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Lin C, Mazor Y, Reppert M. Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis. J Phys Chem B 2024; 128:2266-2280. [PMID: 38442033 DOI: 10.1021/acs.jpcb.3c06488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.
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Affiliation(s)
- Chientzu Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| | - Yuval Mazor
- School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
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Kosumi D, Bandou-Uotani M, Kato S, Kawakami K, Yonekura K, Kamiya N. Reinvestigation on primary processes of PSII-dimer from Thermosynechococcus vulcanus by femtosecond pump-probe spectroscopy. PHOTOSYNTHESIS RESEARCH 2024; 159:79-91. [PMID: 38363474 DOI: 10.1007/s11120-024-01076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
Cyanobacterial photosynthetic apparatus efficiently capture sunlight, and the energy is subsequently transferred to photosystem I (PSI) and II (PSII), to produce electrochemical potentials. PSII is a unique membrane protein complex that photo-catalyzes oxidation of water and majorly contains photosynthetic pigments of chlorophyll a and carotenoids. In the present study, the ultrafast energy transfer and charge separation dynamics of PSII from a thermophilic cyanobacterium Thermosynechococcus vulcanus were reinvestigated by femtosecond pump-probe spectroscopic measurements under low temperature and weak intensity excitation condition. The results imply the two possible models of the energy transfers and subsequent charge separation in PSII. One is the previously suggested "transfer-to-trapped limit" model. Another model suggests that the energy transfers from core CP43 and CP47 antennas to the primary electron donor ChlD1 with time-constants of 0.71 ps and 3.28 ps at 140 K (0.17 and 1.33 ps at 296 K), respectively and that the pheophytin anion (PheoD1-) is generated with the time-constant of 43.0 ps at 140 K (14.8 ps at 296 K) upon excitation into the Qy band of chlorophyll a at 670 nm. The secondary electron transfer to quinone QA: PheoD1-QA → PheoD1QA- is observed with the time-constant of 650 ps only at 296 K. On the other hand, an inefficient β-carotene → chlorophyll a energy transfer (33%) occurred after excitation to the S2 state of β-carotene at 500 nm. Instead, the carotenoid triplet state appeared in an ultrafast timescale after excitation at 500 nm.
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Affiliation(s)
- Daisuke Kosumi
- Institute of Industrial Nanomaterials, Kumamoto University, 2-39-1 Kurokami, Chuo-Ku, Kumamoto, 860-8555, Japan.
| | - Miki Bandou-Uotani
- School of Graduate Studies, The Open University of Japan, 2-11 Wakaba, Mihama-Ku, Chiba, 261-8586, Japan
- Division of Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-Ku, Kumamoto, 860-8555, Japan
| | - Shunya Kato
- Department of Physics, Faculty of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-Ku, Kumamoto, 860-8555, Japan
| | - Keisuke Kawakami
- Biostructual Mechanism Laboratory, RIKEN, SPring-8 Center, 1-1-1, Kouto, Sayo, Hyougo, 679-5148, Japan.
| | - Koji Yonekura
- Biostructual Mechanism Laboratory, RIKEN, SPring-8 Center, 1-1-1, Kouto, Sayo, Hyougo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Nobuo Kamiya
- The OCU Research Center for Artificial Photosynthesis, Osaka Metropolitan University, 3-3-138Sumiyoshi-Ku, SugimotoOsaka City, Osaka, 558-8585, Japan
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Mohamed A, Nishi S, Kawakami K, Shen JR, Itoh S, Fukumura H, Shibata Y. Exciton quenching by oxidized chlorophyll Z across the two adjacent monomers in a photosystem II core dimer. PHOTOSYNTHESIS RESEARCH 2022; 154:277-289. [PMID: 35976595 DOI: 10.1007/s11120-022-00948-1] [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: 05/11/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
This study aimed to clarify (1) which pigment in a photosystem II (PSII) core complex is responsible for the 695-nm emission at 77 K and (2) the molecular basis for the oxidation-induced fluorescence quenching in PSII. Picosecond time-resolved fluorescence dynamics was compared between the dimeric and monomeric PSII with and without addition of an oxidant. The results indicated that the excitation-energy flow to the 695-nm-emitting chlorophyll (Chl) at 36 K and 77 K was hindered upon monomerization, clearly demonstrating significant exciton migration from the Chls on one monomer to the 695-nm-emitting pigment on the adjacent monomer. Oxidation of the redox-active Chl, which is named ChlZ caused almost equal quenching of the 684-nm and 695-nm emission bands in the dimer, and lower quenching of the 695-nm band in the monomer. These results suggested two possible scenarios responsible for the 695-nm emission band: (A) Chl11-13 pair and the oxidized ChlZD1 work as the 695-nm emitting Chl and the quenching site, respectively, and (B) Chl29 and the oxidized ChlZD2 work as the 695-nm emitting Chl and the quenching site, respectively.
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Affiliation(s)
- Ahmed Mohamed
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki Aza Aoba, Aoba-Ku, Sendai, 980-8578, Japan
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650, Boul. Lionel-Boulet, Varennes, QC, J3X 1S2, Canada
| | - Shunsuke Nishi
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN Spring-8 Center, Hyogo, 679-5148, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shigeru Itoh
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Hiroshi Fukumura
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki Aza Aoba, Aoba-Ku, Sendai, 980-8578, Japan
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Yutaka Shibata
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki Aza Aoba, Aoba-Ku, Sendai, 980-8578, Japan.
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Fujita Y, Zhang X, Mohamed A, Ye S, Shibata Y. Accumulation of quenched LHCII around PSI in Chlamydomonas cells in state2 revealed by cryo-fluorescence lifetime imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 236:112584. [PMID: 36272337 DOI: 10.1016/j.jphotobiol.2022.112584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/20/2022] [Accepted: 10/02/2022] [Indexed: 02/17/2023]
Abstract
Fluorescence-spectral microscope observations of photosynthetic organisms at cryogenic temperatures have the ability to spectrally resolve the two photosystems (PSs) and thus provide a powerful tool to elucidate the functional analysis of photosynthesis in vivo. In the present study, a measurement channel of the fluorescence lifetime at 680 nm was added to the cryo-microscope system previously developed by the authors. This provides access to information on the functional state of the light-harvesting system in living cells during regulation by a mechanism called state transitions. The observations of state1-locked and state2-locked Chlamydomonas cells at 80 K enabled us to identify a component showing rapidly decaying fluorescence with a lifetime of ca. 3 ps and emitting at around 676 nm. The component was assigned to the light-harvesting complex II (LHCII) that is isolated from both PSs and in a quenched state, probably due to the formation of aggregates. Simultaneous spectral observations revealed the accumulation of this free LHCII in the photosystem I (PSI)-enriched region within each state2-locked cell. To the best of our knowledge, this is the first in-vivo observation which suggests the localization of the quenched LHCII aggregates.
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Affiliation(s)
- Yuki Fujita
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan
| | - XianJun Zhang
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan; Division for Interdisciplinary Advanced Research and Education, Tohoku University, 980-8578 Sendai, Japan
| | - Ahmed Mohamed
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan
| | - Shen Ye
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan
| | - Yutaka Shibata
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan.
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Sirohiwal A, Neese F, Pantazis DA. Chlorophyll excitation energies and structural stability of the CP47 antenna of photosystem II: a case study in the first-principles simulation of light-harvesting complexes. Chem Sci 2021; 12:4463-4476. [PMID: 34163712 PMCID: PMC8179452 DOI: 10.1039/d0sc06616h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Natural photosynthesis relies on light harvesting and excitation energy transfer by specialized pigment-protein complexes. Their structure and the electronic properties of the embedded chromophores define the mechanisms of energy transfer. An important example of a pigment-protein complex is CP47, one of the integral antennae of the oxygen-evolving photosystem II (PSII) that is responsible for efficient excitation energy transfer to the PSII reaction center. The charge-transfer excitation induced among coupled reaction center chromophores resolves into charge separation that initiates the electron transfer cascade driving oxygenic photosynthesis. Mapping the distribution of site energies among the 16 chlorophyll molecules of CP47 is essential for understanding excitation energy transfer and overall antenna function. In this work, we demonstrate a multiscale quantum mechanics/molecular mechanics (QM/MM) approach utilizing full time-dependent density functional theory with modern range-separated functionals to compute for the first time the excitation energies of all CP47 chlorophylls in a complete membrane-embedded cyanobacterial PSII dimer. The results quantify the electrostatic effect of the protein on the site energies of CP47 chlorophylls, providing a high-level quantum chemical excitation profile of CP47 within a complete computational model of "near-native" cyanobacterial PSII. The ranking of site energies and the identity of the most red-shifted chlorophylls (B3, followed by B1) differ from previous hypotheses in the literature and provide an alternative basis for evaluating past approaches and semiempirically fitted sets. Given that a lot of experimental studies on CP47 and other light-harvesting complexes utilize extracted samples, we employ molecular dynamics simulations of isolated CP47 to identify which parts of the polypeptide are most destabilized and which pigments are most perturbed when the antenna complex is extracted from PSII. We demonstrate that large parts of the isolated complex rapidly refold to non-native conformations and that certain pigments (such as chlorophyll B1 and β-carotene h1) are so destabilized that they are probably lost upon extraction of CP47 from PSII. The results suggest that the properties of isolated CP47 are not representative of the native complexed antenna. The insights obtained from CP47 are generalizable, with important implications for the information content of experimental studies on biological light-harvesting antenna systems.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany.,Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum 44780 Bochum Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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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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Hsieh ST, Zhang L, Ye DW, Huang X, Cheng YC. A theoretical study on the dynamics of light harvesting in the dimeric photosystem II core complex: regulation and robustness of energy transfer pathways. Faraday Discuss 2019; 216:94-115. [PMID: 31016302 DOI: 10.1039/c8fd00205c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Here we present our theoretical investigations into the light reaction in the dimeric photosystem II (PSII) core complex. An effective model for excitation energy transfer (EET) and primary charge separation (CS) in the PSII core complex was developed, with model parameters constructed based on molecular dynamics (MD) simulation data. Compared to experimental results, we demonstrated that this model faithfully reproduces the absorption spectra of the RC and core light-harvesting complexes (CP43 and CP47) as well as the full EET dynamics among the chromophores in the PSII core complex. We then applied master equation simulations and network analysis to investigate detailed EET plus CS dynamics in the system, allowing us to identify key EET pathways and produce a coarse-grained cluster model for the light reaction in the dimeric PSII core complex. We show that non-equilibrium energy transfer channels play important roles in the efficient light harvesting process and that multiple EET pathways exist between subunits of PSII to ensure the robustness of light harvesting in the system. Furthermore, we revealed that inter-monomer energy transfer dominated by the coupling between the two CLA625 molecules enables efficient energy exchange between two CP47s in the dimeric PSII core complex, which leads to significant energy pooling in the CP47 domain during the light reaction. Our study provides a blueprint for the design of light harvesting in the PSII core and show that a structure-based approach using molecular dynamics simulations and quantum chemistry calculations can be effectively utilized to elucidate the dynamics of light harvesting in complex photosynthetic systems.
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Affiliation(s)
- Shou-Ting Hsieh
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan.
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou, Fujian CN 350002, China
| | - De-Wei Ye
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan.
| | - Xuhui Huang
- Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.
| | - Yuan-Chung Cheng
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan.
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Jassas M, Chen J, Khmelnitskiy A, Casazza AP, Santabarbara S, Jankowiak R. Structure-Based Exciton Hamiltonian and Dynamics for the Reconstituted Wild-type CP29 Protein Antenna Complex of the Photosystem II. J Phys Chem B 2018; 122:4611-4624. [DOI: 10.1021/acs.jpcb.8b00032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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