1
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Chenchiliyan M, Kübel J, Ooi SA, Salvadori G, Mennucci B, Westenhoff S, Maj M. Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy. J Chem Phys 2023; 158:085103. [PMID: 36859103 DOI: 10.1063/5.0135268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.
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Affiliation(s)
- Manoop Chenchiliyan
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry-Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
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2
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Yang Y, Stensitzki T, Lang C, Hughes J, Mroginski MA, Heyne K. Ultrafast protein response in the Pfr state of Cph1 phytochrome. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023; 22:919-930. [PMID: 36653574 DOI: 10.1007/s43630-023-00362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
Photoisomerization is a fundamental process in several classes of photoreceptors. Phytochromes sense red and far-red light in their Pr and Pfr states, respectively. Upon light absorption, these states react via individual photoreactions to the other state. Cph1 phytochrome shows a photoisomerization of its phycocyanobilin (PCB) chromophore in the Pfr state with a time constant of 0.7 ps. The dynamics of the PCB chromophore has been described, but whether or not the apoprotein exhibits an ultrafast response too, is not known. Here, we compare the photoreaction of 13C/15N labeled apoprotein with unlabeled apoprotein to unravel ultrafast apoprotein dynamics in Cph1. In the spectral range from 1750 to 1620 cm-1 we assigned several signals due to ultrafast apoprotein dynamics. A bleaching signal at 1724 cm-1 is tentatively assigned to deprotonation of a carboxylic acid, probably Asp207, and signals around 1670 cm-1 are assigned to amide I vibrations of the capping helix close to the chromophore. These signals remain after photoisomerization. The apoprotein dynamics appear upon photoexcitation or concomitant with chromophore isomerization. Thus, apoprotein dynamics occur prior to and after photoisomerization on an ultrafast time-scale. We discuss the origin of the ultrafast apoprotein response with the 'Coulomb hammer' mechanism, i.e. an impulsive change of electric field and Coulombic force around the chromophore upon excitation.
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Affiliation(s)
- Yang Yang
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Till Stensitzki
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Maria Andrea Mroginski
- Institut Für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Karsten Heyne
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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3
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Rydzewski J, Walczewska-Szewc K, Czach S, Nowak W, Kuczera K. Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. J Phys Chem B 2022; 126:2647-2657. [PMID: 35357137 PMCID: PMC9014414 DOI: 10.1021/acs.jpcb.2c00131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability of phytochromes
to act as photoswitches in plants and
microorganisms depends on interactions between a bilin-like chromophore
and a host protein. The interconversion occurs between the spectrally
distinct red (Pr) and far-red (Pfr) conformers. This conformational
change is triggered by the photoisomerization of the chromophore D-ring
pyrrole. In this study, as a representative example of a phytochrome-bilin
system, we consider biliverdin IXα (BV) bound to bacteriophytochrome
(BphP) from Deinococcus radiodurans. In the absence
of light, we use an enhanced sampling molecular dynamics (MD) method
to overcome the photoisomerization energy barrier. We find that the
calculated free energy (FE) barriers between essential metastable
states agree with spectroscopic results. We show that the enhanced
dynamics of the BV chromophore in BphP contributes to triggering nanometer-scale
conformational movements that propagate by two experimentally determined
signal transduction pathways. Most importantly, we describe how the
metastable states enable a thermal transition known as the dark reversion
between Pfr and Pr, through a previously unknown intermediate state
of Pfr. We present the heterogeneity of temperature-dependent Pfr
states at the atomistic level. This work paves a way toward understanding
the complete mechanism of the photoisomerization of a bilin-like chromophore
in phytochromes.
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Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Katarzyna Walczewska-Szewc
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Sylwia Czach
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Krzysztof Kuczera
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States.,Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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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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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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Takala H, Edlund P, Ihalainen JA, Westenhoff S. Tips and turns of bacteriophytochrome photoactivation. Photochem Photobiol Sci 2021; 19:1488-1510. [PMID: 33107538 DOI: 10.1039/d0pp00117a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.
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Affiliation(s)
- Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland. and Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Janne A Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland.
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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7
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Sineshchekov VA, Bekasova OD. Two Distinct Photoprocesses in Cyanobacterial Bilin Pigments: Energy Migration in Light‐Harvesting Phycobiliproteins versus Photoisomerization in Phytochromes. Photochem Photobiol 2020; 96:750-767. [DOI: https:/doi.org/10.1111/php.13197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/17/2019] [Indexed: 12/17/2023]
Abstract
AbstractThe evolution of oxygenic photosynthesis, respiration and photoperception are connected with the appearance of cyanobacteria. The key compounds, which are involved in these processes, are tetrapyrroles: open chain — bilins and cyclic — chlorophylls and heme. The latter are characterized by their covalent bond with the apoprotein resulting in the formation of biliproteins. This type of photoreceptors is unique in that it can perform important and opposite functions—light‐harvesting in photosynthesis with the participation of phycobiliproteins and photoperception mediated by phycochromes and phytochromes. In this review, cyanobacterial phycobiliproteins and phytochrome Cph1 are considered from a comparative point of view. Structural features of these pigments, which provide their contrasting photophysical and photochemical characteristics, are analyzed. The determining factor in the case of energy migration with the participation of phycobiliproteins is blocking the torsional relaxations of the chromophore, its D‐ring, in the excited state and their freedom, in the case of phytochrome photoisomerization. From the energetics point of view, this distinction is preconditioned by the height of the activation barrier for the photoreaction and relaxation in the excited state, which depends on the degree of the chromophore fixation by its protein surroundings.
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Affiliation(s)
| | - Olga D. Bekasova
- Bach Institute of Biochemistry Fundamentals of Biotechnology Federal Research Centre Russian Academy of Sciences Moscow Russia
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8
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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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9
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Sadeghi M, Balke J, Schneider C, Nagano S, Stellmacher J, Lochnit G, Lang C, Weise C, Hughes J, Alexiev U. Transient Deprotonation of the Chromophore Affects Protein Dynamics Proximal and Distal to the Linear Tetrapyrrole Chromophore in Phytochrome Cph1. Biochemistry 2020; 59:1051-1062. [PMID: 32069394 DOI: 10.1021/acs.biochem.9b00967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phytochromes are biological red/far-red light sensors found in many organisms. Prototypical phytochromes, including Cph1 from the cyanobacterium Synechocystis 6803, act as photochemical switches that interconvert between stable red (Pr)- and metastable far-red (Pfr)-absorbing states induced by photoisomerization of the bilin chromophore. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY) and the C-terminal transmitter (output) module, usually a histidine kinase, as in the case of Cph1. The chromophore deprotonates transiently during the Pr → Pfr photoconversion in association with extensive global structural changes required for signal transmission. Here, we performed equilibrium studies in the Pr state, involving pH titration of the linear tetrapyrrole chromophore in different Cph1 constructs, and measurement of pH-dependent structural changes at various positions in the protein using picosecond time-resolved fluorescence anisotropy. The fluorescent reporter group was attached at positions 371 (PHY domain), 305 (GAF domain), and 120 (PAS domain), as well as at sites in the PAS-GAF bidomain. We show direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains. Our results suggest that chromophore deprotonation is closely associated with a higher protein mobility (conformational space) both in proximal and in distal protein sites, implying a causal relationship that might be important for the global large protein arrangements and thus intramolecular signal transduction.
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Affiliation(s)
- Maryam Sadeghi
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Jens Balke
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Constantin Schneider
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Soshichiro Nagano
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Johannes Stellmacher
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Günter Lochnit
- Justus-Liebig-Universität, Institut für Medizinische Biochemie, D-35390 Giessen, Germany
| | - Christina Lang
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Chris Weise
- Freie Universität Berlin, Institut für Chemie und Biochemie, D-14195 Berlin, Germany
| | - Jon Hughes
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Ulrike Alexiev
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
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10
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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11
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Kübel J, Chenchiliyan M, Ooi SA, Gustavsson E, Isaksson L, Kuznetsova V, Ihalainen JA, Westenhoff S, Maj M. Transient IR spectroscopy identifies key interactions and unravels new intermediates in the photocycle of a bacterial phytochrome. Phys Chem Chem Phys 2020; 22:9195-9203. [DOI: 10.1039/c9cp06995j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Infra-red spectroscopy advances our understanding of how photosensory proteins carry their function.
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Affiliation(s)
- Joachim Kübel
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- Gothenburg 40530
- Sweden
| | - Manoop Chenchiliyan
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- Gothenburg 40530
- Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- Gothenburg 40530
- Sweden
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- Gothenburg 40530
- Sweden
| | - Linnéa Isaksson
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- Gothenburg 40530
- Sweden
| | - Valentyna Kuznetsova
- Nanoscience Center
- Department of Biological and Environmental Science
- University of Jyväskylä
- Jyväskylä 40014
- Finland
| | - Janne A. Ihalainen
- Nanoscience Center
- Department of Biological and Environmental Science
- University of Jyväskylä
- Jyväskylä 40014
- Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- Gothenburg 40530
- Sweden
| | - Michał Maj
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- Gothenburg 40530
- Sweden
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12
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Buhrke D, Battocchio G, Wilkening S, Blain-Hartung M, Baumann T, Schmitt FJ, Friedrich T, Mroginski MA, Hildebrandt P. Red, Orange, Green: Light- and Temperature-Dependent Color Tuning in a Cyanobacteriochrome. Biochemistry 2019; 59:509-519. [PMID: 31840994 DOI: 10.1021/acs.biochem.9b00931] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptor proteins that photoconvert between two parent states and thereby regulate various biological processes. An intriguing property is their variable ultraviolet-visible (UV-vis) absorption that covers the entire spectral range from the far-red to the near-UV region and thus makes CBCRs promising candidates for optogenetic applications. Here, we have studied Slr1393, a CBCR that photoswitches between red- and green-absorbing states (Pr and Pg, respectively). Using UV-vis absorption, fluorescence, and resonance Raman (RR) spectroscopy, a further orange-absorbing state O600 that is in thermal equilibrium with Pr was identified. The different absorption properties of the three states were attributed to the different lengths of the conjugated π-electron system of the phycocyanobilin chromophore. In agreement with available crystal structures and supported by quantum mechanics/molecular mechanics (QM/MM) calculations, the most extended conjugation holds for Pr whereas it is substantially reduced in Pg. Here, the two outer pyrrole rings D and A are twisted out of the plane defined by inner pyrrole rings B and C. For the O600 state, the comparison of the experimental RR spectra with QM/MM-calculated spectra indicates a partially distorted ZZZssa geometry in which ring A is twisted while ring D and the adjacent methine bridge display essentially the same geometry as Pr. The quantitative analysis of temperature-dependent spectra yields an enthalpy barrier of ∼30 kJ/mol for the transition from Pr to O600. This reaction is associated with the movement of a conserved tryptophan residue from the chromophore binding pocket to a solvent-exposed position.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Giovanni Battocchio
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Svea Wilkening
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Matthew Blain-Hartung
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Tobias Baumann
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Franz-Josef Schmitt
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Thomas Friedrich
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Maria-Andrea Mroginski
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Peter Hildebrandt
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
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13
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Sineshchekov VA, Bekasova OD. Two Distinct Photoprocesses in Cyanobacterial Bilin Pigments: Energy Migration in Light-Harvesting Phycobiliproteins versus Photoisomerization in Phytochromes. Photochem Photobiol 2019; 96:750-767. [PMID: 31869438 DOI: 10.1111/php.13197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/17/2019] [Indexed: 01/29/2023]
Abstract
The evolution of oxygenic photosynthesis, respiration and photoperception are connected with the appearance of cyanobacteria. The key compounds, which are involved in these processes, are tetrapyrroles: open chain - bilins and cyclic - chlorophylls and heme. The latter are characterized by their covalent bond with the apoprotein resulting in the formation of biliproteins. This type of photoreceptors is unique in that it can perform important and opposite functions-light-harvesting in photosynthesis with the participation of phycobiliproteins and photoperception mediated by phycochromes and phytochromes. In this review, cyanobacterial phycobiliproteins and phytochrome Cph1 are considered from a comparative point of view. Structural features of these pigments, which provide their contrasting photophysical and photochemical characteristics, are analyzed. The determining factor in the case of energy migration with the participation of phycobiliproteins is blocking the torsional relaxations of the chromophore, its D-ring, in the excited state and their freedom, in the case of phytochrome photoisomerization. From the energetics point of view, this distinction is preconditioned by the height of the activation barrier for the photoreaction and relaxation in the excited state, which depends on the degree of the chromophore fixation by its protein surroundings.
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Affiliation(s)
| | - Olga D Bekasova
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Centre, Russian Academy of Sciences, Moscow, Russia
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14
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Gustavsson E, Isaksson L, Persson C, Mayzel M, Brath U, Vrhovac L, Ihalainen JA, Karlsson BG, Orekhov V, Westenhoff S. Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching. Biophys J 2019; 118:415-421. [PMID: 31839260 DOI: 10.1016/j.bpj.2019.11.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 11/16/2022] Open
Abstract
Phytochromes sense red/far-red light and control many biological processes in plants, fungi, and bacteria. Although the crystal structures of dark- and light-adapted states have been determined, the molecular mechanisms underlying photoactivation remain elusive. Here, we demonstrate that the conserved tongue region of the PHY domain of a 57-kDa photosensory module of Deinococcus radiodurans phytochrome changes from a structurally heterogeneous dark state to an ordered, light-activated state. The results were obtained in solution by utilizing a laser-triggered activation approach detected on the atomic level with high-resolution protein NMR spectroscopy. The data suggest that photosignaling of phytochromes relies on careful modulation of structural heterogeneity of the PHY tongue.
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Affiliation(s)
- Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Persson
- Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Maxim Mayzel
- Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Ulrika Brath
- Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Janne A Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - B Göran Karlsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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15
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Consiglieri E, Gutt A, Gärtner W, Schubert L, Viappiani C, Abbruzzetti S, Losi A. Dynamics and efficiency of photoswitching in biliverdin-binding phytochromes. Photochem Photobiol Sci 2019; 18:2484-2496. [DOI: 10.1039/c9pp00264b] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A full scale analysis of the kinetic processes in the μ-to-millisecond time scale for red-and far red-triggered processes in biliverdin-binding bacterial and fungal phytochromes.
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Affiliation(s)
- Eleonora Consiglieri
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Alexander Gutt
- Max-Planck-Institute for Chemical Energy Conversion
- 45470 Mülheim an der Ruhr
- Germany
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry
- University of Leipzig
- 04103 Leipzig
- Germany
| | - Luiz Schubert
- Institute for Physical Chemistry
- Heinrich-Heine-University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Cristiano Viappiani
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Stefania Abbruzzetti
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Aba Losi
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
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16
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Li X, Hu D, Xie Y, Lan Z. Analysis of trajectory similarity and configuration similarity in on-the-fly surface-hopping simulation on multi-channel nonadiabatic photoisomerization dynamics. J Chem Phys 2018; 149:244104. [DOI: 10.1063/1.5048049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Xusong Li
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deping Hu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Xie
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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17
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Assafa TE, Anders K, Linne U, Essen LO, Bordignon E. Light-Driven Domain Mechanics of a Minimal Phytochrome Photosensory Module Studied by EPR. Structure 2018; 26:1534-1545.e4. [DOI: 10.1016/j.str.2018.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/30/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
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18
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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: 33] [Impact Index Per Article: 5.5] [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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19
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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20
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Velázquez Escobar F, Buhrke D, Michael N, Sauthof L, Wilkening S, Tavraz NN, Salewski J, Frankenberg-Dinkel N, Mroginski MA, Scheerer P, Friedrich T, Siebert F, Hildebrandt P. Common Structural Elements in the Chromophore Binding Pocket of the Pfr State of Bathy Phytochromes. Photochem Photobiol 2017; 93:724-732. [DOI: 10.1111/php.12742] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/06/2017] [Indexed: 01/17/2023]
Affiliation(s)
| | - David Buhrke
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | - Norbert Michael
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | - Luisa Sauthof
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
- Institute of Medical Physics and Biophysics (CCO); Group Protein X-ray Crystallography & Signal Transduction; Charité - University Medicine Berlin; Berlin Germany
| | - Svea Wilkening
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | | | | | - Nicole Frankenberg-Dinkel
- Fachbereich Biologie; Abt. Mikrobiologie; Technische Universität Kaiserslautern; Kaiserslautern Germany
| | | | - Patrick Scheerer
- Institute of Medical Physics and Biophysics (CCO); Group Protein X-ray Crystallography & Signal Transduction; Charité - University Medicine Berlin; Berlin Germany
| | - Thomas Friedrich
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | - Friedrich Siebert
- Institut für Molekulare Medizin und Zellforschung; Sektion Biophysik; Albert-Ludwigs-Universität Freiburg; Freiburg Germany
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21
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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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22
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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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23
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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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24
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Nagano S. From photon to signal in phytochromes: similarities and differences between prokaryotic and plant phytochromes. JOURNAL OF PLANT RESEARCH 2016; 129:123-135. [PMID: 26818948 DOI: 10.1007/s10265-016-0789-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/03/2016] [Indexed: 06/05/2023]
Abstract
Phytochromes represent a diverse family of red/far-red-light absorbing chromoproteins which are widespread across plants, cyanobacteria, non-photosynthetic bacteria, and more. Phytochromes play key roles in regulating physiological activities in response to light, a critical element in the acclimatization to the environment. The discovery of prokaryotic phytochromes facilitated structural studies which deepened our understanding on the general mechanisms of phytochrome action. An extrapolation of this information to plant phytochromes is justified for universally conserved functional aspects, but it is also true that there are many aspects which are unique to plant phytochromes. Here I summarize some structural studies carried out to date on both prokaryotic and plant phytochromes. I also attempt to identify aspects which are common or unique to plant and prokaryotic phytochromes. Phytochrome themselves, as well as the downstream signaling pathway in plants are more complex than in their prokaryotic counterparts. Thus many structural and functional aspects of plant phytochrome remain unresolved.
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Affiliation(s)
- Soshichiro Nagano
- Institute for Plant Physiology, Justus Liebig University Giessen, Senckenbergstrasse 3, 35390, Giessen, Germany.
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25
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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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