1
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Blain-Hartung M, Johannes von Sass G, Plaickner J, Katz S, Tu Hoang O, Andrea Mroginski M, Esser N, Budisa N, Forest KT, Hildebrandt P. On the Role of a Conserved Tryptophan in the Chromophore Pocket of Cyanobacteriochrome. J Mol Biol 2024; 436:168227. [PMID: 37544357 DOI: 10.1016/j.jmb.2023.168227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
The cyanobacteriochrome Slr1393 can be photoconverted between a red (Pr) and green absorbing form (Pg). The recently determined crystal structures of both states suggest a major movement of Trp496 from a stacking interaction with ring D of the phycocyanobilin (PCB) chromophore in Pr to a position outside the chromophore pocket in Pg. Here, we investigated the role of this amino acid during photoconversion in solution using engineered protein variants in which Trp496 was substituted by natural and non-natural amino acids. These variants and the native protein were studied by various spectroscopic techniques (UV-vis absorption, fluorescence, IR, NIR and UV resonance Raman) complemented by theoretical approaches. Trp496 is shown to affect the electronic transition of PCB and to be essential for the thermal equilibrium between Pr and an intermediate state O600. However, Trp496 is not required to stabilize the tilted orientation of ring D in Pr, and does not play a role in the secondary structure changes of Slr1393 during the Pr/Pg transition. The present results confirm the re-orientation of Trp496 upon Pr → Pg conversion, but do not provide evidence of a major change in the microenvironment of this residue. Structural models indicate the penetration of water molecules into the chromophore pocket in both Pr and Pg states and thus water-Trp contacts, which can readily account for the subtle spectral changes between Pr and Pg. Thus, we conclude that reorientation of Trp496 during the Pr-to-Pg photoconversion in solution is not associated with a major change in the dielectric environment in the two states.
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Affiliation(s)
- Matthew Blain-Hartung
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Georg Johannes von Sass
- Technische Universität Berlin, Institut für Chemie, Sekr. CL1, Müller-Breslau-Str.10, D-10623 Berlin, Germany
| | - Julian Plaickner
- Technische Universität Berlin, Institut für Festkörperphysik, Sekr. EW 6-1, Hardenbergstraße 36, 10623 Berlin, Germany
| | - Sagie Katz
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Oanh Tu Hoang
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Esser
- Technische Universität Berlin, Institut für Festkörperphysik, Sekr. EW 6-1, Hardenbergstraße 36, 10623 Berlin, Germany; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Schwarzschildstraße 8, 12489 Berlin, Germany
| | - Nediljko Budisa
- Technische Universität Berlin, Institut für Chemie, Sekr. CL1, Müller-Breslau-Str.10, D-10623 Berlin, Germany; Department of Chemistry, University of Manitoba, 144 Dysart Rd, 360 Parker Building, R3T 2N2 Winnipeg, Manitoba, Canada
| | - Katrina T Forest
- University of Wisconsin-Madison, Department of Bacteriology, 1550 Linden Dr., Madison, WI 53706, USA
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
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2
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Hildebrandt P. Vibrational Spectroscopy of Phytochromes. Biomolecules 2023; 13:1007. [PMID: 37371587 DOI: 10.3390/biom13061007] [Citation(s) in RCA: 0] [Impact Index Per Article: 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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3
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Light- and pH-dependent structural changes in cyanobacteriochrome AnPixJg2. Photochem Photobiol Sci 2022; 21:447-469. [PMID: 35394641 DOI: 10.1007/s43630-022-00204-4] [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: 12/22/2021] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
Abstract
Cyanobacteriochromes (CBCRs) are phytochrome-related photosensory proteins that play an essential role in regulating phototaxis, chromatic acclimation, and cell aggregation in cyanobacteria. Here, we apply solid-state NMR spectroscopy to the red/green GAF2 domain of the CBCR AnPixJ assembled in vitro with a uniformly 13C- and 15N-labeled bilin chromophore, tracking changes in electronic structure, geometry, and structural heterogeneity of the chromophore as well as intimate contacts between the chromophore and protein residues in the photocycle. Our data confirm that the bilin ring D is strongly twisted with respect to the B-C plane in both dark and photoproduct states. We also identify a greater structural heterogeneity of the bilin chromophore in the photoproduct than in the dark state. In addition, the binding pocket is more hydrated in the photoproduct. Observation of interfacial 1H contacts of the photoproduct chromophore, together with quantum mechanics/molecular mechanics (QM/MM)-based structural models for this photoproduct, clearly suggests the presence of a biprotonated (cationic) imidazolium side-chain for a conserved histidine residue (322) at a distance of ~2.7 Å, generalizing the recent theoretical findings that explicitly link the structural heterogeneity of the dark-state chromophore to the protonation of this specific residue. Moreover, we examine pH effects on this in vitro assembled holoprotein, showing a substantially altered electronic structure and protonation of the photoproduct chromophore even with a small pH drop from 7.8 to 7.2. Our studies provide further information regarding the light- and pH-induced changes of the chromophore and the rearrangements of the hydrogen-bonding and electrostatic interaction network around it. Possible correlations between structural heterogeneity of the chromophore, protonation of the histidine residue nearby, and hydration of the pocket in both photostates are discussed.
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4
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Okuda Y, Miyoshi R, Kamo T, Fujisawa T, Nagae T, Mishima M, Eki T, Hirose Y, Unno M. Raman Spectroscopy of an Atypical C15-E,syn Bilin Chromophore in Cyanobacteriochrome RcaE. J Phys Chem B 2022; 126:813-821. [DOI: 10.1021/acs.jpcb.1c09652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuji Okuda
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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5
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Kraskov A, Buhrke D, Scheerer P, Shaef I, Sanchez JC, Carrillo M, Noda M, Feliz D, Stojković EA, Hildebrandt P. On the Role of the Conserved Histidine at the Chromophore Isomerization Site in Phytochromes. J Phys Chem B 2021; 125:13696-13709. [PMID: 34843240 DOI: 10.1021/acs.jpcb.1c08245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phytochromes are sensory photoreceptors that use light to drive protein structural changes, which in turn trigger physiological reaction cascades. The process starts with a double-bond photoisomerization of the linear methine-bridged tetrapyrrole chromophore in the photosensory core module. The molecular mechanism of the photoconversion depends on the structural and electrostatic properties of the chromophore environment, which are highly conserved in related phytochromes. However, the specific role of individual amino acids is yet not clear. A histidine in the vicinity of the isomerization site is highly conserved and almost invariant among all phytochromes. The present study aimed at analyzing its role by taking advantage of a myxobacterial phytochrome SaBphP1 from Stigmatella aurantiaca, where this histidine is naturally substituted with a threonine (Thr289), and comparing it to its normal, His-containing counterpart from the same organism SaBphP2 (His275). We have carried out a detailed resonance Raman and IR spectroscopic investigation of the wild-type proteins and their respective His- or Thr-substituted variants (SaBphP1-T289H and SaBphP2-H275T) using the well-characterized prototypical phytochrome Agp1 from Agrobacterium fabrum as a reference. The overall mechanism of the photoconversion is insensitive toward the His substitution. However, the chromophore geometry at the isomerization site appears to be affected, with a slightly stronger twist of ring D in the presence of Thr, which is sufficient to cause different light absorption properties in SaBphP1 and SaBphP2. Furthermore, the presence of His allows for multiple hydrogen-bonding interactions with the ring D carbonyl which may be the origin for the geometric differences of the C-D methine bridge compared to the Thr-containing variants. Other structural and mechanistic differences are independent of the presence of His. The most striking finding is the protonation of the ring C propionate in the Pfr states of SaBphP2, which is common among bathy phytochromes but so far has not been reported in prototypical phytochromes.
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Affiliation(s)
- Anastasia Kraskov
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - David Buhrke
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Charité─Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Ida Shaef
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Juan C Sanchez
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Melissa Carrillo
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Moraima Noda
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, Illinois 60625, United States
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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6
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Velazquez Escobar F, Kneip C, Michael N, Hildebrandt T, Tavraz N, Gärtner W, Hughes J, Friedrich T, Scheerer P, Mroginski MA, Hildebrandt P. The Lumi-R Intermediates of Prototypical Phytochromes. J Phys Chem B 2020; 124:4044-4055. [PMID: 32330037 DOI: 10.1021/acs.jpcb.0c01059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phytochromes are photoreceptors that upon light absorption initiate a physiological reaction cascade. The starting point is the photoisomerization of the tetrapyrrole cofactor in the parent Pr state, followed by thermal relaxation steps culminating in activation of the physiological signal. Here we have employed resonance Raman (RR) spectroscopy to study the chromophore structure in the primary photoproduct Lumi-R, trapped between 130 and 200 K. The investigations covered phytochromes from plants (phyA) and prokaryotes (Cph1, Agp1, CphB, and RpBphP2) including phytochromobilin (PΦB), phycocyanobilin (PCB), and biliverdin (BV). In PΦB- and PCB-binding phyA and Cph1, two Lumi-R states (Lumi-R1, Lumi-R2) were identified and discussed in terms of sequential and parallel reaction models. In Lumi-R1, the chromophore structural changes are restricted to the C-D methine bridge isomerization site but extended throughout the chromophore in Lumi-R2. Formation and decay kinetics as well as photochemical activity depend on the specific protein-chromophore interactions and thus account for the different distribution between Lumi-R1 and Lumi-R2 in the photostationary mixtures of the various PΦB(PCB)-binding phytochromes. For BV-binding bacteriophytochromes, only a single Lumi-R(BV) state was found. In this state, which is similar for Agp1, CphB, and RpBphP2, the chromophore structural changes comprise major torsions of the C-D methine bridge but also perturbations at the A-B methine bridge remote from the isomerization site. The different structures of the photoproducts in PΦB(PCB)-binding phytochromes and BV-binding bacteriophytochromes are attributed to the different disposition of ring D upon isomerization, which leads to distinct protein-chromophore interactions in the Lumi-R states of these two classes of phytochromes.
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Affiliation(s)
- Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Christa Kneip
- Grünenthal GmbH, Zieglerstraße 6, D-52078 Aachen, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Thomas Hildebrandt
- Universitätsklinikum Düsseldorf, Klinik für Neurologie, Moorenstr. 5, D-40225 Düsseldorf, Germany
| | - Neslihan Tavraz
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Wolfgang Gärtner
- Universität Leipzig, Institut für Analytische Chemie, Linnéstr. 3, D-04103 Leipzig, Germany
| | - Jon Hughes
- Plant Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
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7
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Nagano S, Guan K, Shenkutie SM, Feiler C, Weiss M, Kraskov A, Buhrke D, Hildebrandt P, Hughes J. Structural insights into photoactivation and signalling in plant phytochromes. NATURE PLANTS 2020; 6:581-588. [PMID: 32366982 DOI: 10.1038/s41477-020-0638-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/16/2020] [Indexed: 05/11/2023]
Abstract
Plant phytochromes are red/far-red photochromic photoreceptors that act as master regulators of development, controlling the expression of thousands of genes. Here, we describe the crystal structures of four plant phytochrome sensory modules, three at about 2 Å resolution or better, including the first of an A-type phytochrome. Together with extensive spectral data, these structures provide detailed insight into the structure and function of plant phytochromes. In the Pr state, the substitution of phycocyanobilin and phytochromobilin cofactors has no structural effect, nor does the amino-terminal extension play a significant functional role. Our data suggest that the chromophore propionates and especially the phytochrome-specific domain tongue act differently in plant and prokaryotic phytochromes. We find that the photoproduct in period-ARNT-single-minded (PAS)-cGMP-specific phosphodiesterase-adenylyl cyclase-FhlA (GAF) bidomains might represent a novel intermediate between MetaRc and Pfr. We also discuss the possible role of a likely nuclear localization signal specific to and conserved in the phytochrome A lineage.
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Affiliation(s)
- Soshichiro Nagano
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Gießen, Germany
| | - Kaoling Guan
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Gießen, Germany
| | | | - Christian Feiler
- BESSY II, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - Manfred Weiss
- BESSY II, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - Anastasia Kraskov
- Institut für Chemie, Sekr. PC14, Technische Universität, Berlin, Germany
| | - David Buhrke
- Institut für Chemie, Sekr. PC14, Technische Universität, Berlin, Germany
| | - Peter Hildebrandt
- Institut für Chemie, Sekr. PC14, Technische Universität, Berlin, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Gießen, Germany.
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8
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Battocchio G, González R, Rao AG, Schapiro I, Mroginski MA. Dynamic Properties of the Photosensory Domain of Deinococcus radiodurans Bacteriophytochrome. J Phys Chem B 2020; 124:1740-1750. [PMID: 31999119 DOI: 10.1021/acs.jpcb.0c00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physicochemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with the main focus on the photoconversion mechanism involving a tetrapyrrole chromophore. In this computational work, we concentrate on the long-scale dynamic motion of the photosensory domain of Deinococcus radiodurans by means of classical all-atom molecular dynamics (MD) simulations. Conventional and accelerated MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB, are tested in long atomistic simulations to confront the dynamics of monomer and dimer forms. These calculations highlight dissimilar equilibrium conformations in aqueous solutions and, in turn, different large-scale dynamic behaviors of the monomer form vs the dimer form. While the phytochrome in a monomer form tends to close the cavity entailed between the GAF and PHY domains, the opposite trend is predicted for the phytochrome dimer, which opens up as a consequence of the formation of strong salt bridges between the PHY domains of two molecules in water.
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Affiliation(s)
- Giovanni Battocchio
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Aditya G Rao
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - 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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9
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Osoegawa S, Miyoshi R, Watanabe K, Hirose Y, Fujisawa T, Ikeuchi M, Unno M. Identification of the Deprotonated Pyrrole Nitrogen of the Bilin-Based Photoreceptor by Raman Spectroscopy with an Advanced Computational Analysis. J Phys Chem B 2019; 123:3242-3247. [PMID: 30913882 DOI: 10.1021/acs.jpcb.9b00965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochrome and cyanobacteriochrome utilize a linear methine-bridged tetrapyrrole (bilin) to control numerous biological processes. They show a reversible photoconversion between two spectrally distinct states. This photocycle is initiated by a C═C double-bond photoisomerization of the bilin followed by its thermal relaxations with transient and/or stationary changes in the protonation state of the pyrrole moiety. However, it has never been identified which of the four pyrrole nitrogen atoms is deprotonated. Here, we report a resonance Raman spectroscopic study on cyanobacteriochrome RcaE, which has been proposed to contain a deprotonated bilin for its green-absorbing 15 Z state. The observed Raman spectra were well reproduced by a simulated structure whose bilin B ring is deprotonated, with the aid of molecular dynamics and quantum mechanics/molecular mechanics calculations. The results revealed that the deprotonation of B and C rings has the distinct effect on the overall bilin structure, which will be relevant to the color tuning and photoconversion mechanisms of the phytochrome superfamily. Furthermore, this study documents the ability of vibrational spectroscopy combined with the advanced spectral analysis to visualize a proton of a cofactor molecule embedded in a protein moiety.
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Affiliation(s)
- Shinsuke Osoegawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Kouhei Watanabe
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences , Toyohashi University of Technology , Toyohashi , Aichi 441-8580 , Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology) , The University of Tokyo , Meguro, Tokyo 153-8902 , Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
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10
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Wojciechowska J, Jędrzejczyk M, Grams J, Keller N, Ruppert AM. Enhanced Production of γ-Valerolactone with an Internal Source of Hydrogen on Ca-Modified TiO 2 Supported Ru Catalysts. CHEMSUSCHEM 2019; 12:639-650. [PMID: 30350463 DOI: 10.1002/cssc.201801974] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/12/2018] [Indexed: 06/08/2023]
Abstract
Calcium-modified titania supported Ru catalysts were synthesized and evaluated for the hydrogenation of levulinic acid with formic acid as an internal hydrogen source and water as a green solvent. A new elegant photoassisted method was developed for the synthesis of uniform-size and evenly distributed Ru particles on the titania surface. Compared with the counterpart catalysts prepared by classical wet impregnation, enhanced levulinic acid conversion and γ-valerolactone yield were obtained and further improved through modification of the support by introduction of calcium into the titania support. This synthesis approach resulted in a change of the surface and bulk properties of the support, namely a decrease in the anatase crystallite size and the formation of a new calcium titanate phase. As a consequence, the properties of the catalysts were modified, and smaller ruthenium particles that had stronger interactions with the support were obtained. This affected the strength of the CO adsorption on the catalyst surface and facilitated the reaction performance. The optimum size of Ru particles that allowed for most efficient levulinic acid conversion was established.
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Affiliation(s)
- Joanna Wojciechowska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Łódź University of Technology, ul. Żeromskiego 116, 90-924, Łódź, Poland
- Institut de Chimie et Procédés pour l'Energie, l'Environnement et la Santé (ICPEES), CNRS, University of Strasbourg, 25 rue Becquerel, 67087, Strasbourg, France
| | - Marcin Jędrzejczyk
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Łódź University of Technology, ul. Żeromskiego 116, 90-924, Łódź, Poland
| | - Jacek Grams
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Łódź University of Technology, ul. Żeromskiego 116, 90-924, Łódź, Poland
| | - Nicolas Keller
- Institut de Chimie et Procédés pour l'Energie, l'Environnement et la Santé (ICPEES), CNRS, University of Strasbourg, 25 rue Becquerel, 67087, Strasbourg, France
| | - Agnieszka M Ruppert
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Łódź University of Technology, ul. Żeromskiego 116, 90-924, Łódź, Poland
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11
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Takeda K, Terazima M. Photoinduced Orientation Change of the Dimer Structure of the Pr-I State of Cph1Δ2. Biochemistry 2018; 57:5058-5071. [DOI: 10.1021/acs.biochem.8b00605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kimitoshi Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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12
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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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13
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Takiden A, Velazquez-Escobar F, Dragelj J, Woelke AL, Knapp EW, Piwowarski P, Bart F, Hildebrandt P, Mroginski MA. Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1. Photochem Photobiol 2017; 93:713-723. [DOI: 10.1111/php.12737] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Aref Takiden
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | | | - Jovan Dragelj
- Institut für Chemie und Biochemie; Freie Universität Berlin; Berlin Germany
| | - Anna Lena Woelke
- Institut für Chemie und Biochemie; Freie Universität Berlin; Berlin Germany
| | - Ernst-Walter Knapp
- Institut für Chemie und Biochemie; Freie Universität Berlin; Berlin Germany
| | - Patrick Piwowarski
- Institute of Medical Physics and Biophysics; Charité-Medical University Berlin; Berlin Germany
| | - Franz Bart
- Institute of Medical Physics and Biophysics; Charité-Medical University Berlin; Berlin Germany
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14
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Velázquez Escobar F, Buhrke D, Fernandez Lopez M, Shenkutie SM, von Horsten S, Essen LO, Hughes J, Hildebrandt P. Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB. FEBS Lett 2017; 591:1258-1265. [DOI: 10.1002/1873-3468.12642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/25/2017] [Accepted: 03/28/2017] [Indexed: 12/19/2022]
Affiliation(s)
| | - David Buhrke
- Institut für Chemie; Technische Universität Berlin; Germany
| | | | | | - Silke von Horsten
- Fachbereich Chemie, Strukturbiochemie; Philipps-Universität Marburg; Marburg Germany
| | - Lars-Oliver Essen
- Fachbereich Chemie, Strukturbiochemie; Philipps-Universität Marburg; Marburg Germany
- LOEWE Center for Synthetic Microbiology; Philipps-Universität; Marburg Germany
| | - Jon Hughes
- Plant Physiology; Justus-Liebig University Gießen; Giessen Germany
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15
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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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16
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Falklöf O, Durbeej B. Steric Effects Govern the Photoactivation of Phytochromes. Chemphyschem 2016; 17:954-7. [DOI: 10.1002/cphc.201501080] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Olle Falklöf
- Division of Theoretical Chemistry, IFM; Linköping University; 581 83 Linköping Sweden
| | - Bo Durbeej
- Division of Theoretical Chemistry, IFM; Linköping University; 581 83 Linköping Sweden
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17
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Siebert E, Rippers Y, Frielingsdorf S, Fritsch J, Schmidt A, Kalms J, Katz S, Lenz O, Scheerer P, Paasche L, Pelmenschikov V, Kuhlmann U, Mroginski MA, Zebger I, Hildebrandt P. Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O2-Tolerant Membrane-Bound Hydrogenase in the Crystalline State. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04119] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elisabeth Siebert
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes Fritsch
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Andrea Schmidt
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Jacqueline Kalms
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Sagie Katz
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Oliver Lenz
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Lars Paasche
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Vladimir Pelmenschikov
- Technische
Universität Berlin, Institut für Chemie, Sekr. C7, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Uwe Kuhlmann
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Ingo Zebger
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
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18
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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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19
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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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20
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Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proc Natl Acad Sci U S A 2014; 111:10179-84. [PMID: 24982198 DOI: 10.1073/pnas.1403096111] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Many aspects of plant photomorphogenesis are controlled by the phytochrome (Phy) family of bilin-containing photoreceptors that detect red and far-red light by photointerconversion between a dark-adapted Pr state and a photoactivated Pfr state. Whereas 3D models of prokaryotic Phys are available, models of their plant counterparts have remained elusive. Here, we present the crystal structure of the photosensing module (PSM) from a seed plant Phy in the Pr state using the PhyB isoform from Arabidopsis thaliana. The PhyB PSM crystallized as a head-to-head dimer with strong structural homology to its bacterial relatives, including a 5(Z)syn, 10(Z)syn, 15(Z)anti configuration of the phytochromobilin chromophore buried within the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain, and a well-ordered hairpin protruding from the Phy-specific domain toward the bilin pocket. However, its Per/Arnt/Sim (PAS) domain, knot region, and helical spine show distinct structural differences potentially important to signaling. Included is an elongated helical spine, an extended β-sheet connecting the GAF domain and hairpin stem, and unique interactions between the region upstream of the PAS domain knot and the bilin A and B pyrrole rings. Comparisons of this structure with those from bacterial Phys combined with mutagenic studies support a toggle model for photoconversion that engages multiple features within the PSM to stabilize the Pr and Pfr end states after rotation of the D pyrrole ring. Taken together, this Arabidopsis PhyB structure should enable molecular insights into plant Phy signaling and provide an essential scaffold to redesign their activities for agricultural benefit and as optogenetic reagents.
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21
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Chizhov I, Zorn B, Manstein DJ, Gärtner W. Kinetic and thermodynamic analysis of the light-induced processes in plant and cyanobacterial phytochromes. Biophys J 2014; 105:2210-20. [PMID: 24209867 DOI: 10.1016/j.bpj.2013.09.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/06/2013] [Accepted: 09/04/2013] [Indexed: 02/08/2023] Open
Abstract
The light-induced processes of the biological photoreceptor phytochrome (recombinant phyA of oat and recombinant CphA from the cyanobacterium Tolypothrix PCC7601) have been investigated in a time-resolved manner in the temperature range from 0 to 30°C. Both proteins were heterologously expressed and assembled in vitro with phycocyanobilin. The Pr state of plant phytochrome phyA is converted to the Pfr state after formation of four intermediates with an overall quantum yield of ~18%. The reversal reaction (Pfr-to-Pr) shows several intermediates, all of which, even the first detectable one, exhibit already all spectral features of the Pr state. The canonical phytochrome CphA from Tolypothrix showed a similar intermediate sequence as its plant ortholog. Whereas the kinetics for the forward reaction (Pr-to-Pfr) was nearly identical for both proteins, the reverse process (Pr formation) in the cyanobacterial phytochrome was slower by a factor of three. As found for the Pfr-to-Pr intermediates in the plant protein, also in CphA all detectable intermediates showed the spectral features of the Pr form. For both phytochromes, activation parameters for both the forward and the backward reaction pathways were determined.
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Affiliation(s)
- Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
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22
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Hauck AFE, Hardman SJO, Kutta RJ, Greetham GM, Heyes DJ, Scrutton NS. The photoinitiated reaction pathway of full-length cyanobacteriochrome Tlr0924 monitored over 12 orders of magnitude. J Biol Chem 2014; 289:17747-57. [PMID: 24817121 PMCID: PMC4067208 DOI: 10.1074/jbc.m114.566133] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The coupling of photochemistry to protein chemical and structural change is crucial to biological light-activated signaling mechanisms. This is typified by cyanobacteriochromes (CBCRs), members of the phytochrome superfamily of photoreceptors that exhibit a high degree of spectral diversity, collectively spanning the entire visible spectrum. CBCRs utilize a basic E/Z isomerization of the bilin chromophore as the primary step in their photocycle, which consists of reversible photoconversion between two photostates. Despite intense interest in these photoreceptors as signal transduction modules a complete description of light-activated chemical and structural changes has not been reported. The CBCR Tlr0924 contains both phycocyanobilin and phycoviolobilin chromophores, and these two species photoisomerize in parallel via spectrally and kinetically equivalent intermediates before the second step of the photoreaction where the reaction pathways diverge, the loss of a thioether linkage to a conserved cysteine residue occurs, and the phycocyanobilin reaction terminates in a red-absorbing state, whereas the phycoviolobilin reaction proceeds more rapidly to a final green-absorbing state. Here time-resolved visible transient absorption spectroscopy (femtosecond to second) has been used, in conjunction with time-resolved IR spectroscopy (femtosecond to nanosecond) and cryotrapping techniques, to follow the entire photoconversion of the blue-absorbing states to the green- and red-absorbing states of the full-length form of Tlr0924 CBCR. Our analysis shows that Tlr0924 undergoes an unprecedented long photoreaction that spans from picoseconds to seconds. We show that the thermally driven, long timescale changes are less complex than those reported for the red/far-red photocycles of the related phytochrome photoreceptors.
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Affiliation(s)
- Anna F E Hauck
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Samantha J O Hardman
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Roger J Kutta
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Gregory M Greetham
- the Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Derren J Heyes
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Nigel S Scrutton
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
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23
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Velazquez Escobar F, Hildebrandt T, Utesch T, Schmitt FJ, Seuffert I, Michael N, Schulz C, Mroginski MA, Friedrich T, Hildebrandt P. Structural parameters controlling the fluorescence properties of phytochromes. Biochemistry 2013; 53:20-9. [PMID: 24328165 DOI: 10.1021/bi401287u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Phytochromes constitute a class of photoreceptors that can be photoconverted between two stable states. The tetrapyrrole chromophore absorbs in the red spectral region and displays fluorescence maxima above 700 nm, albeit with low quantum yields. Because this wavelength region is particularly advantageous for fluorescence-based deep tissue imaging, there is a strong interest to engineer phytochrome variants with increased fluorescence yields. Such targeted design efforts would substantially benefit from a deeper understanding of those structural parameters that control the photophysical properties of the protein-bound chromophore. Here we have employed resonance Raman (RR) spectroscopy and molecular dynamics simulations for elucidating the chromophore structural changes in a fluorescence-optimized mutant (iRFP) derived from the PAS-GAF domain of the bacteriophytochrome RpBphP2 from Rhodopseudomas palustris . Both methods consistently reveal the structural consequences of the amino acid substitutions in the vicinity of the biliverdin chromophore that may account for lowering the propability of nonradiative excited state decays. First, compared to the wild-type protein, the tilt angle of the terminal ring D with respect to ring C is increased in iRFP, accompanied by the loss of hydrogen bond interactions of the ring D carbonyl function and the reduction of the number of water molecules in that part of the chromophore pocket. Second, the overall flexibility of the chromophore is significantly reduced, particularly in the region of rings D and A, thereby reducing the conformational heterogeneity of the methine bridge between rings A and B and the ring A carbonyl group, as concluded from the RR spectra of the wild-type proteins.
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Affiliation(s)
- Francisco Velazquez Escobar
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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24
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Zhuang X, Wang J, Lan Z. Tracking of the Molecular Motion in the Primary Event of Photoinduced Reactions of a Phytochromobilin Model. J Phys Chem B 2013; 117:15976-86. [DOI: 10.1021/jp408799b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xuhui Zhuang
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
| | - Jun Wang
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
| | - Zhenggang Lan
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
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25
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Zienicke B, Molina I, Glenz R, Singer P, Ehmer D, Escobar FV, Hildebrandt P, Diller R, Lamparter T. Unusual spectral properties of bacteriophytochrome Agp2 result from a deprotonation of the chromophore in the red-absorbing form Pr. J Biol Chem 2013; 288:31738-51. [PMID: 24036118 DOI: 10.1074/jbc.m113.479535] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phytochromes are widely distributed photoreceptors with a bilin chromophore that undergo a typical reversible photoconversion between the two spectrally different forms, Pr and Pfr. The phytochrome Agp2 from Agrobacterium tumefaciens belongs to the group of bathy phytochromes that have a Pfr ground state as a result of the Pr to Pfr dark conversion. Agp2 has untypical spectral properties in the Pr form reminiscent of a deprotonated chromophore as confirmed by resonance Raman spectroscopy. UV/visible absorption spectroscopy showed that the pKa is >11 in the Pfr form and ∼7.6 in the Pr form. Unlike other phytochromes, photoconversion thus results in a pKa shift of more than 3 units. The Pr/Pfr ratio after saturating irradiation with monochromatic light is strongly pH-dependent. This is partially due to a back-reaction of the deprotonated Pr chromophore at pH 9 after photoexcitation as found by flash photolysis. The chromophore protonation and dark conversion were affected by domain swapping and site-directed mutagenesis. A replacement of the PAS or GAF domain by the respective domain of the prototypical phytochrome Agp1 resulted in a protonated Pr chromophore; the GAF domain replacement afforded an inversion of the dark conversion. A reversion was also obtained with the triple mutant N12S/Q190L/H248Q, whereas each single point mutant is characterized by decelerated Pr to Pfr dark conversion.
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Affiliation(s)
- Benjamin Zienicke
- From the Botanical Institute, Karlsruhe Institute of Technology, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
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Velazquez Escobar F, Utesch T, Narikawa R, Ikeuchi M, Mroginski MA, Gärtner W, Hildebrandt P. Photoconversion mechanism of the second GAF domain of cyanobacteriochrome AnPixJ and the cofactor structure of its green-absorbing state. Biochemistry 2013; 52:4871-80. [PMID: 23808413 DOI: 10.1021/bi400506a] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacteriochromes are members of the phytochrome superfamily. In contrast to classical phytochromes, these small photosensors display a considerable variability of electronic absorption maxima. We have studied the light-induced conversions of the second GAF domain of AnPixJ, AnPixJg2, a phycocyanobilin-binding protein from the cyanobacterium Anabaena PCC 7120, using low-temperature resonance Raman spectroscopy combined with molecular dynamics simulations. AnPixJg2 is formed biosynthetically as a red-absorbing form (Pr) and can be photoconverted into a green-absorbing form (Pg). Forward and backward phototransformations involve the same reaction sequences and intermediates of similar cofactor structures as the corresponding processes in canonical phytochromes, including a transient cofactor deprotonation. Whereas the cofactor of the Pr state shows far-reaching similarities to the Pr states of classical phytochromes, the Pg form displays significant upshifts of the methine bridge stretching frequencies concomitant to the hypsochromically shifted absorption maximum. However, the cofactor in Pg is protonated and adopts a conformation very similar to the Pfr state of classical phytochromes. The spectral differences are probably related to an increased solvent accessibility of the chromophore which may reduce the π-electron delocalization in the phycocyanobilin and thus raise the energies of the first electronic transition and the methine bridge stretching modes. Molecular dynamics simulations suggest that the Z → E photoisomerization of the chromophore at the C-D methine bridge alters the interactions with the nearby Trp90 which in turn may act as a gate, allowing the influx of water molecules into the chromophore pocket. Such a mechanism of color tuning AnPixJg2 is unique among the cyanobacteriochromes studied so far.
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Affiliation(s)
- Francisco Velazquez Escobar
- Institut für Chemie, Technische Universität Berlin , Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
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Salewski J, Escobar FV, Kaminski S, von Stetten D, Keidel A, Rippers Y, Michael N, Scheerer P, Piwowarski P, Bartl F, Frankenberg-Dinkel N, Ringsdorf S, Gärtner W, Lamparter T, Mroginski MA, Hildebrandt P. Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes. J Biol Chem 2013; 288:16800-16814. [PMID: 23603902 DOI: 10.1074/jbc.m113.457531] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion.
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Affiliation(s)
- Johannes Salewski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Francisco Velazquez Escobar
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Steve Kaminski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - David von Stetten
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany; Structural Biology Group, European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Anke Keidel
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Michael
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Protein X-ray Crystallography, D-10117 Berlin, Germany
| | - Patrick Piwowarski
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Franz Bartl
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Nicole Frankenberg-Dinkel
- AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Simone Ringsdorf
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Tilman Lamparter
- Institut für Allgemeine Botanik, Karlsruher Institut für Technologie, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
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Falklöf O, Durbeej B. Modeling of phytochrome absorption spectra. J Comput Chem 2013; 34:1363-74. [DOI: 10.1002/jcc.23265] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Olle Falklöf
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
| | - Bo Durbeej
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
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Song C, Rohmer T, Tiersch M, Zaanen J, Hughes J, Matysik J. Solid-State NMR Spectroscopy to Probe Photoactivation in Canonical Phytochromes. Photochem Photobiol 2013; 89:259-73. [DOI: 10.1111/php.12029] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/28/2012] [Indexed: 01/17/2023]
Affiliation(s)
| | - Thierry Rohmer
- Leids Instituut voor Chemisch Onderzoek; Universiteit Leiden; Leiden; The Netherlands
| | | | - Jan Zaanen
- Instituut-Lorentz for Theoretical Physics; Universiteit Leiden; Leiden; The Netherlands
| | - Jon Hughes
- Pflanzenphysiologie; Justus-Liebig-Universität; Giessen; Germany
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Zhou G, Hou Y, Liu L, Liu H, Liu C, Liu J, Qiao H, Liu W, Fan Y, Shen S, Rong L. Preparation and characterization of NiW-nHA composite catalyst for hydrocracking. NANOSCALE 2012; 4:7698-7703. [PMID: 23128670 DOI: 10.1039/c2nr31486j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The synthesis, characterization and catalytic capability of the NiW-nano-hydroxyapatite (NiW-nHA) composite were investigated in this paper. The NiW-nHA catalyst was prepared by a co-precipitation method. Then Fourier transform infrared (FT-IR) spectroscopy, transmission electron microscopy (TEM), X-ray diffraction (XRD) and energy dispersive spectroscopy (EDX) were used to analyze this material. In addition, the catalytic capacity of the NiW-nHA composite was also examined by FT-IR and gas chromatography (GC). The results of FT-IR analysis indicated that Ni, W and nHA combined closely. TEM observation revealed that this catalyst was needle shaped and the crystal retained a nanometer size. XRD data also suggested that a new phase of CaWO(4) appeared and the lattice parameters of nHA changed in this system. nHA was the carrier of metals. The rates of Ni/W-loading were 73.24% and 65.99% according to the EDX data, respectively. Furthermore, the conversion of 91.88% Jatropha oil was achieved at 360 °C and 3 MPa h(-1) over NiW-nHA catalyst. The straight chain alkanes ranging from C(15) to C(18) were the main components in the production. The yield of C(15)-C(18) alkanes was up to 83.56 wt%. The reaction pathway involved hydrocracking of the C═C bonds of these triglycerides from Jatropha oil. This paper developed a novel non-sulfided catalyst to obtain a "green biofuel" from vegetable oil.
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Affiliation(s)
- Gang Zhou
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, XueYuan Road No.37, Haidian District, Beijing, 100191, China
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31
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Wang GY, Gao YX, Wang WD, Huang WX. Selective CO Methanation over Ru Catalysts Supported on Nanostructured TiO2 with Different Crystalline Phases and Morphology. CHINESE J CHEM PHYS 2012. [DOI: 10.1088/1674-0068/25/04/475-480] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Song C, Essen LO, Gärtner W, Hughes J, Matysik J. Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A. MOLECULAR PLANT 2012; 5:698-715. [PMID: 22419823 DOI: 10.1093/mp/sss017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Despite extensive study, the molecular structure of the chromophore-binding pocket of phytochrome A (phyA), the principal photoreceptor controlling photomorphogenesis in plants, has not yet been successfully resolved. Here, we report a series of two-dimensional (2-D) magic-angle spinning solid-state NMR experiments on the recombinant N-terminal, 65-kDa PAS-GAF-PHY light-sensing module of phytochrome A3 from oat (Avena sativa), assembled with uniformly 13C- and 15N-labeled phycocyanobilin (u-[13C,15N]-PCB-As.phyA3). The Pr state of this protein was studied regarding the electronic structure of the chromophore and its interactions with the proximal amino acids. Using 2-D 13C-13C and 1H-15N experiments, a complete set of 13C and 15N assignments for the chromophore were obtained. Also, a large number of 1H-13C distance restraints between the chromophore and its binding pocket were revealed by interfacial heteronuclear correlation spectroscopy. 13C doublings of the chromophore A-ring region and the C-ring carboxylate moiety, together with the observation of two Pr isoforms, Pr-I and Pr-II, demonstrate the local mobility of the chromophore and the plasticity of its protein environment. It appears that the interactions and dynamics in the binding pocket of phyA in the Pr state are remarkably similar to those of cyanobacterial phytochrome (Cph1). The N-terminus of the region modeled (residues 56-66 of phyA) is highly mobile. Differences in the regulatory processes involved in plant and Cph1 phytochromes are discussed.
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Affiliation(s)
- Chen Song
- Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden, PO Box 9502, 2300 RA Leiden, The Netherlands
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Gärtner W. Kurt Schaffner: from organic photochemistry to photobiology. Photochem Photobiol Sci 2012; 11:872-80. [DOI: 10.1039/c2pp05405a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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34
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Elucidating photoinduced structural changes in phytochromes by the combined application of resonance Raman spectroscopy and theoretical methods. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.02.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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