1
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Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024; 20:906-915. [PMID: 38831036 DOI: 10.1038/s41589-024-01626-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
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Affiliation(s)
- Nathan M Ennist
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shunzhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison A Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | | | | | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anthony V Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ash Sueh Hua
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Avi Z Swartz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ralph A Cacho
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Novy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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2
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Riedl M, Renger T, Seibt J. Theory of 2D electronic spectroscopy of water soluble chlorophyll-binding protein (WSCP): Signatures of Chl b derivate. J Chem Phys 2024; 160:184114. [PMID: 38726933 DOI: 10.1063/5.0200876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/21/2024] [Indexed: 06/29/2024] Open
Abstract
We investigate how electronic excitations and subsequent dissipative dynamics in the water soluble chlorophyll-binding protein (WSCP) are connected to features in two-dimensional (2D) electronic spectra, thereby comparing results from our theoretical approach with experimental data from the literature. Our calculations rely on third-order response functions, which we derived from a second-order cumulant expansion of the dissipative dynamics involving the partial ordering prescription, assuming a fast vibrational relaxation in the potential energy surfaces of excitons. Depending on whether the WSCP complex containing a tetrameric arrangement of pigments composed of two dimers with weak excitonic coupling between them binds the chlorophyll variant Chl a or Chl b, the resulting linear absorption and circular dichroism spectra and particularly the 2D spectra exhibit substantial differences in line shapes. These differences between Chl a WSCP and Chl b WSCP cannot be explained by the slightly modified excitonic couplings within the two variants. In the case of Chl a WSCP, the assumption of equivalent dimer subunits facilitates a reproduction of substantial features from the experiment by the calculations. In contrast, for Chl b WSCP, we have to assume that the sample, in addition to Chl b dimers, contains a small but distinct fraction of chemically modified Chl b pigments. The existence of such Chl b derivates has been proposed by Pieper et al. [J. Phys. Chem. B 115, 4042 (2011)] based on low-temperature absorption and hole-burning spectroscopy. Here, we provide independent evidence.
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Affiliation(s)
- Michael Riedl
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Joachim Seibt
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
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3
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Gustin I, Kim CW, McCamant DW, Franco I. Mapping electronic decoherence pathways in molecules. Proc Natl Acad Sci U S A 2023; 120:e2309987120. [PMID: 38015846 PMCID: PMC10710033 DOI: 10.1073/pnas.2309987120] [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: 06/13/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.
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Affiliation(s)
- Ignacio Gustin
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Chang Woo Kim
- Department of Chemistry, Chonnam National University, Gwangju61186, South Korea
| | - David W. McCamant
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, NY14627
- Department of Physics, University of Rochester, Rochester, NY14627
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4
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Cherepanov DA, Neverov KV, Obukhov YN, Maleeva YV, Gostev FE, Shelaev IV, Aybush AV, Kritsky MS, Nadtochenko VA. Femtosecond Dynamics of Excited States of Chlorophyll Tetramer in Water-Soluble Chlorophyll-Binding Protein BoWSCP. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1580-1595. [PMID: 38105026 DOI: 10.1134/s0006297923100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 12/19/2023]
Abstract
The paper reports on the absorption dynamics of chlorophyll a in a symmetric tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP. It was measured by a broadband femtosecond laser pump-probe spectroscopy within the range from 400 to 750 nm and with a time resolution of 20 fs-200 ps. When BoWSCP was excited in the region of the Soret band at a wavelength of 430 nm, nonradiative intramolecular conversion S3→S1 was observed with a characteristic time of 83 ± 9 fs. When the complex was excited in the region of the Qy band at 670 nm, relaxation transition between two excitonic states of the chlorophyll dimer was observed in the range of 105 ± 10 fs. Absorption spectra of the excited singlet states S1 and S3 of chlorophyll a were obtained. The delocalization of the excited state between exciton-coupled Chl molecules in BoWSCP tetramer changed in time and depended on the excitation energy. When BoWSCP is excited in the Soret band region, an ultrafast photochemical reaction is observed. This could result from the reduction of tryptophan in the vicinity of chlorophyll.
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Affiliation(s)
- Dmitry A Cherepanov
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
- Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Konstantin V Neverov
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yuriy N Obukhov
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Yulia V Maleeva
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Feodor E Gostev
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Ivan V Shelaev
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
- Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Arseny V Aybush
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Michail S Kritsky
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Victor A Nadtochenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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5
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Fresch E, Collini E. The Role of H-Bonds in the Excited-State Properties of Multichromophoric Systems: Static and Dynamic Aspects. Molecules 2023; 28:molecules28083553. [PMID: 37110786 PMCID: PMC10141795 DOI: 10.3390/molecules28083553] [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: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Given their importance, hydrogen bonds (H-bonds) have been the subject of intense investigation since their discovery. Indeed, H-bonds play a fundamental role in determining the structure, the electronic properties, and the dynamics of complex systems, including biologically relevant materials such as DNA and proteins. While H-bonds have been largely investigated for systems in their electronic ground state, fewer studies have focused on how the presence of H-bonds could affect the static and dynamic properties of electronic excited states. This review presents an overview of the more relevant progress in studying the role of H-bond interactions in modulating excited-state features in multichromophoric biomimetic complex systems. The most promising spectroscopic techniques that can be used for investigating the H-bond effects in excited states and for characterizing the ultrafast processes associated with their dynamics are briefly summarized. Then, experimental insights into the modulation of the electronic properties resulting from the presence of H-bond interactions are provided, and the role of the H-bond in tuning the excited-state dynamics and the related photophysical processes is discussed.
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Affiliation(s)
- Elisa Fresch
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Elisabetta Collini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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6
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Seibt J, Lindorfer D, Renger T. Signatures of intramolecular vibrational and vibronic Q[Formula: see text]-Q[Formula: see text] coupling effects in absorption and CD spectra of chlorophyll dimers. PHOTOSYNTHESIS RESEARCH 2023; 156:19-37. [PMID: 36040654 PMCID: PMC10070234 DOI: 10.1007/s11120-022-00946-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
An electron-vibrational coupling model that includes the vibronic (non-adiabatic) coupling between the Q[Formula: see text] and Q[Formula: see text] transitions of chlorophyll (Chl), created by Reimers and coworkers (Scientific Rep. 3, 2761, 2013) is extended here to chlorophyll dimers with interchlorophyll excitonic coupling. The model is applied to a Chl a dimer of the water-soluble chlorophyll binding protein (WSCP). As for isolated chlorophyll, the vibronic coupling is found to have a strong influence on the high-frequency vibrational sideband in the absorption spectrum, giving rise to a band splitting. In contrast, in the CD spectrum the interplay of vibronic coupling and static disorder leads to a strong suppression of the vibrational sideband in excellent agreement with the experimental data. The conservative nature of the CD spectrum in the low-energy region is found to be caused by a delicate balance of the intermonomer excitonic coupling between the purely electronic Q[Formula: see text] transition and the Q[Formula: see text] transition involving intramolecular vibrational excitations on one hand and the coupling to higher-energy electronic transitions on the other hand.
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Affiliation(s)
- Joachim Seibt
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria.
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria
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7
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Ciuti S, Agostini A, Barbon A, Bortolus M, Paulsen H, Di Valentin M, Carbonera D. Magnetophotoselection in the Investigation of Excitonically Coupled Chromophores: The Case of the Water-Soluble Chlorophyll Protein. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123654. [PMID: 35744779 PMCID: PMC9227413 DOI: 10.3390/molecules27123654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/01/2022]
Abstract
A magnetophotoselection (MPS) investigation of the photoexcited triplet state of chlorophyll a both in a frozen organic solvent and in a protein environment, provided by the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum, is reported. The MPS experiment combines the photoselection achieved by exciting with linearly polarized light with the magnetic selection of electron paramagnetic resonance (EPR) spectroscopy, allowing the determination of the relative orientation of the optical transition dipole moment and the zero-field splitting tensor axes in both environments. We demonstrate the robustness of the proposed methodology for a quantitative description of the excitonic interactions among pigments. The orientation of the optical transition dipole moments determined by the EPR analysis in WSCP, identified as an appropriate model system, are in excellent agreement with those calculated in the point-dipole approximation. In addition, MPS provides information on the electronic properties of the triplet state, localized on a single chlorophyll a pigment of the protein cluster, in terms of orientation of the zero-field splitting tensor axes in the molecular frame.
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Affiliation(s)
- Susanna Ciuti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
| | - Alessandro Agostini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Antonio Barbon
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim Becher-Weg 7, 55128 Mainz, Germany;
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
- Correspondence: (M.D.V.); (D.C.); Tel.: +39-0498275139 (M.D.V.); +39-0498275144 (D.C.)
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
- Correspondence: (M.D.V.); (D.C.); Tel.: +39-0498275139 (M.D.V.); +39-0498275144 (D.C.)
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8
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Friedl C, Fedorov DG, Renger T. Towards a quantitative description of excitonic couplings in photosynthetic pigment-protein complexes: quantum chemistry driven multiscale approaches. Phys Chem Chem Phys 2022; 24:5014-5038. [PMID: 35142765 PMCID: PMC8865841 DOI: 10.1039/d1cp03566e] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A structure-based quantitative calculation of excitonic couplings between photosynthetic pigments has to describe the dynamical polarization of the protein/solvent environment of the pigments, giving rise to reaction field and screening effects. Here, this challenging problem is approached by combining the fragment molecular orbital (FMO) method with the polarizable continuum model (PCM). The method is applied to compute excitonic couplings between chlorophyll a (Chl a) pigments of the water-soluble chlorophyll-binding protein (WSCP). By calibrating the vacuum dipole strength of the 0–0 transition of the Chl a chromophores according to experimental data, an excellent agreement between calculated and experimental linear absorption and circular dichroism spectra of WSCP is obtained. The effect of the mutual polarization of the pigment ground states is calculated to be very small. The simple Poisson-Transition-charge-from-Electrostatic-potential (Poisson-TrEsp) method is found to accurately describe the screening part of the excitonic coupling, obtained with FMO/PCM. Taking into account that the reaction field effects of the latter method can be described by a scalar constant leads to an improvement of Poisson-TrEsp that is expected to provide the basis for simple and realistic calculations of optical spectra and energy transfer in photosynthetic light-harvesting complexes. In addition, we present an expression for the estimation of Huang–Rhys factors of high-frequency pigment vibrations from experimental fluorescence line-narrowing spectra that takes into account the redistribution of oscillator strength by the interpigment excitonic coupling. Application to WSCP results in corrected Huang–Rhys factors that are less than one third of the original values obtained by the standard electronic two-state analysis that neglects the above redistribution. These factors are important for the estimation of the dipole strength of the 0–0 transition of the chromophores and for the development of calculation schemes for the spectral density of the exciton-vibrational coupling. The importance of reaction field and screening effects on the excitonic couplings is demonstrated, and from quantum-chemical calculations a single scaling factor is derived that can be used to improve simple models based on the Poisson equation.![]()
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Affiliation(s)
- Christian Friedl
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
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9
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Ohtsuki T, Uchida A, Nishigaki A, Nagashima U, Takahashi S, Ohshima S. Excitonic Energy Level of Homo- and Hetero-Dimers and Their Composition in the Native Water-Soluble Chlorophyll Protein from Lepidium Virginicum. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Takayuki Ohtsuki
- Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Akira Uchida
- Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Atsuko Nishigaki
- Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Umpei Nagashima
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa 236-0027, Japan
| | | | - Shigeru Ohshima
- Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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10
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Pieper J, Irrgang KD. Nature of low-energy exciton levels in light-harvesting complex II of green plants as revealed by satellite hole structure. PHOTOSYNTHESIS RESEARCH 2020; 146:279-285. [PMID: 32405995 DOI: 10.1007/s11120-020-00752-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Persistent non-photochemical hole burning at 4.2 K is an efficient experimental tool to unravel position and nature of low-energy excitonic states in pigment-protein complexes. This is demonstrated here for the case of the trimeric chlorophyll (Chl) a/b light-harvesting complexes of Photosystem II (LHC II) of green plants, where previous work (Pieper et al. J Phys Chem B 103:2412, 1999a) reported a highly localized lowest energy state at 680 nm. At that time, this finding appeared to be consistent with the contemporary knowledge about the LHC II structure, which mainly suggested the presence of weakly coupled Chl heterodimers. Currently, however, it is widely accepted that the lowest state is associated with an excitonically coupled trimer of Chl molecules at physiological temperatures. This raises the question, why an excitonically coupled state has not been identified by spectral hole burning. A re-inspection of the hole burning data reveals a remarkable dependence of satellite hole structure on burn fluence, which is indicative of the excitonic coupling of the low-energy states of trimeric LHC II. At low fluence, the satellite hole structure of the lowest/fluorescing ~ 680 nm state is weak with only one shallow satellite hole at 649 nm in the Chl b spectral range. These findings suggest that the lowest energy state at ~ 680 nm is essentially localized on a Chl a molecule, which may belong to a Chl a/b heterodimer. At high fluence, however, the lowest energy hole shifts blue to ~ 677 nm and is accompanied by two satellite holes at ~ 673 and 663 nm, respectively, indicating that this state is excitonically coupled to other Chl a molecules. In conclusion, LHC II seems to possess two different, but very closely spaced lowest energy states at cryogenic temperatures of 4.2 K.
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Affiliation(s)
- Jörg Pieper
- Institute of Physics, University of Tartu, W. Ostwald str. 1, Tartu, 50411, Estonia.
| | - Klaus-Dieter Irrgang
- Department of Life Science & Technology, Laboratory of Biochemistry, University for Applied Sciences, Berlin, Germany
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11
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Fresch E, Meneghin E, Agostini A, Paulsen H, Carbonera D, Collini E. How the Protein Environment Can Tune the Energy, the Coupling, and the Ultrafast Dynamics of Interacting Chlorophylls: The Example of the Water-Soluble Chlorophyll Protein. J Phys Chem Lett 2020; 11:1059-1067. [PMID: 31952446 PMCID: PMC7995254 DOI: 10.1021/acs.jpclett.9b03628] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The interplay between active molecules and the protein environment in light-harvesting complexes tunes the photophysics and the dynamical properties of pigment-protein complexes in a subtle way, which is not fully understood. Here we characterized the photophysics and the ultrafast dynamics of four variants of the water-soluble chlorophyll protein (WSCP) as an ideal model system to study the behavior of strongly interacting chlorophylls. We found that when coordinated by the WSCP protein, the presence of the formyl group in chlorophyll b replacing the methyl group in chlorophyll a strongly affects the exciton energy and the dynamics of the system, opening up the possibility of tuning the photophysics and the transport properties of multichromophores by engineering specific interactions with the surroundings.
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Affiliation(s)
- Elisa Fresch
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padua, Italy
| | - Elena Meneghin
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padua, Italy
| | - Alessandro Agostini
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padua, Italy
- Institute
of Molecular Physiology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Harald Paulsen
- Institute
of Molecular Physiology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Donatella Carbonera
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padua, Italy
| | - Elisabetta Collini
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padua, Italy
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12
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Prabahar V, Afriat-Jurnou L, Paluy I, Peleg Y, Noy D. New homologues of Brassicaceae water-soluble chlorophyll proteins shed light on chlorophyll binding, spectral tuning, and molecular evolution. FEBS J 2019; 287:991-1004. [PMID: 31549491 DOI: 10.1111/febs.15068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/02/2019] [Accepted: 09/18/2019] [Indexed: 01/06/2023]
Abstract
Type-II water-soluble chlorophyll (Chl) proteins (WSCPs) of Brassicaceae are promising models for understanding how protein sequence and structure affect Chl binding and spectral tuning in photosynthetic Chl-protein complexes. However, to date, their use has been limited by the small number of known WSCPs, which also limited understanding their physiological roles. To overcome these limitations, we performed a phylogenetic analysis to compile a more comprehensive and complete set of natural type-II WSCP homologues. The identified homologues were heterologously expressed in Escherichia coli, purified, tested for assembly with chlorophylls, and spectroscopically characterized. The analyses led to the discovery of previously unrecognized type-IIa and IIb subclass WSCPs, as well as of a new subclass that did not bind chlorophylls. Further analysis by ancestral sequence reconstruction yielded sequences of putative ancestors of the three subclasses, which were subsequently recombinantly expressed in E. coli, purified and characterized. Combining the phylogenetic and spectroscopic data with molecular structural information revealed distinct Chl-binding motifs, and identified residues critically impacting spectral tuning. The distinct Chl-binding properties of the WSCP archetypes suggest that the non-Chl-binding subclass evolved from a Chl-binding ancestor that most likely lost its Chl-binding capacity upon localization in the plant tissues with low Chl content. This dual evolutionary trajectory is consistent with WSCPs association with the Kunitz-type protease inhibitors superfamily, and indications of their inhibitory activity in response to various forms of stress in plants. These findings suggest new directions for exploring the physiological roles of WSCPs and the correlation, if any, between Chl-binding and protease inhibition functionality.
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Affiliation(s)
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona, Israel.,Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| | - Irina Paluy
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Dror Noy
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
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13
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Zazubovich V, Jankowiak R. How Well Does the Hole-Burning Action Spectrum Represent the Site-Distribution Function of the Lowest-Energy State in Photosynthetic Pigment-Protein Complexes? J Phys Chem B 2019; 123:6007-6013. [PMID: 31265294 DOI: 10.1021/acs.jpcb.9b03806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the first time, we combined Monte Carlo and nonphotochemical hole burning (NPHB) master equation approaches to allow for ultrahigh-resolution (<0.005 cm-1, smaller than the typical homogeneous line widths at 5 K) simulations of the NPHB spectra of dimers and trimers of interacting pigments. These simulations reveal significant differences between the zero-phonon hole (ZPH) action spectrum and the site-distribution function (SDF) of the lowest-energy state. The NPHB of the lowest-energy pigment, following the excitation energy transfer (EET) from the higher-energy pigments which are excited directly, results in the shifts of all excited states. These shifts affect the ZPH action spectra and EET times derived from the widths of the spectral holes burned in the donor-dominated regions. The effect is present for a broad variety of realistic antihole functions, and it is maximal at relatively low values of interpigment coupling (V ≤ 5 cm-1) where the use of the Förster approximation is justified. These findings need to be considered in interpreting various optical spectra of photosynthetic pigment-protein complexes for which SDFs (describing the inhomogeneous broadening) are often obtained directly from the ZPH action spectra. Water-soluble chlorophyll-binding protein (WSCP) was considered as an example.
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Affiliation(s)
- Valter Zazubovich
- Department of Physics , Concordia University , 7141 Sherbrooke Street West , Montreal H4B 1R6 , Quebec , Canada
| | - Ryszard Jankowiak
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , United States
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14
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Jakučionis M, Chorošajev V, Abramavičius D. Vibrational damping effects on electronic energy relaxation in molecular aggregates. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Adolphs J, Maier F, Renger T. Wavelength-Dependent Exciton-Vibrational Coupling in the Water-Soluble Chlorophyll Binding Protein Revealed by Multilevel Theory of Difference Fluorescence Line-Narrowing. J Phys Chem B 2018; 122:8891-8899. [PMID: 30183300 DOI: 10.1021/acs.jpcb.8b08410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the most powerful line-narrowing techniques used to unravel the homogeneous lineshapes of inhomogeneously broadened systems is difference fluorescence line-narrowing spectroscopy. When this spectroscopy was applied to multichromophoric systems so far, the spectra were analyzed by an effective two-level system approach, composed of the electronic ground state and the lowest exciton state. An effective Huang-Rhys factor was assigned for the coupling of this state to the vibrations. Here, we extend this approach by including a multilevel line shape theory, which takes into account the excitonic coupling between pigments and thereby the effect of the delocalization of the excited states explicitly. In this way, it becomes possible to extract the spectral density of the local exciton-vibrational coupling. The theory is applied to the recombinant water-soluble chlorophyll binding protein reconstituted with chlorophyll a or b and reveals a significant decrease of the Huang-Rhys factor of the local exciton-vibrational coupling with decreasing transition energy of the chlorophylls. This decrease could be due to the increase in steric interactions reducing the flexibility of the environment and red-shifting the site energy of the pigments.
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Affiliation(s)
- Julian Adolphs
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
| | - Franziska Maier
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
| | - Thomas Renger
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
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16
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Pieper J, Artene P, Rätsep M, Pajusalu M, Freiberg A. Evaluation of Electron–Phonon Coupling and Spectral Densities of Pigment–Protein Complexes by Line-Narrowed Optical Spectroscopy. J Phys Chem B 2018; 122:9289-9301. [DOI: 10.1021/acs.jpcb.8b05220] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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17
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Golub M, Rusevich L, Irrgang KD, Pieper J. Rigid versus Flexible Protein Matrix: Light-Harvesting Complex II Exhibits a Temperature-Dependent Phonon Spectral Density. J Phys Chem B 2018; 122:7111-7121. [DOI: 10.1021/acs.jpcb.8b02948] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Leonid Rusevich
- Institute of Physical Energetics, Krivu 11, LV-1006 Riga, Latvia
- Institute of Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga, Latvia
| | - Klaus-Dieter Irrgang
- Department of Life Science & Technology, Laboratory of Biochemistry, University for Applied Sciences, 10318 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
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18
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Agostini A, Palm DM, Paulsen H, Carbonera D. Optically Detected Magnetic Resonance of Chlorophyll Triplet States in Water-Soluble Chlorophyll Proteins from Lepidium virginicum: Evidence for Excitonic Interaction among the Four Pigments. J Phys Chem B 2018; 122:6156-6163. [DOI: 10.1021/acs.jpcb.8b01906] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alessandro Agostini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Institute of Molecular Physiology, Johannes-Gutenberg University Mainz, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Daniel M. Palm
- Institute of Molecular Physiology, Johannes-Gutenberg University Mainz, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes-Gutenberg University Mainz, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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19
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Pieper J, Rätsep M, Golub M, Schmitt FJ, Artene P, Eckert HJ. Excitation energy transfer in phycobiliproteins of the cyanobacterium Acaryochloris marina investigated by spectral hole burning. PHOTOSYNTHESIS RESEARCH 2017; 133:225-234. [PMID: 28560566 DOI: 10.1007/s11120-017-0396-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/06/2017] [Indexed: 06/07/2023]
Abstract
The cyanobacterium Acaryochloris marina developed two types of antenna complexes, which contain chlorophyll-d (Chl d) and phycocyanobilin (PCB) as light-harvesting pigment molecules, respectively. The latter membrane-extrinsic complexes are denoted as phycobiliproteins (PBPs). Spectral hole burning was employed to study excitation energy transfer and electron-phonon coupling in PBPs. The data reveal a rich spectral substructure with a total of four low-energy electronic states whose absorption bands peak at 633, 644, 654, and at about 673 nm. The electronic states at ~633 and 644 nm can be tentatively attributed to phycocyanin (PC) and allophycocyanin (APC), respectively. The remaining low-energy electronic states including the terminal emitter at 673 nm may be associated with different isoforms of PC, APC, or the linker protein. Furthermore, the hole burning data reveal a large number of excited state vibrational frequencies, which are characteristic for the chromophore PCB. In summary, the results are in good agreement with the low-energy level structure of PBPs and electron-phonon coupling parameters reported by Gryliuk et al. (BBA 1837:1490-1499, 2014) based on difference fluorescence line-narrowing experiments.
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Affiliation(s)
- Jörg Pieper
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia.
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Maksym Golub
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Franz-Josef Schmitt
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University Berlin, Berlin, Germany
| | - Petrica Artene
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Hann-Jörg Eckert
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University Berlin, Berlin, Germany
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20
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Kell A, Bednarczyk D, Acharya K, Chen J, Noy D, Jankowiak R. New Insight into the Water-Soluble Chlorophyll-Binding Protein fromLepidium virginicum. Photochem Photobiol 2016; 92:428-35. [DOI: 10.1111/php.12581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/18/2016] [Indexed: 01/20/2023]
Affiliation(s)
- Adam Kell
- Department of Chemistry; Kansas State University; Manhattan Kansas 66506
| | - Dominika Bednarczyk
- Department of Biological Chemistry; Weizmann Institute of Sciences; Rehovot 76100 Israel
| | - Khem Acharya
- Department of Chemistry; Kansas State University; Manhattan Kansas 66506
| | - Jinhai Chen
- Department of Chemistry; Kansas State University; Manhattan Kansas 66506
| | - Dror Noy
- Migal-Galilee Research Institute; Kiryat Shmona 11016 Israel
| | - Ryszard Jankowiak
- Department of Chemistry; Kansas State University; Manhattan Kansas 66506
- Department of Physics; Kansas State University; Manhattan Kansas 66506
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21
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Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
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22
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Adolphs J, Berrer M, Renger T. Hole-Burning Spectroscopy on Excitonically Coupled Pigments in Proteins: Theory Meets Experiment. J Am Chem Soc 2016; 138:2993-3001. [PMID: 26811003 PMCID: PMC4786881 DOI: 10.1021/jacs.5b08246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A theory for the calculation of resonant
and nonresonant hole-burning
(HB) spectra of pigment–protein complexes is presented and
applied to the water-soluble chlorophyll-binding protein (WSCP) from
cauliflower. The theory is based on a non-Markovian line shape theory
(Renger and Marcus2002, 116, 9997) and includes exciton delocalization, vibrational
sidebands, and lifetime broadening. An earlier approach by Reppert
(2011, 2, 2716) is found to describe nonresonant HB spectra only. Here we present
a theory that can be used for a quantitative description of HB data
for both nonresonant and resonant burning conditions. We find that
it is important to take into account the excess energy of the excitation
in the HB process. Whereas excitation of the zero-phonon transition
of the lowest exciton state, that is, resonant burning allows the
protein to access only its conformational substates in the neighborhood
of the preburn state, any higher excitation gives the protein full
access to all conformations present in the original inhomogeneous
ensemble. Application of the theory to recombinant WSCP from cauliflower,
reconstituted with chlorophyll a or chlorophyll b, gives excellent agreement with experimental data by Pieper
et al. (2011, 115, 405321417356) and allows us to obtain an upper bound of the lifetime of the upper
exciton state directly from the HB experiments in agreement with lifetimes
measured recently in time domain 2D experiments by Alster et al. (2014, 118, 352424627983).
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Affiliation(s)
- Julian Adolphs
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
| | - Manuel Berrer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
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23
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Rosnik AM, Curutchet C. Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:5826-37. [DOI: 10.1021/acs.jctc.5b00891] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreana M. Rosnik
- Department
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona, Barcelona 08028, Spain
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Carles Curutchet
- Department
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona, Barcelona 08028, Spain
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24
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Rancova O, Jankowiak R, Abramavicius D. Probing environment fluctuations by two-dimensional electronic spectroscopy of molecular systems at temperatures below 5 K. J Chem Phys 2015; 142:212428. [DOI: 10.1063/1.4918584] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Olga Rancova
- Department of Theoretical Physics, Vilnius University, Sauletekio al 9-III, 10222 Vilnius, Lithuania
| | - Ryszard Jankowiak
- Department of Chemistry and Department of Physics, Kansas State University, 213 CBC Building Manhattan, Kansas 66506-0401, USA
| | - Darius Abramavicius
- Department of Theoretical Physics, Vilnius University, Sauletekio al 9-III, 10222 Vilnius, Lithuania
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25
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Bednarczyk D, Takahashi S, Satoh H, Noy D. Assembly of water-soluble chlorophyll-binding proteins with native hydrophobic chlorophylls in water-in-oil emulsions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:307-313. [DOI: 10.1016/j.bbabio.2014.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 11/15/2022]
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26
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Vrandecic K, Rätsep M, Wilk L, Rusevich L, Golub M, Reppert M, Irrgang KD, Kühlbrandt W, Pieper J. Protein dynamics tunes excited state positions in light-harvesting complex II. J Phys Chem B 2015; 119:3920-30. [PMID: 25664910 DOI: 10.1021/jp5112873] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Light harvesting and excitation energy transfer in photosynthesis are relatively well understood at cryogenic temperatures up to ∼100 K, where crystal structures of several photosynthetic complexes including the major antenna complex of green plants (LHC II) are available at nearly atomic resolution. The situation is much more complex at higher or even physiological temperatures, because the spectroscopic properties of antenna complexes typically undergo drastic changes above ∼100 K. We have addressed this problem using a combination of quasielastic neutron scattering (QENS) and optical spectroscopy on native LHC II and mutant samples lacking the Chl 2/Chl a 612 pigment molecule. Absorption difference spectra of the Chl 2/Chl a 612 mutant of LHC II reveal pronounced changes of spectral position and their widths above temperatures as low as ∼80 K. The complementary QENS data indicate an onset of conformational protein motions at about the same temperature. This finding suggests that excited state positions in LHC II are affected by protein dynamics on the picosecond time scale. In more detail, this means that at cryogenic temperatures the antenna complex is trapped in certain protein conformations. At higher temperature, however, a variety of conformational substates with different spectral position may be thermally accessible. At the same time, an analysis of the widths of the absorption difference spectra of Chl 2/Chl a 612 reveals three different reorganization energies or Huang-Rhys factors in different temperature ranges, respectively. These findings imply that (dynamic) pigment-protein interactions fine-tune electronic energy levels and electron-phonon coupling of LHC II for efficient excitation energy transfer at physiological temperatures.
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Affiliation(s)
- Kamarniso Vrandecic
- Institute of Physics, University of Tartu , Ravila 14C, 50411 Tartu, Estonia
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27
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Rusevich L, Embs J, Bektas I, Paulsen H, Renger G, Pieper J. Protein and solvent dynamics of the water-soluble chlorophyll-binding protein (WSCP). EPJ WEB OF CONFERENCES 2015. [DOI: 10.1051/epjconf/20158302016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Zazubovich V. Fluorescence Line Narrowing and Δ-FLN Spectra in the Presence of Excitation Energy Transfer between Weakly Coupled Chromophores. J Phys Chem B 2014; 118:13535-43. [DOI: 10.1021/jp509056z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valter Zazubovich
- Department of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal H4B 1R6, Quebec, Canada
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29
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Takahashi S, Abe E, Nakayama K, Satoh H. Identification of genes encoding photoconvertible (Class I) water-soluble chlorophyll-binding proteins from Chenopodium ficifolium. Biosci Biotechnol Biochem 2014; 79:205-10. [PMID: 25333387 DOI: 10.1080/09168451.2014.972326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Photoconvertible water-soluble chlorophyll-binding proteins, called Class I WSCPs, have been detected in Chenopodiaceae, Amaranthaceae and Polygonaceae plant species. To date, Chenopodium album WSCP (CaWSCP) is the only cloned gene encoding a Class I WSCP. In this study, we identified two cDNAs encoding Chenopodium ficifolium Class I WSCPs, CfWSCP1, and CfWSCP2. Sequence analyses revealed that the open reading frames of CfWSCP1 and CfWSCP2 were 585 and 588 bp, respectively. Furthermore, both CfWSCPs contain cystein2 and cystein30, which are essential for the chlorophyll-binding ability of CaWSCP. Recombinant CfWSCP1 and CfWSCP2, expressed in Escherichia coli as hexa-histidine fusion proteins (CfWSCP1-His and CfWSCP2-His), formed inclusion bodies; however, we were able to solubilize these using a buffer containing 8 M urea and then refold them by dialysis. The refolded CfWSCP1-His and CfWSCP2-His could bind chlorophylls and exhibited photoconvertibility, confirming that the cloned CfWSCPs are further examples of Class I WSCPs.
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Affiliation(s)
- Shigekazu Takahashi
- a Faculty of Science, Department of Biomolecular Science , Toho University , Funabashi , Japan
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30
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Barone V, Biczysko M, Borkowska-Panek M, Bloino J. A Multifrequency Virtual Spectrometer for Complex Bio-Organic Systems: Vibronic and Environmental Effects on the UV/Vis Spectrum of Chlorophylla. Chemphyschem 2014; 15:3355-64. [DOI: 10.1002/cphc.201402300] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Indexed: 11/07/2022]
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31
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Takahashi S, Seki Y, Uchida A, Nakayama K, Satoh H. Cysteine-2 and Cys30 are essential for chlorophyll-binding activity of the water-soluble chlorophyll-binding protein (WSCP) of Chenopodium album. Biosci Biotechnol Biochem 2014; 78:1825-32. [PMID: 25060234 DOI: 10.1080/09168451.2014.940274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chenopodium album has a non-photosynthetic chlorophyll protein known as the water-soluble chlorophyll (Chl)-binding protein (WSCP). The C. album WSCP (CaWSCP) is able to photoconvert the chlorin skeleton of Chl a into a bacteriochlorin-like skeleton. Reducing reagents such as β-mercaptoethanol or dithiothreitol inhibit photoconversion, indicating that S-S bridge(s) in CaWSCP are quite important for it. Recently, we found that the mature region of CaWSCP contains five cysteine residues; Cys2, Cys30, Cys48, Cys63, and Cys144. To identify which cysteine residues are involved in the photoconversion, we generated five mutants (C2S, C30S, C48S, C63S, and C144S) by site-directed mutagenesis. Interestingly, C48S, C63S, and C144S mutants showed the same Chl-binding activity and photoconvertibility as those of the recombinant wild-type CaWSCP-His, while the C2S and C30S mutants completely lost Chl-binding activity. Our findings indicated that the S-S bridge between Cys2 and Cys30 in each CaWSCP subunit is essential for Chl-binding activity.
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32
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Takahashi S, Uchida A, Nakayama K, Satoh H. Three-step photoconversion of only three subunits of the water-soluble chlorophyll-binding protein tetramer from Chenopodium album. Protein J 2014; 33:337-43. [PMID: 24824829 DOI: 10.1007/s10930-014-9565-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Water-soluble chlorophyll (Chl)-binding proteins (WSCPs) have been found in various plants. WSCPs are categorized into two classes based on their photoconvertibility: Class I (photoconvertible) and Class II (non-photoconvertible). Based on their absorption peaks, which occur in the red wavelengths, the pre- and post-photoconverted forms of Chenopodium album WSCP (CaWSCP) are called CP668 and CP742, respectively. Although various biochemical and biophysical properties of CaWSCP have already been characterized, questions remain regarding the structural dynamics of the photoconversion from CP668 to CP742, and the relationship between the photoconversion activity and incident light wavelength. To address how the wavelength of incident light affects the photoconversion, we performed time-course analyses of CaWSCP photoconversion by using light-emitting diodes that emit either white light, or at the discrete wavelengths 670, 645, 525, 470, or 430 nm. The most efficient photoconversion was observed under irradiation at 430 nm. Less efficient photoconversion was observed under irradiation with 670, 645, 470, or 525 nm light, in that order. The relationship between photoconversion activity and wavelength corresponded with the absorption peak intensities of Chls in the CaWSCP complex. The observed time dependence of the A(742)/A(668) ratio during photoconversion of the CaWSCP complex indicated that the photoconversion from CP668 to CP742 occurs in a three-step reaction, and that only three subunits in the complex could be photoconverted.
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Affiliation(s)
- Shigekazu Takahashi
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
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Alster J, Lokstein H, Dostál J, Uchida A, Zigmantas D. 2D Spectroscopy Study of Water-Soluble Chlorophyll-Binding Protein from Lepidium virginicum. J Phys Chem B 2014; 118:3524-31. [DOI: 10.1021/jp411174t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Alster
- Department
of Chemical Physics, Lund University, P.O. Box 124, SE-221-00 Lund, Sweden
| | - Heiko Lokstein
- Glasgow
Biomedical Research Centre, Institute of Molecular, Cell and Systems
Biology, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland/U.K
| | - Jakub Dostál
- Department
of Chemical Physics, Lund University, P.O. Box 124, SE-221-00 Lund, Sweden
| | - Akira Uchida
- Department
of Biomolecular Science, Faculty of Science, Toho University, 2-2-1
Miyama, Funabashi, Chiba 274-8510, Japan
| | - Donatas Zigmantas
- Department
of Chemical Physics, Lund University, P.O. Box 124, SE-221-00 Lund, Sweden
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Excitation energy transfer and electron-vibrational coupling in phycobiliproteins of the cyanobacterium Acaryochloris marina investigated by site-selective spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1490-9. [PMID: 24560813 DOI: 10.1016/j.bbabio.2014.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/26/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
In adaption to its specific environmental conditions, the cyanobacterium Acaryochloris marina developed two different types of light-harvesting complexes: chlorophyll-d-containing membrane-intrinsic complexes and phycocyanobilin (PCB) - containing phycobiliprotein (PBP) complexes. The latter complexes are believed to form a rod-shaped structure comprising three homo-hexamers of phycocyanin (PC), one hetero-hexamer of phycocyanin and allophycocyanin (APC) and probably a linker protein connecting the PBPs to the reaction centre. Excitation energy transfer and electron-vibrational coupling in PBPs have been investigated by selectively excited fluorescence spectra. The data reveal a rich spectral substructure with a total of five low-energy electronic states with fluorescence bands at 635nm, 645nm, 654nm, 659nm and a terminal emitter at about 673 nm. The electronic states at ~635 and 645 nm are tentatively attributed to PC and APC, respectively, while an apparent heterogeneity among PC subunits may also play a role. The other fluorescence bands may be associated with three different isoforms of the linker protein. Furthermore, a large number of vibrational features can be identified for each electronic state with intense phonon sidebands peaking at about 31 to 37cm⁻¹, which are among the highest phonon frequencies observed for photosynthetic antenna complexes. The corresponding Huang-Rhys factors S fall in the range between 0.98 (terminal emitter), 1.15 (APC), and 1.42 (PC). Two characteristic vibronic lines at about 1580 and 1634cm⁻¹ appear to reflect CNH⁺ and CC stretching modes of the PCB chromophore, respectively. The exact phonon and vibrational frequencies vary with electronic state implying that the respective PCB chromophores are bound to different protein environments. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.
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Takahashi S, Uchida A, Nakayama K, Satoh H. The C-terminal Extension Peptide of Non-photoconvertible Water-Soluble Chlorophyll-Binding Proteins (Class II WSCPs) Affects Their Solubility and Stability: Comparative Analyses of the Biochemical and Chlorophyll-Binding Properties of Recombinant Brassica, Raphanus and Lepidium WSCPs with or Without Their C-terminal Extension Peptides. Protein J 2014; 33:75-84. [DOI: 10.1007/s10930-013-9539-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Takahashi S, Yanai H, Oka-Takayama Y, Zanma-Sohtome A, Fujiyama K, Uchida A, Nakayama K, Satoh H. Molecular cloning, characterization and analysis of the intracellular localization of a water-soluble chlorophyll-binding protein (WSCP) from Virginia pepperweed (Lepidium virginicum), a unique WSCP that preferentially binds chlorophyll b in vitro. PLANTA 2013; 238:1065-1080. [PMID: 23995835 DOI: 10.1007/s00425-013-1952-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
Various plants possess non-photosynthetic, hydrophilic chlorophyll (Chl) proteins called water-soluble Chl-binding proteins (WSCPs). WSCPs are categorized into two classes; Class I (photoconvertible type) and Class II (non-photoconvertible type). Among Class II WSCPs, only Lepidium virginicum WSCP (LvWSCP) exhibits a low Chl a/b ratio compared with that found in the leaf. Although the physicochemical properties of LvWSCP have been characterized, its molecular properties have not yet been documented. Here, we report the characteristics of the LvWSCP gene, the biochemical properties of a recombinant LvWSCP, and the intracellular localization of LvWSCP. The cloned LvWSCP gene possesses a 669-bp open reading frame. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis revealed that the precursor of LvWSCP contains both N- and C-terminal extension peptides. RT-PCR analysis revealed that LvWSCP was transcribed in various tissues, with the levels being higher in developing tissues. A recombinant LvWSCP and hexa-histidine fusion protein (LvWSCP-His) could remove Chls from the thylakoid in aqueous solution and showed an absorption spectrum identical to that of native LvWSCP. Although LvWSCP-His could bind both Chl a and Chl b, it bound almost exclusively to Chl b when reconstituted in 40 % methanol. To clarify the intracellular targeting functions of the N- and C-terminal extension peptides, we constructed transgenic Arabidopsis thaliana lines expressing the Venus protein fused with the LvWSCP N- and/or C-terminal peptides, as well as Venus fused at the C-terminus of LvWSCP. The results showed that the N-terminal peptide functioned in ER body targeting, while the C-terminal sequence did not act as a trailer peptide.
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Affiliation(s)
- Shigekazu Takahashi
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Haruna Yanai
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Yuko Oka-Takayama
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Aya Zanma-Sohtome
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Kosaku Fujiyama
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Akira Uchida
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Katsumi Nakayama
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Hiroyuki Satoh
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan.
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Takahashi S, Yoshikawa M, Kamada A, Ohtsuki T, Uchida A, Nakayama K, Satoh H. The photoconvertible water-soluble chlorophyll-binding protein of Chenopodium album is a member of DUF538, a superfamily that distributes in Embryophyta. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1549-1552. [PMID: 23820553 DOI: 10.1016/j.jplph.2013.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/03/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
Various plants possess hydrophilic chlorophyll (Chl) proteins known as water-soluble Chl-binding proteins (WSCPs). WSCPs exist in two forms: Class I and Class II, of which Class I alone exhibits unique photoconvertibility. Although numerous genes encoding Class II WSCPs have been identified and the molecular properties of their recombinant proteins have been well characterized, no Class I WSCP gene has been identified to date. In this study, we cloned the cDNA and a gene encoding the Class I WSCP of Chenopodium album (CaWSCP). Sequence analyses revealed that CaWSCP comprises a single exon corresponding to 585bp of an open reading frame encoding 195 amino acid residues. The CaWSCP protein sequence possesses a signature of DUF538, a protein superfamily of unknown function found almost exclusively in Embryophyta. The recombinant CaWSCP was expressed in Escherichia coli as a hexa-histidine fusion protein (CaWSCP-His) that removes Chls from the thylakoid. Under visible light illumination, the reconstituted CaWSCP-His was successfully photoconverted into a different pigment with an absorption spectrum identical to that of native CaWSCP. Interestingly, while CaWSCP-His could bind both Chl a and Chl b, photoconversion occurred only in CaWSCP-His reconstituted with Chl a.
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Affiliation(s)
- Shigekazu Takahashi
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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Bektas I, Fellenberg C, Paulsen H. Water-soluble chlorophyll protein (WSCP) of Arabidopsis is expressed in the gynoecium and developing silique. PLANTA 2012; 236:251-259. [PMID: 22350767 DOI: 10.1007/s00425-012-1609-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/02/2012] [Indexed: 05/27/2023]
Abstract
Water-soluble chlorophyll protein (WSCP) has been found in many Brassicaceae, most often in leaves. In many cases, its expression is stress-induced, therefore, it is thought to be involved in some stress response. In this work, recombinant WSCP from Arabidopsis thaliana (AtWSCP) is found to form chlorophyll-protein complexes in vitro that share many properties with recombinant or native WSCP from Brassica oleracea, BoWSCP, including an unusual heat resistance up to 100°C in aqueous solution. A polyclonal antibody raised against the recombinant apoprotein is used to identify plant tissues expressing AtWSCP. The only plant organs containing significant amounts of AtWSCP are the gynoecium in open flowers and the septum of developing siliques, specifically the transmission tract. In fully grown but still green siliques, the protein has almost disappeared. Possible implications for AtWSCP functions are discussed.
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Affiliation(s)
- Inga Bektas
- Institut f. Allgemeine Botanik der Johannes-Gutenberg-Universität, Johannes-von-Müller-Weg 6, 55099, Mainz, Germany
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Zucchelli G, Santabarbara S, Jennings RC. The Qy Absorption Spectrum of the Light-Harvesting Complex II As Determined by Structure-Based Analysis of Chlorophyll Macrocycle Deformations. Biochemistry 2012; 51:2717-36. [DOI: 10.1021/bi201677q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Giuseppe Zucchelli
- CNR-Istituto di Biofisica, Sezione di Milano
and Dipartimento di Biologia, Università degli Studi di Milano, via Giovanni Celoria 26, 20133
Milano Italy
| | - Stefano Santabarbara
- CNR-Istituto di Biofisica, Sezione di Milano
and Dipartimento di Biologia, Università degli Studi di Milano, via Giovanni Celoria 26, 20133
Milano Italy
| | - Robert C. Jennings
- CNR-Istituto di Biofisica, Sezione di Milano
and Dipartimento di Biologia, Università degli Studi di Milano, via Giovanni Celoria 26, 20133
Milano Italy
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