Radiation damage in biological material: Electronic properties and electron impact ionization in urea

Caleman, Carl; Ortiz, Carlos; Marklund, Erik; Bultmark, Fredrik; Gabrysch, Markus; Parak, F.; Hajdu, János; Klintenberg, Mattias; Tı̂mneanu, Nicuşor

doi:10.1209/0295-5075/88/29901

Cited by 14 publications

(26 citation statements)

References 29 publications

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“…Moreover, secondary electrons represent the main source of radiation damage following tissue irradiation. Thus knowledge of inelastic electron scattering in a dielectric, such as liquid water, is essential to fully understand how radiation affects living organisms [3][4][5] .…”

Section: Main Textmentioning

confidence: 99%

Attosecond chronoscopy of electron scattering in dielectric nanoparticles

et al. 2017

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Section: Main Textmentioning

confidence: 99%

Attosecond chronoscopy of electron scattering in dielectric nanoparticles

et al. 2017

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“…Although proof of principle experiments have demonstrated that it is possible to obtain structural information from solid targets at low resolution (60 nm),29 issues like sample dynamics,30 and irreproducible scattering from bound solvent molecules31 will in practice probably limit the resolution of such experiments. Radiation damage to samples at atomic wavelengths is not completely understood either27, 32–36 and this may preclude obtaining high resolution structural information as well. Nevertheless, this technique may provide a powerful complement to IMS in the near future.…”

Section: Introductionmentioning

confidence: 99%

Proteins, Lipids, and Water in the Gas Phase

Spoel

Marklund

Larsson

et al. 2010

Macromolecular Bioscience

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Evidence from mass‐spectrometry experiments and molecular dynamics simulations suggests that it is possible to transfer proteins, or in general biomolecular aggregates, from solution to the gas‐phase without grave impact on the structure. If correct, this allows interpretation of such experiments as a probe of physiological behavior. Here, we survey recent experimental results from mass spectrometry and ion‐mobility spectroscopy and combine this with observations based on molecular dynamics simulation, in order to give a comprehensive overview of the state of the art in gas‐phase studies. We introduce a new concept in protein structure analysis by determining the fraction of the theoretical possible numbers of hydrogen bonds that are formed in solution and in the gas‐phase. In solution on average 43% of the hydrogen bonds is realized, while in vacuo this fraction increases to 56%. The hydrogen bonds stabilizing the secondary structure (α‐helices, β‐sheets) are maintained to a large degree, with additional hydrogen bonds occurring when side chains make new hydrogen bonds to rest of the protein rather than to solvent. This indicates that proteins that are transported to the gas phase in a native‐like manner in many cases will be kinetically trapped in near‐physiological structures. Simulation results for lipid‐ and detergent‐aggregates and lipid‐coated (membrane) proteins in the gas phase are discussed, which in general point to the conclusion that encapsulating proteins in “something” aids in the conservation of native‐like structure. Isolated solvated micelles of cetyl‐tetraammonium bromide quickly turn into reverse micelles whereas dodecyl phosphocholine micelles undergo much slower conversions, and do not quite reach a reverse micelle conformation within 100 ns. magnified image

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“…Thus, urea crystals are a good model for protein nanocrystals, known to contain 30%-60% water. We refer to [5,9,16] and the supplementary material for further details of these calculations and how the model compares with experiments on diamond [17]. Considering m i to be the mass of electron i and r i the position of electron i with respect to the center of mass of all free electrons, the radius of gyration, used in Figure 2, is defined as…”

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confidence: 99%

On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses

et al. 2010

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Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters, or nanoparticles. Coherent flash imaging will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single-shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain inaccessible using conventional X-ray sources.

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Radiation damage in biological material: Electronic properties and electron impact ionization in urea

Cited by 14 publications

References 29 publications

Attosecond chronoscopy of electron scattering in dielectric nanoparticles

Attosecond chronoscopy of electron scattering in dielectric nanoparticles

Proteins, Lipids, and Water in the Gas Phase

On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses

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