1
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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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2
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Influence of the PHY domain on the ms-photoconversion dynamics of a knotless phytochrome. Photochem Photobiol Sci 2022; 21:1627-1636. [PMID: 35687310 DOI: 10.1007/s43630-022-00245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
The ability of some knotless phytochromes to photoconvert without the PHY domain allows evaluation of the distinct effect of the PHY domain on their photodynamics. Here, we compare the ms dynamics of the single GAF domain (g1) and the GAF-PHY (g1g2) construct of the knotless phytochrome All2699 from cyanobacterium Nostoc punctiforme. While the spectral signatures and occurrence of the intermediates are mostly unchanged by the domain composition, the presence of the PHY domain slows down the early forward and reverse dynamics involving chromophore and protein binding pocket relaxation. We assign this effect to a more restricted binding pocket imprinted by the PHY domain. The photoproduct formation is also slowed down by the presence of the PHY domain but to a lesser extent than the early dynamics. This indicates a rate limiting step within the GAF and not the PHY domain. We further identify a pH dependence of the biphasic photoproduct formation hinting towards a pKa dependent tuning mechanism. Our findings add to the understanding of the role of the individual domains in the photocycle dynamics and provide a basis for engineering of phytochromes towards biotechnological applications.
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3
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Morozov D, Modi V, Mironov V, Groenhof G. The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization. J Phys Chem Lett 2022; 13:4538-4542. [PMID: 35576453 PMCID: PMC9150100 DOI: 10.1021/acs.jpclett.2c00899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.
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Affiliation(s)
- Dmitry Morozov
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vaibhav Modi
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Gerrit Groenhof
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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4
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Ultrafast proton-coupled isomerization in the phototransformation of phytochrome. Nat Chem 2022; 14:823-830. [PMID: 35577919 PMCID: PMC9252900 DOI: 10.1038/s41557-022-00944-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/01/2022] [Indexed: 11/08/2022]
Abstract
The biological function of phytochromes is triggered by an ultrafast photoisomerization of the tetrapyrrole chromophore biliverdin between two rings denoted C and D. The mechanism by which this process induces extended structural changes of the protein is unclear. Here we report ultrafast proton-coupled photoisomerization upon excitation of the parent state (Pfr) of bacteriophytochrome Agp2. Transient deprotonation of the chromophore's pyrrole ring D or ring C into a hydrogen-bonded water cluster, revealed by a broad continuum infrared band, is triggered by electronic excitation, coherent oscillations and the sudden electric-field change in the excited state. Subsequently, a dominant fraction of the excited population relaxes back to the Pfr state, while ~35% follows the forward reaction to the photoproduct. A combination of quantum mechanics/molecular mechanics calculations and ultrafast visible and infrared spectroscopies demonstrates how proton-coupled dynamics in the excited state of Pfr leads to a restructured hydrogen-bond environment of early Lumi-F, which is interpreted as a trigger for downstream protein structural changes.
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5
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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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6
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Tachibana SR, Tang L, Chen C, Zhu L, Takeda Y, Fushimi K, Seevers TK, Narikawa R, Sato M, Fang C. Transient electronic and vibrational signatures during reversible photoswitching of a cyanobacteriochrome photoreceptor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 250:119379. [PMID: 33401182 DOI: 10.1016/j.saa.2020.119379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/12/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacteriochromes (CBCRs) are an emerging class of photoreceptors that are distant relatives of the phytochromes family. Unlike phytochromes, CBCRs have gained popularity in optogenetics due to their highly diverse spectral properties spanning the UV to near-IR region and only needing a single compact binding domain. AnPixJg2 is a CBCR that can reversibly photoswitch between its red-absorbing (15ZPr) and green-absorbing (15EPg) forms of the phycocyanobilin (PCB) cofactor. To reveal primary events of photoconversion, we implemented femtosecond transient absorption spectroscopy with a homemade LED box and a miniature peristaltic pump flow cell to track transient electronic responses of the photoexcited AnPixJg2 on molecular time scales. The 525 nm laser-induced Pg-to-Pr reverse conversion exhibits a ~3 ps excited-state lifetime before reaching the conical intersection (CI) and undergoing further relaxation on the 30 ps time scale to generate a long-lived Lumi-G ground state intermediate en route to Pr. The 650 nm laser-induced Pr-to-Pg forward conversion is less efficient than reverse conversion, showing a longer-lived excited state which requires two steps with ~13 and 217 ps time constants to enter the CI region. Furthermore, using a tunable ps Raman pump with broadband Raman probe on both the Stokes and anti-Stokes sides, we collected the pre-resonance ground-state femtosecond stimulated Raman spectroscopy (GS-FSRS) data with mode assignments aided by quantum calculations. Key vibrational marker bands at ~850, 1050, 1615, and 1649 cm-1 of the Pr conformer exhibit a notable blueshift to those of the Pg conformer inside AnPixJg2, reflecting the PCB chromophore terminal D (major) and A (minor) ring twist along the primary photoswitching reaction coordinate. This integrated ultrafast spectroscopy and computational platform has the potential to elucidate photochemistry and photophysics of more CBCRs and photoactive proteins in general, providing the highly desirable mechanistic insights to facilitate the rational design of functional molecular sensors and devices.
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Affiliation(s)
- Sean R Tachibana
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, United States
| | - Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, United States
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, United States
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, United States
| | - Yuka Takeda
- Graduate School of Integrated Science and Technology, Shizuoka University, 422-8529 Shizuoka, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, 422-8529 Shizuoka, Japan
| | - Travis K Seevers
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, United States
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, 422-8529 Shizuoka, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 332-0012 Saitama, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, University of Tokyo, 153-8902 Tokyo, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 332-0012 Saitama, Japan
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, United States.
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7
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Altmayer S, Jähnigen S, Köhler L, Wiebeler C, Song C, Sebastiani D, Matysik J. Hydrogen Bond between a Tyrosine Residue and the C-Ring Propionate Has a Direct Influence on Conformation and Absorption of the Bilin Cofactor in Red/Green Cyanobacteriochromes. J Phys Chem B 2021; 125:1331-1342. [PMID: 33523656 DOI: 10.1021/acs.jpcb.0c08518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptors of the phytochrome superfamily showing remarkable variability in the wavelengths of the first electronic transition-sometimes denoted as Q band-compared to canonical phytochromes. Both classes carry the same cofactor, a bilin, but the molecular basis for the wide variation of their absorption properties is still a matter of debate. The interaction between the cofactor and the surrounding protein moiety has been proposed as a possible tuning factor. Here, we address the impact of hydrogen-bonding interaction between the covalently bound tetrapyrrole cofactor (phycocyanobilin, PCB) and a conserved tyrosine residue (Y302) in the second GAF (cGMP-specific phosphodiesterase, adenylyl cyclases, and FhlA) domain of the red-/green-switching CBCR AnPixJ (AnPixJg2). In the wild type, AnPixJg2 shows absorption maxima of 648 and 543 nm for the dark-adapted (Pr) and photoproduct (Pg) states, respectively. The Y302F mutation leads to the occurrence of an additional absorption band at 687 nm, which is assigned to a new spectroscopically identified sub-state called PIII. Similar spectral changes result upon mutating the Y302F-homologue in another representative red-/green-switching CBCR, Slr1393g3. Molecular dynamics simulations on the dark-adapted state suggest that the removal of the hydrogen bond leads to an additional PCB sub-state differing in its A- and D-ring geometries. The origin of the Q band satellite in the dark-adapted state is discussed.
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Affiliation(s)
- Susanne Altmayer
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Sascha Jähnigen
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Lisa Köhler
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Christian Wiebeler
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.,Leibniz-Institut für Oberflächenmodifizierung, Permoserstraße 15, 04318 Leipzig, Germany
| | - Chen Song
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Daniel Sebastiani
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
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8
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Jähnigen S, Sebastiani D. Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ. Molecules 2020; 25:E5505. [PMID: 33255423 PMCID: PMC7727823 DOI: 10.3390/molecules25235505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics-statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.
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Affiliation(s)
| | - Daniel Sebastiani
- Institut für Chemie, Naturwissenschaftliche Fakultät II, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany;
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9
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Song JY, Lee HY, Yang HW, Song JJ, Lagarias JC, Park YI. Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes. J Biol Chem 2020; 295:6754-6766. [PMID: 32184354 DOI: 10.1074/jbc.ra120.012950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/13/2020] [Indexed: 11/06/2022] Open
Abstract
The atypical trichromatic cyanobacterial phytochrome NpTP1 from Nostoc punctiforme ATCC 29133 is a linear tetrapyrrole (bilin)-binding photoreceptor protein that possesses tandem-cysteine residues responsible for shifting its light-sensing maximum to the violet spectral region. Using bioinformatics and phylogenetic analyses, here we established that tandem-cysteine cyanobacterial phytochromes (TCCPs) compose a well-supported monophyletic phytochrome lineage distinct from prototypical red/far-red cyanobacterial phytochromes. To investigate the light-sensing diversity of this family, we compared the spectroscopic properties of NpTP1 (here renamed NpTCCP) with those of three phylogenetically diverged TCCPs identified in the draft genomes of Tolypothrix sp. PCC7910, Scytonema sp. PCC10023, and Gloeocapsa sp. PCC7513. Recombinant photosensory core modules of ToTCCP, ScTCCP, and GlTCCP exhibited violet-blue-absorbing dark-states consistent with dual thioether-linked phycocyanobilin (PCB) chromophores. Photoexcitation generated singly-linked photoproduct mixtures with variable ratios of yellow-orange and red-absorbing species. The photoproduct ratio was strongly influenced by pH and by mutagenesis of TCCP- and phytochrome-specific signature residues. Our experiments support the conclusion that both photoproduct species possess protonated 15E bilin chromophores, but differ in the ionization state of the noncanonical "second" cysteine sulfhydryl group. We found that the ionization state of this and other residues influences subsequent conformational change and downstream signal transmission. We also show that tandem-cysteine phytochromes present in eukaryotes possess similar amino acid substitutions within their chromophore-binding pocket, which tune their spectral properties in an analogous fashion. Taken together, our findings provide a roadmap for tailoring the wavelength specificity of plant phytochromes to optimize plant performance in diverse natural and artificial light environments.
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Affiliation(s)
- Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ha Yong Lee
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ji-Joon Song
- Department of Biological Science and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
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10
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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 2020; 295:539-551. [PMID: 31801828 PMCID: PMC6956517 DOI: 10.1074/jbc.ra119.011915] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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11
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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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12
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Bizimana LA, Farfan CA, Brazard J, Turner DB. E to Z Photoisomerization of Phytochrome Cph1Δ Exceeds the Born-Oppenheimer Adiabatic Limit. J Phys Chem Lett 2019; 10:3550-3556. [PMID: 31181167 DOI: 10.1021/acs.jpclett.9b01137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Born-Oppenheimer adiabatic limit applies broadly in chemistry because most reactions occur on the ground electronic state. Photochemical reactions involve two or more electronic states and need not be subject to this adiabatic limit. The spectroscopic signatures of nonadiabatic processes are subtle, and therefore, experimental investigations have been limited to the few systems dominated by single photochemical outcomes. Systems with branched excited-state pathways have been neglected, despite their potential to reveal insights into photochemical reactivity. Here we present experimental evidence from coherent three-dimensional electronic spectroscopy that the E to Z photoisomerization of phytochrome Cph1 is strongly nonadiabatic, and the simulations reproduce the measured features only when the photoisomerization proceeds nonadiabatically near, but not through, a conical intersection. The results broaden the general understanding of photoisomerization mechanisms and motivate future studies of nonadiabatic processes with multiple outcomes arising from branching on excited-state potential energy surfaces.
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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
| | - Camille A Farfan
- 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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13
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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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14
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Kirpich JS, Mix LT, Martin SS, Rockwell NC, Lagarias JC, Larsen DS. Protonation Heterogeneity Modulates the Ultrafast Photocycle Initiation Dynamics of Phytochrome Cph1. J Phys Chem Lett 2018; 9:3454-3462. [PMID: 29874080 PMCID: PMC6247788 DOI: 10.1021/acs.jpclett.8b01133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phytochrome proteins utilize ultrafast photoisomerization of a linear tetrapyrrole chromophore to detect the ratio of red to far-red light. Femtosecond photodynamics in the PAS-GAF-PHY photosensory core of the Cph1 phytochrome from Synechocystis sp. PCC6803 (Cph1Δ) were resolved with a dual-excitation-wavelength-interleaved pump-probe (DEWI) approach with two excitation wavelengths (600 and 660 nm) at three pH values (6.5, 8.0, and 9.0). Observed spectral and kinetic heterogeneity in the excited-state dynamics were described with a self-consistent model comprised of three spectrally distinct populations with different protonation states (Pr-I, Pr-II, and Pr-III), each composed of multiple kinetically distinct subpopulations. Apparent partitioning among these populations is dictated by pH, temperature, and excitation wavelength. Our studies provide insight into photocycle initiation dynamics at physiological temperatures, implicate the low-pH/low-temperature Pr-I state as the photoactive state in vitro, and implicate an internal hydrogen-bonding network in regulating the photochemical quantum yield.
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Affiliation(s)
- Julia S. Kirpich
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
| | - L. Tyler Mix
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
| | - Shelley S. Martin
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
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15
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Song C, Mroginski MA, Lang C, Kopycki J, Gärtner W, Matysik J, Hughes J. 3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function. FRONTIERS IN PLANT SCIENCE 2018; 9:498. [PMID: 29740459 PMCID: PMC5928327 DOI: 10.3389/fpls.2018.00498] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 05/25/2023]
Abstract
We present structural information for oat phyA3 in the far-red-light-absorbing (Pfr) signaling state, to our knowledge the first three-dimensional (3D) information for a plant phytochrome as Pfr. Solid-state magic-angle spinning (MAS) NMR was used to detect interatomic contacts in the complete photosensory module [residues 1-595, including the NTE (N-terminal extension), PAS (Per/Arnt/Sim), GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) and PHY (phytochrome-specific) domains but with the C-terminal PAS repeat and transmitter-like module deleted] auto-assembled in vitro with 13C- and 15N-labeled phycocyanobilin (PCB) chromophore. Thereafter, quantum mechanics/molecular mechanics (QM/MM) enabled us to refine 3D structural models constrained by the NMR data. We provide definitive atomic assignments for all carbon and nitrogen atoms of the chromophore, showing the Pfr chromophore geometry to be periplanar ZZEssa with the D -ring in a β-facial disposition incompatible with many earlier notions regarding photoconversion yet supporting circular dichroism (CD) data. The Y268 side chain is shifted radically relative to published Pfr crystal structures in order to accommodate the β-facial ring D . Our findings support a photoconversion sequence beginning with Pr photoactivation via an anticlockwise D -ring Za→Ea photoflip followed by significant shifts at the coupling of ring A to the protein, a B -ring propionate partner swap from R317 to R287, changes in the C -ring propionate hydrogen-bonding network, breakage of the D272-R552 salt bridge accompanied by sheet-to-helix refolding of the tongue region stabilized by Y326-D272-S554 hydrogen bonding, and binding of the NTE to the hydrophobic side of ring A . We discuss phyA photoconversion, including the possible roles of mesoscopic phase transitions and protonation dynamics in the chromophore pocket. We also discuss possible associations between structural changes and translocation and signaling processes within the cell.
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Affiliation(s)
- Chen Song
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
- Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden, Leiden, Netherlands
| | | | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Jakub Kopycki
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Wolfgang Gärtner
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
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16
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Correlating structural and photochemical heterogeneity in cyanobacteriochrome NpR6012g4. Proc Natl Acad Sci U S A 2018; 115:4387-4392. [PMID: 29632180 DOI: 10.1073/pnas.1720682115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytochrome photoreceptors control plant growth, development, and the shade avoidance response that limits crop yield in high-density agricultural plantings. Cyanobacteriochromes (CBCRs) are distantly related photosensory proteins that control cyanobacterial metabolism and behavior in response to light. Photoreceptors in both families reversibly photoconvert between two photostates via photoisomerization of linear tetrapyrrole (bilin) chromophores. Spectroscopic and biochemical studies have demonstrated heterogeneity in both photostates, but the structural basis for such heterogeneity remains unclear. We report solution NMR structures for both photostates of the red/green CBCR NpR6012g4 from Nostoc punctiforme In addition to identifying structural changes accompanying photoconversion, these structures reveal structural heterogeneity for residues Trp655 and Asp657 in the red-absorbing NpR6012g4 dark state, yielding two distinct environments for the phycocyanobilin chromophore. We use site-directed mutagenesis and fluorescence and absorbance spectroscopy to assign an orange-absorbing population in the NpR6012g4 dark state to the minority configuration for Asp657. This population does not undergo full, productive photoconversion, as shown by time-resolved spectroscopy and absorption spectroscopy at cryogenic temperature. Our studies thus elucidate the spectral and photochemical consequences of structural heterogeneity in a member of the phytochrome superfamily, insights that should inform efforts to improve photochemical or fluorescence quantum yields in the phytochrome superfamily.
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17
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Scarbath-Evers LK, Jähnigen S, Elgabarty H, Song C, Narikawa R, Matysik J, Sebastiani D. Structural heterogeneity in a parent ground-state structure of AnPixJg2 revealed by theory and spectroscopy. Phys Chem Chem Phys 2018; 19:13882-13894. [PMID: 28513754 DOI: 10.1039/c7cp01218g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We investigated the red absorbing, dark stable state (Pr state) of the second GAF domain of the cyanobacteriochrome AnPixJ (AnPixJg2) by a molecular dynamics simulation of 1 μs duration. Our results reveal two distinct conformational isoforms of the chromophore, from which only one was known from crystallographic experiments. The interconversion between both isoforms is accompanied by alterations in the hydrogen bond pattern between the chromophore and the protein and the solvation structure of the chromophore binding pocket. The existence of sub-states in the Pr form of AnPixJg2 is supported by the results from experimental 13C MAS NMR spectroscopy. Our finding is consistent with the observation of structural heterogeneity in other cyanobacteriochromes and phytochromes.
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Affiliation(s)
- Laura Katharina Scarbath-Evers
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany.
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18
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Rockwell NC, Martin SS, Li FW, Mathews S, Lagarias JC. The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2. THE NEW PHYTOLOGIST 2017; 214:1145-1157. [PMID: 28106912 PMCID: PMC5388591 DOI: 10.1111/nph.14422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/04/2016] [Indexed: 05/11/2023]
Abstract
Land plant phytochromes perceive red and far-red light to control growth and development, using the linear tetrapyrrole (bilin) chromophore phytochromobilin (PΦB). Phytochromes from streptophyte algae, sister species to land plants, instead use phycocyanobilin (PCB). PCB and PΦB are synthesized by different ferredoxin-dependent bilin reductases (FDBRs): PΦB is synthesized by HY2, whereas PCB is synthesized by PcyA. The pathway for PCB biosynthesis in streptophyte algae is unknown. We used phylogenetic analysis and heterologous reconstitution of bilin biosynthesis to investigate bilin biosynthesis in streptophyte algae. Phylogenetic results suggest that PcyA is present in chlorophytes and prasinophytes but absent in streptophytes. A system reconstituting bilin biosynthesis in Escherichia coli was modified to utilize HY2 from the streptophyte alga Klebsormidium flaccidum (KflaHY2). The resulting bilin was incorporated into model cyanobacterial photoreceptors and into phytochrome from the early-diverging streptophyte alga Mesostigma viride (MvirPHY1). All photoreceptors tested incorporate PCB rather than PΦB, indicating that KflaHY2 is sufficient for PCB synthesis without any other algal protein. MvirPHY1 exhibits a red-far-red photocycle similar to those seen in other streptophyte algal phytochromes. These results demonstrate that streptophyte algae use HY2 to synthesize PCB, consistent with the hypothesis that PΦB synthesis arose late in HY2 evolution.
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Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Shelley S. Martin
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Sarah Mathews
- CSIRO National Research Collections Australia, Australian National Herbarium, Canberra, ACT, 2601, Australia
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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19
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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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20
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Velazquez Escobar F, Lang C, Takiden A, Schneider C, Balke J, Hughes J, Alexiev U, Hildebrandt P, Mroginski MA. Protonation-Dependent Structural Heterogeneity in the Chromophore Binding Site of Cyanobacterial Phytochrome Cph1. J Phys Chem B 2016; 121:47-57. [DOI: 10.1021/acs.jpcb.6b09600] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Francisco Velazquez Escobar
- Institut
für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Christina Lang
- Plant
Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Aref Takiden
- Plant
Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Constantin Schneider
- Institut
für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jens Balke
- Institut
für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jon Hughes
- Plant
Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Ulrike Alexiev
- Institut
für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Peter Hildebrandt
- Institut
für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Institut
für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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21
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Rockwell NC, Martin SS, Lagarias JC. Identification of Cyanobacteriochromes Detecting Far-Red Light. Biochemistry 2016; 55:3907-19. [DOI: 10.1021/acs.biochem.6b00299] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
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22
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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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23
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Tracking the secondary photodynamics of the green/red cyanobacteriochrome RcaE from Fremyella diplosiphon. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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24
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Yang Y, Heyne K, Mathies RA, Dasgupta J. Non-Bonded Interactions Drive the Sub-Picosecond Bilin Photoisomerization in the P(fr) State of Phytochrome Cph1. Chemphyschem 2015; 17:369-74. [PMID: 26630441 DOI: 10.1002/cphc.201501073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 01/26/2023]
Abstract
Phytochromes are protein-based photoreceptors harboring a bilin-based photoswitch in the active site. The timescale of photosignaling via C15 =C16 E-to-Z photoisomerization has been ambiguous in the far-red-absorbing Pfr state. Here we present a unified view of the structural events in phytochrome Cph1 post excitation with femtosecond precision, obtained via stimulated Raman and polarization-resolved transient IR spectroscopy. We demonstrate that photoproduct formation occurs within 700 fs, determined by a two-step partitioning process initiated by a planarization on the electronic excited state with a 300 fs time scale. The ultrafast isomerization timescale for Pfr -to-Pr conversion highlights the active role of the nonbonding methyl-methyl clash initiating the reaction in the excited state. We envision that our results will motivate the synthesis of new artificial photoswitches with precisely tuned non-bonded interactions for ultrafast response.
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Affiliation(s)
- Yang Yang
- Department of Physics, Freie Universitat Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Karsten Heyne
- Department of Physics, Freie Universitat Berlin, Arnimallee 14, 14195, Berlin, Germany.
| | - Richard A Mathies
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai, 400005, India.
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25
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Lehtivuori H, Bhattacharya S, Angenent-Mari NM, Satyshur KA, Forest KT. Removal of Chromophore-Proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor. Front Mol Biosci 2015; 2:65. [PMID: 26636092 PMCID: PMC4658570 DOI: 10.3389/fmolb.2015.00065] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/02/2015] [Indexed: 11/13/2022] Open
Abstract
Genetically encoded fluorescent markers have revolutionized cell and molecular biology due to their biological compatibility, controllable spatiotemporal expression, and photostability. To achieve in vivo imaging in whole animals, longer excitation wavelength probes are needed due to the superior ability of near infrared light to penetrate tissues unimpeded by absorbance from biomolecules or autofluorescence of water. Derived from near infrared-absorbing bacteriophytochromes, phytofluors are engineered to fluoresce in this region of the electromagnetic spectrum, although high quantum yield remains an elusive goal. An invariant aspartate residue is of utmost importance for photoconversion in native phytochromes, presumably due to the proximity of its backbone carbonyl to the pyrrole ring nitrogens of the biliverdin (BV) chromophore as well as the size and charge of the side chain. We hypothesized that the polar interaction network formed by the charged side chain may contribute to the decay of the excited state via proton transfer. Thus, we chose to further probe the role of this amino acid by removing all possibility for polar interactions with its carboxylate side chain by incorporating leucine instead. The resultant fluorescent protein, WiPhy2, maintains BV binding, monomeric status, and long maximum excitation wavelength while minimizing undesirable protoporphyrin IXα binding in cells. A crystal structure and time-resolved fluorescence spectroscopy reveal that water near the BV chromophore is excluded and thus validate our hypothesis that removal of polar interactions leads to enhanced fluorescence by increasing the lifetime of the excited state. This new phytofluor maintains its fluorescent properties over a broad pH range and does not suffer from photobleaching. WiPhy2 achieves the best compromise to date between high fluorescence quantum yield and long illumination wavelength in this class of fluorescent proteins.
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Affiliation(s)
- Heli Lehtivuori
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA ; Department of Physics, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
| | | | | | - Kenneth A Satyshur
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
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26
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Song C, Lang C, Kopycki J, Hughes J, Matysik J. NMR chemical shift pattern changed by ammonium sulfate precipitation in cyanobacterial phytochrome Cph1. Front Mol Biosci 2015; 2:42. [PMID: 26284254 PMCID: PMC4516977 DOI: 10.3389/fmolb.2015.00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
Phytochromes are dimeric biliprotein photoreceptors exhibiting characteristic red/far-red photocycles. Full-length cyanobacterial phytochrome Cph1 from Synechocystis 6803 is soluble initially but tends to aggregate in a concentration-dependent manner, hampering attempts to solve the structure using NMR and crystallization methods. Otherwise, the Cph1 sensory module (Cph1Δ2), photochemically indistinguishable from the native protein and used extensively in structural and other studies, can be purified to homogeneity in >10 mg amounts at mM concentrations quite easily. Bulk precipitation of full-length Cph1 by ammonium sulfate (AmS) was expected to allow us to produce samples for solid-state magic-angle spinning (MAS) NMR from dilute solutions before significant aggregation began. It was not clear, however, what effects the process of partial dehydration might have on the molecular structure. Here we test this by running solid-state MAS NMR experiments on AmS-precipitated Cph1Δ2 in its red-absorbing Pr state carrying uniformly 13C/15N-labeled phycocyanobilin (PCB) chromophore. 2D 13C–13C correlation experiments allowed a complete assignment of 13C responses of the chromophore. Upon precipitation, 13C chemical shifts for most of PCB carbons move upfield, in which we found major changes for C4 and C6 atoms associated with the A-ring positioning. Further, the broad spectral lines seen in the AmS 13C spectrum reflect primarily the extensive inhomogeneous broadening presumably due to an increase in the distribution of conformational states in the protein, in which less free water is available to partake in the hydration shells. Our data suggest that the effect of dehydration process indeed leads to changes of electronic structure of the bilin chromophore and a decrease in its mobility within the binding pocket, but not restricted to the protein surface. The extent of the changes induced differs from the freezing process of the solution samples routinely used in previous MAS NMR and crystallographic studies. AmS precipitation might nevertheless provide useful protein structure/functional information for full-length Cph1 in cases where neither X-ray crystallography nor conventional NMR methods are available.
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Affiliation(s)
- Chen Song
- Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden Leiden, Netherlands ; Institut für Analytische Chemie, Fakultät für Chemie and Mineralogie, Universität Leipzig Leipzig, Germany
| | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität Gießen Gießen, Germany
| | - Jakub Kopycki
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität Gießen Gießen, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität Gießen Gießen, Germany
| | - Jörg Matysik
- Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden Leiden, Netherlands ; Institut für Analytische Chemie, Fakultät für Chemie and Mineralogie, Universität Leipzig Leipzig, Germany
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27
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Anders K, Essen LO. The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful. Curr Opin Struct Biol 2015; 35:7-16. [PMID: 26241319 DOI: 10.1016/j.sbi.2015.07.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 11/17/2022]
Abstract
Bilin-dependent GAF domain photoreceptors cover the whole spectrum of light with their absorbance properties. They can be divided into three groups according to the domain architecture of their photosensory module. Group I and Group II harbor phytochromes with PAS-GAF-PHY and GAF-PHY domain architecture, respectively. Group III consists of stand-alone GAF domain photoreceptors, the cyanobacteriochromes. Crystal structures of all three groups are now available to shed light on possible downstream signaling pathways. Structures of Group I and III photoreceptors in both states display changes in the secondary structures during photoconversion. The knowledge about the photoconversion in phytochromes and CBCRs make them promising targets for applications in life science and synthetic biology.
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Affiliation(s)
- Katrin Anders
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany.
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28
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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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29
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Song C, Narikawa R, Ikeuchi M, Gärtner W, Matysik J. Color Tuning in Red/Green Cyanobacteriochrome AnPixJ: Photoisomerization at C15 Causes an Excited-State Destabilization. J Phys Chem B 2015; 119:9688-95. [DOI: 10.1021/acs.jpcb.5b04655] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chen Song
- Leids
Instituut voor Chemisch Onderzoek, Universiteit Leiden, P.O. Box 9502, 2300
RA Leiden, The Netherlands
- Institut
für Analytische Chemie, Universität Leipzig, Johannisallee
29, D-04103 Leipzig, Germany
| | - Rei Narikawa
- Department
of Biological Science, Faculty of Science, Shizuoka University, Ohya, Suruga-ku,
Shizuoka 422-8529, Japan
- Graduate
School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
- Precursory
Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Masahiko Ikeuchi
- Department
of Biological Science, Faculty of Science, Shizuoka University, Ohya, Suruga-ku,
Shizuoka 422-8529, Japan
- Core Research
for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Wolfgang Gärtner
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Jörg Matysik
- Leids
Instituut voor Chemisch Onderzoek, Universiteit Leiden, P.O. Box 9502, 2300
RA Leiden, The Netherlands
- Institut
für Analytische Chemie, Universität Leipzig, Johannisallee
29, D-04103 Leipzig, Germany
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30
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Gottlieb SM, Kim PW, Chang CW, Hanke SJ, Hayer RJ, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Conservation and Diversity in the Primary Forward Photodynamics of Red/Green Cyanobacteriochromes. Biochemistry 2015; 54:1028-42. [DOI: 10.1021/bi5012755] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean M. Gottlieb
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Che-Wei Chang
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Samuel J. Hanke
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Randeep J. Hayer
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Nathan C. Rockwell
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Delmar S. Larsen
- Department of Chemistry and ‡Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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