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  1. Article: Time-resolved serial crystallography to reveal protein structural changes.

    Meszaros, Petra / Westenhoff, Sebastian

    Trends in biochemical sciences

    2023  Volume 49, Issue 2, Page(s) 183–184

    MeSH term(s) Crystallography ; Proteins/chemistry ; Crystallography, X-Ray
    Chemical Substances Proteins
    Language English
    Publishing date 2023-10-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2023.09.009
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1207: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  2. Article ; Online: Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins.

    Westenhoff, Sebastian / Meszaros, Petra / Schmidt, Marius

    Current opinion in structural biology

    2022  Volume 77, Page(s) 102481

    Abstract: Proteins are dynamic objects and undergo conformational changes when functioning. These changes range from interconversion between states in equilibrium to ultrafast and coherent structural motions within one perturbed state. Time-resolved serial ... ...

    Abstract Proteins are dynamic objects and undergo conformational changes when functioning. These changes range from interconversion between states in equilibrium to ultrafast and coherent structural motions within one perturbed state. Time-resolved serial femtosecond crystallography at free-electron X-ray lasers can unravel structural changes with atomic resolution and down to femtosecond time scales. In this review, we summarize recent advances on detecting structural changes for phytochrome photosensor proteins and a bacterial photosynthetic reaction center. In the phytochrome structural changes are extensive and involve major rearrangements of many amino acids and water molecules, accompanying the regulation of its biochemical activity, whereas in the photosynthetic reaction center protein the structural changes are smaller, more localized, and are optimized to facilitate electron transfer along the chromophores. The detected structural motions underpin the proteins' function, providing a showcase for the importance of detecting ultrafast protein structural dynamics.
    Language English
    Publishing date 2022-10-14
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2022.102481
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3206: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article: Cryo-Electron Microscopy of

    Wahlgren, Weixiao Yuan / Golonka, David / Westenhoff, Sebastian / Möglich, Andreas

    Frontiers in plant science

    2021  Volume 12, Page(s) 663751

    Abstract: Phytochrome photoreceptors regulate vital adaptations of plant development, growth, and physiology depending on the ratio of red and far-red light. The light- ... ...

    Abstract Phytochrome photoreceptors regulate vital adaptations of plant development, growth, and physiology depending on the ratio of red and far-red light. The light-triggered
    Language English
    Publishing date 2021-04-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2021.663751
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  4. Article ; Online: Dynamic band-shift signal in two-dimensional electronic spectroscopy: A case of bacterial reaction center.

    Bukartė, Eglė / Paleček, David / Edlund, Petra / Westenhoff, Sebastian / Zigmantas, Donatas

    The Journal of chemical physics

    2021  Volume 154, Issue 11, Page(s) 115102

    Abstract: Optical nonlinear spectroscopies carry a high amount of information about the systems under investigation; however, as they report polarization signals, the resulting spectra are often congested and difficult to interpret. To recover the landscape of ... ...

    Abstract Optical nonlinear spectroscopies carry a high amount of information about the systems under investigation; however, as they report polarization signals, the resulting spectra are often congested and difficult to interpret. To recover the landscape of energy states and physical processes such as energy and electron transfer, a clear interpretation of the nonlinear signals is prerequisite. Here, we focus on the interpretation of the electrochromic band-shift signal, which is generated when an internal electric field is established in the system following optical excitation. Whereas the derivative shape of the band-shift signal is well understood in transient absorption spectroscopy, its emergence in two-dimensional electronic spectroscopy (2DES) has not been discussed. In this work, we employed 2DES to follow the dynamic band-shift signal in reaction centers of purple bacteria Rhodobacter sphaeroides at 77 K. The prominent two-dimensional derivative-shape signal appears with the characteristic formation time of the charge separated state. To explain and characterize the band-shift signal, we use expanded double-sided Feynman diagram formalism. We propose to distinguish two types of Feynman diagrams that lead to signals with negative amplitude: excited state absorption and re-excitation. The presented signal decomposition and modeling analysis allows us to recover precise electrochromic shifts of accessory bacteriochlorophylls, identify additional signals in the B band range, and gain a further insight into the electron transfer mechanism. In a broader perspective, expanded Feynman diagram formalism will allow for interpretation of all 2D signals in a clearer and more intuitive way and therefore facilitate studying the underlying photophysics.
    MeSH term(s) Electrons ; Photosynthetic Reaction Center Complex Proteins/chemistry ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Rhodobacter sphaeroides/enzymology ; Spectrum Analysis
    Chemical Substances Photosynthetic Reaction Center Complex Proteins
    Language English
    Publishing date 2021-03-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0033805
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  5. Article ; Online: Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy.

    Chenchiliyan, Manoop / Kübel, Joachim / Ooi, Saik Ann / Salvadori, Giacomo / Mennucci, Benedetta / Westenhoff, Sebastian / Maj, Michał

    The Journal of chemical physics

    2023  Volume 158, Issue 8, Page(s) 85103

    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 ... ...

    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
    MeSH term(s) Biliverdine ; Vibration ; Spectrophotometry, Infrared ; Phytochrome ; Hydrogen
    Chemical Substances Biliverdine (O9MIA842K9) ; Phytochrome (11121-56-5) ; Hydrogen (7YNJ3PO35Z)
    Language English
    Publishing date 2023-03-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0135268
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  6. Article ; Online: Tips and turns of bacteriophytochrome photoactivation.

    Takala, Heikki / Edlund, Petra / Ihalainen, Janne A / Westenhoff, Sebastian

    Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology

    2020  Volume 19, Issue 11, Page(s) 1488–1510

    Abstract: Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, ...

    Abstract Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Models, Molecular ; Photochemical Processes ; Phytochrome/chemistry ; Phytochrome/metabolism ; Protein Conformation ; Signal Transduction
    Chemical Substances Bacterial Proteins ; Phytochrome (11121-56-5)
    Language English
    Publishing date 2020-10-26
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2072584-X
    ISSN 1474-9092 ; 1474-905X
    ISSN (online) 1474-9092
    ISSN 1474-905X
    DOI 10.1039/d0pp00117a
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  7. Article: Erratum: MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins. Erratum.

    Niebling, Stephan / Björling, Alexander / Westenhoff, Sebastian

    Journal of applied crystallography

    2018  Volume 51, Issue Pt 3, Page(s) 968

    Abstract: This corrects the article DOI: 10.1107/S1600576714009959.]. ...

    Abstract [This corrects the article DOI: 10.1107/S1600576714009959.].
    Language English
    Publishing date 2018-05-18
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2020879-0
    ISSN 1600-5767 ; 0021-8898
    ISSN (online) 1600-5767
    ISSN 0021-8898
    DOI 10.1107/S1600576718007331
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  8. Article ; Online: Structural mechanism of signal transduction in a phytochrome histidine kinase.

    Wahlgren, Weixiao Yuan / Claesson, Elin / Tuure, Iida / Trillo-Muyo, Sergio / Bódizs, Szabolcs / Ihalainen, Janne A / Takala, Heikki / Westenhoff, Sebastian

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 7673

    Abstract: Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the ... ...

    Abstract Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the availability of three-dimensional structures of phytochromes and other two-component proteins, the conformational changes, which lead to activation of the protein, are not understood. We reveal cryo electron microscopy structures of the complete phytochrome from Deinoccocus radiodurans in its resting and photoactivated states at 3.6 Å and 3.5 Å resolution, respectively. Upon photoactivation, the photosensory core module hardly changes its tertiary domain arrangement, but the connector helices between the photosensory and the histidine kinase modules open up like a zipper, causing asymmetry and disorder in the effector domains. The structures provide a framework for atom-scale understanding of signaling in phytochromes, visualize allosteric communication over several nanometers, and suggest that disorder in the dimeric arrangement of the effector domains is important for phosphatase activity in a two-component system. The results have implications for the development of optogenetic applications.
    MeSH term(s) Phytochrome/metabolism ; Histidine Kinase/metabolism ; Models, Molecular ; Bacterial Proteins/metabolism ; Signal Transduction ; Light ; Bacteria/metabolism
    Chemical Substances Phytochrome (11121-56-5) ; Histidine Kinase (EC 2.7.13.1) ; Bacterial Proteins
    Language English
    Publishing date 2022-12-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-34893-3
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  9. Article ; Online: Potential pitfalls of the early-time dynamics in two-dimensional electronic spectroscopy.

    Paleček, David / Edlund, Petra / Gustavsson, Emil / Westenhoff, Sebastian / Zigmantas, Donatas

    The Journal of chemical physics

    2019  Volume 151, Issue 2, Page(s) 24201

    Abstract: Two-dimensional electronic spectroscopy, and especially the polarization-controlled version of it, is the cutting edge technique for disentangling various types of coherences in molecules and molecular aggregates. In order to evaluate the electronic ... ...

    Abstract Two-dimensional electronic spectroscopy, and especially the polarization-controlled version of it, is the cutting edge technique for disentangling various types of coherences in molecules and molecular aggregates. In order to evaluate the electronic coherences, which often decay on a 100 fs time scale, the early population times have to be included in the analysis. However, signals in this region are typically plagued by several artifacts, especially in the unavoidable pulse overlap region. In this paper, we show that, in the case of polarization-controlled two-dimensional spectroscopy experiment, the early-time dynamics can be dominated by the "incorrect" pulse ordering signals. These signals can affect kinetics at positive times well beyond the pulse overlap region, especially when the "correct" pulse ordering signals are much weaker. Moreover, the "incorrect" pulse ordering contributions are oscillatory and overlap with the spectral signatures of energy transfer, which may lead to misinterpretation of "incorrect" pulse ordering signals for fast-decaying coherences.
    Language English
    Publishing date 2019-07-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/1.5079817
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  10. Article ; Online: Quantum coherence as a witness of vibronically hot energy transfer in bacterial reaction center.

    Paleček, David / Edlund, Petra / Westenhoff, Sebastian / Zigmantas, Donatas

    Science advances

    2017  Volume 3, Issue 9, Page(s) e1603141

    Abstract: Photosynthetic proteins have evolved over billions of years so as to undergo optimal energy transfer to the sites of charge separation. On the basis of spectroscopically detected quantum coherences, it has been suggested that this energy transfer is ... ...

    Abstract Photosynthetic proteins have evolved over billions of years so as to undergo optimal energy transfer to the sites of charge separation. On the basis of spectroscopically detected quantum coherences, it has been suggested that this energy transfer is partially wavelike. This conclusion depends critically on the assignment of the coherences to the evolution of excitonic superpositions. We demonstrate that, for a bacterial reaction center protein, long-lived coherent spectroscopic oscillations, which bear canonical signatures of excitonic superpositions, are essentially vibrational excited-state coherences shifted to the ground state of the chromophores. We show that the appearance of these coherences arises from a release of electronic energy during energy transfer. Our results establish how energy migrates on vibrationally hot chromophores in the reaction center, and they call for a reexamination of claims of quantum energy transfer in photosynthesis.
    MeSH term(s) Bacteria/metabolism ; Bacterial Physiological Phenomena ; Chlorophyll/metabolism ; Energy Transfer ; Photosynthesis ; Quantum Theory
    Chemical Substances Chlorophyll (1406-65-1)
    Language English
    Publishing date 2017-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.1603141
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