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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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2
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Cherepanov DA, Milanovsky GE, Neverov KV, Obukhov YN, Maleeva YV, Aybush AV, Kritsky MS, Nadtochenko VA. Exciton interactions of chlorophyll tetramer in water-soluble chlorophyll-binding protein BoWSCP. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123847. [PMID: 38217986 DOI: 10.1016/j.saa.2024.123847] [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: 07/31/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The exciton interaction of four chlorophyll a (Chl a) molecules in a symmetrical tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP was analyzed in the pH range of 3-11. Exciton splitting ΔE = 232 ± 2 cm-1 of the Qy band of Chl a into two subcomponents with relative intensities of 78.1 ± 0.7 % and 21.9 ± 0.7 % was determined by a joint decomposition of the absorption and circular dichroism spectra into Gaussian functions. The exciton coupling parameters were calculated based on the BoWSCP atomic structure in three approximations: the point dipole model, the distributed atomic monopoles, and direct ab initio calculations in the TDDFT/PCM approximation. The Coulomb interactions of monomers were calculated within the continuum model using three values of optical permittivity. The models based on the properties of free Chl a in solution suffer from significant errors both in estimating the absolute value of the exciton interaction and in the relative intensity of exciton transitions. Calculations within the TDDFT/PCM approximation reproduce the experimentally determined parameters of the exciton splitting and the relative intensities of the exciton bands. The following factors of pigment-protein and pigment-pigment interactions were examined: deviation of the macrocycle geometry from the planar conformation of free Chl; the formation of hydrogen bonds between the macrocycle and water molecules; the overlap of wave functions of monomers at close distances. The most significant factor is the geometrical deformation of the porphyrin macrocycle, which leads to an increase in the dipole moment of Chl monomer from 5.5 to 6.9 D and to a rotation of the dipole moment by 15° towards the cyclopentane ring. The contributions of resonant charge-transfer states to the wave functions of the Chl dimer were determined and the transition dipole moments of the symmetric and antisymmetric charge-transfer states were estimated.
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Affiliation(s)
- D A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation; A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Leninskye gory, 1b.40, Russian Federation.
| | - G E Milanovsky
- A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Leninskye gory, 1b.40, Russian Federation
| | - K V Neverov
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation; Faculty of Biology, Moscow State University, 119234 Moscow, Leninskye gory, 1b.12, Russian Federation
| | - Yu N Obukhov
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation
| | - Yu V Maleeva
- Faculty of Biology, Moscow State University, 119234 Moscow, Leninskye gory, 1b.12, Russian Federation
| | - A V Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation
| | - M S Kritsky
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation
| | - V A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation; Department of Chemistry, Moscow State University, 119991 Moscow, Leninskye gory, 1b.3, Russian Federation
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3
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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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Jana S, Do TN, Nowakowski PJ, Khyasudeen MF, Le DV, Lim IJY, Prasad S, Zhang J, Tan HS. Measuring the Ultrafast Correlation Dynamics of a Multilevel System Using the Center Line Slope Analysis in Two-Dimensional Electronic Spectroscopy. J Phys Chem B 2023; 127:7309-7322. [PMID: 37579317 DOI: 10.1021/acs.jpcb.3c02521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
In a two-dimensional (2D) optical spectrum of a multilevel system, there are diagonal peaks and off-diagonal cross-peaks that correlate the different levels. The time-dependent properties of these diagonal peaks and cross-peaks contain much information about the dynamics of the multilevel system. The time-dependent diagonal peakshape that depends on the spectral diffusion dynamics of the associated transition and characterized by the frequency-fluctuation correlation function (FFCF) is well studied. However, the time-dependent peakshape of a cross-peak that provides the correlation dynamics between different transitions is much less studied or understood. We derived the third-order nonlinear response functions that describe the cross-peaks in a 2D electronic spectrum of a multilevel system that arise from processes sharing a common ground state and/or from internal conversion and population transfer. We can use the center line slope (CLS) analysis to characterize the cross-peaks in conjunction with the diagonal peaks. This allows us to recover the frequency-fluctuation cross-correlation functions (FXCFs) between two transitions. The FXCF and its subsidiary quantities such as the initial correlation and the initial covariance between different transitions are important for studying the correlation effects between states in complex systems, such as energy-transfer processes. Furthermore, knowledge of how various molecular processes over different timescales affect simultaneously different transitions can also be obtained from the measured FXCF. We validated and tested our derived equations and analysis process by studying, as an example, the 2D electronic spectra of metal-free phthalocyanine in solution. We measured and analyzed the diagonal peaks of the Qx and Qy transitions and the cross-peaks between these two transitions of this multilevel electronic system and obtained the associated FFCFs and FXCFs. In this model system, we measured negative components of FXCF over the tens of picosecond timescale. This suggests that in phthalocyanine, the Qx and Qy transitions coupling with the solvent molecule motion are anticorrelated to each other.
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Affiliation(s)
- Sanjib Jana
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Thanh Nhut Do
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Paweł J Nowakowski
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - M Faisal Khyasudeen
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Duc Viet Le
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Ian Jing Yan Lim
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Sachin Prasad
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Jianjun Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
- Laboratory of Solar Fuel, Faculty of Materials Science and Chemistry, China University of Geosciences, 68 Jincheng Street, Wuhan 430078, China
| | - Howe-Siang Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
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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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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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7
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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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/31/2021] [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.
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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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Lahav Y, Noy D, Schapiro I. Spectral tuning of chlorophylls in proteins - electrostatics vs. ring deformation. Phys Chem Chem Phys 2021; 23:6544-6551. [PMID: 33690760 DOI: 10.1039/d0cp06582j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Recombinant type II water soluble chlorophyll-binding proteins from Brassicaceae (WSCPs) are useful for studying spectral tuning mechanisms due to their symmetric homotetramer structure, and the ability to rigorously modify the chlorophyll's protein surroundings. Our previous comparison of the crystal structures of two WSCP homologues suggested that protein-induced chlorophyll ring deformation is the predominant spectral tuning mechanism. Here, we implement a more rigorous analysis based on hybrid quantum mechanics and molecular mechanics calculations to quantify the relative contributions of geometrical and electrostatic factors to the absorption spectra of WSCP-chlorophyll complexes. We show that when considering conformational dynamics, geometry distortions such as chlorophyll ring deformation accounts for about one-third of the spectral shift, whereas the direct polarization of the electron density accounts for the remaining two-thirds. From a practical perspective, protein electrostatics is easier to manipulate than chlorophyll conformations, thus, it may be more readily implemented in designing artificial protein-chlorophyll complexes.
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Affiliation(s)
- Yigal Lahav
- Fritz Haber Centre for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Israel.
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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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Oetama VSP, Pentzold S, Boland W. The fate of chlorophyll in phytophagous insects goes beyond nutrition. Z NATURFORSCH C 2021; 76:1-9. [PMID: 32887212 DOI: 10.1515/znc-2020-0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
Chlorophyll (Chl) is a natural compound that is found in all autotrophic plants. Since phytophagous insects ingest the photosynthetically active material with the plant leaves, the question arises if and how herbivores deal with Chl and its degradation products. Here we review findings on Chl degradation in phytophagous insects and highlight the role of these ubiquitous plant metabolites for plant-feeding insects. Due to the anaerobic gut of many insects, the degradation is limited to the removal of the peripheral substituents, while the tetrapyrrole core remains intact. Proteins, such as red fluorescent protein, P252 (a novel 252-kDa protein), and chlorophyllide binding protein have been reported to occur in the insect gut and might be indirectly connected to Chl degradation. Besides of an nutritional value, e.g., by taking up Mg2+ ions or by sequestration of carbon from the phytol side chain, the Chl degradation products may serve the insect, after binding to certain proteins, as antimicrobial, antifungal, and antiviral factors. The protein complexes may also confer protection against reactive oxygen species. The antibiotic potential of proteins and degradation products does not only benefit phytophagous insects but also human being in medical application of cancer treatment for instance. This review highlights these aspects from a molecular, biochemical, and ecological point of view.
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Affiliation(s)
- Vincensius S P Oetama
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knvll-Stra_e 8, 07745 Jena, Germany
| | - Stefan Pentzold
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knvll-Stra_e 8, 07745 Jena, Germany.,Friedrich Schiller University Jena, University Hospital, Am Klinikum 1, 07747 Jena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knvll-Stra_e 8, 07745 Jena, Germany
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11
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Gelzinis A, Augulis R, Büchel C, Robert B, Valkunas L. Confronting FCP structure with ultrafast spectroscopy data: evidence for structural variations. Phys Chem Chem Phys 2021; 23:806-821. [PMID: 33427836 DOI: 10.1039/d0cp05578f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diatoms are a major group of algae, responsible for a quarter of the global primary production on our planet. Their adaptation to marine environments is ensured by their light-harvesting antenna - the fucoxanthin-chlorophyll protein (FCP) complex, which absorbs strongly in the blue-green spectral region. Although these essential proteins have been the subject of many studies, for a long time their comprehensive description was not possible in the absence of structural data. Last year, the 3D structures of several FCP complexes were revealed. The structure of an FCP dimer was resolved by crystallography for the pennate diatom Phaeodactylum tricornutum [W. Wang et al., Science, 2019, 363, 6427] and the structure of the PSII supercomplex from the centric diatom Chaetoceros gracilis, containing several FCPs, was obtained by electron microscopy [X. Pi et al., Science, 2019, 365, 6452; R. Nagao et al., Nat. Plants, 2019, 5, 890]. In this Perspective article, we evaluate how precisely these structures may account for previously published ultrafast spectroscopy results, describing the excitation energy transfer in the FCP from another centric diatom Cyclotella meneghiniana. Surprisingly, we find that the published FCP structures cannot explain several observations obtained from ultrafast spectroscopy. Using the available structures, and results from electron microscopy, we construct a trimer-based FCP model for Cyclotella meneghiniana, consistent with ultrafast experimental data. As a whole, our observations suggest that the structures from the proteins belonging to the FCP family display larger variations than the equivalent LHC proteins in plants, which may reflect species-specific adaptations or original strategies for adapting to rapidly changing marine environments.
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Affiliation(s)
- Andrius Gelzinis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania. and Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
| | - Ramūnas Augulis
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straβe 9, 60438 Frankfurt, Germany
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania. and Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
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12
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Girr P, Paulsen H. How water-soluble chlorophyll protein extracts chlorophyll from membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183479. [PMID: 32961122 DOI: 10.1016/j.bbamem.2020.183479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
Water-soluble chlorophyll proteins (WSCPs) found in Brassicaceae are non-photosynthetic proteins that bind only a small number of chlorophylls. Their biological function remains unclear, but recent data indicate that WSCPs are involved in stress response and pathogen defense as producers of reactive oxygen species and/or Chl-regulated protease inhibitors. For those functions, WSCP apoprotein supposedly binds Chl to become physiologically active or inactive, respectively. Thus, Chl-binding seems to be a pivotal step for the biological function of WSCP. WSCP can extract Chl from the thylakoid membrane but little is known about the mechanism of how Chl is sequestered from the membrane into the binding sites. Here, we investigate the interaction of WSCP with the thylakoid membrane in detail. The extraction of Chl from the thylakoid by WSCP apoprotein is a slow and inefficient reaction, because WSCP presumably does not directly extract Chl from other Chl-binding proteins embedded in the membrane. WSCP apoprotein interacts with model membranes that contain the thylakoid lipids MGDG, DGDG or PG, and can extract Chl from those. Furthermore, the WSCP-Chl complex, once formed, no longer interacts with membranes. We concluded that the surroundings of the WSCP pigment-binding site are involved in the WSCP-membrane interaction and identified a ring of hydrophobic amino acids with two conserved Trp residues around the Chl-binding site. Indeed, WSCP variants, in which one of the Trp residues was exchanged for Phe, still interact with the membrane but are no longer able to extract Chl.
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Affiliation(s)
- Philipp Girr
- 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.
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13
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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: 20] [Impact Index Per Article: 5.0] [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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14
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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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15
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Application of decay- and evolution-associated spectra for molecular systems with spectral shifts or inherent inhomogeneities. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Tamascelli D, Smirne A, Lim J, Huelga SF, Plenio MB. Efficient Simulation of Finite-Temperature Open Quantum Systems. PHYSICAL REVIEW LETTERS 2019; 123:090402. [PMID: 31524443 DOI: 10.1103/physrevlett.123.090402] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 06/10/2023]
Abstract
Chain-mapping techniques in combination with the time-dependent density matrix renormalization group are a powerful tool for the simulation of open-system quantum dynamics. For finite-temperature environments, however, this approach suffers from an unfavorable algorithmic scaling with increasing temperature. We prove that the system dynamics under thermal environments can be nonperturbatively described by temperature-dependent system-environmental couplings with the initial environment state being in its pure vacuum state, instead of a mixed thermal state. As a consequence, as long as the initial system state is pure, the global system-environment state remains pure at all times. The resulting speed-up and relaxed memory requirements of this approach enable the efficient simulation of open quantum systems interacting with highly structured environments in any temperature range, with applications extending from quantum thermodynamics to quantum effects in mesoscopic systems.
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Affiliation(s)
- D Tamascelli
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, 89069 Ulm, Germany
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, via Celoria 16, 20133 Milano, Italy
| | - A Smirne
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, 89069 Ulm, Germany
| | - J Lim
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, 89069 Ulm, Germany
| | - S F Huelga
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, 89069 Ulm, Germany
| | - M B Plenio
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, 89069 Ulm, Germany
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17
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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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18
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Gelzinis A, Augulis R, Butkus V, Robert B, Valkunas L. Two-dimensional spectroscopy for non-specialists. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:271-285. [DOI: 10.1016/j.bbabio.2018.12.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/14/2018] [Accepted: 12/08/2018] [Indexed: 12/20/2022]
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19
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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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20
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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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21
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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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22
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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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23
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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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24
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Butkus V, Dong H, Fleming GR, Abramavicius D, Valkunas L. Disorder-Induced Quantum Beats in Two-Dimensional Spectra of Excitonically Coupled Molecules. J Phys Chem Lett 2016; 7:277-282. [PMID: 26720834 DOI: 10.1021/acs.jpclett.5b02642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Quantum superposition of molecular electronic states is very fragile because of thermal energy fluctuations and the static conformational disorder induced by the intimate surrounding of constituent molecules of the system. However, the nature of the long-lived quantum beats, observed in time-resolved spectra of molecular aggregates at physiological conditions, is still being debated. We present our study of the conditions when long-lived electronic quantum coherences originating from recently proposed inhomogeneous broadening mechanism are enhanced and reflected in the two-dimensional electronic spectra of the excitonically coupled molecular dimer. We show that depending on the amount of inhomogeneous broadening, the excitonically coupled molecular system can establish long-lived electronic coherences, caused by a disordered subensemble, for which the dephasing due to static energy disorder becomes significantly reduced. On the basis of these considerations, we present explanations for why the electronic or vibrational coherences were or were not observed in a range of recent experiments.
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Affiliation(s)
- Vytautas Butkus
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
| | - Hui Dong
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Graham R Fleming
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Leonas Valkunas
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
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25
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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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26
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Takahashi S, Aizawa K, Nakayama K, Satoh H. Water-soluble chlorophyll-binding proteins from Arabidopsis thaliana and Raphanus sativus target the endoplasmic reticulum body. BMC Res Notes 2015; 8:365. [PMID: 26289422 PMCID: PMC4546050 DOI: 10.1186/s13104-015-1333-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 08/12/2015] [Indexed: 11/18/2022] Open
Abstract
Background Non-photosynthetic chlorophyll (Chl) proteins called water-soluble Chl-binding proteins are distributed in Brassicaceae plants. Brassica oleracea WSCP (BoWSCP) and Lepidium virginicum WSCP (LvWSCP) are highly expressed in leaves and stems, while Arabidopsis thaliana WSCP (AtWSCP) and Raphanus sativus WSCP (RshWSCP) are highly transcribed in floral organs. BoWSCP and LvWSCP exist in the endoplasmic reticulum (ER) body. However, the subcellular localization of AtWSCP and RshWSCP is still unclear. To determine the subcellular localization of these WSCPs, we constructed transgenic plants expressing Venus-fused AtWSCP or RshWSCP. Results Open reading frames corresponding to full-length AtWSCP and RshWSCP were cloned and ligated between the cauliflower mosaic virus 35S promoter and Venus, a gene encoding a yellow fluorescent protein. We introduced the constructs into A. thaliana by the floral dip method. We succeeded in constructing a number of transformants expressing Venus-fused chimeric AtWSCP (AtWSCP::Venus) or RshWSCP (RshWSCP::Venus). We detected fluorescence derived from the chimeric proteins using a fluorescence microscope system. In cotyledons, fluorescence derived from AtWSCP::Venus and RshWSCP::Venus was detected in spindle structures. The spindle structures altered their shape to a globular form under blue light excitation. In true leaves, the number of spindle structures was drastically reduced. These observations indicate that the spindle structure was the ER body. Conclusions AtWSCP and RshWSCP have the potential for ER body targeting like BoWSCP and LvWSCP.
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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.
| | - Kyoko Aizawa
- 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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27
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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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28
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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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29
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Gelzinis A, Butkus V, Songaila E, Augulis R, Gall A, Büchel C, Robert B, Abramavicius D, Zigmantas D, Valkunas L. Mapping energy transfer channels in fucoxanthin–chlorophyll protein complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:241-247. [DOI: 10.1016/j.bbabio.2014.11.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/11/2014] [Accepted: 11/14/2014] [Indexed: 11/15/2022]
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30
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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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31
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Dinh TC, Renger T. Towards an exact theory of linear absorbance and circular dichroism of pigment-protein complexes: Importance of non-secular contributions. J Chem Phys 2015; 142:034104. [DOI: 10.1063/1.4904928] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Thanh-Chung Dinh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
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