| 1. |
- Berntsson, Oskar, 1989, et al.
(author)
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Sequential conformational transitions and alpha-helical supercoiling regulate a sensor histidine kinase
- 2017
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Journal article (peer-reviewed)abstract
- Sensor histidine kinases are central to sensing in bacteria and in plants. They usually contain sensor, linker, and kinase modules and the structure of many of these components is known. However, it is unclear how the kinase module is structurally regulated. Here, we use nano- to millisecond time-resolved X-ray scattering to visualize the solution structural changes that occur when the light-sensitive model histidine kinase YF1 is activated by blue light. We find that the coiled coil linker and the attached histidine kinase domains undergo a left handed rotation within microseconds. In a much slower second step, the kinase domains rearrange internally. This structural mechanism presents a template for signal transduction in sensor histidine kinases.
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| 2. |
- Björling, Alexander, 1983, et al.
(author)
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Structural photoactivation of a full-length bacterial phytochrome
- 2016
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In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 2:8
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Journal article (peer-reviewed)abstract
- Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that propagates from the chromophore through the entire protein. However, the structure of the photoactivated state and the conformational changes that lead to it are not known. We report time-resolved x-ray scattering of the full-length phytochrome from Deinococcus radiodurans on micro-and millisecond time scales. We identify a twist of the histidine kinase output domains with respect to the chromophore-binding domains as the dominant change between the photoactivated and resting states. The time-resolved data further show that the structural changes up to the microsecond time scales are small and localized in the chromophore-binding domains. The global structural change occurs within a few milliseconds, coinciding with the formation of the spectroscopic meta-Rc state. Our findings establish key elements of the signaling mechanism of full-length bacterial phytochromes.
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| 3. |
- Björling, Alexander, 1983, et al.
(author)
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Ubiquitous Structural Signaling in Bacterial Phytochromes
- 2015
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In: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 6:17, s. 3379-3383
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Journal article (peer-reviewed)abstract
- The phytochrome family of light-switchable proteins has long been studied by biochemical, spectroscopic and crystallographic means, while a direct probe for global conformational signal propagation has been lacking. Using solution X-ray scattering, we find that the photosensory cores of several bacterial phytochromes undergo similar large-scale structural changes upon red-light excitation. The data establish that phytochromes with ordinary and inverted photocycles share a structural signaling mechanism and that a particular conserved histidine, previously proposed to be involved in signal propagation, in fact tunes photoresponse.
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| 4. |
- Nimmrich, Amke, 1995, et al.
(author)
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Solvent-Dependent Structural Dynamics in the Ultrafast Photodissociation Reaction of Triiodide Observed with Time-Resolved X-ray Solution Scattering
- 2023
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 145:29, s. 15754-15765
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Journal article (peer-reviewed)abstract
- Resolving the structural dynamics of bond breaking, bond formation, and solvation is required for a deeper understanding of solutionphase chemical reactions. In this work, we investigate the photodissociation of triiodide in four solvents using femtosecond time-resolved X-ray solution scattering following 400 nm photoexcitation. Structural analysis of the scattering data resolves the solvent-dependent structural evolution during the bond cleavage, internal rearrangements, solvent-cage escape, and bond reformation in real time. The nature and structure of the reaction intermediates during the recombination are determined, elucidating the full mechanism of photodissociation and recombination on ultrafast time scales. We resolve the structure of the precursor state for recombination as a geminate pair. Further, we determine the size of the solvent cages from the refined structures of the radical pair. The observed structural dynamics present a comprehensive picture of the solvent influence on structure and dynamics of dissociation reactions.
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| 5. |
- Takala, Heikki, et al.
(author)
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Light-induced structural changes in a monomeric bacteriophytochrome
- 2016
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In: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 3:5
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Journal article (peer-reviewed)abstract
- Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes. © Author(s) 2016.
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| 6. |
- Berntsson, Oskar, 1989, et al.
(author)
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Time-Resolved X-Ray Solution Scattering Reveals the Structural Photoactivation of a Light-Oxygen-Voltage Photoreceptor
- 2017
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In: Structure. - : Elsevier BV. - 0969-2126. ; 25:6
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Journal article (peer-reviewed)abstract
- Light-oxygen-voltage (LOV) receptors are sensory proteins controlling a wide range of organismal adaptations in multiple kingdoms of life. Because of their modular nature, LOV domains are also attractive for use as optogenetic actuators. A flavin chromophore absorbs blue light, forms a bond with a proximal cysteine residue, and induces changes in the surroundings. There is a gap of knowledge on how this initial signal is relayed further through the sensor to the effector module. To characterize these conformational changes, we apply time-resolved X-ray scattering to the homodimeric LOV domain from Bacillus subtilis YtvA. We observe a global structural change in the LOV dimer synchronous with the formation of the chromophore photoproduct state. Using molecular modeling, this change is identified as splaying apart and relative rotation of the two monomers, which leads to an increased separation at the anchoring site of the effector modules.
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| 7. |
- Björling, Alexander, 1983, et al.
(author)
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Deciphering solution scattering data with experimentally guided molecular dynamics simulations
- 2015
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:2, s. 780-787
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Journal article (peer-reviewed)abstract
- Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.
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| 8. |
- Björling, Alexander, 1983
(author)
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Detecting and Identifying Solution-structural Change in Photoactive Proteins
- 2015
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Doctoral thesis (other academic/artistic)abstract
- Conformational dynamics allow proteins to fulfil their biological roles, yet the understanding of these molecular machines is largely limited to structural snapshots. Time-resolved X-ray scattering provides a possible way of uncovering such dynamics, but hinges on the ability to trigger reactions, and most critically on the ability to interpret the resulting data. This thesis explores how such experiments can be carried out and analysed. First, a computational tool for the interpretation of time-resolved X-ray scattering data is presented and tested. It is found that the method works for systems which undergo concerted domain movements, but fails for those where the structure changes in more subtle ways. The method is a potential starting point for systematic, molecular dynamics based interpretation schemes, and provides the most general and unbiased scheme yet. Further, the time-resolved X-ray scattering technique is applied to the phytochrome family of light-sensing proteins. The results establish a comprehensive mechanism of signal transduction in a particular member of the family. A comparative study shows that this mechanism is also found in several other protein relatives, implying that a core structural apparatus has been conserved and reused for various purposes during evolution.
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| 9. |
- Björling, Alexander, 1983, et al.
(author)
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Kinetics of surface modification induced by submonolayer electrochemical oxygen adsorption on Pt(1 1 1)
- 2010
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In: Electrochemistry Communications. - : Elsevier BV. - 1388-2481. ; 12:3, s. 359-361
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Journal article (peer-reviewed)abstract
- Electrochemical oxygen adsorption/desorption below monolayer level leads to a disordering of platinum single-crystal surfaces vicinal to the (1 1 1) plane. The kinetics can be described by means of a consecutive reaction from (1 1 1)-terrace sites to (1 1 0)-defect sites, in which (1 0 0)-defects act as intermediates. The first oxidation of the electrode reflects independent contributions from terrace and step sites, the latter being structure sensitive. Oxygen adsorption charges amount to a mean value of one electron per step site.
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| 10. |
- Jirkovský, Jakub S, 1980, et al.
(author)
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Reduction of Oxygen on Dispersed Nanocrystalline CoS2
- 2012
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In: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 116:46, s. 24436-24444
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Journal article (peer-reviewed)abstract
- The electrocatalytic properties of nanocrystalline CoS2 have been investigated for the oxygen reduction reaction (ORR) in 0.1 M HClO4. CoS2 with pyrite structure was prepared by hydrothermal synthesis and attached to a glassy carbon electrode from solution with a mixture of carbon and Nafion. The prepared CoS2 electrode layers showed high activity toward the ORR and very good stability under oxygen reducing conditions. Selectivity of the ORR toward H2O2 was determined by rotating (ring) disk electrode measurements, and relatively high selectivity was obtained with up to 80% H2O2 formation around 0.4 V (vs Ag/AgCl), but this dropped to zero for potentials below 0.0 V. The amount of H2O2 produced between 0.6 and 0.0 V was dependent on the quality of the CoS2 dispersion within the electrode layer, and decreasing CoS2 particle size resulted in significant improvement in the ORR electrocatalytic activity, both by increasing the turnover frequency and through decreasing the selectivity toward H2O2 production.
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| 11. |
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| 12. |
- Niebling, Stephan, et al.
(author)
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MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins
- 2014
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In: Journal of Applied Crystallography. - 0021-8898 .- 1600-5767. ; 47:4, s. 1190-1198
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Journal article (peer-reviewed)abstract
- Time-resolved small- and wide-angle X-ray scattering (SAXS and WAXS) methods probe the structural dynamics of proteins in solution. Although technologically advanced, these methods are in many cases limited by data interpretation. The calculation of X-ray scattering profiles is computationally demanding and poses a bottleneck for all SAXS/WAXS-assisted structural refinement and, in particular, for the analysis of time-resolved data. A way of speeding up these calculations is to represent biomolecules as collections of coarse-grained scatterers. Here, such coarse-graining schemes are presented and discussed and their accuracies examined. It is demonstrated that scattering factors coincident with the popular MARTINI coarse-graining scheme produce reliable difference scattering in the range 0 < q < 0.75 Å-1. The findings are promising for future attempts at X-ray scattering data analysis, and may help to bridge the gap between time-resolved experiments and their interpretation.
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| 13. |
- Sharma, Amit, et al.
(author)
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A simple adaptation to a protein crystallography station to facilitate difference X-ray scattering studies
- 2019
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In: Journal of Applied Crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 52, s. 378-386
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Journal article (peer-reviewed)abstract
- The X-ray crystallography station I911-2 at MAXLab II (Lund, Sweden) has been adapted to enable difference small- and wide-angle X-ray scattering (SAXS/WAXS) data to be recorded. Modifications to the beamline included a customized flow cell, a motorized flow cell holder, a helium cone, a beam stop, a sample stage and a sample delivery system. This setup incorporated external devices such as infrared lasers, LEDs and reaction mixers to induce conformational changes in macromolecules. This platform was evaluated through proof-of-principle experiments capturing light-induced conformational changes in phytochromes. A difference WAXS signature of conformational changes in a plant aquaporin was also demonstrated using caged calcium.
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| 14. |
- Takala, Heikki, et al.
(author)
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Light-induced Changes in the Dimerization Interface of Bacteriophytochromes.
- 2015
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In: The Journal of biological chemistry. - 1083-351X. ; 290:26, s. 16383-92
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Journal article (peer-reviewed)abstract
- Phytochromes are dimeric photoreceptor proteins that sense red light levels in plants, fungi, and bacteria. The proteins are structurally divided into a light-sensing photosensory module consisting of PAS, GAF, and PHY domains and a signaling output module, which in bacteriophytochromes typically is a histidine kinase (HK) domain. Existing structural data suggest that two dimerization interfaces exist between the GAF and HK domains, but their functional roles remain unclear. Using mutational, biochemical, and computational analyses of the Deinococcus radiodurans phytochrome, we demonstrate that two dimerization interfaces between sister GAF and HK domains stabilize the dimer with approximately equal contributions. The existence of both dimerization interfaces is critical for thermal reversion back to the resting state. We also find that a mutant in which the interactions between the GAF domains were removed monomerizes under red light. This implies that the interactions between the HK domains are significantly altered by photoconversion. The results suggest functional importance of the dimerization interfaces in bacteriophytochromes.
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| 15. |
- Takala, Heikki, et al.
(author)
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Signal amplification and transduction in phytochrome photosensors
- 2014
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 509:7499, s. 245-248
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Journal article (peer-reviewed)abstract
- Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi(1-9). Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain(10,11). Structures of photosensory cores are reported in the resting state(12-18) and conformational responses to light activation have been proposed in the vicinity of the chromophore(19-23). However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved 'tongue', which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into ana angstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism is a blueprint for understanding how phytochromes connect to the cellular signalling network.
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