by Esser et al Collectively, these joint works provide strong evidence for the potential impact of this exciting new field.…”

Section: Discussionmentioning

confidence: 74%

Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes

Westphall,

Lee,

Hemme

et al. 2023

Anal. Chem.

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We describe an apparatus for the cryogenic landing of particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. We demonstrate that as compared to room temperature landings, the use of this cryogenic landing device greatly improves the structural preservation of deposited protein−protein complexes. Furthermore, landing under cryogenic conditions can increase the diversity of particle orientations, allowing for improved 3D structural interpretation. We conclude that this approach allows for the direct coupling of mass spectrometry with cryo-electron microscopy.

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Section: Discussionmentioning

confidence: 74%

Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes

Westphall,

Lee,

Hemme

et al. 2023

Anal. Chem.

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“…Native MS is also being leveraged to improve other structural biology techniques, such as soft-landing of mass-selected protein complexes for further structural characterization (e.g., cryo-electron microscopy). [407][408][409][682][683][684][685][686] Hydrogen deuterium exchange and protein footprinting have also seen substantive gains due to steady improvements in instrumentation. 168,[312][313][314]687,688 At the peptide level, methods for crosslinking MS (XL-MS) have enabled large-scale structural proteomics studies, owing in part to the advanced instrumentation discussed herein.…”

Section: Top-down Proteomicsmentioning

confidence: 99%

Instrumentation at the leading edge of proteomics

Peters-Clarke,

Coon,

Riley

2023

Preprint

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The proteome, or collection of proteoforms expressed in a biological system, is dynamic and heterogeneous. As our appreciation for the complexity of the proteome has evolved, so have the technologies we use to interrogate its composition. More than three decades ago, a rapid expansion in the field of proteomics was driven by the advent of soft ionization techniques focusing on capturing protein sequence information using mass spectrometry (MS). As tools to automate peptide and protein sequencing with tandem MS (MS/MS) matured, our field recognized the limits of qualitatively cataloguing gene products.1,2 This realization drove a multi-pronged expansion of MS-centric technologies that seek to capture various aspects of proteins, including their abundance, modification states, conformation and structure, and spatiotemporal relationships.3–7 Here we review innovations in MS-based instrumentation that continue to expand our ability to survey the proteome with ever increasing sensitivity, speed, and flexibility. The march of progress in MS instrumentation has been steady over the better half of the past century, but our discussion here focuses on developments within the past five years that have ushered in an exciting era in proteomics, where MS is poised to be the dominant platform for exploring biological phenotypes in basic and translational sciences for the foreseeable future.

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“…Most recently, a preprint has been published, that reported the combination of native MS with soft landing techniques. Here intact proteins were landed on cryoEM targets after ionization and mass spectrometry separation [82]. The resulting cryoEM data showed that the protein remained largely its original fold during native MS.…”

Section: Tools To Investigate Protein-metabolome Interactionsmentioning

confidence: 99%

Decoding the molecular interplay in the central dogma: An overview of mass spectrometry‐based methods to investigate protein‐metabolite interactions

Stincone,

Naimi,

Saviola

et al. 2023

Proteomics

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With the emergence of next‐generation nucleotide sequencing and mass spectrometry‐based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry‐based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry‐based tools to probe metabolite‐protein interactions—from individual interaction pairs to interactions at the proteome‐metabolome scale.

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Cryo-EM of soft-landedβ-galactosidase: Gas-phase and native structures are remarkably similar

Cited by 10 publications

References 68 publications

Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes

Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes

Instrumentation at the leading edge of proteomics

Decoding the molecular interplay in the central dogma: An overview of mass spectrometry‐based methods to investigate protein‐metabolite interactions

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