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Ahad S, Lin C, Reppert M. PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations. J Chem Phys 2024; 160:154111. [PMID: 38639311 DOI: 10.1063/5.0198443] [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: 01/18/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.
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Affiliation(s)
- S Ahad
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - C Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - M Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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2
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Zazubovich V, Jankowiak R. High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes. Int J Mol Sci 2024; 25:3850. [PMID: 38612659 PMCID: PMC11011720 DOI: 10.3390/ijms25073850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.
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Affiliation(s)
- Valter Zazubovich
- Department of Physics, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
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3
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Toutounji M. Empirical asymmetric phonon sideband due to phonons in the protein matrix present in photosynthetic complexes: Time-domain response theory. BIOPHYSICAL REPORTS 2024; 4:100146. [PMID: 38375357 PMCID: PMC10875334 DOI: 10.1016/j.bpr.2024.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024]
Abstract
The phonon spectral density plays a key role in probing the dynamical and spectral behavior of molecular aggregates. One may utilize the intimate connection between the one-phonon profile and the phonon spectral density to extract a plausible form of the spectral density of media with rich structure using advanced optical spectroscopy. The excitonic transition is normally accompanied by a broad, asymmetric phonon-side band due to the coupling to the phonons in the surrounding protein matrix present in photosynthetic complexes. The asymmetry in the one-phonon profile of a homogeneous absorption spectrum and other experiments performed on photosynthetic bacterial reaction centers (BRCs) led the Small group to employ a half-Gaussian distribution function on the red side and half-Lorentzian distribution function on the blue side of the absorption lineshape to account for the one-phonon profile asymmetrical shape and relaxation effects contributing to spectroscopy and dynamics of BRCs at hand. Different research groups successfully employed the theory of Small to simulate their photosynthetic spectral data so they could calculate the homogeneous absorption and hole-burned spectra of photosynthetic complexes. Although this report does not directly use the formulae of homogeneous absorption, hole-burning, and fluorescence line-narrowed spectra of BRCs, and photosynthetic complexes, developed by Hayes-Small, it builds on their idea of the phonon sideband asymmetric shape in deriving an accurate and computationally efficient linear electronic transition dipole moment time correlation function. Besides the compelling tractability and efficiency of this correlation function, it accounts for excitonic coupling and eliminates all the inconsistencies arising in the Hayes-Small theory.
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Affiliation(s)
- Mohamad Toutounji
- College of Science, Department of Chemistry, UAE University, Al-Ain, UAE
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Santabarbara S, Agostini A, Petrova AA, Bortolus M, Casazza AP, Carbonera D. Chlorophyll triplet states in thylakoid membranes of Acaryochloris marina. Evidence for a triplet state sitting on the photosystem I primary donor populated by intersystem crossing. PHOTOSYNTHESIS RESEARCH 2024; 159:133-152. [PMID: 37191762 DOI: 10.1007/s11120-023-01023-z] [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: 03/16/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Photo-induced triplet states in the thylakoid membranes isolated from the cyanobacterium Acaryocholoris marina, that harbours Chlorophyll (Chl) d as its main chromophore, have been investigated by Optically Detected Magnetic Resonance (ODMR) and time-resolved Electron Paramagnetic Resonance (TR-EPR). Thylakoids were subjected to treatments aimed at poising the redox state of the terminal electron transfer acceptors and donors of Photosystem II (PSII) and Photosystem I (PSI), respectively. Under ambient redox conditions, four Chl d triplet populations were detectable, identifiable by their characteristic zero field splitting parameters, after deconvolution of the Fluorescence Detected Magnetic Resonance (FDMR) spectra. Illumination in the presence of the redox mediator N,N,N',N'-Tetramethyl-p-phenylenediamine (TMPD) and sodium ascorbate at room temperature led to a redistribution of the triplet populations, with T3 (|D|= 0.0245 cm-1, |E|= 0.0042 cm-1) becoming dominant and increasing in intensity with respect to untreated samples. A second triplet population (T4, |D|= 0.0248 cm-1, |E|= 0.0040 cm-1) having an intensity ratio of about 1:4 with respect to T3 was also detectable after illumination in the presence of TMPD and ascorbate. The microwave-induced Triplet-minus-Singlet spectrum acquired at the maximum of the |D|-|E| transition (610 MHz) displays a broad minimum at 740 nm, accompanied by a set of complex spectral features that overall resemble, despite showing further fine spectral structure, the previously reported Triplet-minus-Singlet spectrum attributed to the recombination triplet of PSI reaction centre,3 P 740 [Schenderlein M, Çetin M, Barber J, et al. Spectroscopic studies of the chlorophyll d containing photosystem I from the cyanobacterium Acaryochloris marina. Biochim Biophys Acta 1777:1400-1408]. However, TR-EPR experiments indicate that this triplet displays an eaeaea electron spin polarisation pattern which is characteristic of triplet sublevels populated by intersystem crossing rather than recombination, for which an aeeaae polarisation pattern is expected instead. It is proposed that the observed triplet, which leads to the bleaching of the P740 singlet state, sits on the PSI reaction centre.
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Affiliation(s)
- Stefano Santabarbara
- Photosynthesis Research Unit, Centro Studi Sulla Biologia Cellulare e Molecolare delle Piante, Consiglio Nazionale Delle Ricerche, Via Celoria 26, 20133, Milan, Italy.
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Bassini 15a, 20133, Milan, Italy.
| | - Alessandro Agostini
- Department of Chemical Sciences, Università di Padova, Via Marzolo 1, 35131, Padua, Italy
| | - Anastasia A Petrova
- Photosynthesis Research Unit, Centro Studi Sulla Biologia Cellulare e Molecolare delle Piante, Consiglio Nazionale Delle Ricerche, Via Celoria 26, 20133, Milan, Italy
- A. N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1 Building 40, Moscow, Russia, 119992
| | - Marco Bortolus
- Department of Chemical Sciences, Università di Padova, Via Marzolo 1, 35131, Padua, Italy
| | - Anna Paola Casazza
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Bassini 15a, 20133, Milan, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, Università di Padova, Via Marzolo 1, 35131, Padua, Italy.
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5
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Mai M, Zazubovich V, Mansbach RA. Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations. J Phys Chem B 2024; 128:1371-1384. [PMID: 38299975 PMCID: PMC10876061 DOI: 10.1021/acs.jpcb.3c06889] [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: 10/17/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Reversible light and thermally induced spectral shifts are universally observed in a wide variety of pigment-protein complexes at temperatures ranging from cryogenic to ambient. In this paper, we employed large-scale molecular dynamics (MD) simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. From simulations of the water-soluble chlorophyll-binding protein complex, we determined that rearrangements of long hydrogen bonds were unlikely to be the origin of the multiwell landscape features necessary to explain observed spectral shifts. We also assessed small motions of amino acid residues and identified side chain rotations of some of these residues as likely candidates for the origin of relevant multiwell landscape features. The protein free-energy landscapes associated with side chain rotations feature energy barriers of around 1100-1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric triple-well landscape and moment of inertia of a relevant magnitude.
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Affiliation(s)
- Martina Mai
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Valter Zazubovich
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Rachael A. Mansbach
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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6
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Toutounji M. Homogeneous Dephasing in Photosynthetic Bacterial Reaction Centers: Time Correlation Function Approach. Chemphyschem 2024; 25:e202300335. [PMID: 37953408 DOI: 10.1002/cphc.202300335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
A new tractable linear electronic transition dipole moment time correlation function (ETDMTCF) that accurately accounts for electronic dephasing, asymmetry, and width of 1-phonon profile, which the zero-phonon line (ZPL) contributes to it, in Rhodopseudomonas viridis bacterial reaction center is derived. This time correlation function proves to be superior to other frequency-domain expressions in case of strong electron-phonon coupling (which is often the case in bacterial RCs and pigment-protein complexes), many vibrational modes involved, and high temperature, whereby more vibronic and electronic (sequence) transitions would arise. The Fourier transform of this ETDMTCF leads to asymmetric multiphonon profiles composed of Lorentzian distribution and Gaussian distribution on the high- and low-energy sides, respectively, whereby the overtone widths fold themselves with that of the one-phonon profile. This ETDMTCF also features expedient computation in large systems using asymmetric phonon profiles to account correctly for dephasing and pigment-protein interaction (electron-phonon coupling). The derived ETDMTCF allows computing all nonlinear optical signals in both time and frequency domains, through the nonlinear dipole moment time correlation functions (as guided by nonlinear optical response theory) in line with the eight Liouville space pathways. The linear transition dipole moment time correlation function is of a central value as the nonlinear transition dipole moment time correlation function is expressed in terms of the linear transition dipole moment time correlation function, derived herein. One of the great advantages of presenting this ETDMTCF is its applicability to nonlinear transition dipole moment time correlation functions in line with the eight Liouville space pathways needed in computing nonlinear signals. As such, there is more to the utility and applicability of the presented ETDMTCF besides computational expediency and efficiency. Results show good agreement with the reported literature. The intimate connection between a one-phonon profile and the corresponding bath spectral density in photosynthetic complexes is discussed.
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Affiliation(s)
- Mohamad Toutounji
- College of Science, Department of Chemistry, P. O. Box 15551, UAE University, Al-Ain, United Arab Emirate
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7
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Abstract
Biological pigment-protein complexes (PPCs) exhibit a remarkable ability to tune the optical properties of biological excitons (bioexcitons) through specific pigment-protein interactions. While such fine-tuning allows natural systems (e.g., photosynthetic proteins) to carry out their native functions with near-optimal performance, native function itself is often suboptimal for applications such as biofuel production or quantum technology development. This perspective offers a look at near-term prospects for the rational reoptimization of PPC bioexcitons for new functions using site-directed mutagenesis. The primary focus is on the "structure-spectrum" challenge of understanding the relationships between structural features and spectroscopic properties. While recent examples demonstrate that site-directed mutagenesis can be used to tune nearly all key bioexciton parameters (e.g., site energies, interpigment couplings, and electronic-vibrational interactions), critical challenges remain before we achieve truly rational design of bioexciton properties.
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Affiliation(s)
- Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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Semenov AN, Gvozdev DA, Zlenko DV, Protasova EA, Khashimova AR, Parshina EY, Baizhumanov AA, Lotosh NY, Kim EE, Kononevich YN, Pakhomov AA, Selishcheva AA, Sluchanko NN, Shirshin EA, Maksimov EG. Modulation of Membrane Microviscosity by Protein-Mediated Carotenoid Delivery as Revealed by Time-Resolved Fluorescence Anisotropy. MEMBRANES 2022; 12:905. [PMID: 36295665 PMCID: PMC9609150 DOI: 10.3390/membranes12100905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Carotenoids are potent antioxidants with a wide range of biomedical applications. However, their delivery into human cells is challenging and relatively inefficient. While the use of natural water-soluble carotenoproteins capable to reversibly bind carotenoids and transfer them into membranes is promising, the quantitative estimation of the delivery remains unclear. In the present work, we studied echinenone (ECN) delivery by cyanobacterial carotenoprotein AnaCTDH (C-terminal domain homolog of the Orange Carotenoid Protein from Anabaena), into liposome membranes labelled with BODIPY fluorescent probe. We observed that addition of AnaCTDH-ECN to liposomes led to the significant changes in the fast-kinetic component of the fluorescence decay curve, pointing on the dipole-dipole interactions between the probe and ECN within the membrane. It may serve as an indirect evidence of ECN delivery into membrane. To study the delivery in detail, we carried out molecular dynamics modeling of the localization of ECN within the lipid bilayer and calculate its orientation factor. Next, we exploited FRET to assess concentration of ECN delivered by AnaCTDH. Finally, we used time-resolved fluorescence anisotropy to assess changes in microviscosity of liposomal membranes. Incorporation of liposomes with β-carotene increased membrane microviscosity while the effect of astaxanthin and its mono- and diester forms was less pronounced. At temperatures below 30 °C addition of AnaCTDH-ECN increased membrane microviscosity in a concentration-dependent manner, supporting the protein-mediated carotenoid delivery mechanism. Combining all data, we propose FRET-based analysis and assessment of membrane microviscosity as potent approaches to characterize the efficiency of carotenoids delivery into membranes.
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Affiliation(s)
- Alexey N. Semenov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Danil A. Gvozdev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Dmitry V. Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Elena A. Protasova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Anastasia R. Khashimova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Evgenia Yu. Parshina
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Adil A. Baizhumanov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Natalia Yu. Lotosh
- National Research Center “Kurchatov Institute”, 1 Acad. Kurchatov Sq., Moscow 123182, Russia
| | - Eleonora E. Kim
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yuriy N. Kononevich
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A. Pakhomov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alla A. Selishcheva
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
- National Research Center “Kurchatov Institute”, 1 Acad. Kurchatov Sq., Moscow 123182, Russia
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology, Russian Academy of Sciences, 33 Leninsky Prospect, Moscow 119071, Russia
| | - Evgeny A. Shirshin
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory St., Moscow 119991, Russia
- Laboratory of Clinical Biophotonics, Biomedical Science and Technology Park, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, Moscow 119991, Russia
- Institute of Spectroscopy, Russian Academy of Sciences, 5 Fizicheskaya Str., Troitsk, Moscow 108840, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory St., Moscow 119991, Russia
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Reinot T, Khmelnitskiy A, Zazubovich V, Toporik H, Mazor Y, Jankowiak R. Frequency-Domain Spectroscopic Study of the Photosystem I Supercomplexes, Isolated IsiA Monomers, and the Intact IsiA Ring. J Phys Chem B 2022; 126:6891-6910. [PMID: 36065077 DOI: 10.1021/acs.jpcb.2c04829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The PSI3-IsiA18 supercomplex is one of the largest and most complicated assemblies in photosynthesis. The IsiA ring, composed of 18 IsiA monomers (IsiA18) surrounding the PSI trimer (PSI3), forms under iron-deficient conditions in cyanobacteria and acts as a peripheral antenna. Based on the supercomplex structure recently determined via cryo-EM imaging, we model various optical spectra of the IsiA monomers and IsiA18 ring. Comparison of the absorption and emission spectra of the isolated IsiA monomers and the full ring reveals that about 2.7 chlorophylls (Chls) are lost in the isolated IsiA monomers. The best fits for isolated monomers spectra are obtained assuming the absence of Chl 508 and Chl 517 and 70% loss of Chl 511. The best model describing all three hexamers and the entire ring suggests that the lowest energy pigments are Chls 511, 514, and 517. Based on the modeling results presented in this work, we conclude that there are most likely three entry points for EET from the IsiA6 hexamer to the PSI core monomer, with two of these entry points likely being located next to each other (i.e., nine entry points from IsiA18 to the PSI3 trimer). Finally, we show that excitation energy transfer inside individual monomers is fast (<2 ps at T = 5 K) and at least 20 times faster than intermonomer energy transfer.
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Affiliation(s)
| | | | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal, H4B 1R6, Canada
| | - Hila Toporik
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, United States
| | - Yuval Mazor
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, United States
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10
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Golub M, Lokstein H, Soloviov D, Kuklin A, Wieland DCF, Pieper J. Light-Harvesting Complex II Adopts Different Quaternary Structures in Solution as Observed Using Small-Angle Scattering. J Phys Chem Lett 2022; 13:1258-1265. [PMID: 35089716 DOI: 10.1021/acs.jpclett.1c03614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The high-resolution crystal structure of the trimeric major light-harvesting complex of photosystem II (LHCII) is often perceived as the basis for understanding its light-harvesting and photoprotective functions. However, the LHCII solution structure and its oligomerization or aggregation state may generally differ from the crystal structure and, moreover, also depend on its functional state. In this regard, small-angle scattering experiments provide the missing link by offering structural information in aqueous solution at physiological temperatures. Herein, we use small-angle scattering to investigate the solution structures of two different preparations of solubilized LHCII employing the nonionic detergents n-octyl-β-d-glucoside (OG) and n-dodecyl-β-D-maltoside (β-DM). The data reveal that the LHCII-OG complex is equivalent to the trimeric crystal structure. Remarkably, however, we observe─for the first time─a stable oligomer composed of three LHCII trimers in the case of the LHCII-β-DM preparation, implying additional pigment-pigment interactions. The latter complex is assumed to mimic trimer-trimer interactions which play an important role in the context of photoprotective nonphotochemical quenching.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 121 16 Prague, Czech Republic
| | - Dmytro Soloviov
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia
- Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
- Institute for Safety Problems of Nuclear Power Plants NAS of Ukraine, Lysogirska str. 12, 03028 Kyiv, Ukraine
| | - Alexander Kuklin
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia
- Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - D C Florian Wieland
- Helmholtz Zentrum Geesthacht, Institute for Materials Research, Department for Metallic Biomaterials, 21502 Geesthacht, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
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11
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Hong YH, Lee YM, Nam W, Fukuzumi S. Molecular Photocatalytic Water Splitting by Mimicking Photosystems I and II. J Am Chem Soc 2022; 144:695-700. [PMID: 34990144 DOI: 10.1021/jacs.1c11707] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In nature, water is oxidized by plastoquinone to evolve O2 and form plastoquinol in Photosystem II (PSII), whereas NADP+ is reduced by plastoquinol to produce NADPH and regenerate plastoquinone in Photosystem I (PSI), using homogeneous molecular photocatalysts. However, water splitting to evolve H2 and O2 in a 2:1 stoichiometric ratio has yet to be achieved using homogeneous molecular photocatalysts, remaining as one of the biggest challenges in science. Herein, we demonstrate overall water splitting to evolve H2 and O2 in a 2:1 ratio using a two liquid membranes system composed of two toluene phases, which are separated by a solvent mixture of water and trifluoroethanol (H2O/TFE, 3:1 v/v), with a glass membrane to combine PSI and PSII molecular models. A PSII model contains plastoquinone analogs [p-benzoquinone derivatives (X-Q)] in toluene and an iron(II) complex as a molecular oxidation catalyst in H2O/TFE (3:1 v/v), which evolves a stoichiometric amount of O2 and forms plastoquinol analogs (X-QH2) under photoirradiation. On the other hand, a PSI model contains nothing in toluene but contains X-QH2, 9-mesityl-10-methylacridinium ion (Acr+-Mes) as a photocatalyst, and a cobalt(III) complex as an H2 evolution catalyst in H2O/TFE (3:1 v/v), which evolves a stoichiometric amount of H2 and forms X-Q under photoirradiation. When a PSII model system is combined with a PSI model system with two glass membranes and two liquid membranes, photocatalytic water splitting with homogeneous molecular photocatalysts is achieved to evolve hydrogen and oxygen with the turnover number (TON) of >100.
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Affiliation(s)
- Young Hyun Hong
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.,School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
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12
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Srivastava A, Ahad S, Wat JH, Reppert M. Accurate prediction of mutation-induced frequency shifts in chlorophyll proteins with a simple electrostatic model. J Chem Phys 2021; 155:151102. [PMID: 34686046 DOI: 10.1063/5.0064567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photosynthetic pigment-protein complexes control local chlorophyll (Chl) transition frequencies through a variety of electrostatic and steric forces. Site-directed mutations can modify this local spectroscopic tuning, providing critical insight into native photosynthetic functions and offering the tantalizing prospect of creating rationally designed Chl proteins with customized optical properties. Unfortunately, at present, no proven methods exist for reliably predicting mutation-induced frequency shifts in advance, limiting the method's utility for quantitative applications. Here, we address this challenge by constructing a series of point mutants in the water-soluble chlorophyll protein of Lepidium virginicum and using them to test the reliability of a simple computational protocol for mutation-induced site energy shifts. The protocol uses molecular dynamics to prepare mutant protein structures and the charge density coupling model of Adolphs et al. [Photosynth. Res. 95, 197-209 (2008)] for site energy prediction; a graphical interface that implements the protocol automatically is published online at http://nanohub.org/tools/pigmenthunter. With the exception of a single outlier (presumably due to unexpected structural changes), we find that the calculated frequency shifts match the experiment remarkably well, with an average error of 1.6 nm over a 9 nm spread in wavelengths. We anticipate that the accuracy of the method can be improved in the future with more advanced sampling of mutant protein structures.
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Affiliation(s)
- Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Safa Ahad
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jacob H Wat
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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13
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Bubilaitis V, Rancova O, Abramavicius D. Vibration-mediated energy transport in bacterial reaction center: Simulation study. J Chem Phys 2021; 154:214115. [PMID: 34240965 DOI: 10.1063/5.0048815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Exciton energy relaxation in a bacterial Reaction Center (bRC) pigment-protein aggregate presumably involves emission of high energy vibrational quanta to cover wide energy gaps between excitons. Here, we assess this hypothesis utilizing vibronic two-particle theory in modeling of the excitation relaxation process in bRC. Specific high frequency molecular vibrational modes are included explicitly one at a time in order to check which high frequency vibrations are involved in the excitation relaxation process. The low frequency bath modes are treated perturbatively within Redfield relaxation theory. The analysis of the population relaxation rate data indicates energy flow pathways in bRC and suggests that specific vibrations may be responsible for the excitation relaxation process.
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Affiliation(s)
- Vytautas Bubilaitis
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius 10222, Lithuania
| | - Olga Rancova
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius 10222, Lithuania
| | - Darius Abramavicius
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius 10222, Lithuania
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14
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Gelin MF, Borrelli R. Simulation of Nonlinear Femtosecond Signals at Finite Temperature via a Thermo Field Dynamics-Tensor Train Method: General Theory and Application to Time- and Frequency-Resolved Fluorescence of the Fenna-Matthews-Olson Complex. J Chem Theory Comput 2021; 17:4316-4331. [PMID: 34076412 DOI: 10.1021/acs.jctc.1c00158] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Addressing needs of contemporary nonlinear femtosecond optical spectroscopy, we have developed a fully quantum, numerically accurate wave function-based approach for the calculation of third-order spectroscopic signals of polyatomic molecules and molecular aggregates at finite temperature. The systems are described by multimode nonadiabatic vibronic-coupling Hamiltonians, in which diagonal terms are treated in harmonic approximation, while off-diagonal interstate couplings are assumed to be coordinate independent. The approach is based on the Thermo Field Dynamics (TFD) representation of quantum mechanics and tensor-train (TT) machinery for efficient numerical simulation of quantum evolution of systems with many degrees of freedom. The developed TFD-TT approach is applied to the calculation of time- and frequency-resolved fluorescence spectra of the Fenna-Matthews-Olson (FMO) antenna complex at room temperature taking into account finite time-frequency resolution in fluorescence detection, orientational averaging, and static disorder.
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Affiliation(s)
- Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
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15
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Du M, Qin M, Cui H, Wang C, Xu Y, Ma X, Yi X. Role of Spatially Correlated Fluctuations in Photosynthetic Excitation Energy Transfer with an Equilibrium and a Nonequilibrium Initial Bath. J Phys Chem B 2021; 125:6417-6430. [PMID: 34105973 DOI: 10.1021/acs.jpcb.1c02041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transfer of excitation energy in photosynthetic light-harvesting complexes has inspired growing interest for its scientific and engineering significance. Recent experimental findings have suggested that spatially correlated environmental fluctuations may account for the existence of long-lived quantum coherent energy transfer observed even at physiological temperature. In this paper, we investigate the effects of spatial correlations on the excitation energy transfer dynamics by including a nonequilibrium initial bath in a simulated donor-acceptor model. The initial bath state, which is assumed to be either equilibrium or nonequilibrium, is expanded in powers of coupling strength within the polaron formalism of a quantum master equation. The spatial correlations of bath fluctuations strongly influence the decay of coherence in the dynamics. The role of a nonequilibrium initial bath is also influenced by spatial correlations and becomes the most conspicuous for certain degrees of spatial correlations from which we propose a picture that the spatial correlations of bath fluctuations open up new energy transfer pathways, playing a role of protecting coherence. Besides, we apply the polaron master equation approach to study the dynamics in a two-site subsystem of the FMO complex and provide a practical example that shows the versatility of this approach.
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Affiliation(s)
- Min Du
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Ming Qin
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Haitao Cui
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Chunyang Wang
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Yuqing Xu
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xiaoguang Ma
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xuexi Yi
- Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
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16
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Trempe A, Levenberg A, Ortega ADG, Lujan MA, Picorel R, Zazubovich V. Effects of Chlorophyll Triplet States on the Kinetics of Spectral Hole Growth. J Phys Chem B 2021; 125:3278-3285. [PMID: 33764072 DOI: 10.1021/acs.jpcb.0c09042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectral hole burning has been employed for decades to study various amorphous solids and proteins. Triplet states and respective transient holes were incorporated into theoretical models and software simulating nonphotochemical spectral hole burning (NPHB) and including all relevant distributions, in particular the distribution of the angle between the electric field of light E and transient dipole moment of the chromophore μ. The presence of a chlorophyll a triplet state with a lifetime of several milliseconds explains the slowdown of NPHB (on the depth vs illumination dose scale) with the increase of the light intensity, as well as larger hole depths observed in weak probe beam experiments, compared to those deduced from the hole growth kinetics (HGK) measurements (signal collected at a fixed wavelength while a stronger burning beam is on) in cytochrome b6f and chemically modified LH2. We also considered the solvent deuteration effects on triplet lifetime and concluded that both triplet states and local heating likely play a role in slowing down the HGK with increasing burn intensity.
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Affiliation(s)
- Alexandra Trempe
- Department of Physics, Concordia University, 7141 Sherbrooke Str. West, Montreal, Quebec H4B 1R6, Canada
| | - Alexander Levenberg
- Department of Physics, Concordia University, 7141 Sherbrooke Str. West, Montreal, Quebec H4B 1R6, Canada
| | | | - Maria A Lujan
- Estacion Experimental de Aula Dei (CSIC), Avda. Montañana 1005, Zaragoza 50059, Spain
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC), Avda. Montañana 1005, Zaragoza 50059, Spain
| | - Valter Zazubovich
- Department of Physics, Concordia University, 7141 Sherbrooke Str. West, Montreal, Quebec H4B 1R6, Canada
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17
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Reinot T, Khmelnitskiy A, Kell A, Jassas M, Jankowiak R. Exciton Lifetime Distributions and Population Dynamics in the FMO Protein Complex from Prosthecochloris aestuarii. ACS OMEGA 2021; 6:5990-6008. [PMID: 33681637 PMCID: PMC7931385 DOI: 10.1021/acsomega.1c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Significant protein rearrangement upon excitation and energy transfer in Fenna-Matthews-Olson protein of Prosthecochloris aestuarii results in a modified energy landscape, which induces more changes in pigment site energies than predicted by the "standard" hole-burning theory. The energy changes are elucidated by simulations while investigating the effects of site-dependent disorder, both static (site-energy distribution widths) and dynamic (spectral density shapes). The resulting optimized site energies and their fluctuations are consistent with relative differences observed in inhomogeneous widths calculated by recent molecular dynamic simulations. Two sets of different spectral densities reveal how their shapes affect the population dynamics and distribution of exciton lifetimes. Calculations revealed the wavelength-dependent distributions of exciton lifetimes (T 1) in the femtosecond to picosecond time frame. We suggest that the calculated multimodal and asymmetric wavelength-dependent T 1 distributions offer more insight into the interpretation of resonant hole-burned (HB) spectra, kinetic traces in two-dimensional (2D) electronic spectroscopy experiments, and widely used global analyses in fitting data from transient absorption experiments.
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Affiliation(s)
- Tonu Reinot
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Anton Khmelnitskiy
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Adam Kell
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mahboobe Jassas
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ryszard Jankowiak
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
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18
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Reinot T, Jassas M, Kell A, Casazza AP, Santabarbara S, Jankowiak R. On wavelength-dependent exciton lifetime distributions in reconstituted CP29 antenna of the photosystem II and its site-directed mutants. J Chem Phys 2021; 154:085101. [PMID: 33639775 DOI: 10.1063/5.0038217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To provide more insight into the excitonic structure and exciton lifetimes of the wild type (WT) CP29 complex of photosystem II, we measured high-resolution (low temperature) absorption, emission, and hole burned spectra for the A2 and B3 mutants, which lack chlorophylls a612 and b614 (Chls), respectively. Experimental and modeling results obtained for the WT CP29 and A2/B3 mutants provide new insight on the mutation-induced changes at the molecular level and shed more light on energy transfer dynamics. Simulations of the A2 and B3 optical spectra, using the second-order non-Markovian theory, and comparison with improved fits of WT CP29 optical spectra provide more insight into their excitonic structure, mutation induced changes, and frequency-dependent distributions of exciton lifetimes (T1). A new Hamiltonian obtained for WT CP29 reveals that deletion of Chls a612 or b614 induces changes in the site energies of all remaining Chls. Hamiltonians obtained for A2 and B3 mutants are discussed in the context of the energy landscape of chlorophylls, excitonic structure, and transfer kinetics. Our data suggest that the lowest exciton states in A2 and B3 mutants are contributed by a611(57%), a610(17%), a615(15%) and a615(58%), a611(20%), a612(15%) Chls, respectively, although other compositions of lowest energy states are also discussed. Finally, we argue that the calculated exciton decay times are consistent with both the hole-burning and recent transient absorption measurements. Wavelength-dependent T1 distributions offer more insight into the interpretation of kinetic traces commonly described by discrete exponentials in global analysis/global fitting of transient absorption experiments.
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Affiliation(s)
- Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Mahboobe Jassas
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Adam Kell
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Anna Paola Casazza
- Istituto di Biologia e Biotecnologia Agraria, C.N.R., Via Bassini 15, 20133 Milano, Italy
| | - Stefano Santabarbara
- Photosynthesis Research Unit, Centro Studi sulla Biologia Cellulare e Molecolare delle Piante, C.N.R., Milano, Italy
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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19
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Chung JW, Kwak M, Yang HK. Improvement of luminescence properties of NaYF 4 :Yb 3+ /Er 3+ upconversion materials by a cross-relaxation mechanism based on co-doped Ho 3+ ion concentrations. LUMINESCENCE 2021; 36:812-818. [PMID: 33404165 DOI: 10.1002/bio.4008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 11/09/2022]
Abstract
NaYF4 :Yb3+ /Er3+ /Ho3+ nanophosphors were successfully synthesized using a solvothermal method and with various concentrations of Ho3+ ions. The crystal structure, grain size, morphology, and luminescence properties were analyzed by X-ray diffraction, field-emission scanning electron microscopy, and photoluminescence measurements. All samples were crystallized as a cubic structure; it was confirmed that all samples exhibited strong green emission and weak red emission generated at a particular level of the activated ions. The strongest upconversion fluorescence intensity was observed in the Ho3+ and Er3+ ions co-doped NaYF4 materials with a Ho3+ ion concentration of 0.005 mol. Only the green fluorescence intensity at the 542 nm centre increased strongly due to the 4 S3/2 →4 I15/2 energy transfer. This increase in upconversion fluorescence intensity at a selected wavelength was described as a cross-relaxation mechanism due to the addition of Ho3+ ions.
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Affiliation(s)
- Jong Won Chung
- Department of Electrical, Electronics and Software Engineering, Pukyong National University, Busan, Republic of Korea
| | - Minseok Kwak
- Department of Chemistry, Pukyong National University, Busan, Republic of Korea
| | - Hyun Kyoung Yang
- Department of Electrical, Electronics and Software Engineering, Pukyong National University, Busan, Republic of Korea
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20
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Reimers JR, Rätsep M, Freiberg A. Asymmetry in the Q y Fluorescence and Absorption Spectra of Chlorophyll a Pertaining to Exciton Dynamics. Front Chem 2020; 8:588289. [PMID: 33344415 PMCID: PMC7738624 DOI: 10.3389/fchem.2020.588289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Significant asymmetry found between the high-resolution Qy emission and absorption spectra of chlorophyll-a is herein explained, providing basic information needed to understand photosynthetic exciton transport and photochemical reactions. The Qy spectral asymmetry in chlorophyll has previously been masked by interference in absorption from the nearby Qx transition, but this effect has recently been removed using extensive quantum spectral simulations or else by analytical inversion of absorption and magnetic circular dichroism data, allowing high-resolution absorption information to be accurately determined from fluorescence-excitation spectra. To compliment this, here, we measure and thoroughly analyze the high-resolution differential fluorescence line narrowing spectra of chlorophyll-a in trimethylamine and in 1-propanol. The results show that vibrational frequencies often change little between absorption and emission, yet large changes in line intensities are found, this effect also being strongly solvent dependent. Among other effects, the analysis in terms of four basic patterns of Duschinsky-rotation matrix elements, obtained using CAM-B3LYP calculations, predicts that a chlorophyll-a molecule excited into a specific vibrational level, may, without phase loss or energy relaxation, reemit the light over a spectral bandwidth exceeding 1,000 cm−1 (0.13 eV) to influence exciton-transport dynamics.
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Affiliation(s)
- Jeffrey R Reimers
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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21
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Chaillet M, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment. J Phys Chem Lett 2020; 11:10306-10314. [PMID: 33227205 PMCID: PMC7751012 DOI: 10.1021/acs.jpclett.0c03123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein with a quantum chemical/electrostatic calculation of local transition energies (site energies) of the pigments. The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site energies. Rotamers of polar amino acid side chains are found to cause bimodal distribution functions of site energy shifts, which can be probed by hole burning and single-molecule spectroscopy. When summing over the large number of contributions, the resulting distribution functions of the site energies become Gaussians, and the correlations in site energy fluctuations at different sites practically average to zero. These results demonstrate that static disorder in the FMO protein is in the realm of the central limit theorem of statistics.
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Affiliation(s)
- Marten
L. Chaillet
- Bijvoet
Centre for Biomolecular Research, University
of Utrecht, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Florian Lengauer
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Julian Adolphs
- Leibniz
Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Frank Müh
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Alexander S. Fokas
- TCM
Group, Cavendish Laboratory, 19 J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Alex W. Chin
- Centre
National de la Recherce Scientifique, Institute des Nanosciences de
Paris, Sorbonne Université, Paris, France
| | - Thomas Renger
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
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22
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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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23
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Reppert M. Delocalization Effects in Chlorophyll Fluorescence: Nonperturbative Line Shape Analysis of a Vibronically Coupled Dimer. J Phys Chem B 2020; 124:10024-10033. [PMID: 33138372 DOI: 10.1021/acs.jpcb.0c05789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-adiabatic vibrational/electronic (vibronic) interactions in photosynthetic pigment/protein complexes (PPCs) have recently attracted considerable interest as a potential source for long-lived dynamic coherence and optimized light harvesting. The analysis of such effects is limited, however, by the complexity of the vibrational spectrum of biological pigments such as chlorophyll (Chl) molecules, which often makes numerical calculations prohibitively expensive and complicates the interpretation of experimental spectroscopic data. This work contributes to both challenges by using numerically exact computational methods to systematically examine vibronic mixing effects in the low-temperature fluorescence spectra of a Chl dimer possessing a full complement of local vibrations, using parameters extracted from experimental data. The results highlight the varying roles local vibrations can play in energy-transfer dynamics, both enhancing delocalization through vibronic resonance and, conversely, inducing dynamic localization by acting as a "self-bath" for local electronic transitions. In the specific context of line-narrowed fluorescence, the results indicate that, while low-frequency features are strongly suppressed by delocalization, high-frequency modes are likely to be dynamically localized in the parameter regime relevant to most photosynthetic complexes.
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Affiliation(s)
- Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2050, United States
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24
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Hong YH, Lee YM, Nam W, Fukuzumi S. Photocatalytic Hydrogen Evolution from Plastoquinol Analogues as a Potential Functional Model of Photosystem I. Inorg Chem 2020; 59:14838-14846. [PMID: 33023288 DOI: 10.1021/acs.inorgchem.0c02254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recent development of a functional model of photosystem II (PSII) has paved a new way to connect the PSII model with a functional model of photosystem I (PSI). However, PSI functional models have yet to be reported. We report herein the first potential functional model of PSI, in which plastoquinol (PQH2) analogues were oxidized to plastoquinone (PQ) analogues, accompanied by hydrogen (H2) evolution. Photoirradiation of a deaerated acetonitrile (MeCN) solution containing hydroquinone derivatives (X-QH2) as a hydrogen source, 9-mesityl-10-methylacridinium ion (Acr+-Mes) as a photoredox catalyst, and a cobalt(III) complex, CoIII(dmgH)2pyCl (dmgH = dimethylglyoximate monoanion; py = pyridine) as a redox catalyst resulted in the evolution of H2 and formation of the corresponding p-benzoquinone derivatives (X-Q) quantitatively. The maximum quantum yield for photocatalytic H2 evolution from tetrachlorohydroquinone (Cl4QH2) with Acr+-Mes and CoIII(dmgH)2pyCl and H2O in deaerated MeCN was determined to be 10%. Photocatalytic H2 evolution is started by electron transfer (ET) from Cl4QH2 to the triplet ET state of Acr+-Mes to produce Cl4QH2•+ and Acr•-Mes with a rate constant of 7.2 × 107 M-1 s-1, followed by ET from Acr•-Mes to CoIII(dmgH)2pyCl to produce [CoII(dmgH)2pyCl]-, accompanied by the regeneration of Acr+-Mes. On the other hand, Cl4QH2•+ is deprotonated to produce Cl4QH•, which transfers either a hydrogen-atom transfer or a proton-coupled electron transfer to [CoII(dmgH)2pyCl]- to produce a cobalt(III) hydride complex, [CoIII(H)(dmgH)2pyCl]-, which reacts with H+ to evolve H2, accompanied by the regeneration of CoIII(dmgH)2pyCl. The formation of [CoII(dmgH)2pyCl]- was detected by electron paramagnetic resonance measurements.
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Affiliation(s)
- Young Hyun Hong
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.,Faculty of Science and Engineering, Meijo University, Nagoya, Aichi 468-0073, Japan
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25
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Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formulations and computational modeling of some of the light harvesting complexes including FMO. The most recent research developments in the photosynthetic light harvesting complexes are thoroughly discussed. The theoretical background related to the spectral density, quantum coherence and density functional theory has been elaborated. Furthermore, details about the transfer and excitation of energy in different sites of the FMO complex along with other vital photosynthetic light harvesting complexes have also been provided. Finally, we conclude this review by providing the current and potential applications in environmental science, energy, health and medicine, where such mathematical and computational studies of the photosynthesis and the light harvesting complexes can be readily integrated.
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Khmelnitskiy A, Toporik H, Mazor Y, Jankowiak R. On the Red Antenna States of Photosystem I Mutants from Cyanobacteria Synechocystis PCC 6803. J Phys Chem B 2020; 124:8504-8515. [DOI: 10.1021/acs.jpcb.0c05201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton Khmelnitskiy
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Hila Toporik
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Yuval Mazor
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
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27
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Leiger K, Linnanto JM, Freiberg A. Establishment of the Qy Absorption Spectrum of Chlorophyll a Extending to Near-Infrared. Molecules 2020; 25:molecules25173796. [PMID: 32825445 PMCID: PMC7503670 DOI: 10.3390/molecules25173796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
A weak absorption tail related to the Qy singlet electronic transition of solvated chlorophyll a is discovered using sensitive anti-Stokes fluorescence excitation spectroscopy. The quasi-exponentially decreasing tail was, at ambient temperature, readily observable as far as -2400 cm-1 from the absorption peak and at relative intensity of 10-7. The tail also weakened rapidly upon cooling the sample, implying its basic thermally activated nature. The shape of the spectrum as well as its temperature dependence were qualitatively well reproduced by quantum chemical calculations involving the pigment intramolecular vibrational modes, their overtones, and pairwise combination modes, but no intermolecular/solvent modes. A similar tail was observed earlier in the case of bacteriochlorophyll a, suggesting generality of this phenomenon. Long vibronic red tails are, thus, expected to exist in all pigments of light-harvesting relevance at physiological temperatures.
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Affiliation(s)
- Kristjan Leiger
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 51011 Tartu, Estonia; (K.L.); (J.M.L.)
| | - Juha Matti Linnanto
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 51011 Tartu, Estonia; (K.L.); (J.M.L.)
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 51011 Tartu, Estonia; (K.L.); (J.M.L.)
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51014 Tartu, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia
- Correspondence:
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28
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Yan Y, Liu Y, Xing T, Shi Q. Theoretical study of excitation energy transfer and nonlinear spectroscopy of photosynthetic light‐harvesting complexes using the nonperturbative reduced dynamics method. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1498] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yaming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
| | - Yanying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
| | - Tao Xing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
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29
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Korsakas S, Bučinskas J, Abramavicius D. Long memory effects in excitonic systems dynamics: Spectral relations and excitation transport. J Chem Phys 2020; 152:244114. [DOI: 10.1063/5.0009926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- S. Korsakas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - J. Bučinskas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - D. Abramavicius
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
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30
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Kell A, Khmelnitskiy AY, Reinot T, Jankowiak R. On uncorrelated inter-monomer Förster energy transfer in Fenna-Matthews-Olson complexes. J R Soc Interface 2020; 16:20180882. [PMID: 30958204 DOI: 10.1098/rsif.2018.0882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Fenna-Matthews-Olson (FMO) light-harvesting antenna protein of green sulfur bacteria is a long-studied pigment-protein complex which funnels energy from the chlorosome to the reaction centre where photochemistry takes place. The structure of the FMO protein from Chlorobaculum tepidum is known as a homotrimeric complex containing eight bacteriochlorophyll a per monomer. Owing to this structure FMO has strong intra-monomer and weak inter-monomer electronic coupling constants. While long-lived (sub-picosecond) coherences within a monomer have been a prevalent topic of study over the past decade, various experimental evidence supports the presence of subsequent inter-monomer energy transfer on a picosecond time scale. The latter has been neglected by most authors in recent years by considering only sub-picosecond time scales or assuming that the inter-monomer coupling between low-energy states is too weak to warrant consideration of the entire trimer. However, Förster theory predicts that energy transfer of the order of picoseconds is possible even for very weak (less than 5 cm-1) electronic coupling between chromophores. This work reviews experimental data (with a focus on emission and hole-burned spectra) and simulations of exciton dynamics which demonstrate inter-monomer energy transfer. It is shown that the lowest energy 825 nm absorbance band cannot be properly described by a single excitonic state. The energy transfer through FMO is modelled by generalized Förster theory using a non-Markovian, reduced density matrix approach to describe the electronic structure. The disorder-averaged inter-monomer transfer time across the 825 nm band is about 27 ps. While only isolated FMO proteins are presented, the presence of inter-monomer energy transfer in the context of the overall photosystem is also briefly discussed.
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Affiliation(s)
- Adam Kell
- 1 Department of Chemistry, Kansas State University , Manhattan, KS , USA
| | | | - Tonu Reinot
- 1 Department of Chemistry, Kansas State University , Manhattan, KS , USA
| | - Ryszard Jankowiak
- 1 Department of Chemistry, Kansas State University , Manhattan, KS , USA.,2 Department of Physics, Kansas State University , Manhattan, KS , USA
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31
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Müh F, Zouni A. Structural basis of light-harvesting in the photosystem II core complex. Protein Sci 2020; 29:1090-1119. [PMID: 32067287 PMCID: PMC7184784 DOI: 10.1002/pro.3841] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
Photosystem II (PSII) is a membrane-spanning, multi-subunit pigment-protein complex responsible for the oxidation of water and the reduction of plastoquinone in oxygenic photosynthesis. In the present review, the recent explosive increase in available structural information about the PSII core complex based on X-ray crystallography and cryo-electron microscopy is described at a level of detail that is suitable for a future structure-based analysis of light-harvesting processes. This description includes a proposal for a consistent numbering scheme of protein-bound pigment cofactors across species. The structural survey is complemented by an overview of the state of affairs in structure-based modeling of excitation energy transfer in the PSII core complex with emphasis on electrostatic computations, optical properties of the reaction center, the assignment of long-wavelength chlorophylls, and energy trapping mechanisms.
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Affiliation(s)
- Frank Müh
- Department of Theoretical Biophysics, Institute for Theoretical Physics, Johannes Kepler University Linz, Linz, Austria
| | - Athina Zouni
- Humboldt-Universität zu Berlin, Institute for Biology, Biophysics of Photosynthesis, Berlin, Germany
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32
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Jassas M, Goodson C, Blankenship RE, Jankowiak R, Kell A. On Excitation Energy Transfer within the Baseplate BChl a-CsmA Complex of Chloroflexus aurantiacus. J Phys Chem B 2019; 123:9786-9791. [PMID: 31660744 DOI: 10.1021/acs.jpcb.9b08043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, a hybrid approach combining solid-state NMR spectroscopy and cryo-electron microscopy showed that the baseplate in green sulfur bacterium Chlorobaculum tepidum is a 2D lattice of BChl a-CsmA dimers [Nielsen, J. T.; et al., Nat. Commun. 2016, 7, 12454-12465]. While the existence of the BChl a-CsmA subunit was previously known, the proposed orientations of the BChl a pigments had only been elucidated from spectral data up to this point. Regarding the electronic structure of the baseplate, two models have been proposed. 2D electronic spectroscopy data were interpreted as revealing that at least four excitonically coupled BChl a might be in close contact. Conversely, spectral hole burning data suggested that the lowest energy state was localized, yet additional states are sometimes observed because of the presence of the Fenna-Matthews-Olson (FMO) antenna protein. To solve this conundrum, this work studies the chlorosome-baseplate complex from Chloroflexus aurantiacus, which does not contain the FMO protein. The results confirm that in both C. tepidum and C. aurantiacus, excitation energy is transferred to a localized low-energy trap state near 818 nm with similar rates, most likely via exciton hopping.
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Affiliation(s)
| | - Carrie Goodson
- Departments of Biology and Chemistry , Washington University in Saint Louis , Saint Louis , Missouri 63130 , United States
| | - Robert E Blankenship
- Departments of Biology and Chemistry , Washington University in Saint Louis , Saint Louis , Missouri 63130 , United States
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33
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Khmelnitskiy A, Williams JC, Allen JP, Jankowiak R. Influence of Hydrogen Bonds on the Electron-Phonon Coupling Strength/Marker Mode Structure and Charge Separation Rates in Reaction Centers from Rhodobacter sphaeroides. J Phys Chem B 2019; 123:8717-8726. [PMID: 31539255 DOI: 10.1021/acs.jpcb.9b08388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Low-temperature persistent and transient hole-burning (HB) spectra are presented for the triple hydrogen-bonded L131LH + M160LH + M197FH mutant of Rhodobacter sphaeroides. These spectra expose the heterogeneous nature of the P-, B-, and H-bands, consistent with a distribution of electron transfer (ET) times and excitation energy transfer (EET) rates. Transient P+QA- holes are observed for fast (tens of picoseconds or faster) ET times and reveal strong coupling to phonons and marker mode(s), while the persistent holes are bleached in a fraction of reaction centers with long-lived excited states characterized by much weaker electron-phonon coupling. Exposed differences in electron-phonon coupling strength, as well as a different coupling to the marker mode(s), appear to affect the ET times. Both resonantly and nonresonantly burned persistent HB spectra show weak blue- (∼150 cm-1) and large, red-shifted (∼300 cm-1) antiholes of the P band. Slower EET times from the H- and B-bands to the special pair dimer provide new insight on the influence of hydrogen bonds on mutation-induced heterogeneity.
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Affiliation(s)
| | - JoAnn C Williams
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - James P Allen
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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34
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Rätsep M, Linnanto JM, Freiberg A. Higher Order Vibronic Sidebands of Chlorophyll a and Bacteriochlorophyll a for Enhanced Excitation Energy Transfer and Light Harvesting. J Phys Chem B 2019; 123:7149-7156. [PMID: 31356081 DOI: 10.1021/acs.jpcb.9b06843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optical absorption and fluorescence spectra of molecules in condensed phases often show extensive sidebands. Originating from electron-vibrational and electron-phonon couplings, these spectral tails bear important information on the dynamics of electronic states and processes the molecules are involved in. The vibronic sidebands observed in conjugate Qy absorption and fluorescence spectra of chlorophyll a and bacteriochlorophyll a are relatively weak, characterized by the total Huang-Rhys factor which is less than one. Therefore, it is widely considered that only fundamental intramolecular modes are responsible for their formation. Here, we provide evidence for extra-long and structured fluorescence tails of chlorophyll a and bacteriochlorophyll a as far as 4000 cm-1 from respective spectral origins, far beyond the frequency range of fundamental modes. According to quantum chemical simulations, these sidebands extending to ∼960 nm in chlorophyll a and ∼1140 nm in bacteriochlorophyll a into the infrared part of the optical spectrum are mainly contributed to by vibrational overtones of the fundamental modes. Because energy transfer and relaxation processes generally depend on vibronic overlap integrals, these findings potentially contribute to better understanding of many vital photo-induced phenomena, including photosynthetic light harvesting.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics , University of Tartu , W. Ostwald Street 1 , 50411 Tartu , Estonia
| | - Juha Matti Linnanto
- Institute of Physics , University of Tartu , W. Ostwald Street 1 , 50411 Tartu , Estonia
| | - Arvi Freiberg
- Institute of Physics , University of Tartu , W. Ostwald Street 1 , 50411 Tartu , Estonia.,Institute of Molecular and Cell Biology , University of Tartu , Riia 23 , 51010 Tartu , Estonia.,Estonian Academy of Sciences , Kohtu 6 , 10130 Tallinn , Estonia
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35
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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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36
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Jang SJ. Robust and Fragile Quantum Effects in the Transfer Kinetics of Delocalized Excitons between B850 Units of LH2 Complexes. J Phys Chem Lett 2018; 9:6576-6583. [PMID: 30383380 DOI: 10.1021/acs.jpclett.8b02641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aggregates of light harvesting 2 (LH2) complexes form the major exciton-relaying domain in the photosynthetic unit of purple bacteria. Application of a generalized master equation to pairs of the B850 units of LH2 complexes, where excitons predominantly reside, provides quantitative information on how the inter-LH2 exciton transfer depends on the distance, relative rotational angle, and the relative energies of the two LH2s. The distance dependence demonstrates significant enhancement of the rate due to quantum delocalization of excitons, the qualitative nature of which remains robust against the disorder. The angle dependence reflects isotropic nature of exciton transfer, which remains similar for the ensemble of disorder. The variation of the rate on relative excitation energies of LH2 exhibits resonance peaks, which, however, is fragile as the disorder becomes significant. Overall, the average transfer times between two LH2s are estimated to be in the range of 4-25 ps for physically plausible inter-LH2 distances.
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Affiliation(s)
- Seogjoo J Jang
- Department of Chemistry and Biochemistry , Queens College, City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States
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37
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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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38
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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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39
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Khmelnitskiy A, Reinot T, Jankowiak R. Impact of Single-Point Mutations on the Excitonic Structure and Dynamics in a Fenna-Matthews-Olson Complex. J Phys Chem Lett 2018; 9:3378-3386. [PMID: 29863366 DOI: 10.1021/acs.jpclett.8b01396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hole burning (HB) spectroscopy and modeling studies reveal significant changes in the excitonic structure and dynamics in several mutants of the FMO trimer from the Chlorobaculum tepidum. The excited-state decay times ( T1) of the high-energy excitons are significantly modified when mutation occurs near bacteriochlorophyll (BChl) 1 (V152N mutant) or BChl 6 (W184F). Longer (averaged) T1 times of highest-energy excitons in V152N and W184F mutants suggest that site energies of BChls 1 and 6, believed to play an important role in receiving excitation from the baseplate BChls, likely play a critical role to ensure the femtosecond (fs) energy relaxation observed in wild-type FMO. HB spectroscopy reveals preferentially slower T1 times (about 1 ps on average) because fs times prohibit HB due to an extremely low HB quantum yield. Uncorrelated (incoherent) excitation energy transfer times between monomers, the composition of exciton states, and average, frequency-dependent, excited-state decay times ( T1) are discussed.
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40
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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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41
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Reprint of “The effect of site-specific spectral densities on the high-dimensional exciton-vibrational dynamics in the FMO complex”. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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Khmelnitskiy A, Saer RG, Blankenship RE, Jankowiak R. Excitonic Energy Landscape of the Y16F Mutant of the Chlorobium tepidum Fenna-Matthews-Olson (FMO) Complex: High Resolution Spectroscopic and Modeling Studies. J Phys Chem B 2018; 122:3734-3743. [PMID: 29554425 DOI: 10.1021/acs.jpcb.7b11763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We report high-resolution (low-temperature) absorption, emission, and nonresonant/resonant hole-burned (HB) spectra and results of excitonic calculations using a non-Markovian reduced density matrix theory (with an improved algorithm for parameter optimization in heterogeneous samples) obtained for the Y16F mutant of the Fenna-Matthews-Olson (FMO) trimer from the green sulfur bacterium Chlorobium tepidum. We show that the Y16F mutant is a mixture of FMO complexes with three independent low-energy traps (located near 817, 821, and 826 nm), in agreement with measured composite emission and HB spectra. Two of these traps belong to mutated FMO subpopulations characterized by significantly modified low-energy excitonic states. Hamiltonians for the two major subpopulations (Sub821 and Sub817) provide new insight into extensive changes induced by the single-point mutation in the vicinity of BChl 3 (where tyrosine Y16 was replaced with phenylalanine F16). The average decay time(s) from the higher exciton state(s) in the Y16F mutant depends on frequency and occurs on a picosecond time scale.
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Affiliation(s)
| | - Rafael G Saer
- Departments of Biology and Chemistry , Washington University in St. Louis , Saint Louis , Missouri 63130 , United States
| | - Robert E Blankenship
- Departments of Biology and Chemistry , Washington University in St. Louis , Saint Louis , Missouri 63130 , United States
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43
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Tiwari V, Jonas DM. Electronic energy transfer through non-adiabatic vibrational-electronic resonance. II. 1D spectra for a dimer. J Chem Phys 2018; 148:084308. [DOI: 10.1063/1.5003193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vivek Tiwari
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
| | - David M. Jonas
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
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44
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Rancova O, Jankowiak R, Abramavicius D. Role of Bath Fluctuations in the Double-Excitation Manifold in Shaping the 2DES of Bacterial Reaction Centers at Low Temperature. J Phys Chem B 2018; 122:1348-1366. [DOI: 10.1021/acs.jpcb.7b08905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Olga Rancova
- Institute
of Chemical 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, United States
| | - Darius Abramavicius
- Institute
of Chemical Physics, Vilnius University, Sauletekio al 9-III, 10222 Vilnius, Lithuania
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Löhner A, Cogdell R, Köhler J. Contribution of low-temperature single-molecule techniques to structural issues of pigment-protein complexes from photosynthetic purple bacteria. J R Soc Interface 2018; 15:rsif.2017.0680. [PMID: 29321265 DOI: 10.1098/rsif.2017.0680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/01/2017] [Indexed: 11/12/2022] Open
Abstract
As the electronic energies of the chromophores in a pigment-protein complex are imposed by the geometrical structure of the protein, this allows the spectral information obtained to be compared with predictions derived from structural models. Thereby, the single-molecule approach is particularly suited for the elucidation of specific, distinctive spectral features that are key for a particular model structure, and that would not be observable in ensemble-averaged spectra due to the heterogeneity of the biological objects. In this concise review, we illustrate with the example of the light-harvesting complexes from photosynthetic purple bacteria how results from low-temperature single-molecule spectroscopy can be used to discriminate between different structural models. Thereby the low-temperature approach provides two advantages: (i) owing to the negligible photobleaching, very long observation times become possible, and more importantly, (ii) at cryogenic temperatures, vibrational degrees of freedom are frozen out, leading to sharper spectral features and in turn to better resolved spectra.
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Affiliation(s)
- Alexander Löhner
- Spectroscopy of Soft Matter, University of Bayreuth, 95440 Bayreuth, Germany
| | - Richard Cogdell
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Jürgen Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, 95440 Bayreuth, Germany .,Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
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Abramavicius D, Chorošajev V, Valkunas L. Tracing feed-back driven exciton dynamics in molecular aggregates. Phys Chem Chem Phys 2018; 20:21225-21240. [DOI: 10.1039/c8cp00682b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excitation, exciton transport, dephasing and energy relaxation, and finally detection processes shift molecular systems into a specific superposition of quantum states causing localization, local heating and finally excitonic polaronic effects.
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Affiliation(s)
| | | | - Leonas Valkunas
- Institute of Chemical Physics
- Vilnius University
- Vilnius
- Lithuania
- Center for Physical Sciences and Technology
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Rätsep M, Timpmann K, Kawakami T, Wang-Otomo ZY, Freiberg A. Spectrally Selective Spectroscopy of Native Ca-Containing and Ba-Substituted LH1-RC Core Complexes from Thermochromatium tepidum. J Phys Chem B 2017; 121:10318-10326. [PMID: 29058423 DOI: 10.1021/acs.jpcb.7b07841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The LH1-RC core complex from the thermophilic photosynthetic purple sulfur bacterium Thermochromatium tepidum has recently attracted interest of many researchers because of its several unique properties, such as increased robustness against environmental hardships and the much red-shifted near-infrared absorption spectrum of the LH1 antenna exciton polarons. The known near-atomic-resolution crystal structure of the complex well supported this attention. Yet several mechanistic aspects of the complex prominence remained to be understood. In this work, samples of the native, Ca2+-containing core complexes were investigated along with those destabilized by Ba2+ substitution, using various spectrally selective steady-state and picosecond time-resolved spectroscopic techniques at physiological and cryogenic temperatures. As a result, the current interpretation of exciton spectra of the complex was significantly clarified. Specifically, by evaluating the homogeneous and inhomogeneous compositions of the spectra, we showed that there is little to no effect of cation substitution on the dynamic or kinetic properties of antenna excitons. Reasons of the extra red shift of absorption/fluorescence spectra observed in the Ca-LH1-RC and not in the Ba-LH1-RC complex should thus be searched in subtle structural differences following the inclusion of different cations into the core complex scaffold.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | | | | | - Arvi Freiberg
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu , Riia 23, 51010 Tartu, Estonia
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Schulze J, Shibl MF, Al-Marri MJ, Kühn O. The effect of site-specific spectral densities on the high-dimensional exciton-vibrational dynamics in the FMO complex. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Kell A, Jassas M, Hacking K, Cogdell RJ, Jankowiak R. On Light-Induced Photoconversion of B800 Bacteriochlorophylls in the LH2 Antenna of the Purple Sulfur Bacterium Allochromatium vinosum. J Phys Chem B 2017; 121:9999-10006. [DOI: 10.1021/acs.jpcb.7b06185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Kirsty Hacking
- Institute
of Molecular, Cell and Systems Biology, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8TA, Scotland
| | - Richard J. Cogdell
- Institute
of Molecular, Cell and Systems Biology, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8TA, Scotland
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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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