showing 26 related works from this author
Ubiquitous Structural Signaling in Bacterial Phytochromes
2015
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.
The Structural Diversity of Benzofuran Resorcinarene Leads to Enhanced Fluorescence
2014
An unexpected and previously unknown resorcinarene mono-crown with a fused benzofuran moiety in its macrocyclic core was obtained as a byproduct from a bridging reaction of tetramethoxy resorcinarene with tetraethylene glycol ditosylate. The formation of the fused benzofuran moiety in the resorcinarene macrocycle resulted in a unique rigid and puckered boat conformation, as shown by XRD studies in the solid state. Modification of the macrocycle was also observed to affect the photophysical properties in solution by enhancing the fluorescence brightness compared with a conventional resorcinarene macrocycle. The fluorescent properties enabled unique detection of structural features, that is, …
Removal of Chromophore-proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor
2015
Genetically encoded fluorescent markers have revolutionized cell and molecular biology due to their biological compatibility, controllable spatiotemporal expression, and photostability. To achieve in vivo imaging in whole animals, longer excitation wavelength probes are needed due to the superior ability of near infrared light to penetrate tissues unimpeded by absorbance from biomolecules or autofluorescence of water. Derived from near infrared-absorbing bacteriophytochromes, phytofluors are engineered to fluoresce in this region of the electromagnetic spectrum, although high quantum yield remains an elusive goal. An invariant aspartate residue is of utmost importance for photoconversion in…
Injection and ultrafast regeneration in dye-sensitized solar cells
2014
Injection of an electron from the excited dye molecule to the semiconductor is the initial charge separation step in dye-sensitized solar cells (DSC's). Though the dynamics of the forward injection process has been widely studied, the results reported so far are controversial, especially for complete DSC's. In this work, the electron injection in titanium dioxide (TiO2) films sensitized with ruthenium bipyridyl dyes N3 and N719 was studied both in neat solvent and in a typical iodide/triiodide (I-/I3 -) DSC electrolyte. Transient absorption (TA) spectroscopy was used to monitor both the formation of the oxidized dye and the arrival of injected electrons to the conduction band of TiO2. Emiss…
Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome
2022
Funding Information: This work was supported by Academy of Finland grants 285461 (H.T.), 330678 (H.T., J.R.), 277194 (H.L.), and 290677 (S.M.). We acknowledge the European Synchrotron Radiation Facility (ESRF) for providing synchrotron access for crystal data collection. We thank Prof. Janne Ihalainen (University of Jyväskylä) for all the help in all aspects of the paper, Prof. Gerrit Groenhof (University of Jyväskylä) for support, and Prof. Nikolai V. Tkachenko (Tampere University) for help and facilities for time-resolved absorption spectroscopy. We also thank M.Sc. Alli Liukkonen (University of Jyväskylä) and Dr. Heikki Häkkänen (University of Jyväskylä) for the assistance in laboratory …
Structural photoactivation of a full-length bacterial phytochrome
2016
Time-resolved x-ray solution scattering reveals the conformational signaling mechanism of a bacterial phytochrome.
Subcellular localization of bacteriophage PRD1 proteins in Escherichia coli
2014
Bacteria possess an intricate internal organization resembling that of the eukaryotes. The complexity is especially prominent at the bacterial cell poles, which are also known to be the preferable sites for some bacteriophages to infect. Bacteriophage PRD1 is a well-known model serving as an ideal system to study structures and functions of icosahedral internal membrane-containing viruses. Our aim was to analyze the localization and interactions of individual PRD1 proteins in its native host Escherichia coli. This was accomplished by constructing a vector library for production of fluorescent fusion proteins. Analysis of solubility and multimericity of the fusion proteins, as well as their …
Retene, pyrene and phenanthrene cause distinct molecular-level changes in the cardiac tissue of rainbow trout (Oncorhynchus mykiss) larvae, Part 2 – …
2020
Polycyclic aromatic hydrocarbons (PAHs) are global contaminants of concern. Despite several decades of research, their mechanisms of toxicity are not very well understood. Early life stages of fish are particularly sensitive with the developing cardiac tissue being a main target of PAHs toxicity. The mechanisms of cardiotoxicity of the three widespread model polycyclic aromatic hydrocarbons (PAHs) retene, pyrene and phenanthrene were explored in rainbow trout (Oncorhynchus mykiss) early life stages. Newly hatched larvae were exposed to sublethal doses of each individual PAH causing no detectable morphometric alterations. Changes in the cardiac proteome and metabolome were assessed after 7 o…
On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome
2018
Phytochromes are photoreceptors in plants, fungi, and various microorganisms and cycle between metastable red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Their light responses are thought to follow a conserved structural mechanism that is triggered by isomerization of the chromophore. Downstream structural changes involve refolding of the so-called tongue extension of the phytochrome-specific GAF-related (PHY) domain of the photoreceptor. The tongue is connected to the chromophore by conserved DIP and PRXSF motifs and a conserved tyrosine, but the role of these residues in signal transduction is not clear. Here, we examine the tongue interactions and their interplay with …
Fluorescence Properties of the Chromophore-Binding Domain of Bacteriophytochrome from Deinococcus radiodurans
2013
Fluorescent proteins are versatile tools for molecular imaging. In this study, we report a detailed analysis of the absorption and fluorescence properties of the chromophore-binding domain from Deinococcus radiodurans and its D207H mutant. Using single photon counting and transient absorption techniques, the average excited state lifetime of both studied systems was about 370 ps. The D207H mutation slightly changed the excited state decay profile but did not have a considerable effect on the average decay time of the system or the shape of the absorption and emission spectra of the biliverdin chromophore. We confirmed that the fluorescence properties of both samples are very similar in vivo…
Light-induced structural changes in a monomeric bacteriophytochrome
2016
International audience; 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 th…
More accuracy to the EROD measurements—The resorufin fluorescence differs between species and individuals
2012
Ethoxyresorufin-O-deethylase (EROD) activity is a biomarker of exposure to planar aromatic hydrocarbons, and it is often measured from the S9 fraction. The effect of the liver S9 fraction of seven boreal freshwater fish species on the fluorescence of resorufin was studied. The S9 fractions diminished resorufin fluorescence by 40–80%, and there were large differences between species. Thus, using a resorufin standard curve without the S9 fraction leads to a large underestimation of the EROD activity. Therefore a microwell plate EROD method was developed that takes into account the effect of each sample on resorufin fluorescence. At least two mechanisms were involved in the decrease of the flu…
Origins of fluorescence in evolved bacteriophytochromes
2014
Use of fluorescent proteins to study in vivo processes in mammals requires near-infrared (NIR) biomarkers that exploit the ability of light in this range to penetrate tissue. Bacteriophytochromes (BphPs) are photoreceptors that couple absorbance of NIR light to photoisomerization, protein conformational changes, and signal transduction. BphPs have been engineered to form NIR fluorophores, including IFP1.4, Wi-Phy, and the iRFP series, initially by replacement of Asp-207 by His. This position was suggestive because its main chain carbonyl is within hydrogen-bonding distance to pyrrole ring nitrogens of the biliverdin chromophore, thus potentially functioning as a crucial transient proton sin…
Signal amplification and transduction in phytochrome photosensors
2014
[Introduction] Page 2 of 20 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 cell ular functions in plants, bacteria, and fungi. 1-9 Bacterial phytochro mes consist of a photosensory core and a C-te rminal regulatory domain. 10,11 Structures of photosensory cores are reported in the resting state 12-18 and conformational responses to light activat ion have been proposed in the vicinity of the chromophore. 19-23 However, the structure of the signalling state and the mechanism of downstream signal re lay through the photosensory core remain e…
Chromophore-Protein Interplay During the Phytochrome Photocycle Revealed by Step-Scan FTIR Spectroscopy
2018
Phytochrome proteins regulate many photoresponses of plants and microorganisms. Light absorption causes isomerization of the biliverdin chromophore, which triggers a series of structural changes to activate the signaling domains of the protein. However, the structural changes are elusive, and therefore the molecular mechanism of signal transduction remains poorly understood. Here, we apply two-color step-scan infrared spectroscopy to the bacteriophytochrome from Deinococcus radiodurans. We show by recordings in H2O and D2O that the hydrogen bonds to the biliverdin D-ring carbonyl become disordered in the first intermediate (Lumi-R) forming a dynamic microenvironment, then completely detach …
Retene, pyrene and phenanthrene cause distinct molecular-level changes in the cardiac tissue of rainbow trout (Oncorhynchus mykiss) larvae, part 1 – …
2020
Polycyclic aromatic hydrocarbons (PAHs) are contaminants of concern that impact every sphere of the environment. Despite several decades of research, their mechanisms of toxicity are still poorly understood. This study explores the mechanisms of cardiotoxicity of the three widespread model PAHs retene, pyrene and phenanthrene in the rainbow trout (Oncorhynchus mykiss) early life stages. Newly hatched larvae were exposed to each individual compound at sublethal doses causing no significant increase in the prevalence of deformities. Changes in the cardiac transcriptome were assessed after 1, 3, 7 and 14 days of exposure using custom Salmo salar microarrays. The highest number of differentiall…
Size-And Wavelength-Dependent Two-Photon Absorption Cross-Section of CsPbBr3 Perovskite Quantum Dots
2017
All-inorganic colloidal perovskite quantum dots (QDs) based on cesium, lead, and halide have recently emerged as promising light emitting materials. CsPbBr3 QDs have also been demonstrated as stable two-photon-pumped lasing medium. However, the reported two photon absorption (TPA) cross sections for these QDs differ by an order of magnitude. Here we present an in-depth study of the TPA properties of CsPbBr3 QDs with mean size ranging from 4.6 to 11.4 nm. By using femtosecond transient absorption (TA) spectroscopy we found that TPA cross section is proportional to the linear one photon absorption. The TPA cross section follows a power law dependence on QDs size with exponent 3.3 +- 0.2. The …
Connection between Absorption Properties and Conformational Changes in Deinococcus radiodurans Phytochrome
2014
Phytochromes consist of several protein domains and a linear tetrapyrrole molecule, which interact as a red-light-sensing system. In this study, size-exclusion chromatography and light-scattering techniques are combined with UV-vis spectroscopy to investigate light-induced changes in dimeric Deinococcus radiodurans bacterial phytochrome (DrBphP) and its subdomains. The photosensory unit (DrCBD-PHY) shows an unusually stable Pfr state with minimal dark reversion, whereas the histidine kinase (HK) domain facilitates dark reversion to the resting state. Size-exclusion chromatography reveals that all phytochrome fragments remain as dimers in the illuminated state and dark state. Still, the elut…
Laatuaikaoppiminen : vuorovaikutteista ja yhteistoiminnallista fysiikan opiskelua
2017
Esittelemme artikkelissa Jyväskylän yliopiston fysiikan laitoksella kehitettyä opetuksen toimintamallia, joka perustuu teknologiatuettuun pienryhmäopiskeluun ja kurssin aikaiseen formatiiviseen arviointiin. Toimintamalli kehittää työelämätaitoja, tehostaa opettajien ja opiskelijoiden ajankäyttöä, vahvistaa opiskelijoiden välistä vuorovaikutusta ja hyödyntää suunnitelmallisesti tuloksia fysiikan opetuksen tutkimuksesta. Alustavat kokemukset toimintamallista ovat rohkaisevia. nonPeerReviewed
Avoimen toimintakulttuurin palveluiden itsearviointityökalu
2022
Toimintakulttuurin avoimen linjauksen tueksi on kehitetty palveluiden itsearviointityökalu, joka huomioi kaikkien aiempien avoimen tieteen kansallisten linjausten suositukset. Työkalun tarkoituksena on auttaa tutkimusorganisaatioita palveluiden itsearvioinnissa, kehittämisessä ja saataville asettamisessa. A self-evaluation tool for services has been developed to support the Policy for Open Scholarship, which takes into account the recommendations of all previous national policies on open science. The purpose of the tool is to assist research organisations in the self-evaluation and development of services and making them available. The organisation may produce the services alone, in coopera…
Subcellular localization of bacteriophage PRD1 proteins in Escherichia coli
2014
Bacteria possess an intricate internal organization resembling that of the eukaryotes. The complexity is especially prominent at the bacterial cell poles, which are also known to be the preferable sites for some bacteriophages to infect. Bacteriophage PRD1 is a well-known model serving as an ideal system to study structures and functions of icosahedral internal membrane-containing viruses. Our aim was to analyze the localization and interactions of individual PRD1 proteins in its native host Escherichia coli. This was accomplished by constructing a vector library for production of fluorescent fusion proteins. Analysis of solubility and multimericity of the fusion proteins, as well as their …
Fast Photochemistry of Prototypical Phytochromes : A Species vs. Subunit Specific Comparison
2015
Phytochromes are multi-domain red light photosensor proteins, which convert red light photons to biological activity utilizing the multitude of structural and chemical reactions. The steady increase in structural information obtained from various bacteriophytochromes has increased understanding about the functional mechanism of the photochemical processes of the phytochromes. Furthermore, a number of spectroscopic studies have revealed kinetic information about the light-induced reactions. The spectroscopic changes are, however, challenging to connect with the structural changes of the chromophore and the protein environment, as the excited state properties of the chromophores are very sens…
CCDC 943017: Experimental Crystal Structure Determination
2014
Related Article: Tiia-Riikka Tero, Kirsi Salorinne, Heli Lehtivuori, Janne A. Ihalainen, Maija Nissinen|2014|Chem.Asian J.|9|1860|doi:10.1002/asia.201402016
CCDC 943016: Experimental Crystal Structure Determination
2014
Related Article: Tiia-Riikka Tero, Kirsi Salorinne, Heli Lehtivuori, Janne A. Ihalainen, Maija Nissinen|2014|Chem.Asian J.|9|1860|doi:10.1002/asia.201402016
CCDC 943015: Experimental Crystal Structure Determination
2014
Related Article: Tiia-Riikka Tero, Kirsi Salorinne, Heli Lehtivuori, Janne A. Ihalainen, Maija Nissinen|2014|Chem.Asian J.|9|1860|doi:10.1002/asia.201402016
CCDC 943014: Experimental Crystal Structure Determination
2014
Related Article: Tiia-Riikka Tero, Kirsi Salorinne, Heli Lehtivuori, Janne A. Ihalainen, Maija Nissinen|2014|Chem.Asian J.|9|1860|doi:10.1002/asia.201402016