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Hajdu, J
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Publications (10 of 65) Show all publications
Andrikopoulos, P. C., Liu, Y., Picchiotti, A., Lenngren, N., Kloz, M., Chaudhari, A. S., . . . Fuertes, G. (2020). Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations. Physical Chemistry, Chemical Physics - PCCP, 22(12), 6538-6552
Open this publication in new window or tab >>Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations
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2020 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 22, no 12, p. 6538-6552Article in journal (Refereed) Published
Abstract [en]

Flavin mononucleotide (FMN) belongs to the large family of flavins, ubiquitous yellow-coloured biological chromophores that contain an isoalloxazine ring system. As a cofactor in flavoproteins, it is found in various enzymes and photosensory receptors, like those featuring the light-oxygen-voltage (LOV) domain. The photocycle of FMN is triggered by blue light and proceeds via a cascade of intermediate states. In this work, we have studied isolated FMN in an aqueous solution in order to elucidate the intrinsic electronic and vibrational changes of the chromophore upon excitation. The ultrafast transitions of excited FMN were monitored through the joint use of femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy encompassing a time window between 0 ps and 6 ns with 50 fs time resolution. Global analysis of the obtained transient visible absorption and transient Raman spectra in combination with extensive quantum chemistry calculations identified unambiguously the singlet and triplet FMN populations and addressed solvent dynamics effects. The good agreement between the experimental and theoretical spectra facilitated the assignment of electronic transitions and vibrations. Our results represent the first steps towards more complex experiments aimed at tracking structural changes of FMN embedded in light-inducible proteins upon photoexcitation.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-411217 (URN)10.1039/c9cp04918e (DOI)000526715200027 ()31994556 (PubMedID)
Available from: 2020-06-01 Created: 2020-06-01 Last updated: 2020-06-01Bibliographically approved
Ho, P. J., Daurer, B. J., Hantke, M., Bielecki, J., Al Haddad, A., Bucher, M., . . . Bostedt, C. (2020). The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters. Nature Communications, 11, Article ID 167.
Open this publication in new window or tab >>The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters
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2020 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 11, article id 167Article in journal (Refereed) Published
Abstract [en]

Intense x-ray free-electron laser (XFEL) pulses hold great promise for imaging function in nanoscale and biological systems with atomic resolution. So far, however, the spatial resolution obtained from single shot experiments lags averaging static experiments. Here we report on a combined computational and experimental study about ultrafast diffractive imaging of sucrose clusters which are benchmark organic samples. Our theoretical model matches the experimental data from the water window to the keV x-ray regime. The large-scale dynamic scattering calculations reveal that transient phenomena driven by non-linear x-ray interaction are decisive for ultrafast imaging applications. Our study illuminates the complex interplay of the imaging process with the rapidly changing transient electronic structures in XFEL experiments and shows how computational models allow optimization of the parameters for ultrafast imaging experiments. X-ray free electron lasers provide high photon flux to explore single particle diffraction imaging of biological samples. Here the authors present dynamic electronic structure calculations and benchmark them to single-particle XFEL diffraction data of sucrose clusters to predict optimal single-shot imaging conditions.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2020
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-406723 (URN)10.1038/s41467-019-13905-9 (DOI)000510942100001 ()31919346 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilSwedish Foundation for Strategic Research The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Wellcome trust, 204732/Z/16/Z
Available from: 2020-03-19 Created: 2020-03-19 Last updated: 2020-03-19Bibliographically approved
Reddy, H. K. .., Carroni, M., Hajdu, J. & Svenda, M. (2019). Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture. eLIFE, 8, Article ID e48496.
Open this publication in new window or tab >>Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture
2019 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 8, article id e48496Article in journal (Refereed) Published
Abstract [en]

Bacteriophage PR772, a member of the Tectiviridae family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 angstrom, while the resolution of the protein capsid is 2.3 angstrom. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.

Place, publisher, year, edition, pages
ELIFE SCIENCES PUBLICATIONS LTD, 2019
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-395312 (URN)10.7554/eLife.48496 (DOI)000486655300001 ()31513011 (PubMedID)
Funder
Swedish Research Council, 828-2012-108Swedish Research Council, 628-2008-1109Swedish Research Council, 822-2010-6157Swedish Research Council, 822-2012-5260Swedish Research Council, 349-2011-6488Swedish Research Council, 2015-06107Knut and Alice Wallenberg Foundation, KAW-2011.081EU, European Research Council, ERC-291602
Available from: 2019-10-18 Created: 2019-10-18 Last updated: 2019-10-18Bibliographically approved
Bielecki, J., Hantke, M. F., Daurer, B. J., Reddy, H. K. N., Hasse, D., Larsson, D. S. D., . . . Maia, F. R. N. (2019). Electrospray sample injection for single-particle imaging with x-ray lasers. Science Advances, 5(5), Article ID eaav8801.
Open this publication in new window or tab >>Electrospray sample injection for single-particle imaging with x-ray lasers
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2019 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-387970 (URN)10.1126/sciadv.aav8801 (DOI)000470125000080 ()31058226 (PubMedID)
Available from: 2019-05-03 Created: 2019-06-27 Last updated: 2019-06-27Bibliographically approved
Helliwell, J. R., Minor, W., Weiss, M. S., Garman, E. F., Read, R. J., Newman, J., . . . Baker, E. N. (2019). Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 75, 455-457
Open this publication in new window or tab >>Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography
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2019 (English)In: ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, ISSN 2059-7983, Vol. 75, p. 455-457Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
INT UNION CRYSTALLOGRAPHY, 2019
Keywords
FAIR, diffraction data, IUCr policy
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-384082 (URN)10.1107/S2059798319004844 (DOI)000467046700001 ()31063147 (PubMedID)
Note

This editorial article is simultaneously published by the IUCr in the journal IUCrJ (doi:10.1107/S2052252519005918) and in the journal Journal of applied crystallography (doi:10.1107/S1600576719005922) and in the journal Acta Crystallographica Section F structural biology communications (doi: 10.1107/S2053230X19005909)

Available from: 2019-06-18 Created: 2019-06-18 Last updated: 2019-06-18Bibliographically approved
Mühlig, K., Ganan-Calvo, A. M., Andreasson, J., Larsson, D. S., Hajdu, J. & Svenda, M. (2019). Nanometre-sized droplets from a gas dynamic virtual nozzle. Journal of applied crystallography, 52, 800-808
Open this publication in new window or tab >>Nanometre-sized droplets from a gas dynamic virtual nozzle
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2019 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 52, p. 800-808Article in journal (Refereed) Published
Abstract [en]

This paper reports on improved techniques to create and characterize nanometre-sized droplets from dilute aqueous solutions by using a gas dynamic virtual nozzle (GDVN). It describes a method to measure the size distribution of uncharged droplets, using an environmental scanning electron microscope, and provides theoretical models for the droplet sizes created. The results show that droplet sizes can be tuned by adjusting the gas and liquid flow rates in the GDVN, and at the lowest liquid flow rates, the size of the water droplets peaks at about 120nm. This droplet size is similar to droplet sizes produced by electrospray ionization but requires neither electrolytes nor charging of the solution. The results presented here identify a new operational regime for GDVNs and show that predictable droplet sizes, comparable to those obtained by electrospray ionization, can be produced by purely mechanical means in GDVNs.

Place, publisher, year, edition, pages
INT UNION CRYSTALLOGRAPHY, 2019
Keywords
aerosols, droplet size, gas dynamic virtual nozzles (GDVNs), environmental scanning electron microscopy, coherent X-ray diffractive imaging (CXDI), single particles, sample delivery, structural biology, nanoscience
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-391281 (URN)10.1107/S1600576719008318 (DOI)000477717400013 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research Council
Available from: 2019-08-22 Created: 2019-08-22 Last updated: 2019-08-22Bibliographically approved
Klimesova, E., Kulyk, O., Gu, Y., Dittrich, L., Korn, G., Hajdu, J., . . . Andreasson, J. (2019). Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector. Scientific Reports, 9, Article ID 8851.
Open this publication in new window or tab >>Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 8851Article in journal (Refereed) Published
Abstract [en]

Aerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 10(16) Wcm(-2). We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2019
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-390094 (URN)10.1038/s41598-019-45120-3 (DOI)000472136900025 ()31221980 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2019-08-05 Created: 2019-08-05 Last updated: 2019-08-05Bibliographically approved
Pietrini, A., Bielecki, J., Timneanu, N., Hantke, M. F., Andreasson, J., Loh, N. D., . . . Nettelblad, C. (2018). A statistical approach to detect protein complexes at X-ray free electron laser facilities. Communications Physics, 1, 92:1-11, Article ID 92.
Open this publication in new window or tab >>A statistical approach to detect protein complexes at X-ray free electron laser facilities
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2018 (English)In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-369876 (URN)10.1038/s42005-018-0092-6 (DOI)000452676300003 ()
Projects
eSSENCE
Available from: 2018-12-07 Created: 2018-12-17 Last updated: 2019-05-06Bibliographically approved
Lundholm, I. V., Sellberg, J. A., Ekeberg, T., Hantke, M. F., Okamoto, K., van der Schot, G., . . . Maia, F. R. N. (2018). Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. IUCrJ, 5, 531-541
Open this publication in new window or tab >>Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
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2018 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-360034 (URN)10.1107/S2052252518010047 (DOI)000444010100003 ()
Projects
eSSENCE
Available from: 2018-09-01 Created: 2018-09-09 Last updated: 2019-07-01Bibliographically approved
Okamoto, K., Miyazaki, N., Reddy, H. K. .., Hantke, M. F., Maia, F. R. .., Larsson, D. S., . . . Svenda, M. (2018). Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly. Virology, 516, 239-245, Article ID S0042-6822(18)30028-X.
Open this publication in new window or tab >>Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly
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2018 (English)In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 516, p. 239-245, article id S0042-6822(18)30028-XArticle in journal (Refereed) Published
Abstract [en]

Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.

Keywords
Amoeba, Capsid, Cryo-electron microscopy, Marseilleviridae, Melbournevirus, NCLDV, Protein complex, Structure, Tomography, Virus
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-370071 (URN)10.1016/j.virol.2018.01.021 (DOI)000428004800025 ()29407382 (PubMedID)
Funder
Swedish Research Council, 628-20081109 822-2010-6157 822-2012-5260 828-2012-108Knut and Alice Wallenberg Foundation, KAW-2011.081EU, European Research Council, ERC-291602The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), JA2014-5721
Available from: 2018-12-18 Created: 2018-12-18 Last updated: 2019-08-25Bibliographically approved
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