Resolution and dose dependence of radiation damage in biomolecular systems

Atakisi, Hakan; Conger, Lauren; Moreau, David; Thorne, Robert

doi:10.1107/s2052252519008777

Cited by 20 publications

(28 citation statements)

References 46 publications

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“…If the dose was increased by a factor of 10, a resolution of 42 nm might have been obtained. The dose would then have been near the radiation-damage limit according to the Howells et al (2009) model but less than that for the Atakisi et al (2019) model (see Fig. 1).…”

Section: Discussionmentioning

confidence: 94%

“…The tolerable dose is much less well determined with possibilities ranging from a 1/d dependence (Howells et al, 2009) to a higher power dependence, e.g. 1/d 1.86 as suggested by Atakisi et al (2019).…”

Section: Discussionmentioning

confidence: 99%

“…1 indicates the positions of some of the examples given in Table 1 on a dose versus resolution plot. In addition, the Howells et al (2009) model of the dose threshold as a function of resolution is shown together with a more recent one (Atakisi et al, 2019) obtained from radiation-damage studies of protein crystals. Similar diagrams occur in the works by Shen et al (2004), Howells et al (2009) andVillanueva-Perez et al (2018).…”

Section: Most Of the Examples Inmentioning

confidence: 99%

“…The highest attainable resolution shown in Fig. 1 is that for coherent imaging at 0.52 keV for protein contrasted against water, assuming the Rose criterion (K = 5) applied to the amplitude in a Shannon voxel and the Atakisi et al (2019) model of tolerable dose applied. All these conditions, plus the assumption of efficient phase determination, would have to be met to realize the 3 nm resolution implied in Fig.…”

Section: Most Of the Examples Inmentioning

confidence: 99%

“…Note that the values of W for the experiments do not necessarily correspond to the simulations in Villaneuva-Perez et al (2018). Plots for the resolution dependence for the tolerable dose at which the intensity decreases by half are shown with a 100 MGy nm À1 dependence (Howells et al, 2009) and a q 1.86 dependence (Atakisi et al, 2019), where q is the wavevector (2/d).…”

Section: Referencementioning

confidence: 99%

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The achievable resolution for X-ray imaging of cells and other soft biological material

Nave

2020

Int Union Crystallogr J

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X-ray imaging of soft materials is often difficult because of the low contrast of the components. This particularly applies to frozen hydrated biological cells where the feature of interest can have a similar density to the surroundings. As a consequence, a high dose is often required to achieve the desired resolution. However, the maximum dose that a specimen can tolerate is limited by radiation damage. Results from 3D coherent diffraction imaging (CDI) of frozen hydrated specimens have given resolutions of ∼80 nm compared with the expected resolution of 10 nm predicted from theoretical considerations for identifying a protein embedded in water. Possible explanations for this include the inapplicability of the dose-fractionation theorem, the difficulty of phase determination, an overall object-size dependence on the required fluence and dose, a low contrast within the biological cell, insufficient exposure, and a variety of practical difficulties such as scattering from surrounding material. A recent article [Villaneuva-Perez et al. (2018), Optica, 5, 450–457] concluded that imaging by Compton scattering gave a large dose advantage compared with CDI because of the object-size dependence for CDI. An object-size dependence would severely limit the applicability of CDI and perhaps related coherence-based methods for structural studies. This article specifically includes the overall object size in the analysis of the fluence and dose requirements for coherent imaging in order to investigate whether there is a dependence on object size. The applicability of the dose-fractionation theorem is also discussed. The analysis is extended to absorption-based imaging and imaging by incoherent scattering (Compton) and fluorescence. This article includes analysis of the dose required for imaging specific low-contrast cellular organelles as well as for protein against water. This article concludes that for both absorption-based and coherent diffraction imaging, the dose-fractionation theorem applies and the required dose is independent of the overall size of the object. For incoherent-imaging methods such as Compton scattering, the required dose depends on the X-ray path length through the specimen. For all three types of imaging, the dependence of fluence and dose on a resolution d goes as 1/d 4 when imaging uniform-density voxels. The independence of CDI on object size means that there is no advantage for Compton scattering over coherent-based imaging methods. The most optimistic estimate of achievable resolution is 3 nm for imaging protein molecules in water/ice using lensless imaging methods in the water window. However, the attainable resolution depends on a variety of assumptions including the model for radiation damage as a function of resolution, the efficiency of any phase-retrieval process, the actual contrast of the feature of interest within the cell and the definition of resolution itself. There is insufficient observational information available regarding the most appropriate model for radiation damage in frozen hydrated biological material. It is advocated that, in order to compare theory with experiment, standard methods of reporting results covering parameters such as the feature examined (e.g. which cellular organelle), resolution, contrast, depth of the material (for 2D), estimate of noise and dose should be adopted.

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Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

Section: Most Of the Examples Inmentioning

confidence: 99%

Section: Most Of the Examples Inmentioning

confidence: 99%

Section: Referencementioning

confidence: 99%

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The achievable resolution for X-ray imaging of cells and other soft biological material

Nave

2020

Int Union Crystallogr J

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Doses for X‐ray and electron diffraction: New features in RADDOSE‐3D including intensity decay models

Dickerson,

McCubbin,

Brooks‐Bartlett

et al. 2024

Protein Science

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New features in the dose estimation program RADDOSE‐3D are summarised. They include the facility to enter a diffraction intensity decay model which modifies the “Diffraction Weighted Dose” output from a “Fluence Weighted Dose” to a “Diffraction‐Decay Weighted Dose”, a description of RADDOSE‐ED for use in electron diffraction experiments, where dose is historically quoted in electrons/Å2 rather than in gray (Gy), and finally the development of a RADDOSE‐3D GUI, enabling easy access to all the options available in the program.

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Radiation damage to biological macromolecules∗

Garman¹,

Weik

2023

Current Opinion in Structural Biology

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Resolution and dose dependence of radiation damage in biomolecular systems

Cited by 20 publications

References 46 publications

The achievable resolution for X-ray imaging of cells and other soft biological material

The achievable resolution for X-ray imaging of cells and other soft biological material

Doses for X‐ray and electron diffraction: New features in RADDOSE‐3D including intensity decay models

Radiation damage to biological macromolecules∗

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