1
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Hildebrandt P. Vibrational Spectroscopy of Phytochromes. Biomolecules 2023; 13:1007. [PMID: 37371587 DOI: 10.3390/biom13061007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Phytochromes are biological photoswitches that translate light into physiological functions. Spectroscopic techniques are essential tools for molecular research into these photoreceptors. This review is directed at summarizing how resonance Raman and IR spectroscopy contributed to an understanding of the structure, dynamics, and reaction mechanism of phytochromes, outlining the substantial experimental and theoretical challenges and describing the strategies to master them. It is shown that the potential of the various vibrational spectroscopic techniques can be most efficiently exploited using integral approaches via a combination of theoretical methods as well as other experimental techniques.
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Affiliation(s)
- Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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2
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Yang Y, Stensitzki T, Lang C, Hughes J, Mroginski MA, Heyne K. Ultrafast protein response in the Pfr state of Cph1 phytochrome. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023; 22:919-930. [PMID: 36653574 DOI: 10.1007/s43630-023-00362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
Photoisomerization is a fundamental process in several classes of photoreceptors. Phytochromes sense red and far-red light in their Pr and Pfr states, respectively. Upon light absorption, these states react via individual photoreactions to the other state. Cph1 phytochrome shows a photoisomerization of its phycocyanobilin (PCB) chromophore in the Pfr state with a time constant of 0.7 ps. The dynamics of the PCB chromophore has been described, but whether or not the apoprotein exhibits an ultrafast response too, is not known. Here, we compare the photoreaction of 13C/15N labeled apoprotein with unlabeled apoprotein to unravel ultrafast apoprotein dynamics in Cph1. In the spectral range from 1750 to 1620 cm-1 we assigned several signals due to ultrafast apoprotein dynamics. A bleaching signal at 1724 cm-1 is tentatively assigned to deprotonation of a carboxylic acid, probably Asp207, and signals around 1670 cm-1 are assigned to amide I vibrations of the capping helix close to the chromophore. These signals remain after photoisomerization. The apoprotein dynamics appear upon photoexcitation or concomitant with chromophore isomerization. Thus, apoprotein dynamics occur prior to and after photoisomerization on an ultrafast time-scale. We discuss the origin of the ultrafast apoprotein response with the 'Coulomb hammer' mechanism, i.e. an impulsive change of electric field and Coulombic force around the chromophore upon excitation.
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Affiliation(s)
- Yang Yang
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Till Stensitzki
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Maria Andrea Mroginski
- Institut Für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Karsten Heyne
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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3
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Fischer T, van Wilderen LJGW, Gnau P, Bredenbeck J, Essen LO, Wachtveitl J, Slavov C. Ultrafast Photoconversion Dynamics of the Knotless Phytochrome SynCph2. Int J Mol Sci 2021; 22:ijms221910690. [PMID: 34639031 PMCID: PMC8508867 DOI: 10.3390/ijms221910690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/03/2022] Open
Abstract
The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast Pr ⇆ Pfr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of Pr* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow Pr* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The Pfr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes.
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Affiliation(s)
- Tobias Fischer
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
| | - Luuk J. G. W. van Wilderen
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Petra Gnau
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
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4
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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] [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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5
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Wang D, Qin Y, Zhang S, Wang L, Yang X, Zhong D. Elucidating the Molecular Mechanism of Ultrafast Pfr-State Photoisomerization in Bathy Bacteriophytochrome PaBphP. J Phys Chem Lett 2019; 10:6197-6201. [PMID: 31577445 PMCID: PMC7268903 DOI: 10.1021/acs.jpclett.9b02446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bacteriophytochromes are photoreceptors that regulate various physiological processes induced by photoisomerization in a linear tetrapyrrole chromophore upon red/far-red light absorption. Here, we investigate the photoinduced Pfr-state isomerization mechanism of a bathy bacteriophytochrome from Pseudomonas aeruginosa combining femtosecond-resolved fluorescence and absorption methods. We observed initial coherent oscillation motions in the first 1 ps with low-frequency modes below 60 cm-1, then a bifurcation of the wavepacket with the distinct excited-state lifetimes in a few picoseconds, and finally chromophore-protein coupled ground-state conformational evolution on nanosecond time scales. Together with systematic mutational studies, we revealed the critical roles of hydrogen bonds in tuning the photoisomerization dynamics. These results provide a clear molecular picture of the Pfr-state photoisomerization, a mechanism likely applicable to the other phytochromes.
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Affiliation(s)
- Dihao Wang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Yangzhong Qin
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Sheng Zhang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
- Corresponding Author
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6
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Consiglieri E, Gutt A, Gärtner W, Schubert L, Viappiani C, Abbruzzetti S, Losi A. Dynamics and efficiency of photoswitching in biliverdin-binding phytochromes. Photochem Photobiol Sci 2019; 18:2484-2496. [DOI: 10.1039/c9pp00264b] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A full scale analysis of the kinetic processes in the μ-to-millisecond time scale for red-and far red-triggered processes in biliverdin-binding bacterial and fungal phytochromes.
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Affiliation(s)
- Eleonora Consiglieri
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Alexander Gutt
- Max-Planck-Institute for Chemical Energy Conversion
- 45470 Mülheim an der Ruhr
- Germany
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry
- University of Leipzig
- 04103 Leipzig
- Germany
| | - Luiz Schubert
- Institute for Physical Chemistry
- Heinrich-Heine-University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Cristiano Viappiani
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Stefania Abbruzzetti
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Aba Losi
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
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7
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Stensitzki T, Yang Y, Wölke AL, Knapp EW, Hughes J, Mroginski MA, Heyne K. Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome. Photochem Photobiol 2018; 93:703-712. [PMID: 28500700 DOI: 10.1111/php.12743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/03/2017] [Indexed: 01/23/2023]
Abstract
Photoisomerization of a protein-bound chromophore is the basis of light sensing and signaling in many photoreceptors. Phytochrome photoreceptors can be photoconverted reversibly between the Pr and Pfr states through photoisomerization of the methine bridge between rings C and D. Ground-state heterogeneity of the chromophore has been reported for both Pr and Pfr. Here, we report ultrafast visible (Vis) pump-probe and femtosecond polarization-resolved Vis pump-infrared (IR) probe studies of the Pfr photoreaction in native and 13 C/15 N-labeled Cph1 phytochrome with unlabeled PCB chromophore, demonstrating different S0 substates, Pfr-I and Pfr-II, with distinct IR absorptions, orientations and dynamics of the carbonyl vibration of ring D. We derived time constants of 0.24 ps, 0.7 ps and 6 ps, describing the complete initial photoreaction. We identified an isomerizing pathway with 0.7 ps for Pfr-I, and silent dynamics with 6 ps for Pfr-II. We discuss different origins of the Pfr substates, and favor different facial orientations of ring D. The model provides a quantum yield for Pfr-I of 38%, in line with ~35% ring D rotation in the electronic excited state. We tentatively assign the silent form Pfr-II to a dark-adapted state that can convert to Pfr-I upon light absorption.
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Affiliation(s)
- Till Stensitzki
- Department of Physics, Free University Berlin, Berlin, Germany
| | - Yang Yang
- Department of Physics, Free University Berlin, Berlin, Germany
| | - Anna Lena Wölke
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig Universität, Gießen, Germany
| | | | - Karsten Heyne
- Department of Physics, Free University Berlin, Berlin, Germany
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8
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Choudry U, Heyes DJ, Hardman SJO, Sakuma M, Sazanovich IV, Woodhouse J, De La Mora E, Pedersen MN, Wulff M, Weik M, Schirò G, Scrutton NS. Photochemical Mechanism of an Atypical Algal Phytochrome. Chembiochem 2018; 19:1036-1043. [DOI: 10.1002/cbic.201800016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Uzma Choudry
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Derren J. Heyes
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Samantha J. O. Hardman
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Igor V. Sazanovich
- Central Laser Facility; Research Complex at Harwell; Science and Technology Facilities Council; Harwell Oxford; Didcot OX11 0QX UK
| | - Joyce Woodhouse
- CNRS; Université Grenoble Alpes; CEA-Institut de Biologie Structurale; Grenoble 38044 France
| | - Eugenio De La Mora
- CNRS; Université Grenoble Alpes; CEA-Institut de Biologie Structurale; Grenoble 38044 France
| | | | - Michael Wulff
- European Synchrotron Radiation Facility; Grenoble 38044 France
| | - Martin Weik
- CNRS; Université Grenoble Alpes; CEA-Institut de Biologie Structurale; Grenoble 38044 France
| | - Giorgio Schirò
- CNRS; Université Grenoble Alpes; CEA-Institut de Biologie Structurale; Grenoble 38044 France
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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9
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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] [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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10
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Lamparter T, Krauß N, Scheerer P. Phytochromes from Agrobacterium fabrum. Photochem Photobiol 2017; 93:642-655. [DOI: 10.1111/php.12761] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/22/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Tilman Lamparter
- Karlsruhe Institute of Technology (KIT); Botanical Institute; Karlsruhe Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology (KIT); Botanical Institute; Karlsruhe Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
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11
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Bizimana LA, Epstein J, Brazard J, Turner DB. Conformational Homogeneity in the P r Isomer of Phytochrome Cph1. J Phys Chem B 2017; 121:2622-2630. [PMID: 28282147 DOI: 10.1021/acs.jpcb.7b02180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Numerous time-resolved studies of the Pr to Pfr photoisomerization in phytochrome Cph1 have revealed multiphasic excited-state decay kinetics. It remains unclear whether these kinetics arise from multiple ground-state conformational subpopulations or from a single ground-state conformation that undergoes an excited-state photoisomerization process-either branching on the excited state or relaxing through multiple sequential intermediates. Many studies have attempted to resolve this debate by fitting the measured dynamics to proposed kinetic models, arriving at different conclusions. Here we probe spectral signatures of ground-state heterogeneity of Pr. Two-dimensional electronic spectra display negligible inhomogeneous line broadening, and vibrational coherence spectra extracted from transient absorption measurements do not contain nodes and phase shifts at the fluorescence maximum. These spectroscopic results support the homogeneous model, in which the primary photochemical transformation of Pr to Lumi-R occurs adiabatically on the excited-state potential energy surface.
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Affiliation(s)
- Laurie A Bizimana
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
| | - Jordan Epstein
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
| | - Johanna Brazard
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
| | - Daniel B Turner
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
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12
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Singer P, Wörner S, Lamparter T, Diller R. Spectroscopic Investigation on the Primary Photoreaction of Bathy Phytochrome Agp2-Pr ofAgrobacterium fabrum: Isomerization in a pH-dependent H-bond Network. Chemphyschem 2016; 17:1288-97. [DOI: 10.1002/cphc.201600199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Patrick Singer
- Department of Physics; University of Kaiserslautern; Erwin-Schrödinger-Strasse, Geb. 46 67663 Kaiserslautern Germany), Fax: +49-631-205-3902
| | - Sybille Wörner
- Botanical Institute; Karlsruhe Institute of Technology; Kaiserstraße 2 76131 Karlsruhe Germany
| | - Tilman Lamparter
- Botanical Institute; Karlsruhe Institute of Technology; Kaiserstraße 2 76131 Karlsruhe Germany
| | - Rolf Diller
- Department of Physics; University of Kaiserslautern; Erwin-Schrödinger-Strasse, Geb. 46 67663 Kaiserslautern Germany), Fax: +49-631-205-3902
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13
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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] [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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14
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Singer P, Fey S, Göller AH, Hermann G, Diller R. Femtosecond Dynamics in the Lactim Tautomer of Phycocyanobilin: A Long-Wavelength Absorbing Model Compound for the Phytochrome Chromophore. Chemphyschem 2014; 15:3824-31. [DOI: 10.1002/cphc.201402383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Indexed: 11/11/2022]
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15
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Kim PW, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Heterogeneous photodynamics of the pfr state in the cyanobacterial phytochrome Cph1. Biochemistry 2014; 53:4601-11. [PMID: 24940993 PMCID: PMC4184438 DOI: 10.1021/bi5005359] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Femtosecond
photodynamics of the Pfr form of the red/far-red
phytochrome N-terminal PAS-GAF-PHY photosensory core module of the
cyanobacterial phytochrome Cph1 (termed Cph1Δ) from Synechocystis were resolved with visible broadband transient
absorption spectroscopy. Multiphasic generation dynamics via global
target analysis revealed parallel evolution of two pathways with distinct
excited- and ground-state kinetics. These measurements resolved two
subpopulations: a majority subpopulation with fast excited-state decay
and slower ground-state dynamics, corresponding to previous descriptions
of Pfr dynamics, and a minority subpopulation with slower
excited-state decay and faster ground-state primary dynamics. Both
excited-state subpopulations generated the isomerized, red-shifted
Lumi-Ff photoproduct (715 nm); subsequent ground-state
evolution to a blue-shifted Meta-Fr population (635 nm)
proceeded on 3 ps and 1.5 ns time scales for the two subpopulations.
Meta-Fr was spectrally similar to a recently described
photoinactive fluorescent subpopulation of Pr (FluorPr). Thus, the reverse Pfr to Pr photoconversion of Cph1Δ involves minor structural deformation
of Meta-Fr to generate the fluorescent, photochemically
refractory form of Pr, with slower subsequent equilibration
with the photoactive Pr subpopulation (PhotoPr).
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Affiliation(s)
- Peter W Kim
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California , One Shields Avenue, Davis, California 95616, United States
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16
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Sineshchekov V, Mailliet J, Psakis G, Feilke K, Kopycki J, Zeidler M, Essen L, Hughes J. Tyrosine 263 in Cyanobacterial Phytochrome Cph1 Optimizes Photochemistry at the prelumi‐ R→lumi‐R Step. Photochem Photobiol 2014; 90:786-795. [DOI: https:/doi.org/10.1111/php.12263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
AbstractWe report a low‐temperature fluorescence spectroscopy study of the PAS‐GAF‐PHY sensory module of Cph1 phytochrome, its Y263F mutant (both with known 3D structures) as well as Y263H and Y263S to connect their photochemical parameters with intramolecular interactions. None of the holoproteins showed photochemical activity at low temperature, and the activation barriers for the Pr→lumi‐R photoreaction (2.5–3.1 kJ mol−1) and fluorescence quantum yields (0.29–0.42) were similar. The effect of the mutations on Pr→Pfr photoconversion efficiency (ΦPr→Pfr) was observed primarily at the prelumi‐R S0 bifurcation point corresponding to the conical intersection of the energy surfaces at which the molecule relaxes to form lumi‐R or Pr, lowering ΦPr→Pfr from 0.13 in the wild type to 0.05–0.07 in the mutants. We suggest that the Ea activation barrier in the Pr* S1 excited state might correspond to the D‐ring (C19) carbonyl – H290 hydrogen bond or possibly to the hindrance caused by the C131/C171 methyl groups of the C and D rings. The critical role of the tyrosine hydroxyl group can be at the prelumi‐R bifurcation point to optimize the yield of the photoprocess and energy storage in the form of lumi‐R for subsequent rearrangement processes culminating in Pfr formation.
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Affiliation(s)
- Vitaly Sineshchekov
- Chair of Physico‐Chemical Biology Department of Biology M. V. Lomonosov Moscow State University Moscow Russia
| | - Joel Mailliet
- Plant Physiology Faculty of Biology and Chemistry Justus Liebig University Giessen Germany
| | - Georgios Psakis
- Plant Physiology Faculty of Biology and Chemistry Justus Liebig University Giessen Germany
| | - Kathleen Feilke
- Plant Physiology Faculty of Biology and Chemistry Justus Liebig University Giessen Germany
| | - Jakub Kopycki
- Plant Physiology Faculty of Biology and Chemistry Justus Liebig University Giessen Germany
| | - Mathias Zeidler
- Plant Physiology Faculty of Biology and Chemistry Justus Liebig University Giessen Germany
| | - Lars‐Oliver Essen
- Structural Biochemistry Faculty of Chemistry Phillipps University Marburg Germany
| | - Jon Hughes
- Plant Physiology Faculty of Biology and Chemistry Justus Liebig University Giessen Germany
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17
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Sineshchekov V, Mailliet J, Psakis G, Feilke K, Kopycki J, Zeidler M, Essen LO, Hughes J. Tyrosine 263 in cyanobacterial phytochrome Cph1 optimizes photochemistry at the prelumi-R→lumi-R step. Photochem Photobiol 2014; 90:786-95. [PMID: 24571438 DOI: 10.1111/php.12263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 02/14/2014] [Indexed: 01/29/2023]
Abstract
We report a low-temperature fluorescence spectroscopy study of the PAS-GAF-PHY sensory module of Cph1 phytochrome, its Y263F mutant (both with known 3D structures) as well as Y263H and Y263S to connect their photochemical parameters with intramolecular interactions. None of the holoproteins showed photochemical activity at low temperature, and the activation barriers for the Pr→lumi-R photoreaction (2.5-3.1 kJ mol(-1)) and fluorescence quantum yields (0.29-0.42) were similar. The effect of the mutations on Pr→Pfr photoconversion efficiency (ΦPr→Pfr) was observed primarily at the prelumi-R S0 bifurcation point corresponding to the conical intersection of the energy surfaces at which the molecule relaxes to form lumi-R or Pr, lowering ΦPr→Pfr from 0.13 in the wild type to 0.05-0.07 in the mutants. We suggest that the Ea activation barrier in the Pr* S1 excited state might correspond to the D-ring (C19) carbonyl - H290 hydrogen bond or possibly to the hindrance caused by the C13(1) /C17(1) methyl groups of the C and D rings. The critical role of the tyrosine hydroxyl group can be at the prelumi-R bifurcation point to optimize the yield of the photoprocess and energy storage in the form of lumi-R for subsequent rearrangement processes culminating in Pfr formation.
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Affiliation(s)
- Vitaly Sineshchekov
- Chair of Physico-Chemical Biology, Department of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
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18
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Kim PW, Pan J, Rockwell NC, Chang CW, Taylor KC, Lagarias JC, Larsen DS. Ultrafast E to Z photoisomerization dynamics of the Cph1 phytochrome. Chem Phys Lett 2012; 549:86-92. [PMID: 23554514 PMCID: PMC3611326 DOI: 10.1016/j.cplett.2012.08.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Femtosecond photodynamics of the reverse ( 15E Pfr→ 15Z Pr) reaction of the red/far-red phytochrome Cph1 from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multi-phasic dynamics were resolved and separated via global target analysis into a fast-decaying (260 fs) excited-state population that bifurcates to generate the isomerized Lumi-F primary photoproduct and a non-isomerizing vibrationally excited ground state that relaxes back into the 15E Pfr ground state on a 2.8-ps time scale. Relaxation on a 1-ms timescale results in the loss of red absorbing region, but not blue region, of Lumi-F, which indicates that formation of 15Z Pr occurs on slower timescales.
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Affiliation(s)
- Peter W. Kim
- Department of Chemistry, One Shields Ave, University of California, Davis, CA 95616, United States
| | - Jie Pan
- Department of Chemistry, One Shields Ave, University of California, Davis, CA 95616, United States
| | - Nathan C. Rockwell
- Department of Molecular and Cell Biology, One Shields Ave, University of California, Davis, CA 95616, United States
| | - Che-Wei Chang
- Department of Chemistry, One Shields Ave, University of California, Davis, CA 95616, United States
| | - Keenan C. Taylor
- Department of Molecular and Cell Biology, One Shields Ave, University of California, Davis, CA 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology, One Shields Ave, University of California, Davis, CA 95616, United States
| | - Delmar S. Larsen
- Department of Chemistry, One Shields Ave, University of California, Davis, CA 95616, United States
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19
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Spillane KM, Dasgupta J, Mathies RA. Conformational homogeneity and excited-state isomerization dynamics of the bilin chromophore in phytochrome Cph1 from resonance Raman intensities. Biophys J 2012; 102:709-17. [PMID: 22325295 DOI: 10.1016/j.bpj.2011.11.4019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/23/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022] Open
Abstract
The ground-state structure and excited-state isomerization dynamics of the P(r) and P(fr) forms of phytochrome Cph1 are investigated using resonance Raman intensity analysis. Electronic absorption and stimulated resonance Raman spectra of P(r) and P(fr) are presented; vibronic analysis of the Raman intensities and absorption spectra reveals that both conformers exist as a single, homogeneous population of molecules in the ground state. The homogeneous and inhomogeneous contributions to the overall electronic broadening are determined, and it is found that the broadening is largely homogeneous in nature, pointing to fast excited-state decay. Franck-Condon displacements derived from the Raman intensity analysis reveal the initial atomic motions in the excited state, including the highly displaced, nontotally symmetric torsional and C(15)-H HOOP modes that appear because of symmetry-reducing distortions about the C(14)-C(15) and C(15)=C(16) bonds. P(fr) is especially well primed for ultrafast isomerization and torsional Franck-Condon analysis predicts a <200 fs P(fr) → P(r) isomerization. This time is significantly faster than the observed 700 fs reaction time, indicating that the P(fr) S(1) surface has a D-ring rotational barrier caused by steric interactions with the protein.
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Affiliation(s)
- Katelyn M Spillane
- Department of Chemistry, University of California, Berkeley, California, USA
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20
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Yang Y, Linke M, von Haimberger T, Hahn J, Matute R, González L, Schmieder P, Heyne K. Real-Time Tracking of Phytochrome’s Orientational Changes During Pr Photoisomerization. J Am Chem Soc 2012; 134:1408-11. [DOI: 10.1021/ja209413d] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yang Yang
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, 14195
Berlin, Germany
- Center for Supramolecular Interactions, Takustr. 3, 14195 Berlin, Germany
| | - Martin Linke
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, 14195
Berlin, Germany
| | | | - Janina Hahn
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle
Str. 10, 13125 Berlin, Germany
| | - Ricardo Matute
- Institut für Physikalische
Chemie, Friedrich-Schiller Universität Jena, Helmholtzweg 4, 07743 Jena, Germany
- Departamento de Quimica, Universidad de Chile, Facultad de Ciencias, Casilla
653, Santiago, Chile
| | - Leticia González
- Institut für Physikalische
Chemie, Friedrich-Schiller Universität Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle
Str. 10, 13125 Berlin, Germany
| | - Karsten Heyne
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, 14195
Berlin, Germany
- Center for Supramolecular Interactions, Takustr. 3, 14195 Berlin, Germany
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21
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Fitzpatrick AE, Lincoln CN, van Wilderen LJGW, van Thor JJ. Pump–Dump–Probe and Pump–Repump–Probe Ultrafast Spectroscopy Resolves Cross Section of an Early Ground State Intermediate and Stimulated Emission in the Photoreactions of the Pr Ground State of the Cyanobacterial Phytochrome Cph1. J Phys Chem B 2012; 116:1077-88. [DOI: 10.1021/jp206298n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ann E. Fitzpatrick
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
| | - Craig N. Lincoln
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
| | | | - Jasper J. van Thor
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
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22
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Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Femtosecond photodynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. 2. reverse dynamics. Biochemistry 2012; 51:619-30. [PMID: 22148731 DOI: 10.1021/bi2017365] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Phytochromes are red/far-red photosensory proteins that utilize photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert reversibly between red- and far-red-absorbing forms (P(r) and P(fr), respectively). Cyanobacteriochromes (CBCRs) are related photosensory proteins with more diverse spectral sensitivity. The mechanisms that underlie this spectral diversity have not yet been fully elucidated. One of the main CBCR subfamilies photoconverts between a red-absorbing 15Z ground state, like the familiar P(r) state of phytochromes, and a green-absorbing photoproduct ((15E)P(g)). We have previously used the red/green CBCR NpR6012g4 from the cyanobacterium Nostoc punctiforme to examine ultrafast photodynamics of the forward photoreaction. Here, we examine the reverse reaction. Using excitation-interleaved transient absorption spectroscopy with broadband detection and multicomponent global analysis, we observed multiphasic excited-state dynamics. Interleaved excitation allowed us to identify wavelength-dependent shifts in the ground-state bleach that equilibrated on a 200 ps time scale, indicating ground-state heterogeneity. Compared to the previously studied forward reaction, the reverse reaction has much faster excited-state decay time constants and significantly higher photoproduct yield. This work thus demonstrates striking differences between the forward and reverse reactions of NpR6012g4 and provides clear evidence of ground-state heterogeneity in the phytochrome superfamily.
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Affiliation(s)
- Peter W Kim
- Department of Chemistry, University of California, Davis, California 95616, United States
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23
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Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome. Nature 2011; 479:428-32. [PMID: 22002602 DOI: 10.1038/nature10506] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 08/23/2011] [Indexed: 11/08/2022]
Abstract
Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C(15) = C(16) double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C(15) methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.
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24
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Wolf MMN, Zimmermann H, Diller R, Domratcheva T. Vibrational Mode Analysis of Isotope-Labeled Electronically Excited Riboflavin. J Phys Chem B 2011; 115:7621-8. [DOI: 10.1021/jp110784t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Herbert Zimmermann
- Max-Planck-Institut für medizinische Forschung, D-69120 Heidelberg, Germany
| | - Rolf Diller
- Fachbereich Physik, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
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25
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Colindres-Rojas M, Wolf MMN, Gross R, Seidel S, Dietzek B, Schmitt M, Popp J, Hermann G, Diller R. Excited-state dynamics of protochlorophyllide revealed by subpicosecond infrared spectroscopy. Biophys J 2011; 100:260-7. [PMID: 21190679 DOI: 10.1016/j.bpj.2010.11.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 11/19/2010] [Accepted: 11/29/2010] [Indexed: 11/24/2022] Open
Abstract
To gain a better understanding of the light-induced reduction of protochlorophyllide (PChlide) to chlorophyllide as a key regulatory step in chlorophyll synthesis, we performed transient infrared absorption measurements on PChlide in d4-methanol. Excitation in the Q-band at 630 nm initiates dynamics characterized by three time constants: τ₁ = 3.6 ± 0.2, τ₂ = 38 ± 2, and τ₃ = 215 ± 8 ps. As indicated by the C13'=O carbonyl stretching mode in the electronic ground state at 1686 cm⁻¹, showing partial ground-state recovery, and in the excited electronic state at 1625 cm⁻¹, showing excited-state decay, τ₂ describes the formation of a state with a strong change in electronic structure, and τ₃ represents the partial recovery of the PChlide electronic ground state. Furthermore, τ₁ corresponds with vibrational energy relaxation. The observed kinetics strongly suggest a branched reaction scheme with a branching ratio of 0.5 for the path leading to the PChlide ground state on the 200 ps timescale and the path leading to a long-lived state (>>700 ps). The results clearly support a branched reaction scheme, as proposed previously, featuring the formation of an intramolecular charge transfer state with ∼25 ps, its decay into the PChlide ground state with 200 ps, and a parallel reaction path to the long-lived PChlide triplet state.
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26
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Toh KC, Stojković EA, Rupenyan AB, van Stokkum IHM, Salumbides M, Groot ML, Moffat K, Kennis JTM. Primary reactions of bacteriophytochrome observed with ultrafast mid-infrared spectroscopy. J Phys Chem A 2010; 115:3778-86. [PMID: 21192725 DOI: 10.1021/jp106891x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. The phytochrome light activation mechanism involves isomerization around the C(15)═C(16) double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its D-ring. In an important recent development, bacteriophytochrome (Bph) has been engineered for use as a fluorescent marker in mammalian tissues. Bphs covalently bind a biliverdin (BV) chromophore, naturally abundant in mammalian cells. Here, we report an ultrafast time-resolved mid-infrared spectroscopic study on the Pr state of two highly related Bphs from Rps. palustris , RpBphP2 (P2) and RpBphP3 (P3) with distinct photoconversion and fluorescence properties. We observed that the BV excited state of P2 decays in 58 ps, while the BV excited state of P3 decays in 362 ps. By combining ultrafast mid-IR spectroscopy with FTIR spectroscopy on P2 and P3 wild type and mutant proteins, we demonstrate that the hydrogen bond strength at the ring D carbonyl of the BV chromophore is significantly stronger in P3 as compared to P2. This result is consistent with the X-ray structures of Bph, which indicate one hydrogen bond from a conserved histidine to the BV ring D carbonyl for classical bacteriophytochromes such as P2, and one or two additional hydrogen bonds from a serine and a lysine side chain to the BV ring D carbonyl for P3. We conclude that the hydrogen-bond strength at BV ring D is a key determinant of excited-state lifetime and fluorescence quantum yield. Excited-state decay is followed by the formation of a primary intermediate that does not decay on the nanosecond time scale of the experiment, which shows a narrow absorption band at ∼1540 cm(-1). Possible origins of this product band are discussed. This work may aid in rational structure- and mechanism-based conversion of BPh into an efficient near-IR fluorescent marker.
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Affiliation(s)
- K C Toh
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, VU University, De Boelelaan 1081, 1081HV Amsterdam, The Netherlands
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27
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Ataka K, Kottke T, Heberle J. Thinner, Smaller, Faster: IR Techniques To Probe the Functionality of Biological and Biomimetic Systems. Angew Chem Int Ed Engl 2010; 49:5416-24. [DOI: 10.1002/anie.200907114] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Ataka K, Kottke T, Heberle J. Dünner, kleiner, schneller - wie die IR-Spektroskopie zur Aufklärung des Funktionsmechanismus biologischer und biomimetischer Systeme beiträgt. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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van Wilderen LJGW, Clark IP, Towrie M, van Thor JJ. Mid-infrared picosecond pump-dump-probe and pump-repump-probe experiments to resolve a ground-state intermediate in cyanobacterial phytochrome Cph1. J Phys Chem B 2010; 113:16354-64. [PMID: 19950906 DOI: 10.1021/jp9038539] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multipulse picosecond mid-infrared spectroscopy has been used to study photochemical reactions of the cyanobacterial phytochrome photoreceptor Cph1. Different photophysical schemes have been discussed in the literature to describe the pathways after photoexcitation, particularly, to identify reaction phases that are linked to photoisomerisation and electronic decay in the 1566-1772 cm(-1) region that probes C=C and C=O stretching modes of the tetrapyrrole chromophore. Here, multipulse spectroscopy is employed, where, compared to conventional visible pump-mid-infrared probe spectroscopy, an additional visible pulse is incorporated that interacts with populations that are evolving on the excited- and ground-state potential energy surfaces. The time delays between the pump and the dump pulse are chosen such that the dump pulse interacts with different phases in the reaction process. The pump and dump pulses are at the same wavelength, 640 nm, and are resonant with the Pr ground state as well as with the excited state and intermediates. Because the dump pulse additionally pumps the remaining, partially recovered, and partially oriented ground-state population, theory is developed for estimating the fraction of excited-state molecules. The calculations take into account the model-dependent ground-state recovery fraction, the angular dependence of the population transfer resulting from the finite bleach that occurs with linearly polarized intense femtosecond optical excitation, and the partially oriented population for the dump field. Distinct differences between the results from the experiments that use a 1 or a 14 ps dump time favor a branching evolution from S1 to an excited state or reconfigured chromophore and to a newly identified ground-state intermediate (GSI). Optical dumping at 1 ps shows the instantaneous induced absorption of a delocalized C=C stretching mode at 1608 cm(-1), where the increased cross section is associated with the electronic ground-state structure of the ZZZ configuration of the linear tetrapyrrole chromophore. The dump-induced absorption decays with time constants of 5 and 19 ps to the Pr ground state. Employing a dump pulse at 14 ps results in an instantaneous decrease of the absorption of the 1608 cm(-1) band, indicating repumping of the GSI. The dump-induced absorption recovers back to the GSI with a 6 ps lifetime. A spectral similarity is observed between the 6 ps phase in the dump experiment and the 3 ps component found in the two-pulse pump-probe measurement. Combined with the dominance of ground-state absorption bands in the dump-induced spectrum, this indicates the presence of a GSI, which is additionally characterized by previously unidentified induced absorption at 1710 and 1570-80 cm(-1). The metastable photoproduct Lumi-R, which is in the electronic ground state and populated at 500 ps after excitation of Pr, is highly efficiently repumped into the Pr ground state with the power density used. After repumping, Lumi-R is not recovered on the 500 ps time scale of the experiment and is distinct from the GSI of Pr since it is not associated with its characteristic induced absorption at 1710 and 1570-80 cm(-1).
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Affiliation(s)
- Luuk J G W van Wilderen
- Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
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30
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Nuernberger P, Lee KF, Bonvalet A, Polack T, Vos MH, Alexandrou A, Joffre M. Suppression of perturbed free-induction decay and noise in experimental ultrafast pump-probe data. OPTICS LETTERS 2009; 34:3226-3228. [PMID: 19838281 DOI: 10.1364/ol.34.003226] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We apply a Fourier filtering technique for the global removal of coherent contributions, like perturbed free-induction decay, and noise, to experimental pump-probe spectra. A further filtering scheme gains access to spectra otherwise only recordable by scanning the probe's center frequency with adjustable spectral resolution. These methods cleanse pump-probe data and allow improved visualization and simpler analysis of the contained dynamics. We demonstrate these filters using visible pump/mid-infrared probe spectroscopy of ligand dissociation in carboxyhemoglobin.
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31
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Inomata K, Khawn H, Chen LY, Kinoshita H, Zienicke B, Molina I, Lamparter T. Assembly of Agrobacterium Phytochromes Agp1 and Agp2 with Doubly Locked Bilin Chromophores. Biochemistry 2009; 48:2817-27. [DOI: 10.1021/bi802334u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Katsuhiko Inomata
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Htoi Khawn
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Li-Yi Chen
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Hideki Kinoshita
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Benjamin Zienicke
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Isabel Molina
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Tilman Lamparter
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
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32
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Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy. Biophys J 2008; 95:4790-802. [PMID: 18708458 DOI: 10.1529/biophysj.108.139246] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD(*-) and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD(*-) to result in FADH(*) on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH(*) C=N stretch marker mode, with tyrosine as the likely proton donor. FADH(*) is reoxidized in 67 ps (180 ps in D(2)O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by approximately 180 degrees through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch.
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