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Prospects for ultrafast single-particle imaging of proteins in solution at X-ray free-electron lasers
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.ORCID iD: 0009-0000-4002-7791
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Lawrence Berkeley National Laboratory, NERSC, Berkeley, CA, 94720, USA.ORCID iD: 0000-0002-2141-438x
2025 (English)Manuscript (preprint) (Other academic)
Abstract [en]

The feasibility of Single Particle Imaging on a protein complex in solution is investigated. We leverage two recent experimental results: the ability to generate stable nano-scale thin liquid sheets, and the availability of a nanometer-sized X-ray focus with unprecedented photon densities. Combining these advances, we show that it is in principle possible to solve for the three-dimensional electron density of a single isolated protein despite significant background scattering due to the water layer. With the 15 nm diameter GroEL protein, a resolution of 0.85 nm was achieved using 106 diffraction patterns. The diffraction patterns were simulated using 9.0 keV hard X-rays with a 7 nm beam radius. 

Place, publisher, year, edition, pages
2025. Vol. 15, no 1, article id 29559
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-571653OAI: oai:DiVA.org:uu-571653DiVA, id: diva2:2014038
Funder
Uppsala UniversityAvailable from: 2025-11-16 Created: 2025-11-16 Last updated: 2025-11-24Bibliographically approved
In thesis
1. From Photon to Protein: Using X-ray Lasers for High-resolution Structure Determination with Single Proteins
Open this publication in new window or tab >>From Photon to Protein: Using X-ray Lasers for High-resolution Structure Determination with Single Proteins
2026 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

X-ray Free-Electron Lasers (XFELs) promise Single Particle Imaging (SPI) of biomolecules through “diffraction before destruction,” but present experiments involving single proteins are limited by weak scattering signals and significant background scattering. This background scattering comes primarily from the sample delivery, and poses a major challenge for small proteins. Recent progress in aerosol sample delivery has shown that the background scattering can be reduced by about 80% by replacing some of the carrier gas with helium. The first paper in this thesis was a large-scale simulation study of a 15 nm diameter GroEL protein, where the impact of reduced gas background on the resolution was investigated. In Paper II the feasibility of SPI is investigated using liquid sheet sample delivery with the same protein. I find that it is indeed possible to do SPI in solution but with demanding requirements: specifically, a large number of diffraction patterns and a high fluence, which currently only a nanofocus can deliver. The second half of this thesis focuses on my contribution to analysis performed on experimental data. Paper III is about work where I developed the initial scripts for data analysis of a Rayleigh-scattering microscope used to characterise the aerosol sample delivery system that is also used during SPI experiments. The final paper is about my contribution to an experiment where the liquid sheet sample delivery was used during an experiment. I end this thesis with an outlook where I provide my perspective on the computational and experimental improvements that can make the biggest impact on the future of SPI.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2026. p. 91
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 2612
Keywords
phase retrieval, single particle imaging, X-ray Free-Electron Laser, structural biology, phase problem, Expand Maximize Compress, UMAP, Coherent X-ray Diffractive Imaging
National Category
Biophysics Atom and Molecular Physics and Optics
Research subject
Molecular Life Sciences
Identifiers
urn:nbn:se:uu:diva-571655 (URN)978-91-513-2667-2 (ISBN)
Public defence
2026-01-21, A1:107a, BMC, Husargatan 3, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2025-12-10 Created: 2025-11-16 Last updated: 2025-12-10

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CiteExportLink to record
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