| 1. |
- Dods, Robert, 1989, et al.
(författare)
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Ultrafast structural changes within a photosynthetic reaction centre.
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 589:7841, s. 310-314
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.
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| 2. |
- Cellini, Andrea, 1991, et al.
(författare)
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The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature
- 2021
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Ingår i: Acta Crystallographica Section D-Structural Biology. - : International Union of Crystallography (IUCr). - 2059-7983. ; 77, s. 1001-1009
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Tidskriftsartikel (refereegranskat)abstract
- (6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 angstrom resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 angstrom resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
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| 3. |
- Chenchiliyan, Manoop, et al.
(författare)
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Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy
- 2023
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 158:8
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm(-1) band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.
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| 4. |
- Claesson, Elin, 1989, et al.
(författare)
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The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser
- 2020
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Ingår i: eLife. - 2050-084X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.
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| 5. |
- Kübel, Joachim, 1988, et al.
(författare)
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Excitation Power Modulates Energy-Transfer Dynamics in a Supramolecular Ru-II-Fe-II-Ru-II Triad
- 2017
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Ingår i: Chemphyschem. - : Wiley. - 1439-4235. ; 18:20, s. 2899-2907
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Tidskriftsartikel (refereegranskat)abstract
- Multichromophoric arrays are key to light harvesting in natural and artificial photosynthesis. A trinuclear, symmetric Ru-II-Fe-II-Ru-II triad may resemble a light-harvesting model system in which excitation energy from donor units (Ru-terpyridine fragments) is efficiently transferred to the acceptor (the Fe-terpyridine fragment). The photoinduced dynamics after simultaneous excitation of more than a single chromophoric unit (donor/acceptor) at varying excitation fluence is investigated in this contribution. Data suggests that energy transfer is decelerated if the acceptor states (on the Fe-II unit) are not depopulated fast enough. As a consequence, the lifetime of a high-lying excited state (centered on either of the Ru-II units) is prolonged. A kinetic model is suggested to account for this effect. Although the proposed model is specifically adopted to account for the experimental data reported here, it might be generalized to other situations in which multiple energy or electron donors are covalently linked to a single acceptor site, a situation of interest in contemporary artificial photosynthesis.
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| 6. |
- Kübel, Joachim, 1988, et al.
(författare)
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Giving voice to the weak: Application of active noise reduction in transient infrared spectroscopy
- 2021
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 783
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Tidskriftsartikel (refereegranskat)abstract
- The analysis and interpretation of time-resolved spectroscopic data is challenging in the presence of high levels of noise. This problem is particularly common when studying light-activated proteins with transient absorption (TA) spectroscopy. For the same reason, transient 2D-IR remains a notoriously challenging technique that so far has mostly been applied to studying strong oscillators, such as metal carbonyls. Here, we present a detailed implementation of transient 1D and 2D-IR spectroscopy that synchronizes three independent laser sources and applies advanced referencing algorithms for efficient noise suppression. The applied referencing method improves data quality considerably and allows for extracting additional spectroscopic information that is otherwise beyond reach due to very low signal-to-noise ratio. We apply the approach to monitor the complete Pr-to-Pfr transition in the Y263F mutant of a bacterial phytochrome (phi Pr_Pfr < 0.1) covering six orders of magnitude in time, from nanoseconds to milliseconds. We further extend the noise suppression method to transient 2D-IR spectroscopy and conduct a technical feasibility test on a solid-state semiconductor sample (InAs). The presented solutions come at no extra cost when a reference detector is present and are expected to find applications in many spectroscopic studies due to the enhanced ability to detect and interpret very weak signals on multiple timescales.
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| 7. |
- Kübel, Joachim, 1988, et al.
(författare)
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Transient IR spectroscopy identifies key interactions and unravels new intermediates in the photocycle of a bacterial phytochrome
- 2020
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Ingår i: Physical chemistry chemical physics : PCCP. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 22:17, s. 9195-9203
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes are photosensory proteins in plants, fungi, and bacteria, which detect red- and far-red light. They undergo a transition between the resting (Pr) and photoactivated (Pfr) states. In bacterial phytochromes, the Pr-to-Pfr transition is facilitated by two intermediate states, called Lumi-R and Meta-R. The molecular structures of the protein in these states are not known and the molecular mechanism of photoconversion is not understood. Here, we apply transient infrared absorption spectroscopy to study the photocycle of the wild-type and Y263F mutant of the phytochrome from Deinococcus radiodurans (DrBphP) from nano- to milliseconds. We identify two sequentially forming Lumi-R states which differ in the local structure surrounding the carbonyl group of the biliverdin D-ring. We also find that the tyrosine at position 263 alters local structure and dynamics around the D-ring and causes an increased rate of Pfr formation. The results shed new light on the mechanism of light-signalling in phytochrome proteins.
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| 8. |
- Kübel, Joachim, 1988, et al.
(författare)
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Ultrafast Chemical Exchange Dynamics of Hydrogen Bonds Observed via Isonitrile Infrared Sensors: Implications for Biomolecular Studies
- 2019
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Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 10:24, s. 7878-7883
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Tidskriftsartikel (refereegranskat)abstract
- Local probes are indispensable to study protein structure and dynamics with site-specificity. The isonitrile functional group is a highly sensitive and H-bonding interaction-specific probe. Isonitriles exhibit large spectral shifts and transition dipole moment changes upon H-bonding while being weakly affected by solvent polarity. These unique properties allow a clear separation of distinct subpopulations of interacting species and an elucidation of their ultrafast dynamics with two-dimensional infrared (2D-IR) spectroscopy. Here, we apply 2D-IR to quantify the picosecond chemical exchange dynamics of solute solvent complexes forming between isonitrile-derivatized alanine and fluorinated ethanol, where the degree of fluorination controls their H-bond-donating ability. We show that the molecules undergo faster exchange in the presence of more acidic H-bond donors, indicating that the exchange process is primarily dependent on the nature of solvent-solvent interactions. We foresee isonitrile as a highly promising probe for studying of H-bonds dynamics in the active site of enzymes.
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| 9. |
- Panman, Matthijs R, 1983, et al.
(författare)
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Observing the Structural Evolution in the Photodissociation of Diiodomethane with Femtosecond Solution X-Ray Scattering
- 2020
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 125:22
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Tidskriftsartikel (refereegranskat)abstract
- Resolving the structural dynamics of the initial steps of chemical reactions is challenging. We report the femtosecond time-resolved wide-angle x-ray scattering of the photodissociation of diiodomethane in cyclohexane. The data reveal with structural detail how the molecule dissociates into radicals, how the radicals collide with the solvent, and how they form the photoisomer. We extract how translational and rotational kinetic energy is dispersed into the solvent. We also find that 85% of the primary radical pairs are confined to their original solvent cage and discuss how this influences the downstream recombination reactions.
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