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Publications (10 of 114) Show all publications
Brodmerkel, M. N., De Santis, E., Uetrecht, C., Caleman, C. & Marklund, E. (2024). Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles. Physical Chemistry, Chemical Physics - PCCP
Open this publication in new window or tab >>Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles
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2024 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed) Published
Abstract [en]

Collision induced unfolding is method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the collision induced unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation. The dimers have highly similar structures, but the activation reveals differences in the dynamics that arises in response to the activation.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2024
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-500271 (URN)10.1039/D3CP06344E (DOI)
Funder
Swedish Research Council, 2021-05988Swedish Research Council, 2020-04825Swedish Research Council, 2018-00740Swedish National Infrastructure for Computing (SNIC), 2022-22-854Swedish National Infrastructure for Computing (SNIC), 2022-22-925Swedish National Infrastructure for Computing (SNIC), 2022-22-947Swedish National Infrastructure for Computing (SNIC), 2022-5-415Swedish National Infrastructure for Computing (SNIC), 2022-23-57EU, Horizon 2020, 801406
Available from: 2023-04-13 Created: 2023-04-13 Last updated: 2024-04-11Bibliographically approved
Wollter, A., De Santis, E., Ekeberg, T., Marklund, E. G. & Caleman, C. (2024). Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging. Journal of Chemical Physics, 160(11), Article ID 114108.
Open this publication in new window or tab >>Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging
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2024 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 160, no 11, article id 114108Article in journal (Refereed) Published
Abstract [en]

Single particle imaging of proteins in the gas phase with x-ray free-electron lasers holds great potential to study fast protein dynamics, but is currently limited by weak and noisy data. A further challenge is to discover the proteins' orientation as each protein is randomly oriented when exposed to x-rays. Algorithms such as the expand, maximize, and compress (EMC) exist that can solve the orientation problem and reconstruct the three-dimensional diffraction intensity space, given sufficient measurements. If information about orientation were known, for example, by using an electric field to orient the particles, the reconstruction would benefit and potentially reach better results. We used simulated diffraction experiments to test how the reconstructions from EMC improve with particles' orientation to a preferred axis. Our reconstructions converged to correct maps of the three-dimensional diffraction space with fewer measurements if biased orientation information was considered. Even for a moderate bias, there was still significant improvement. Biased orientations also substantially improved the results in the case of missing central information, in particular in the case of small datasets. The effects were even more significant when adding a background with 50% the strength of the averaged diffraction signal photons to the diffraction patterns, sometimes reducing the data requirement for convergence by a factor of 10. This demonstrates the usefulness of having biased orientation information in single particle imaging experiments, even for a weaker bias than what was previously known. This could be a key component in overcoming the problems with background noise that currently plague these experiments.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2024
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-528478 (URN)10.1063/5.0188772 (DOI)001187986000015 ()38506290 (PubMedID)
Funder
EU, Horizon 2020, 801406EU, Horizon 2020, 101120312Swedish Research Council, 2020-04825Swedish Research Council, 2018-00740Swedish Foundation for Strategic Research, ITM17-0455Swedish Research Council, 2017-05336
Available from: 2024-05-23 Created: 2024-05-23 Last updated: 2024-05-23Bibliographically approved
Svensson, P., Schwob, L., Grånäs, O., Unger, I., Björneholm, O., Timneanu, N., . . . Berholts, M. (2024). Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics. Physical Chemistry, Chemical Physics - PCCP, 26(2), 770-779
Open this publication in new window or tab >>Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics
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2024 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 2, p. 770-779Article in journal (Refereed) Published
Abstract [en]

The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. These molecules possess dual functionality: improved photoabsorption capabilities and the ability to generate species that are relevant to cancer sensitization upon photofragmentation. Four samples were investigated by scanning the generated fragments in the energy regions around C 1s, N 1s, O 1s, and I 3d-edges with a particular focus on NO2+ production. The experimental summed ion yield spectra are explained using the theoretical near-edge X-ray absorption fine structure spectrum based on density functional theory. Born-Oppenheimer-based molecular dynamics simulations were performed to investigate the fragmentation processes.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2024
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-522697 (URN)10.1039/d3cp03800a (DOI)001090175100001 ()37888897 (PubMedID)
Funder
Swedish Research Council, 2019-03935Swedish Research Council, 2017-05128Swedish Research Council, 2018-00740Swedish Foundation for Strategic ResearchSwedish National Infrastructure for Computing (SNIC), 2022/1-36Swedish National Infrastructure for Computing (SNIC), 2022/22-597
Available from: 2024-02-08 Created: 2024-02-08 Last updated: 2024-02-08Bibliographically approved
Pihlava, L., Svensson, P., Kukk, E., Kooser, K., De Santis, E., Tonisoo, A., . . . Berholts, M. (2024). Shell-dependent photofragmentation dynamics of a heavy-atom-containing bifunctional nitroimidazole radiosensitizer. Physical Chemistry, Chemical Physics - PCCP, 26(11), 8879-8890
Open this publication in new window or tab >>Shell-dependent photofragmentation dynamics of a heavy-atom-containing bifunctional nitroimidazole radiosensitizer
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2024 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 11, p. 8879-8890Article in journal (Refereed) Published
Abstract [en]

Radiation therapy uses ionizing radiation to break chemical bonds in cancer cells, thereby causing DNA damage and leading to cell death. The therapeutic effectiveness can be further increased by making the tumor cells more sensitive to radiation. Here, we investigate the role of the initial halogen atom core hole on the photofragmentation dynamics of 2-bromo-5-iodo-4-nitroimidazole, a potential bifunctional radiosensitizer. Bromine and iodine atoms were included in the molecule to increase the photoionization cross-section of the radiosensitizer at higher photon energies. The fragmentation dynamics of the molecule was studied experimentally in the gas phase using photoelectron-photoion-photoion coincidence spectroscopy and computationally using Born-Oppenheimer molecular dynamics. We observed significant changes between shallow core (I 4d, Br 3d) and deep core (I 3d) ionization in fragment formation and their kinetic energies. Despite the fact, that the ions ejected after deep core ionization have higher kinetic energies, we show that in a cellular environment, the ion spread is not much larger, keeping the damage well-localized. A study on photodissociation dynamics of 2-bromo-5-iodo-nitroimidazole - a model radiosensitizer - using coincidence spectroscopy and computational methods.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2024
National Category
Atom and Molecular Physics and Optics Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-528495 (URN)10.1039/d4cp00367e (DOI)001175892400001 ()38426309 (PubMedID)
Funder
Swedish Research Council, 2023-04346Swedish Research Council, 2018-00740
Available from: 2024-05-22 Created: 2024-05-22 Last updated: 2024-05-22Bibliographically approved
Walz, M.-M., Signorelli, M. R., Caleman, C., Costa, L. T. & Björneholm, O. (2024). The Surface of Ionic Liquids in Water: From an Ionic Tug of War to a Quasi-Ordered Two-Dimensional Layer. ChemPhysChem, 25(1), Article ID e202300551.
Open this publication in new window or tab >>The Surface of Ionic Liquids in Water: From an Ionic Tug of War to a Quasi-Ordered Two-Dimensional Layer
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2024 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 25, no 1, article id e202300551Article in journal (Refereed) Published
Abstract [en]

The sustainable development encompasses the search for new materials for energy storage, gas capture, separation, and solvents in industrial processes that can substitute conventional ones in an efficient and clean manner. Ionic liquids (ILs) emerged and have been advanced as alternative materials for such applications, but an obstacle is their hygroscopicity and the effects on their physical properties in the presence of humidity. Several industrial processes depend on the aqueous interfacial properties, and the main focus of this work is the water/IL interface. The behavior of the aqueous ionic liquids at the water-vacuum interface is representative for their water interfacial properties. Using X-ray photoelectron spectroscopy in combination with molecular dynamics simulations we investigate four aqueous IL systems, and provide molecular level insight on the interfacial behaviour of the ionic liquids, such as ion-pair formation, orientation and surface concentration. We find that ionic liquids containing a chloride anion have a lowered surface enrichment due to the low surface propensity of chloride. In contrast, the ionic liquids containing a bistriflimide anion are extremely surface-enriched due to cooperative surface propensity between the cations and anions, forming a two-dimensional ionic liquid on the water surface at low concentrations. Ionic liquids are interesting materials for many applications related to sustainable development, but the effects of water on their properties are insufficiently known. Using X-ray photoelectron spectroscopy and molecular dynamics simulations, we show how the surface propensity of four ionic liquids in aqueous solution vary with the molecular structure of the ions, and discuss the underlying driving forces.+image

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2024
Keywords
ionic liquids, molecular dynamics, water-IL interface, water surface, XPS
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-528473 (URN)10.1002/cphc.202300551 (DOI)001105563800001 ()37991256 (PubMedID)
Funder
Swedish Research Council, VR 2017-04162
Available from: 2024-05-23 Created: 2024-05-23 Last updated: 2024-05-23Bibliographically approved
Kierspel, T., Kadek, A., Barran, P., Bellina, B., Bijedic N, A., Brodmerkel, M. N., . . . Uetrecht, C. (2023). Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC. Analytical and Bioanalytical Chemistry, 415(18 SI), 4209-4220
Open this publication in new window or tab >>Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC
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2023 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 415, no 18 SI, p. 4209-4220Article in journal (Refereed) Published
Abstract [en]

MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm−1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.

Place, publisher, year, edition, pages
Springer Nature, 2023
Keywords
SPI, X-ray, Native MS, Protein complex structure, Viral particles, Simulation, Modeling
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-500359 (URN)10.1007/s00216-023-04658-y (DOI)000963181300001 ()37014373 (PubMedID)
Funder
Swedish Research Council, 2018-00740Swedish Research Council, 2020-04825EU, Horizon 2020, 801406
Available from: 2023-04-14 Created: 2023-04-14 Last updated: 2024-01-26Bibliographically approved
Cardoch, S., Trost, F., Scott, H. A., Chapman, H. N., Caleman, C. & Timneanu, N. (2023). Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions. Physical review. E, 107(1), Article ID 015205.
Open this publication in new window or tab >>Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions
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2023 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 107, no 1, article id 015205Article in journal (Refereed) Published
Abstract [en]

Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the temporal duration of transmitted x-ray laser pulses, but a detailed account of changes in opacity and emergence of resonances is still missing. In this computational work, we employ nonlocal thermodynamic equilibrium plasma simulations to study the interaction of femtosecond x rays and copper. Following the onset of frustrated absorption, we find that a K–M resonant transition occurring at highly charged states turns copper opaque again. The changes in absorption generate a transient transparent window responsible for the shortened transmission signal. We also propose using fluorescence induced by the incident beam as an alternative source to achieve shorter x-ray pulses. Intense femtosecond x rays are valuable to probe the structure and dynamics of biological samples or to reach extreme states of matter. Shortened pulses could be relevant for emerging imaging techniques.

Place, publisher, year, edition, pages
American Physical SocietyAmerican Physical Society (APS), 2023
National Category
Atom and Molecular Physics and Optics Fusion, Plasma and Space Physics
Identifiers
urn:nbn:se:uu:diva-495128 (URN)10.1103/physreve.107.015205 (DOI)000923229600007 ()
Funder
Swedish Research Council, 2019-03935Swedish Research Council, 2018-00740German Research Foundation (DFG), 390715994
Available from: 2023-01-24 Created: 2023-01-24 Last updated: 2024-01-15Bibliographically approved
Trost, F., Ayyer, K., Prasciolu, M., Fleckenstein, H., Barthelmess, M., Yefanov, O., . . . Chapman, H. (2023). Imaging via Correlation of X-Ray Fluorescence Photons. Physical Review Letters, 130(17), Article ID 173201.
Open this publication in new window or tab >>Imaging via Correlation of X-Ray Fluorescence Photons
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2023 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 130, no 17, article id 173201Article in journal (Refereed) Published
Abstract [en]

We demonstrate that x-ray fluorescence emission, which cannot maintain a stationary interference pattern, can be used to obtain images of structures by recording photon-photon correlations in the manner of the stellar intensity interferometry of Hanbury Brown and Twiss. This is achieved utilizing femtosecondduration pulses of a hard x-ray free-electron laser to generate the emission in exposures comparable to the coherence time of the fluorescence. Iterative phasing of the photon correlation map generated a model-free real-space image of the structure of the emitters. Since fluorescence can dominate coherent scattering, this may enable imaging uncrystallised macromolecules.

Place, publisher, year, edition, pages
American Physical Society, 2023
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-503245 (URN)10.1103/PhysRevLett.130.173201 (DOI)000979791600002 ()37172237 (PubMedID)
Funder
German Research Foundation (DFG), EXC 2056German Research Foundation (DFG), 390715994Swedish Research Council, 2018-00740Swedish Research Council, 2019-03935
Available from: 2023-06-14 Created: 2023-06-14 Last updated: 2023-06-14Bibliographically approved
Kim, S., Sattorov, M., Hong, D., Kang, H., Park, J., Lee, J. H., . . . Park, G.-S. (2023). Observing ice structure of micron-sized vapor-deposited ice with an x-ray free-electron laser. Structural Dynamics, 10(4), Article ID 044302.
Open this publication in new window or tab >>Observing ice structure of micron-sized vapor-deposited ice with an x-ray free-electron laser
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2023 (English)In: Structural Dynamics, E-ISSN 2329-7778, Vol. 10, no 4, article id 044302Article in journal (Refereed) Published
Abstract [en]

The direct observation of the structure of micrometer-sized vapor-deposited ice is performed at Pohang Accelerator Laboratory x-ray free electron laser (PAL-XFEL). The formation of micrometer-sized ice crystals and their structure is important in various fields, including atmospheric science, cryobiology, and astrophysics, but understanding the structure of micrometer-sized ice crystals remains challenging due to the lack of direct observation. Using intense x-ray diffraction from PAL-XFEL, we could observe the structure of micrometer-sized vapor-deposited ice below 150K with a thickness of 2-50 mu m grown in an ultrahigh vacuum chamber. The structure of the ice grown comprises cubic and hexagonal sequences that are randomly arranged to produce a stacking-disordered ice. We observed that ice with a high cubicity of more than 80% was transformed to partially oriented hexagonal ice when the thickness of the ice deposition grew beyond 5 mu m. This suggests that precise temperature control and clean deposition conditions allow mu m-thick ice films with high cubicity to be grown on hydrophilic Si3N4 membranes. The low influence of impurities could enable in situ diffraction experiments of ice nucleation and growth from interfacial layers to bulk ice.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2023
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:uu:diva-510783 (URN)10.1063/4.0000185 (DOI)001045012300001 ()37577135 (PubMedID)
Funder
Swedish Research Council, 2017-05128Swedish Research Council, 2021-1st-XSS-025Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of Technology, 1808
Available from: 2023-09-07 Created: 2023-09-07 Last updated: 2023-09-07Bibliographically approved
Gopakumar, G., Unger, I., Slavicek, P., Hergenhahn, U., Oehrwall, G., Malerz, S., . . . Björneholm, O. (2023). Radiation damage by extensive local water ionization from two-step electron-transfer-mediated decay of solvated ions. Nature Chemistry, 15(10), 1408-+
Open this publication in new window or tab >>Radiation damage by extensive local water ionization from two-step electron-transfer-mediated decay of solvated ions
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2023 (English)In: Nature Chemistry, ISSN 1755-4330, E-ISSN 1755-4349, Vol. 15, no 10, p. 1408-+Article in journal (Refereed) Published
Abstract [en]

Biomolecular radiation damage is largely mediated by radicals and low-energy electrons formed by water ionization rather than by direct ionization of biomolecules. It was speculated that such an extensive, localized water ionization can be caused by ultrafast processes following excitation by core-level ionization of hydrated metal ions. In this model, ions relax via a cascade of local Auger-Meitner and, importantly, non-local charge- and energy-transfer processes involving the water environment. Here, we experimentally and theoretically show that, for solvated paradigmatic intermediate-mass Al3+ ions, electronic relaxation involves two sequential solute-solvent electron transfer-mediated decay processes. The electron transfer-mediated decay steps correspond to sequential relaxation from Al5+ to Al3+ accompanied by formation of four ionized water molecules and two low-energy electrons. Such charge multiplication and the generated highly reactive species are expected to initiate cascades of radical reactions.

Place, publisher, year, edition, pages
Nature Publishing Group, 2023
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-526069 (URN)10.1038/s41557-023-01302-1 (DOI)001188164500001 ()37620544 (PubMedID)
Available from: 2024-04-05 Created: 2024-04-05 Last updated: 2024-04-05Bibliographically approved
Projects
Structural and electronic rearrangement in bio-molecules induced by X-ray Free-electron Laser pulses [2013-03940_VR]; Uppsala UniversitySolving the orientation problem in Single Particle Imaging using XFEL [2018-00740_VR]; Uppsala University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-2638-1940

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