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Impact of gas background on XFEL single-particle imaging
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)In: Scientific Reports, E-ISSN 2045-2322, Vol. 15, no 1, article id 29559Article in journal (Refereed) Published
Abstract [en]

Single-particle imaging (SPI) using X-ray free-electron Lasers (XFELs) offers the potential to determine protein structures at high spatial and temporal resolutions without the need for crystallization or vitrification. However, the technique faces challenges due to weak diffraction signals from single proteins and significant background scattering from gases used for sample delivery. A recent observation of a diffraction pattern from an isolated GroEL protein complex Ekeberg T et al. (Light Sci Appl 13:15, 2024. https://doi.org/10.1038/274s41377-023-01352-7) had similar numbers of signal and background photons. Ongoing efforts aim to reduce the background created by sample delivery, with one approach replacing most of the used gas with helium Yenupuri T et al. (Sci Rep 14:4401, 2024. https://doi.org/10.1038/s41598-024-54605-9). In this study, we investigate the effects of a reduced background on the resolution limits for SPI of isolated proteins under different experiment conditions. As a test case, we used GroEL, and we used experimentally derived parameters for our simulations. We observe that background significantly impacts the achievable resolution, particularly when the signal strength is comparable to the background. This is best exemplified at 6.0 keV, where a background reduction by a factor of 10 leads to a resolution improvement from 1.9 to 1.2 nm, for a dataset of 104 patterns.

Place, publisher, year, edition, pages
Springer Nature, 2025. Vol. 15, no 1, article id 29559
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-565202DOI: 10.1038/s41598-025-15092-8ISI: 001550641400028PubMedID: 40796631Scopus ID: 2-s2.0-105013165399OAI: oai:DiVA.org:uu-565202DiVA, id: diva2:1989606
Part of project
The Torrent Ahead: Algorithms for X-ray Lasers to Study Structure, Function and Dynamics, Swedish Research CouncilStructural biology under biological conditions: Fluctuation Correlation X-ray scattering., Swedish Research Council
Funder
Uppsala UniversityAvailable from: 2025-08-18 Created: 2025-08-18 Last updated: 2025-11-16Bibliographically 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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You, TongMaia, Filipe R. N. C.

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