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Mass-selective and ice-free cryo-EM protein sample preparation via native electrospray ion-beam deposition

View ORCID ProfileTim K. Esser, View ORCID ProfileJan Böhning, Paul Fremdling, Mark T. Agasid, View ORCID ProfileAdam Costin, View ORCID ProfileKyle Fort, Albert Konijnenberg, Alan Bahm, View ORCID ProfileAlexander Makarov, View ORCID ProfileCarol V. Robinson, View ORCID ProfileJustin L. P. Benesch, Lindsay Baker, View ORCID ProfileTanmay A.M. Bharat, View ORCID ProfileJoseph Gault, View ORCID ProfileStephan Rauschenbach
doi: https://doi.org/10.1101/2021.10.18.464782
Tim K. Esser
1Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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Jan Böhning
2Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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Paul Fremdling
1Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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Mark T. Agasid
1Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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Adam Costin
3Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK; Australian Centre for Microscopy and Microanalysis, University of Sydney, Sydney, NSW 2006, Australia
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Kyle Fort
4Thermo Fisher Scientific, Bremen, 28199, Germany
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Albert Konijnenberg
5Thermo Fisher Scientific, Zwaanstraat 31G/H, 5651 CA, Eindhoven, The Netherlands
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Alan Bahm
6Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR, 97124, USA
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Alexander Makarov
4Thermo Fisher Scientific, Bremen, 28199, Germany
7Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Carol V. Robinson
1Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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Justin L. P. Benesch
1Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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Lindsay Baker
8Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Kavli Institute for Nanoscience Discovery, Department of Biochemistry, University of Oxford, Oxford, OX1 3QZ, UK
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Tanmay A.M. Bharat
2Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
9Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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Joseph Gault
1Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
10Vertex Pharmaceuticals, 86-88 Jubilee Avenue, Milton Park, Abingdon, OX14 4RW, UK
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Stephan Rauschenbach
1Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
11Max Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart, DE-70569, Germany
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  • For correspondence: stephan.rauschenbach@chem.ox.ac.uk
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Abstract

Electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA) have revolutionized structure determination of homogeneous proteins. However, obtaining high-resolution structures from heterogeneous samples remains a major challenge, as the various protein states embedded in thin films of vitreous ice may be classified incorrectly, resulting in detrimental averaging of features. Here we present native electrospray ion-beam deposition (native ES-IBD) for the preparation of extremely high-purity cryo-EM samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, mass-filtered, and gently deposited on cryo-EM grids, and subsequently frozen in liquid nitrogen. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected proteins and protein assemblies. SPA reveals that they remain structurally intact, but variations in secondary and tertiary structure are currently limiting information in 2D classes and 3D EM density maps. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM structure determination.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 19, 2021.
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Mass-selective and ice-free cryo-EM protein sample preparation via native electrospray ion-beam deposition
Tim K. Esser, Jan Böhning, Paul Fremdling, Mark T. Agasid, Adam Costin, Kyle Fort, Albert Konijnenberg, Alan Bahm, Alexander Makarov, Carol V. Robinson, Justin L. P. Benesch, Lindsay Baker, Tanmay A.M. Bharat, Joseph Gault, Stephan Rauschenbach
bioRxiv 2021.10.18.464782; doi: https://doi.org/10.1101/2021.10.18.464782
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Mass-selective and ice-free cryo-EM protein sample preparation via native electrospray ion-beam deposition
Tim K. Esser, Jan Böhning, Paul Fremdling, Mark T. Agasid, Adam Costin, Kyle Fort, Albert Konijnenberg, Alan Bahm, Alexander Makarov, Carol V. Robinson, Justin L. P. Benesch, Lindsay Baker, Tanmay A.M. Bharat, Joseph Gault, Stephan Rauschenbach
bioRxiv 2021.10.18.464782; doi: https://doi.org/10.1101/2021.10.18.464782

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