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López MF, Dahl M, Escobar FV, Bonomi HR, Kraskov A, Michael N, Mroginski MA, Scheerer P, Hildebrandt P. Photoinduced reaction mechanisms in prototypical and bathy phytochromes. Phys Chem Chem Phys 2022; 24:11967-11978. [PMID: 35527718 DOI: 10.1039/d2cp00020b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phytochromes, found in plants, fungi, and bacteria, exploit light as a source of information to control physiological processes via photoswitching between two states of different physiological activity, i.e. a red-absorbing Pr and a far-red-absorbing Pfr state. Depending on the relative stability in the dark, bacterial phytochromes are divided into prototypical and bathy phytochromes, where the stable state is Pr and Pfr, respectively. In this work we studied representatives of these groups (prototypical Agp1 and bathy Agp2 from Agrobacterium fabrum) together with the bathy-like phytochrome XccBphP from Xanthomonas campestris by resonance Raman and IR difference spectroscopy. In all three phytochromes, the photoinduced conversions display the same mechanistic pattern as reflected by the chromophore structures in the various intermediate states. We also observed in each case the secondary structure transition of the tongue, which is presumably crucial for the function of phytochrome. The three phytochromes differ in details of the chromophore conformation in the various intermediates and the energetic barrier of their respective decay reactions. The specific protein environment in the chromophore pocket, which is most likely the origin for these small differences, also controls the proton transfer processes concomitant to the photoconversions. These proton translocations, which are tightly coupled to the structural transition of the tongue, presumably proceed via the same mechanism along the Pr → Pfr conversion whereas the reverse Pfr → Pr photoconversion includes different proton transfer pathways. Finally, classification of phytochromes in prototypical and bathy (or bathy-like) phytochromes is discussed in terms of molecular structure and mechanistic properties.
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Affiliation(s)
- María Fernández López
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Margarethe Dahl
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Francisco Velázquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Hernán Ruy Bonomi
- Leloir Institute Foundation, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Anastasia Kraskov
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
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Kraskov A, von Sass J, Nguyen AD, Hoang TO, Buhrke D, Katz S, Michael N, Kozuch J, Zebger I, Siebert F, Scheerer P, Mroginski MA, Budisa N, Hildebrandt P. Local Electric Field Changes during the Photoconversion of the Bathy Phytochrome Agp2. Biochemistry 2021; 60:2967-2977. [PMID: 34570488 DOI: 10.1021/acs.biochem.1c00426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochromes switch between a physiologically inactive and active state via a light-induced reaction cascade, which is initiated by isomerization of the tetrapyrrole chromophore and leads to the functionally relevant secondary structure transition of a protein segment (tongue). Although details of the underlying cause-effect relationships are not known, electrostatic fields are likely to play a crucial role in coupling chromophores and protein structural changes. Here, we studied local electric field changes during the photoconversion of the dark state Pfr to the photoactivated state Pr of the bathy phytochrome Agp2. Substituting Tyr165 and Phe192 in the chromophore pocket by para-cyanophenylalanine (pCNF), we monitored the respective nitrile stretching modes in the various states of photoconversion (vibrational Stark effect). Resonance Raman and IR spectroscopic analyses revealed that both pCNF-substituted variants undergo the same photoinduced structural changes as wild-type Agp2. Based on a structural model for the Pfr state of F192pCNF, a molecular mechanical-quantum mechanical approach was employed to calculate the electric field at the nitrile group and the respective stretching frequency, in excellent agreement with the experiment. These calculations serve as a reference for determining the electric field changes in the photoinduced states of F192pCNF. Unlike F192pCNF, the nitrile group in Y165pCNF is strongly hydrogen bonded such that the theoretical approach is not applicable. However, in both variants, the largest changes of the nitrile stretching modes occur in the last step of the photoconversion, supporting the view that the proton-coupled restructuring of the tongue is accompanied by a change of the electric field.
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Affiliation(s)
- Anastasia Kraskov
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes von Sass
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anh Duc Nguyen
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Tu Oanh Hoang
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Sagie Katz
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Jacek Kozuch
- Freie Universität Berlin, Fachbereich für Physik, Arnimallee 14, D-14195 Berlin, Germany
| | - Ingo Zebger
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Friedrich Siebert
- Albert-Ludwigs-Universität Freiburg, Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Hermann-Herderstr. 9, D-79104 Freiburg, Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd, 360 Parker Building, R3T 2N2 Winnipeg, Manitoba, Canada
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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Merga G, Lopez MF, Fischer P, Piwowarski P, Nogacz Ż, Kraskov A, Buhrke D, Escobar FV, Michael N, Siebert F, Scheerer P, Bartl F, Hildebrandt P. Light- and temperature-dependent dynamics of chromophore and protein structural changes in bathy phytochrome Agp2. Phys Chem Chem Phys 2021; 23:18197-18205. [PMID: 34612283 DOI: 10.1039/d1cp02494a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial phytochromes are sensoric photoreceptors that transform light absorbed by the photosensor core module (PCM) to protein structural changes that eventually lead to the activation of the enzymatic output module. The underlying photoinduced reaction cascade in the PCM starts with the isomerization of the tetrapyrrole chromophore, followed by conformational relaxations, proton transfer steps, and a secondary structure transition of a peptide segment (tongue) that is essential for communicating the signal to the output module. In this work, we employed various static and time-resolved IR and resonance Raman spectroscopic techniques to study the structural and reaction dynamics of the Meta-F intermediate of both the PCM and the full-length (PCM and output module) variant of the bathy phytochrome Agp2 from Agrobacterium fabrum. In both cases, this intermediate represents a branching point of the phototransformation, since it opens an unproductive reaction channel back to the initial state and a productive pathway to the final active state, including the functional protein structural changes. It is shown that the functional quantum yield, i.e. the events of tongue refolding per absorbed photons, is lower by a factor of ca. two than the quantum yield of the primary photochemical process. However, the kinetic data derived from the spectroscopic experiments imply an increased formation of the final active state upon increasing photon flux or elevated temperature under photostationary conditions. Accordingly, the branching mechanism does not only account for the phytochrome's function as a light intensity sensor but may also modulate its temperature sensitivity.
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Affiliation(s)
- Galaan Merga
- Humboldt Universität zu Berlin, Institut für Biologie, Biophysikalische Chemie, Invalidenstr. 42, D-10115 Berlin, Germany
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Sandys D, Tyyger M, Al-Qaisieh B, Michael N. PO-1715: Predicting dosimetric impact of (auto)contouring errors for OARs in prostate VMAT radiotherapy. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)01733-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Xu Y, Jun L, Michael N, Han X, Pei W. Identification of novel tumor suppressors for pancreatic cancer initiation and progression from normal human pancreatic acinar cells. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31146-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Velazquez Escobar F, Kneip C, Michael N, Hildebrandt T, Tavraz N, Gärtner W, Hughes J, Friedrich T, Scheerer P, Mroginski MA, Hildebrandt P. The Lumi-R Intermediates of Prototypical Phytochromes. J Phys Chem B 2020; 124:4044-4055. [PMID: 32330037 DOI: 10.1021/acs.jpcb.0c01059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phytochromes are photoreceptors that upon light absorption initiate a physiological reaction cascade. The starting point is the photoisomerization of the tetrapyrrole cofactor in the parent Pr state, followed by thermal relaxation steps culminating in activation of the physiological signal. Here we have employed resonance Raman (RR) spectroscopy to study the chromophore structure in the primary photoproduct Lumi-R, trapped between 130 and 200 K. The investigations covered phytochromes from plants (phyA) and prokaryotes (Cph1, Agp1, CphB, and RpBphP2) including phytochromobilin (PΦB), phycocyanobilin (PCB), and biliverdin (BV). In PΦB- and PCB-binding phyA and Cph1, two Lumi-R states (Lumi-R1, Lumi-R2) were identified and discussed in terms of sequential and parallel reaction models. In Lumi-R1, the chromophore structural changes are restricted to the C-D methine bridge isomerization site but extended throughout the chromophore in Lumi-R2. Formation and decay kinetics as well as photochemical activity depend on the specific protein-chromophore interactions and thus account for the different distribution between Lumi-R1 and Lumi-R2 in the photostationary mixtures of the various PΦB(PCB)-binding phytochromes. For BV-binding bacteriophytochromes, only a single Lumi-R(BV) state was found. In this state, which is similar for Agp1, CphB, and RpBphP2, the chromophore structural changes comprise major torsions of the C-D methine bridge but also perturbations at the A-B methine bridge remote from the isomerization site. The different structures of the photoproducts in PΦB(PCB)-binding phytochromes and BV-binding bacteriophytochromes are attributed to the different disposition of ring D upon isomerization, which leads to distinct protein-chromophore interactions in the Lumi-R states of these two classes of phytochromes.
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Affiliation(s)
- Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Christa Kneip
- Grünenthal GmbH, Zieglerstraße 6, D-52078 Aachen, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Thomas Hildebrandt
- Universitätsklinikum Düsseldorf, Klinik für Neurologie, Moorenstr. 5, D-40225 Düsseldorf, Germany
| | - Neslihan Tavraz
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Wolfgang Gärtner
- Universität Leipzig, Institut für Analytische Chemie, Linnéstr. 3, D-04103 Leipzig, Germany
| | - Jon Hughes
- Plant Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
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7
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Kraskov A, Nguyen AD, Goerling J, Buhrke D, Velazquez Escobar F, Fernandez Lopez M, Michael N, Sauthof L, Schmidt A, Piwowarski P, Yang Y, Stensitzki T, Adam S, Bartl F, Schapiro I, Heyne K, Siebert F, Scheerer P, Mroginski MA, Hildebrandt P. Intramolecular Proton Transfer Controls Protein Structural Changes in Phytochrome. Biochemistry 2020; 59:1023-1037. [DOI: 10.1021/acs.biochem.0c00053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anastasia Kraskov
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anh Duc Nguyen
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Jan Goerling
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Fernandez Lopez
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Luisa Sauthof
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Andrea Schmidt
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Patrick Piwowarski
- Humboldt Universität zu Berlin, Institut für Biologie, Experimentelle Biophysik, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Yang Yang
- Freie Universität Berlin, Experimentelle Physik, Arnimallee 14, D-14195 Berlin, Germany
| | - Till Stensitzki
- Freie Universität Berlin, Experimentelle Physik, Arnimallee 14, D-14195 Berlin, Germany
| | - Suliman Adam
- Institute of Chemistry, Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Franz Bartl
- Humboldt Universität zu Berlin, Institut für Biologie, Experimentelle Biophysik, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Igor Schapiro
- Institute of Chemistry, Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Karsten Heyne
- Freie Universität Berlin, Experimentelle Physik, Arnimallee 14, D-14195 Berlin, Germany
| | - Friedrich Siebert
- Albert-Ludwigs-Universität Freiburg, Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Hermann-Herderstraße 9, D-79104 Freiburg, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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8
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Buhrke D, Gourinchas G, Müller M, Michael N, Hildebrandt P, Winkler A. Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase. J Biol Chem 2019; 295:539-551. [PMID: 31801828 PMCID: PMC6956517 DOI: 10.1074/jbc.ra119.011915] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/04/2019] [Indexed: 01/31/2023] Open
Abstract
Sensing of red and far-red light by bacteriophytochromes involves intricate interactions between their bilin chromophore and the protein environment. The light-triggered rearrangements of the cofactor configuration and eventually the protein conformation enable bacteriophytochromes to interact with various protein effector domains for biological modulation of diverse physiological functions. Excitation of the holoproteins by red or far-red light promotes the photoconversion to their far-red light–absorbing Pfr state or the red light-absorbing Pr state, respectively. Because prototypical bacteriophytochromes have a parallel dimer architecture, it is generally assumed that symmetric activation with two Pfr state protomers constitutes the signaling-active species. However, the bacteriophytochrome from Idiomarina species A28L (IsPadC) has recently been reported to enable long-range signal transduction also in asymmetric dimers containing only one Pfr protomer. By combining crystallography, hydrogen–deuterium exchange coupled to MS, and vibrational spectroscopy, we show here that Pfr of IsPadC is in equilibrium with an intermediate “Pfr-like” state that combines features of Pfr and Meta-R states observed in other bacteriophytochromes. We also show that structural rearrangements in the N-terminal segment (NTS) can stabilize this Pfr-like state and that the PHY-tongue conformation of IsPadC is partially uncoupled from the initial changes in the NTS. This uncoupling enables structural asymmetry of the overall homodimeric assembly and allows signal transduction to the covalently linked physiological diguanylate cyclase output module in which asymmetry might play a role in the enzyme-catalyzed reaction. The functional differences to other phytochrome systems identified here highlight opportunities for using additional red-light sensors in artificial sensor–effector systems.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany.
| | - Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Melanie Müller
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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Thomas R, Waickman A, Ehrenberg P, Geretz A, Eller M, Tovanabutra S, Ananworanich J, Chomont N, Currier J, Michael N. Single cell RNA-seq identifies host genes that correlate with HIV-1 reservoir size. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30176-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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10
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Hsu D, Silsorn D, Imerbsin R, Pegu A, Mascola J, Geleziunas R, Koup R, Barouch D, Michael N, Vasan S. Delay in viral rebound with TLR7 agonist, N6-LS and PGT121 in SHIV-infected macaques. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30111-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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11
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Fernandez Lopez M, Nguyen AD, Velazquez Escobar F, González R, Michael N, Nogacz Ż, Piwowarski P, Bartl F, Siebert F, Heise I, Scheerer P, Gärtner W, Mroginski MA, Hildebrandt P. Role of the Propionic Side Chains for the Photoconversion of Bacterial Phytochromes. Biochemistry 2019; 58:3504-3519. [DOI: 10.1021/acs.biochem.9b00526] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Maria Fernandez Lopez
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anh Duc Nguyen
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ronald González
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Żaneta Nogacz
- Humboldt Universität zu Berlin, Institut für Biologie, Biophysikalische Chemie, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Patrick Piwowarski
- Humboldt Universität zu Berlin, Institut für Biologie, Biophysikalische Chemie, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Franz Bartl
- Humboldt Universität zu Berlin, Institut für Biologie, Biophysikalische Chemie, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Friedrich Siebert
- Albert-Ludwigs-Universität Freiburg, Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Hermann-Herderstraße 9, D-79104 Freiburg, Germany
| | - Inge Heise
- Max Planck Institut für Chemische Energiekonversion, Stiftstraße 34-36, D-45470 Mülheim, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, D-10117 Berlin, Germany
| | - Wolfgang Gärtner
- Max Planck Institut für Chemische Energiekonversion, Stiftstraße 34-36, D-45470 Mülheim, Germany
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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Schmidt A, Sauthof L, Szczepek M, Lopez MF, Escobar FV, Qureshi BM, Michael N, Buhrke D, Stevens T, Kwiatkowski D, von Stetten D, Mroginski MA, Krauß N, Lamparter T, Hildebrandt P, Scheerer P. Structural snapshot of a bacterial phytochrome in its functional intermediate state. Nat Commun 2018; 9:4912. [PMID: 30464203 PMCID: PMC6249285 DOI: 10.1038/s41467-018-07392-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/31/2018] [Indexed: 11/09/2022] Open
Abstract
Phytochromes are modular photoreceptors of plants, bacteria and fungi that use light as a source of information to regulate fundamental physiological processes. Interconversion between the active and inactive states is accomplished by a photoinduced reaction sequence which couples the sensor with the output module. However, the underlying molecular mechanism is yet not fully understood due to the lack of structural data of functionally relevant intermediate states. Here we report the crystal structure of a Meta-F intermediate state of an Agp2 variant from Agrobacterium fabrum. This intermediate, the identity of which was verified by resonance Raman spectroscopy, was formed by irradiation of the parent Pfr state and displays significant reorientations of almost all amino acids surrounding the chromophore. Structural comparisons allow identifying structural motifs that might serve as conformational switch for initiating the functional secondary structure change that is linked to the (de-)activation of these photoreceptors.
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Affiliation(s)
- Andrea Schmidt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany
| | - Luisa Sauthof
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany
| | - Michal Szczepek
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany
| | - Maria Fernandez Lopez
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623, Germany
| | - Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623, Germany
| | - Bilal M Qureshi
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany
- Division of Biological & Environmental Sciences & Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623, Germany
| | - David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623, Germany
| | - Tammo Stevens
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany
| | - Dennis Kwiatkowski
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220 F-38043, Grenoble Cedex 9, France
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, Hamburg, D-22607, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623, Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Fritz-Haber-Weg 4, Karlsruhe, D-76131, Germany
| | - Tilman Lamparter
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Fritz-Haber-Weg 4, Karlsruhe, D-76131, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623, Germany.
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany.
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Losi A, Bonomi HR, Michael N, Tang K, Zhao KH. Time-Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome-Related Photoreceptors. Photochem Photobiol 2018; 93:733-740. [PMID: 28500712 DOI: 10.1111/php.12728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022]
Abstract
Time-resolved photoacoustics (PA) is uniquely able to explore the energy landscape of photoactive proteins and concomitantly detects light-induced volumetric changes (ΔV) accompanying the formation and decay of transient species in a time window between ca. 20 ns and 5 μs. Here, we report PA measurements on diverse photochromic bilin-binding photoreceptors of prokaryotic origin: (1) the chromophore-binding GAF3 domain of the red (R)/green (G) switching cyanobacteriochrome 1393 (Slr1393g3) from Synechocystis; (2) the red/far red (R/FR) Synechocystis Cph1 phytochrome; (3) full-length and truncated constructs of Xanthomonas campestris bacteriophytochrome (XccBphP), absorbing up to the NIR spectral region. In almost all cases, photoisomerization results in a large fraction of energy dissipated as heat (up to 90%) on the sub-ns scale, reflecting the low photoisomerization quantum yield (<0.2). This "prompt" step is accompanied by a positive ΔV1 = 5-12.5 mL mol-1 . Formation of the first intermediate is the sole process accessible to PA, with the notable exception of Slr1393g3-G for which ΔV1 = +4.5 mL mol-1 is followed by a time-resolved, energy-conserving contraction ΔV2 = -11.4 mL mol-1 , τ2 = 180 ns at 2.4°C. This peculiarity is possibly due to a larger solvent occupancy of the chromophore cavity for Slr1393g3-G.
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Affiliation(s)
- Aba Losi
- Department of Physics and Earth Science, University of Parma, Parma, Italy
| | - Hernán R Bonomi
- Immunology and Molecular Microbiology Laboratory, Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Norbert Michael
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Kun Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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Biava H, Schreiber T, Katz S, Völler JS, Stolarski M, Schulz C, Michael N, Budisa N, Kozuch J, Utesch T, Hildebrandt P. Long-Range Modulations of Electric Fields in Proteins. J Phys Chem B 2018; 122:8330-8342. [PMID: 30109934 DOI: 10.1021/acs.jpcb.8b03870] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Electrostatic interactions are essential for controlling the protein structure and function. Whereas so far experimental and theoretical efforts focused on the effect of local electrostatics, this work aims at elucidating the long-range modulation of electric fields in proteins upon binding to charged surfaces. The study is based on cytochrome c (Cytc) variants carrying nitrile reporters for the vibrational Stark effect that are incorporated into the protein via genetic engineering and chemical modification. The Cytc variants were thoroughly characterized with respect to possible structural perturbations due to labeling. For the proteins in solution, the relative hydrogen bond occupancy and the calculated electric fields, both obtained from molecular dynamics (MD) simulations, and the experimental nitrile stretching frequencies were used to develop a relationship for separating hydrogen-bonding and non-hydrogen-bonding electric field effects. This relationship provides an excellent description for the stable Cytc variants in solution. For the proteins bound to Au electrodes coated with charged self-assembled monolayers (SAMs), the underlying MD simulations can only account for the electric field changes Δ Eads due to the formation of the electrostatic SAM-Cytc complexes but not for the additional contribution, Δ Eint, representing the consequences of the potential drops over the electrode/SAM/protein interfaces. Both Δ Eads and Δ Eint, determined at distances between 20 and 30 Å with respect to the SAM surface, are comparable in magnitude to the non-hydrogen-bonding electric field in the unbound protein. This long-range modulation of the internal electric field may be of functional relevance for proteins in complexes with partner proteins (Δ Eads) and attached to membranes (Δ Eads + Δ Eint).
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Affiliation(s)
- Hernan Biava
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Toni Schreiber
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Sagie Katz
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Jan-Stefan Völler
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Michael Stolarski
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Claudia Schulz
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Norbert Michael
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Nediljko Budisa
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Jacek Kozuch
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Tillmann Utesch
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Peter Hildebrandt
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
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Buhrke D, Kuhlmann U, Michael N, Hildebrandt P. The Photoconversion of Phytochrome Includes an Unproductive Shunt Reaction Pathway. Chemphyschem 2018; 19:566-570. [DOI: 10.1002/cphc.201701311] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Indexed: 11/08/2022]
Affiliation(s)
- David Buhrke
- Institut für Chemie, Sekr. PC14; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Germany
| | - Uwe Kuhlmann
- Institut für Chemie, Sekr. PC14; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Germany
| | - Norbert Michael
- Institut für Chemie, Sekr. PC14; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Sekr. PC14; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Germany
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16
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Velázquez Escobar F, Buhrke D, Michael N, Sauthof L, Wilkening S, Tavraz NN, Salewski J, Frankenberg-Dinkel N, Mroginski MA, Scheerer P, Friedrich T, Siebert F, Hildebrandt P. Common Structural Elements in the Chromophore Binding Pocket of the Pfr State of Bathy Phytochromes. Photochem Photobiol 2017; 93:724-732. [DOI: 10.1111/php.12742] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/06/2017] [Indexed: 01/17/2023]
Affiliation(s)
| | - David Buhrke
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | - Norbert Michael
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | - Luisa Sauthof
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
- Institute of Medical Physics and Biophysics (CCO); Group Protein X-ray Crystallography & Signal Transduction; Charité - University Medicine Berlin; Berlin Germany
| | - Svea Wilkening
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | | | | | - Nicole Frankenberg-Dinkel
- Fachbereich Biologie; Abt. Mikrobiologie; Technische Universität Kaiserslautern; Kaiserslautern Germany
| | | | - Patrick Scheerer
- Institute of Medical Physics and Biophysics (CCO); Group Protein X-ray Crystallography & Signal Transduction; Charité - University Medicine Berlin; Berlin Germany
| | - Thomas Friedrich
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | - Friedrich Siebert
- Institut für Molekulare Medizin und Zellforschung; Sektion Biophysik; Albert-Ludwigs-Universität Freiburg; Freiburg Germany
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17
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Kissane DW, Bobevski I, Gaitanis P, Brooker J, Michael N, Lethborg C, Richardson G, Webster P, Hempton C. Exploratory examination of the utility of demoralization as a diagnostic specifier for adjustment disorder and major depression. Gen Hosp Psychiatry 2017. [PMID: 28622810 DOI: 10.1016/j.genhosppsych.2017.01.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Demoralization, a state of lowered morale and poor coping, has a prevalence of 13-18% among patients with advanced cancer. We surveyed clinicians' perspectives of the utility of "with demoralization" as a diagnostic specifier for adjustment and depressive disorders. METHOD Using comparative clinical vignettes in a field survey, clinicians from a range of disciplines were asked their perception of the utility of diagnosis and treatment options. Response frequencies were compared using Cochran's Q and McNemar's tests, with sensitivity and specificity rated against expert rankings of diagnosis. Analysis of variance and paired t-tests examined significant differences in ratings of utility. RESULTS Vignettes were assessed by 280 clinicians; 77% supported utility of the category 'adjustment disorder with demoralization' compared to 33% supporting 'adjustment disorder with anxiety' (McNemar test, p<0.001), while 83% supported the utility of 'with demoralization' for major depressive episode, matching 83% perceiving utility for 'with melancholia.' Sensitivity and specificity ratings were 77% and 94% for adjustment disorder with demoralization and 83% and 91% for major depression with demoralization. CONCLUSION Clinicians perceived the specifier 'with demoralization' to deepen diagnostic understanding, treatment choice, and ability to communicate with clinicians and patients, particularly for the category of adjustment disorder with demoralization.
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Affiliation(s)
- D W Kissane
- Department of Psychiatry, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia; Szalmuk Family Psycho-Oncology Research Unit, Cabrini Health, Malvern, VIC, Australia.
| | - I Bobevski
- Department of Psychiatry, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - P Gaitanis
- Department of Psychiatry, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - J Brooker
- Department of Psychiatry, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia; Szalmuk Family Psycho-Oncology Research Unit, Cabrini Health, Malvern, VIC, Australia
| | - N Michael
- Palliative Care Research Department, Cabrini Health, Malvern, VIC, Australia; University of Notre Dame, Sydney School of Medicine, Sydney, Australia
| | - C Lethborg
- Department of Psychiatry, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia; Department of Oncology, St Vincent's Hospital Melbourne, Fitzroy, VIC, Australia
| | - G Richardson
- Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia; Department of Oncology, Cabrini Health, Malvern, VIC, Australia
| | - P Webster
- Department of General Practice, Monash University, Clayton, VIC, Australia
| | - C Hempton
- Department of Psychiatry, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia; Szalmuk Family Psycho-Oncology Research Unit, Cabrini Health, Malvern, VIC, Australia
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18
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Krauß N, Nagano S, Scheerer P, Zubow K, Michael N, Inomata K, Lamparter T. Structures of the photosensory core module of bacteriophytochrome Agp1 from two crystal forms reveal plasticity of the Pr state. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Nagano S, Scheerer P, Zubow K, Michael N, Inomata K, Lamparter T, Krauß N. The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers. J Biol Chem 2016; 291:20674-91. [PMID: 27466363 DOI: 10.1074/jbc.m116.739136] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 11/06/2022] Open
Abstract
Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion.
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Affiliation(s)
- Soshichiro Nagano
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Patrick Scheerer
- the Institute of Medical Physics and Biophysics (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Kristina Zubow
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Norbert Michael
- the Institut für Chemie, Technische Universität Berlin, Sekretariat PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Katsuhiko Inomata
- the Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan, and
| | - Tilman Lamparter
- the Botanical Institute, Karlsruhe Institute of Technology (KIT), Kaiserstraße 2, D-76131 Karlsruhe, Germany
| | - Norbert Krauß
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom, the Botanical Institute, Karlsruhe Institute of Technology (KIT), Kaiserstraße 2, D-76131 Karlsruhe, Germany
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O’Callaghan C, Baird A, Michael N. O-47 “A useful icebreaker” or “jumping the gun”: examining the usefulness of the vignette technique in cancer specific advance care planning. BMJ Support Palliat Care 2015. [DOI: 10.1136/bmjspcare-2015-000978.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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21
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Velazquez Escobar F, von Stetten D, Günther-Lütkens M, Keidel A, Michael N, Lamparter T, Essen LO, Hughes J, Gärtner W, Yang Y, Heyne K, Mroginski MA, Hildebrandt P. Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes. Front Mol Biosci 2015. [PMID: 26217669 PMCID: PMC4498102 DOI: 10.3389/fmolb.2015.00037] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Phytochromes are biological photoreceptors that can be reversibly photoconverted between a dark and photoactivated state. The underlying reaction sequences are initiated by the photoisomerization of the tetrapyrrole cofactor, which in plant and cyanobacterial phytochromes are a phytochromobilin (PΦB) and a phycocyanobilin (PCB), respectively. The transition between the two states represents an on/off-switch of the output module activating or deactivating downstream physiological processes. In addition, the photoactivated state, i.e., Pfr in canonical phytochromes, can be thermally reverted to the dark state (Pr). The present study aimed to improve our understanding of the specific reactivity of various PΦB- and PCB-binding phytochromes in the Pfr state by analysing the cofactor structure by vibrational spectroscopic techniques. Resonance Raman (RR) spectroscopy revealed two Pfr conformers (Pfr-I and Pfr-II) forming a temperature-dependent conformational equilibrium. The two sub-states—found in all phytochromes studied, albeit with different relative contributions—differ in structural details of the C-D and A-B methine bridges. In the Pfr-I sub-state the torsion between the rings C and D is larger by ca. 10° compared to Pfr-II. This structural difference is presumably related to different hydrogen bonding interactions of ring D as revealed by time-resolved IR spectroscopic studies of the cyanobacterial phytochrome Cph1. The transitions between the two sub-states are evidently too fast (i.e., nanosecond time scale) to be resolved by NMR spectroscopy which could not detect a structural heterogeneity of the chromophore in Pfr. The implications of the present findings for the dark reversion of the Pfr state are discussed.
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Affiliation(s)
| | | | | | - Anke Keidel
- Institut für Chemie, Technische Universität Berlin Berlin, Germany
| | - Norbert Michael
- Institut für Chemie, Technische Universität Berlin Berlin, Germany
| | - Tilman Lamparter
- Botanisches Institut, Karlsruher Institut für Technologie Karlsruhe, Germany
| | | | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus Liebig University Gießen, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institut für Chemische Energiekonversion Mülheim, Germany
| | - Yang Yang
- Institut für Experimentalphysik, Freie Universität Berlin Berlin, Germany
| | - Karsten Heyne
- Institut für Experimentalphysik, Freie Universität Berlin Berlin, Germany
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Velazquez Escobar F, Piwowarski P, Salewski J, Michael N, Fernandez Lopez M, Rupp A, Qureshi BM, Scheerer P, Bartl F, Frankenberg-Dinkel N, Siebert F, Andrea Mroginski M, Hildebrandt P. A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes. Nat Chem 2015; 7:423-30. [DOI: 10.1038/nchem.2225] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 03/02/2015] [Indexed: 11/09/2022]
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Velazquez Escobar F, Hildebrandt T, Utesch T, Schmitt FJ, Seuffert I, Michael N, Schulz C, Mroginski MA, Friedrich T, Hildebrandt P. Structural parameters controlling the fluorescence properties of phytochromes. Biochemistry 2013; 53:20-9. [PMID: 24328165 DOI: 10.1021/bi401287u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Phytochromes constitute a class of photoreceptors that can be photoconverted between two stable states. The tetrapyrrole chromophore absorbs in the red spectral region and displays fluorescence maxima above 700 nm, albeit with low quantum yields. Because this wavelength region is particularly advantageous for fluorescence-based deep tissue imaging, there is a strong interest to engineer phytochrome variants with increased fluorescence yields. Such targeted design efforts would substantially benefit from a deeper understanding of those structural parameters that control the photophysical properties of the protein-bound chromophore. Here we have employed resonance Raman (RR) spectroscopy and molecular dynamics simulations for elucidating the chromophore structural changes in a fluorescence-optimized mutant (iRFP) derived from the PAS-GAF domain of the bacteriophytochrome RpBphP2 from Rhodopseudomas palustris . Both methods consistently reveal the structural consequences of the amino acid substitutions in the vicinity of the biliverdin chromophore that may account for lowering the propability of nonradiative excited state decays. First, compared to the wild-type protein, the tilt angle of the terminal ring D with respect to ring C is increased in iRFP, accompanied by the loss of hydrogen bond interactions of the ring D carbonyl function and the reduction of the number of water molecules in that part of the chromophore pocket. Second, the overall flexibility of the chromophore is significantly reduced, particularly in the region of rings D and A, thereby reducing the conformational heterogeneity of the methine bridge between rings A and B and the ring A carbonyl group, as concluded from the RR spectra of the wild-type proteins.
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Affiliation(s)
- Francisco Velazquez Escobar
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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Michael N, Stepanov N, Spruyt O, Pollard A, Clayton J, O'Callaghan C. UNDERSTANDING HOW CANCER PATIENTS ACTUALISE, RELINQUISH, AND REJECT ADVANCE CARE PLANNING: IMPLICATIONS FOR PRACTICE. BMJ Support Palliat Care 2013. [DOI: 10.1136/bmjspcare-2013-000491.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Michael N, Hiscock N, Baird A, O'Callaghan C. AN EXPLORATORY STUDY ON THE VIEWS OF CANCER PATIENTS' INFORMAL CAREGIVERS ABOUT ADVANCE CARE PLANNING. BMJ Support Palliat Care 2013. [DOI: 10.1136/bmjspcare-2013-000491.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Salewski J, Escobar FV, Kaminski S, von Stetten D, Keidel A, Rippers Y, Michael N, Scheerer P, Piwowarski P, Bartl F, Frankenberg-Dinkel N, Ringsdorf S, Gärtner W, Lamparter T, Mroginski MA, Hildebrandt P. Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes. J Biol Chem 2013; 288:16800-16814. [PMID: 23603902 DOI: 10.1074/jbc.m113.457531] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion.
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Affiliation(s)
- Johannes Salewski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Francisco Velazquez Escobar
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Steve Kaminski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - David von Stetten
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany; Structural Biology Group, European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Anke Keidel
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Michael
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Protein X-ray Crystallography, D-10117 Berlin, Germany
| | - Patrick Piwowarski
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Franz Bartl
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Nicole Frankenberg-Dinkel
- AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Simone Ringsdorf
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Tilman Lamparter
- Institut für Allgemeine Botanik, Karlsruher Institut für Technologie, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
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Sarikaya H, Yilmaz M, Michael N, Miserez AR, Steinmann B, Baumgartner RW. Zurich Fabry study - prevalence of Fabry disease in young patients with first cryptogenic ischaemic stroke or TIA. Eur J Neurol 2012; 19:1421-6. [DOI: 10.1111/j.1468-1331.2012.03737.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 03/02/2012] [Indexed: 01/30/2023]
Affiliation(s)
- H. Sarikaya
- Department of Neurology; University Hospital of Zürich; Zurich Switzerland
| | - M. Yilmaz
- Department of Neurology; University Hospital of Zürich; Zurich Switzerland
| | - N. Michael
- Department of Neurology; University Hospital of Zürich; Zurich Switzerland
| | | | - B. Steinmann
- Division of Metabolism; University Children's Hospital; Zurich Switzerland
| | - R. W. Baumgartner
- Department of Neurology; University Hospital of Zürich; Zurich Switzerland
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Mutengu LN, Kibuuka H, Millard M, Sekiziyivu A, Wakabi S, Nanyondo J, Kawooya G, Robb M, Michael N. Referral and access to care of HIV prevalent cases; experience from the early capture HIV cohort study in Kampala. Retrovirology 2012. [PMCID: PMC3441750 DOI: 10.1186/1742-4690-9-s2-o28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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29
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Hu H, Nau M, Ehrenberg P, Chenine A, Daye Z, Wei Z, Michael N, Vahey M, Kim J, Marovich M, Ratto-Kim S. Distinct gene expression profiles associated with the susceptibility of pathogen-specific CD4+ T cells to HIV-1 infection. Retrovirology 2012. [PMCID: PMC3441412 DOI: 10.1186/1742-4690-9-s2-o46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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30
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Pollara J, Bonsignori M, Moody M, Alam M, Liao H, Hwang K, Pickeral J, Kappes J, Ochsenbauer C, Soderberg K, Gurley TC, Kozink DM, Marshall DJ, Whitesides JF, Montefiori D, Robinson JE, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Kim J, Michael N, Tomaras G, Haynes BF, Ferrari G. Vaccine-induced ADCC-mediating antibodies target unique and overlapping envelope epitopes. Retrovirology 2012. [PMCID: PMC3441773 DOI: 10.1186/1742-4690-9-s2-o39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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31
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Chung A, Dugast A, Robinson H, Chan Y, Ackerman ME, Cox J, Koff W, Barouch D, Rerks-Ngarm S, Michael N, Kim J, Alter G. Vector induced skewing of antibody Fc-effector functions. Retrovirology 2012. [PMCID: PMC3442037 DOI: 10.1186/1742-4690-9-s2-p361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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32
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Slike BM, Tassaneetrithep B, Nitayaphan S, Rono K, Sanga E, Sekiziyivu A, Stablein D, Eller L, Eller MA, Kim J, Michael N, Robb M, Marovich M. Early immune events during acute HIV infection. Retrovirology 2012. [PMCID: PMC3441840 DOI: 10.1186/1742-4690-9-s2-p181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Franchini G, Pegu P, Gordon S, Keele B, Doster M, Guan Y, Ferrari G, Pal R, Ferrari MG, Whitney S, Hudacik L, Billings E, Rao M, Montefiori D, Venzon D, Fenizia C, Lifson J, Stablein D, Tartaglia J, Michael N, Kim J. Antibodies to the envelope protein protect macaques from SIVmac251 acquisition in an immunization regimen that mimics the RV-144 Thai trial. Retrovirology 2012. [PMCID: PMC3441518 DOI: 10.1186/1742-4690-9-s2-o2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Kibuuka HN, Rono K, Maganga L, Millard M, Sekiziyivu A, Maboko L, Shaffer D, Valenzuela A, Michael N, Robb M. Pattern of HIV risk behavior in a cohort of high risk women in East Africa. Retrovirology 2012. [PMCID: PMC3441943 DOI: 10.1186/1742-4690-9-s2-p124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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Cincotta CDM, Wieczorek LM, Barrows B, Brown B, Asher L, Michael N, Marovich M, Polonis VR. The impact of differences in viral entry and trafficking on the mechanism of HIV-1 neutralization. Retrovirology 2012. [PMCID: PMC3442047 DOI: 10.1186/1742-4690-9-s2-p58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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36
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Wieczorek L, Rao M, Peachman K, Steers N, Marovich M, Michael N, Polonis V, Rao V. Immunogenic selection of HIV-1 MPER epitopes for improved vaccine design. Retrovirology 2012. [PMCID: PMC3441291 DOI: 10.1186/1742-4690-9-s2-p322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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37
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Polonis V, Wieczorek L, Kalyanaraman V, Matyas G, Whitney S, Williams C, Tovanabutra S, Sanders-Buell E, Wesberry M, Ochsenbauer C, Chenine A, Rao M, Tong T, Alving C, Cheng H, Zolla-Pazner S, Michael N, VanCott T, Marovich M. Antigenicity and immunogenicity of a novel, acute HIV-1 Tanzanian subtype C gp145 envelope protein for clinical development. Retrovirology 2012. [PMCID: PMC3441268 DOI: 10.1186/1742-4690-9-s2-p323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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38
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Zwanzger P, Zavorotnyy M, Diemer J, Ruland T, Domschke K, Christ M, Michael N, Pfleiderer B. Auditory processing in remitted major depression: a long-term follow-up investigation using 3T-fMRI. J Neural Transm (Vienna) 2012; 119:1565-73. [DOI: 10.1007/s00702-012-0871-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 07/20/2012] [Indexed: 11/24/2022]
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39
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Piwowarski P, Ritter E, Hofmann KP, Hildebrandt P, von Stetten D, Scheerer P, Michael N, Lamparter T, Bartl F. Light-induced activation of bacterial phytochrome Agp1 monitored by static and time-resolved FTIR spectroscopy. Chemphyschem 2010; 11:1207-14. [PMID: 20333618 DOI: 10.1002/cphc.200901008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phytochromes, which regulate many biological processes in plants, bacteria, and fungi, can exist in two stable states, Pr and Pfr, that can be interconverted by light, via a number of intermediates such as meta-Rc. Herein we employ FTIR spectroscopy to study the Pr-to-Pfr conversion of the bacteriophytochrome Agp1 from Agrobacterium tumefaciens. Static FTIR Pfr/Pr and meta-Rc/Pr difference spectra are disentangled in terms of cofactor and protein structural changes. Guided by DFT calculations on cofactor models, the chromophore conformational changes can be grouped into structural adjustments of the cofactor-protein interactions localized in the C-D dipyrrole moiety, that is, the photoisomerisation site, and in the A-B dipyrrole moiety including the protein attachment site. Whereas changes at the C and D rings appear to be largely completed in the meta-Rc state, the structural changes in the A-B unit occur during the transition from meta-Rc to Pfr, concomitant with the main protein structural changes, as demonstrated by static and time-resolved FTIR difference spectroscopy. We employ this technique to monitor, for the first time, the dynamics of the photocycle of phytochrome on the millisecond timescale. By extending the studies to genetically engineered protein variants of Agp1, we further demonstrate that H250 and D197 as well as the PHY domain are essential for formation of the Pfr state. Based on the IR spectroscopic and available crystallographic data we discuss the role of critical amino acid residues for the protein-cofactor interactions during the photoinduced reaction cycle.
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Affiliation(s)
- Patrick Piwowarski
- Institut für Medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10098 Berlin, Germany
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Scheerer P, Michael N, Park JH, Nagano S, Choe HW, Inomata K, Borucki B, Krauß N, Lamparter T. Light-Induced Conformational Changes of the Chromophore and the Protein in Phytochromes: Bacterial Phytochromes as Model Systems. Chemphyschem 2010; 11:1090-105. [DOI: 10.1002/cphc.200900913] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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41
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Mariottini G, Morbidi F, Prattichizzo D, Vander Valk N, Michael N, Pappas G, Daniilidis K. Vision-Based Localization for Leader–Follower Formation Control. IEEE T ROBOT 2009. [DOI: 10.1109/tro.2009.2032975] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Bakari M, Aboud S, Nilsson C, Francis J, Buma D, Moshiro C, Aris EA, Lyamuya E, Janabi M, Mbwana J, Mwanyika L, Stout R, Hejdeman B, Brave A, Robb M, Marovich M, Michael N, Earl P, Moss B, Wahren B, Biberfeld G, Pallangyo K, Mhalu F, Sandstrom E. P14-14 LB. A low dose of multigene, multiclade HIV DNA given intradermally induces strong and broad immune responses after boosting with heterologous HIV MVA. Retrovirology 2009. [PMCID: PMC2767919 DOI: 10.1186/1742-4690-6-s3-p403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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43
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Currier JR, De Souza M, Ratto-Kim S, Paris R, Nguay V, Cox J, Earl P, Moss B, Sriplienchan S, Thongcharoen P, Kim J, Robb M, Michael N, Marovich M. OA04-03. Characterization of cell-mediated immune responses generated by recombinant modified vaccinia Ankara (rMVA)-HIV-1 in a phase I vaccine trial. Retrovirology 2009. [PMCID: PMC2767548 DOI: 10.1186/1742-4690-6-s3-o27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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44
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Zavorotnyy M, Zwanzger P, Diemer J, Christ M, Michael N, Arolt V, Pfleiderer B. Altered Auditive Processing as a Possible Trait-Marker of Major Depressive Disorder. Pharmacopsychiatry 2009. [DOI: 10.1055/s-0029-1240258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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45
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Moshtagh N, Michael N, Jadbabaie A, Daniilidis K. Vision-Based, Distributed Control Laws for Motion Coordination of Nonholonomic Robots. IEEE T ROBOT 2009. [DOI: 10.1109/tro.2009.2022439] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Tollkötter M, Sörös P, Michael N, Pfleiderer B. 129. Effects of antidepressive therapy on auditory processing on auditory processing in severely depressed patients: A combined MRS and MEG study. Clin Neurophysiol 2009. [DOI: 10.1016/j.clinph.2008.07.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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47
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Krieger A, Molina I, Oberpichler I, Michael N, Lamparter T. Spectral properties of phytochrome Agp2 from Agrobacterium tumefaciens are specifically modified by a compound of the cell extract. Journal of Photochemistry and Photobiology B: Biology 2008; 93:16-22. [DOI: 10.1016/j.jphotobiol.2008.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 05/24/2008] [Accepted: 07/04/2008] [Indexed: 11/29/2022]
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48
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Tollkötter M, Sörös P, Michael N, Pfleiderer B. Effects of antidepressive therapy on auditory processing on auditory processing in severely depressed patients: A combined MRS and MEG study. KLIN NEUROPHYSIOL 2008. [DOI: 10.1055/s-2008-1072923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Werth E, Michael N, Siccoli M, Bassetti C. Behaviourally induced insufficient sleep syndrome: A case series of 31 patients. Clin Neurophysiol 2008. [DOI: 10.1016/j.clinph.2007.09.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Schumann C, Gross R, Michael N, Lamparter T, Diller R. Sub-picosecond mid-infrared spectroscopy of phytochrome Agp1 from Agrobacterium tumefaciens. Chemphyschem 2007; 8:1657-63. [PMID: 17614346 DOI: 10.1002/cphc.200700210] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The photoinduced primary reaction of the biliverdin binding phytochrome Agp1 (Agp1-BV) from Agrobacterium tumefaciens was investigated by sub-picosecond time-resolved Vis pump-IR probe spectroscopy. Three time constants of tau(1)=0.7+/-0.05 ps, tau(2)=3.3+/-0.2 ps and tau(3)=33.3+/-1.5 ps could be isolated from the dynamics of structurally specific marker bands of the BV chromophore. These results together with those of accompanying sub-picosecond Vis pump-Vis probe spectroscopy allow the extension of the reaction scheme for the primary process by a vibrationally excited electronic ground state. The isomerization at the C15=C16 bond occurs within the lifetime of the excited electronic state. A quantum yield of 0.094 for the primary reaction is determined, suggesting that the quantum yield of formation of the P(fr) far-red-absorbing form is already established in the primary photoreaction of the P(r) (red-absorbing) form.
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Affiliation(s)
- Christian Schumann
- Technische Universität Kaiserslautern, Fachbereich Physik, 67653 Kaiserslautern, Germany
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