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Davidsson, Jan
Publications (10 of 17) Show all publications
Marcellini, M., Nasedkin, A., Zietz, B., Petersson, J., Vincent, J., Palazzetti, F., . . . Davidsson, J. (2018). Transient isomers in the photodissociation of bromoiodomethane. Journal of Chemical Physics, 148(13), Article ID 134307.
Open this publication in new window or tab >>Transient isomers in the photodissociation of bromoiodomethane
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2018 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 148, no 13, article id 134307Article in journal (Refereed) Published
Abstract [en]

The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 mu s. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2018
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-352489 (URN)10.1063/1.5005595 (DOI)000429359200029 ()29626862 (PubMedID)
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2018-06-05 Created: 2018-06-05 Last updated: 2018-06-05Bibliographically approved
Dods, R., Båth, P., Arnlund, D., Beyerlein, K. R., Nelson, G., Liang, M., . . . Neutze, R. (2017). From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography. Structure, 25(9), 1461-1468
Open this publication in new window or tab >>From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography
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2017 (English)In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 25, no 9, p. 1461-1468Article in journal (Refereed) Published
Abstract [en]

Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RCvir). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RCvir serial femtosecond crystallography (SFX) structure from 3.3-angstrom to 2.4-angstrom resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography.

Place, publisher, year, edition, pages
CELL PRESS, 2017
National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-335396 (URN)10.1016/j.str.2017.07.002 (DOI)000409243200019 ()28781082 (PubMedID)
Funder
Swedish Research Council, 2015-00560, 349-2011-6485Swedish Foundation for Strategic Research , SRL10-0036Knut and Alice Wallenberg Foundation, KAW 2012.0284, KAW 2014.0275, KAW 2012.0106
Available from: 2017-12-05 Created: 2017-12-05 Last updated: 2017-12-05Bibliographically approved
Kubo, M., Nango, E., Tono, K., Kimura, T., Owada, S., Song, C., . . . Iwata, S. (2017). Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA. Journal of Synchrotron Radiation, 24, 1086-1091
Open this publication in new window or tab >>Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA
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2017 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, p. 1086-1091Article in journal (Refereed) Published
Abstract [en]

X-ray free-electron lasers (XFELs) have opened new opportunities for timeresolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TRSFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.

Place, publisher, year, edition, pages
INT UNION CRYSTALLOGRAPHY, 2017
Keywords
XFEL, serial femtosecond crystallography, time-resolved X-ray crystallography, pump and probe
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-335648 (URN)10.1107/S160057751701030X (DOI)000408902800024 ()28862633 (PubMedID)
Available from: 2017-12-08 Created: 2017-12-08 Last updated: 2017-12-08Bibliographically approved
Nasedkin, A., Davidsson, J., Niemi, A. J. & Peng, X. (2017). Solution x-ray scattering and structure formation in protein dynamics. Physical review. E, 96(6), Article ID 062405.
Open this publication in new window or tab >>Solution x-ray scattering and structure formation in protein dynamics
2017 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 6, article id 062405Article in journal (Refereed) Published
Abstract [en]

We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

National Category
Subatomic Physics
Identifiers
urn:nbn:se:uu:diva-339801 (URN)10.1103/PhysRevE.96.062405 (DOI)000417759900002 ()29347365 (PubMedID)
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2018-02-23 Created: 2018-02-23 Last updated: 2018-02-23Bibliographically approved
Nango, E., Royant, A., Kubo, M., Nakane, T., Wickstrand, C., Kimura, T., . . . Iwata, S. (2016). A three-dimensional movie of structural changes in bacteriorhodopsin. Science, 354(6319), 1552-1557
Open this publication in new window or tab >>A three-dimensional movie of structural changes in bacteriorhodopsin
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2016 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 354, no 6319, p. 1552-1557Article in journal (Refereed) Published
Abstract [en]

Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.

National Category
Biophysics Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-313523 (URN)10.1126/science.aah3497 (DOI)000390254300044 ()
Funder
Swedish Research Council, VR 349-2011-6485 2015-00560Knut and Alice Wallenberg Foundation, KAW 2012.0284EU, FP7, Seventh Framework Programme, 290605
Available from: 2017-02-06 Created: 2017-01-20 Last updated: 2017-11-29Bibliographically approved
Arnlund, D., Johansson, L. C., Wickstrand, C., Barty, A., Williams, G. J., Malmerberg, E., . . . Neutze, R. (2014). Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Nature Methods, 11(9), 923-926
Open this publication in new window or tab >>Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
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2014 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 9, p. 923-926Article in journal (Refereed) Published
Abstract [en]

We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-232831 (URN)10.1038/nmeth.3067 (DOI)000341409700019 ()25108686 (PubMedID)
Available from: 2014-09-25 Created: 2014-09-25 Last updated: 2017-12-05Bibliographically approved
Nasedkin, A., Davidsson, J. & Kumpugdee-Vollrath, M. (2013). Determination of nanostructure of liposomes containing two model drugs by X-ray scattering from a synchrotron source. Journal of Synchrotron Radiation, 20, 721-728
Open this publication in new window or tab >>Determination of nanostructure of liposomes containing two model drugs by X-ray scattering from a synchrotron source
2013 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 20, p. 721-728Article in journal (Refereed) Published
Abstract [en]

Small-angle X-ray scattering has been employed to study how the introduction of paracetamol and acetylsalicylic acid into a liposome bilayer system affects the system's nanostructure. An X-ray scattering model, developed for multilamellar liposome systems [Pabst et al. (2000), Phys. Rev. E, 62, 4000-4009], has been used to fit the experimental data and to extract information on how structural parameters, such as the number and thickness of the bilayers of the liposomes, thickness of the water layer in between the bilayers, size and volume of the head and tail groups, are affected by the drugs and their concentration. Even though the experimental data reveal a complicated picture of the drug-bilayer interaction, they clearly show a correlation between nanostructure, drug and concentration in some aspects. The localization of the drugs in the bilayers is discussed.

Keywords
SAXS, WAXS, acetylsalicylic acid, paracetamol, drug-loaded liposomes
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-207517 (URN)10.1107/S0909049513020074 (DOI)000323282800007 ()
Available from: 2013-09-17 Created: 2013-09-16 Last updated: 2017-12-06Bibliographically approved
Johansson, L. C., Arnlund, D., Katona, G., White, T. A., Barty, A., DePonte, D. P., . . . Neutze, R. (2013). Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nature Communications, 4(Article nr:2911)
Open this publication in new window or tab >>Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography
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2013 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, no Article nr:2911Article in journal (Refereed) Published
Abstract [en]

Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 angstrom resolution and determine its serial femtosecond crystallography structure to 3.5 angstrom resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-218603 (URN)10.1038/ncomms3911 (DOI)000329396400012 ()
Available from: 2014-02-13 Created: 2014-02-13 Last updated: 2017-12-06Bibliographically approved
Johansson, L. C., Arnlund, D., White, T. A., Katona, G., DePonte, D. P., Weierstall, U., . . . Neutze, R. (2012). Lipidic phase membrane protein serial femtosecond crystallography. Nature Methods, 9(3), 263-265
Open this publication in new window or tab >>Lipidic phase membrane protein serial femtosecond crystallography
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2012 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 3, p. 263-265Article in journal (Refereed) Published
Abstract [en]

X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.

National Category
Structural Biology Biophysics
Identifiers
urn:nbn:se:uu:diva-169658 (URN)10.1038/nmeth.1867 (DOI)000300890400021 ()
Available from: 2012-03-05 Created: 2012-03-05 Last updated: 2017-12-07Bibliographically approved
Barty, A., Caleman, C., Aquila, A., Timneanu, N., Lomb, L., White, T. A., . . . Chapman, H. N. (2012). Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nature Photonics, 6(1), 35-40
Open this publication in new window or tab >>Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements
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2012 (English)In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 6, no 1, p. 35-40Article in journal (Refereed) Published
Abstract [en]

X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis(1). For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information(1-4). Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology(5) should enable structural determination from submicrometre protein crystals with atomic resolution.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-167165 (URN)10.1038/NPHOTON.2011.297 (DOI)000298416200013 ()
Available from: 2012-01-25 Created: 2012-01-23 Last updated: 2017-12-08Bibliographically approved
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