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Rankelytė G, Gelzinis A, Robert B, Valkunas L, Chmeliov J. Environment-dependent chlorophyll-chlorophyll charge transfer states in Lhca4 pigment-protein complex. FRONTIERS IN PLANT SCIENCE 2024; 15:1412750. [PMID: 39170787 PMCID: PMC11335733 DOI: 10.3389/fpls.2024.1412750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/02/2024] [Indexed: 08/23/2024]
Abstract
Photosystem I (PSI) light-harvesting antenna complexes LHCI contain spectral forms that absorb and emit photons of lower energy than that of its primary electron donor, P700. The most red-shifted fluorescence is associated with the Lhca4 complex. It has been suggested that this red emission is related to the inter-chlorophyll charge transfer (CT) states. In this work we present a systematic quantum-chemical study of the CT states in Lhca4, accounting for the influence of the protein environment by estimating the electrostatic interactions. We show that significant energy shifts result from these interactions and propose that the emission of the Lhca4 complex is related not only to the previously proposed a603+-a608- state, but also to the a602+-a603- state. We also investigate how different protonation patterns of protein amino acids affect the energetics of the CT states.
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Affiliation(s)
- Gabrielė Rankelytė
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Andrius Gelzinis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Leonas Valkunas
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Jevgenij Chmeliov
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
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2
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Zhang YZ, Li K, Qin BY, Guo JP, Zhang QB, Zhao DL, Chen XL, Gao J, Liu LN, Zhao LS. Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex. Nat Commun 2024; 15:4999. [PMID: 38866834 PMCID: PMC11169493 DOI: 10.1038/s41467-024-49453-0] [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: 01/16/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs.
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Affiliation(s)
- Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Kang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Bing-Yue Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Ping Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Quan-Bao Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Dian-Li Zhao
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Lu-Ning Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Long-Sheng Zhao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
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Shi HX, Bao HW, Wu GY. Solvation controlled excited-state dynamics in a donor-acceptor phenazine-imidazole derivative. RSC Adv 2024; 14:17071-17076. [PMID: 38808230 PMCID: PMC11130646 DOI: 10.1039/d4ra02417f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024] Open
Abstract
In the past few decades, significant efforts have been devoted to developing phenazine derivatives in various fields such as medicine, pesticides, dyes, and conductive materials owing to their highly Stokes-shifted fluorescence and distinctive photophysical properties. The modulation of the surrounding environment can effectively influence the luminescent behavior of phenazine derivatives, prompting us to investigate the solvent effect on the excited state dynamics. Herein, we present the solvent controlled excited state dynamics of a novel triphenylamine-based phenazine-imidazole molecule (TPAIP) through steady-state spectra and femtosecond transient absorption spectra. The fluorescence emission spectrum exhibited a redshift with increasing solvent polarity, indicating the existence of a charge transfer state. Furthermore, by tracking the femtosecond transient absorption spectra of TPAIP, we found that the nature of the relaxed S1 state was strongly influenced by the solvent polarity: intersystem crossing character appears in apolar solvent, whereas intramolecular charge transfer character occurs in polar solvent because of solvation. These findings provide significant theoretical insights into the impact of solvents on the excited state dynamics within phenazine derivatives. This understanding supports diverse applications ranging from advanced biological probe design to photocatalysis and pharmaceutical research.
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Affiliation(s)
- Hai-Xiong Shi
- School of Chemical Engineering, Lanzhou University of Arts and Science Lanzhou Gansu 730000 China
| | - Hong-Wei Bao
- School of Chemical Engineering, Lanzhou University of Arts and Science Lanzhou Gansu 730000 China
| | - Gui-Yuan Wu
- Anhui Province Key Laboratory for Control and Applications of Optoelectronic Information Materials, School of Physics and Electronic Information, Anhui Normal University Wuhu 241002 China
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4
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Sirohiwal A, Pantazis DA. Reaction Center Excitation in Photosystem II: From Multiscale Modeling to Functional Principles. Acc Chem Res 2023; 56:2921-2932. [PMID: 37844298 PMCID: PMC10634305 DOI: 10.1021/acs.accounts.3c00392] [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: 07/14/2023] [Indexed: 10/18/2023]
Abstract
Oxygenic photosynthesis is the fundamental energy-converting process that utilizes sunlight to generate molecular oxygen and the organic compounds that sustain life. Protein-pigment complexes harvest light and transfer excitation energy to specialized pigment assemblies, reaction centers (RC), where electron transfer cascades are initiated. A molecular-level understanding of the primary events is indispensable for elucidating the principles of natural photosynthesis and enabling development of bioinspired technologies. The primary enzyme in oxygenic photosynthesis is Photosystem II (PSII), a membrane-embedded multisubunit complex, that catalyzes the light-driven oxidation of water. The RC of PSII consists of four chlorophyll a and two pheophytin a pigments symmetrically arranged along two core polypeptides; only one branch participates in electron transfer. Despite decades of research, fundamental questions remain, including the origin of this functional asymmetry, the nature of primary charge-transfer states and the identity of the initial electron donor, the origin of the capability of PSII to enact charge separation with far-red photons, i.e., beyond the "red limit" where individual chlorophylls absorb, and the role of protein conformational dynamics in modulating charge-separation pathways.In this Account, we highlight developments in quantum-chemistry based excited-state computations for multipigment assemblies and the refinement of protocols for computing protein-induced electrochromic shifts and charge-transfer excitations calibrated with modern local correlation coupled cluster methods. We emphasize the importance of multiscale atomistic quantum-mechanics/molecular-mechanics and large-scale molecular dynamics simulations, which enabled direct and accurate modeling of primary processes in RC excitation at the quantum mechanical level.Our findings show how differential protein electrostatics enable spectral tuning of RC pigments and generate functional asymmetry in PSII. A chlorophyll pigment on the active branch (ChlD1) has the lowest site energy in PSII and is the primary electron donor. The complete absence of low-lying charge-transfer states within the central pair of chlorophylls excludes a long-held assumption about the initial charge separation. Instead, we identify two primary charge separation pathways, both with the same pheophytin acceptor (PheoD1): a fast pathway with ChlD1 as the primary electron donor (short-range charge-separation) and a slow pathway with PD1PD2 as the initial donor (long-range charge separation). The low-energy spectrum is dominated by two states with significant charge-transfer character, ChlD1δ+PheoD1δ- and PD1δ+PheoD1δ-. The conformational dynamics of PSII allows these charge-transfer states to span wide energy ranges, pushing oxygenic photosynthesis beyond the "red limit". These results provide a quantum mechanical picture of the primary events in the RC of oxygenic photosynthesis, forming a solid basis for interpreting experimental observations and for extending photosynthesis research in new directions.
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Affiliation(s)
- Abhishek Sirohiwal
- Department
of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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5
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Brütting M, Foerster JM, Kümmel S. Understanding Primary Charge Separation in the Heliobacterial Reaction Center. J Phys Chem Lett 2023; 14:3092-3102. [PMID: 36951395 DOI: 10.1021/acs.jpclett.3c00377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The homodimeric reaction center of heliobacteria retains features of the ancestral reaction center and can thus provide insights into the evolution of photosynthesis. Primary charge separation is expected to proceed in a two-step mechanism along either of the two reaction center branches. We reveal the first charge-separation step from first-principles calculations based on time-dependent density functional theory with an optimally tuned range-separated hybrid and ab initio Born-Oppenheimer molecular dynamics: the electron is most likely localized on the electron transfer cofactor 3 (EC3, OH-chlorophyll a), and the hole on the adjacent EC2. Including substantial parts of the surrounding protein environment into the calculations shows that a distinct structural mechanism is decisive for the relative energetic positioning of the electronic excitations: specific charged amino acids in the vicinity of EC3 lower the energy of charge-transfer excitations and thus facilitate efficient charge separation. These results are discussed considering recent experimental insights.
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Saito K, Mitsuhashi K, Tamura H, Ishikita H. Quantum mechanical analysis of excitation energy transfer couplings in photosystem II. Biophys J 2023; 122:470-483. [PMID: 36609140 PMCID: PMC9941724 DOI: 10.1016/j.bpj.2023.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/21/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
We evaluated excitation energy transfer (EET) coupling (J) between all pairs of chlorophylls (Chls) and pheophytins (Pheos) in the protein environment of photosystem II based on the time-dependent density functional theory with a quantum mechanical/molecular mechanics approach. In the reaction center, the EET coupling between Chls PD1 and PD2 is weaker (|J(PD1/PD2)| = 79 cm-1), irrespective of a short edge-to-edge distance of 3.6 Å (Mg-to-Mg distance of 8.1 Å), than the couplings between PD1 and the accessory ChlD1 (|J(PD1/ChlD2)| = 104 cm-1) and between PD2 and ChlD2 (|J(PD2/ChlD1)| = 101 cm-1), suggesting that PD1 and PD2 are two monomeric Chls rather than a "special pair". There exist strongly coupled Chl pairs (|J| > ∼100 cm-1) in the CP47 and CP43 core antennas, which may be candidates for the red-shifted Chls observed in spectroscopic studies. In CP47 and CP43, Chls ligated to CP47-His26 and CP43-His56, which are located in the middle layer of the thylakoid membrane, play a role in the "hub" that mediates the EET from the lumenal to stromal layers. In the stromal layer, Chls ligated to CP47-His466, CP43-His441, and CP43-His444 mediate the EET from CP47 to ChlD2/PheoD2 and from CP43 to ChlD1/PheoD1 in the reaction center. Thus, the excitation energy from both CP47 and CP43 can always be utilized for the charge-separation reaction in the reaction center.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Koji Mitsuhashi
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Tamura
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
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Förster A, Visscher L. Quasiparticle Self-Consistent GW-Bethe-Salpeter Equation Calculations for Large Chromophoric Systems. J Chem Theory Comput 2022; 18:6779-6793. [PMID: 36201788 PMCID: PMC9648197 DOI: 10.1021/acs.jctc.2c00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The GW-Bethe–Salpeter equation
(BSE) method
is promising for calculating the low-lying excitonic states of molecular
systems. However, so far it has only been applied to rather small
molecules and in the commonly implemented diagonal approximations
to the electronic self-energy, it depends on a mean-field starting
point. We describe here an implementation of the self-consistent and
starting-point-independent quasiparticle self-consistent (qsGW)-BSE approach, which is suitable for calculations on
large molecules. We herein show that eigenvalue-only self-consistency
can lead to an unfaithful description of some excitonic states for
chlorophyll dimers while the qsGW-BSE vertical excitation
energies (VEEs) are in excellent agreement with spectroscopic experiments
for chlorophyll monomers and dimers measured in the gas phase. Furthermore,
VEEs from time-dependent density functional theory calculations tend
to disagree with experimental values and using different range-separated
hybrid (RSH) kernels does change the VEEs by up to 0.5 eV. We use
the new qsGW-BSE implementation to calculate the
lowest excitation energies of the six chromophores of the photosystem
II (PSII) reaction center (RC) with nearly 2000 correlated electrons.
Using more than 11,000 (6000) basis functions, the calculation could
be completed in less than 5 (2) days on a single modern compute node.
In agreement with previous TD-DFT calculations using RSH kernels on
models that also do not include environmental effects, our qsGW-BSE calculations only yield states with local characters
in the low-energy spectrum of the hexameric complex. Earlier works
with RSH kernels have demonstrated that the protein environment facilitates
the experimentally observed interchromophoric charge transfer. Therefore,
future research will need to combine correlation effects beyond TD-DFT
with an explicit treatment of environmental electrostatics.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
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8
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Brütting M, Foerster JM, Kümmel S. Investigating Primary Charge Separation in the Reaction Center of Heliobacterium modesticaldum. J Phys Chem B 2021; 125:3468-3475. [PMID: 33788561 DOI: 10.1021/acs.jpcb.0c10283] [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
We compute the primary charge separation step in the homodimeric reaction center (RC) of Heliobacterium modesticaldum from first principles. Using time-dependent density functional theory with the optimally tuned range-separated hybrid functional ωPBE, we calculate the excitations of a system comprising the special pair, the adjacent accessory bacteriochlorophylls, and the most relevant parts of the surrounding protein environment. The structure of the excitation spectrum can be rationalized from coupling of the individual bacteriochlorophyll pigments similar to molecular J- and H-aggregates. We find excited states corresponding to forward-charge transfer along the individual branches of the RC of H. modesticaldum. In the spectrum, these are located at an energy between the coupled Qy and Qx transitions. With ab initio Born-Oppenheimer molecular dynamics simulations, we reveal the influence of thermal vibrations on the excited states. The results show that the energy gap between the coupled Qy and the forward-charge transfer excitations is ∼0.4 eV, which we consider to conflict with the concept of a direct transfer mechanism. Our calculations, however, reveal a certain spectral overlap of the forward-charge transfer and the coupled Qx excitations. The reliability and robustness of the results are demonstrated by several numerical tests.
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Sirohiwal A, Neese F, Pantazis DA. How Can We Predict Accurate Electrochromic Shifts for Biochromophores? A Case Study on the Photosynthetic Reaction Center. J Chem Theory Comput 2021; 17:1858-1873. [PMID: 33566610 PMCID: PMC8023663 DOI: 10.1021/acs.jctc.0c01152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 01/28/2023]
Abstract
Protein-embedded chromophores are responsible for light harvesting, excitation energy transfer, and charge separation in photosynthesis. A critical part of the photosynthetic apparatus are reaction centers (RCs), which comprise groups of (bacterio)chlorophyll and (bacterio)pheophytin molecules that transform the excitation energy derived from light absorption into charge separation. The lowest excitation energies of individual pigments (site energies) are key for understanding photosynthetic systems, and form a prime target for quantum chemistry. A major theoretical challenge is to accurately describe the electrochromic (Stark) shifts in site energies produced by the inhomogeneous electric field of the protein matrix. Here, we present large-scale quantum mechanics/molecular mechanics calculations of electrochromic shifts for the RC chromophores of photosystem II (PSII) using various quantum chemical methods evaluated against the domain-based local pair natural orbital (DLPNO) implementation of the similarity-transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD). We show that certain range-separated density functionals (ωΒ97, ωΒ97X-V, ωΒ2PLYP, and LC-BLYP) correctly reproduce RC site energy shifts with time-dependent density functional theory (TD-DFT). The popular CAM-B3LYP functional underestimates the shifts and is not recommended. Global hybrid functionals are too insensitive to the environment and should be avoided, while nonhybrid functionals are strictly nonapplicable. Among the applicable approximate coupled cluster methods, the canonical versions of CC2 and ADC(2) were found to deviate significantly from the reference results both for the description of the lowest excited state and for the electrochromic shifts. By contrast, their spin-component-scaled (SCS) and particularly the scale-opposite-spin (SOS) variants compare well with the reference DLPNO-STEOM-CCSD and the best range-separated DFT methods. The emergence of RC excitation asymmetry is discussed in terms of intrinsic and protein electrostatic potentials. In addition, we evaluate a minimal structural scaffold of PSII, the D1-D2-CytB559 RC complex often employed in experimental studies, and show that it would have the same site energy distribution of RC chromophores as the full PSII supercomplex, but only under the unlikely conditions that the core protein organization and cofactor arrangement remain identical to those of the intact enzyme.
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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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10
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Montepietra D, Bellingeri M, Ross AM, Scotognella F, Cassi D. Modelling photosystem I as a complex interacting network. J R Soc Interface 2020; 17:20200813. [PMID: 33171073 DOI: 10.1098/rsif.2020.0813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this paper, we model the excitation energy transfer (EET) of photosystem I (PSI) of the common pea plant Pisum sativum as a complex interacting network. The magnitude of the link energy transfer between nodes/chromophores is computed by Forster resonant energy transfer (FRET) using the pairwise physical distances between chromophores from the PDB 5L8R (Protein Data Bank). We measure the global PSI network EET efficiency adopting well-known network theory indicators: the network efficiency (Eff) and the largest connected component (LCC). We also account the number of connected nodes/chromophores to P700 (CN), a new ad hoc measure we introduce here to indicate how many nodes in the network can actually transfer energy to the P700 reaction centre. We find that when progressively removing the weak links of lower EET, the Eff decreases, while the EET paths integrity (LCC and CN) is still preserved. This finding would show that the PSI is a resilient system owning a large window of functioning feasibility and it is completely impaired only when removing most of the network links. From the study of different types of chromophore, we propose different primary functions within the PSI system: chlorophyll a (CLA) molecules are the central nodes in the EET process, while other chromophore types have different primary functions. Furthermore, we perform nodes removal simulations to understand how the nodes/chromophores malfunctioning may affect PSI functioning. We discover that the removal of the CLA triggers the fastest decrease in the Eff, confirming that CAL is the main contributors to the high EET efficiency. Our outcomes open new perspectives of research, such comparing the PSI energy transfer efficiency of different natural and agricultural plant species and investigating the light-harvesting mechanisms of artificial photosynthesis both in plant agriculture and in the field of solar energy applications.
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Affiliation(s)
- D Montepietra
- Dipartimento di Fisica, Università di Modena e Reggio Emilia, via Campi, 213/a, 41125 Modena, Italy.,CNR NANO S3, Via Campi 213/A, 41125 Modena, Italy
| | - M Bellingeri
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, via G.P. Usberti, 7/a, 43124 Parma, Italy.,Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - A M Ross
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - F Scotognella
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.,Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milan, Italy
| | - D Cassi
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, via G.P. Usberti, 7/a, 43124 Parma, Italy
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11
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Sirohiwal A, Neese F, Pantazis DA. Protein Matrix Control of Reaction Center Excitation in Photosystem II. J Am Chem Soc 2020; 142:18174-18190. [PMID: 33034453 PMCID: PMC7582616 DOI: 10.1021/jacs.0c08526] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Indexed: 02/06/2023]
Abstract
Photosystem II (PSII) is a multisubunit pigment-protein complex that uses light-induced charge separation to power oxygenic photosynthesis. Its reaction center chromophores, where the charge transfer cascade is initiated, are arranged symmetrically along the D1 and D2 core polypeptides and comprise four chlorophyll (PD1, PD2, ChlD1, ChlD2) and two pheophytin molecules (PheoD1 and PheoD2). Evolution favored productive electron transfer only via the D1 branch, with the precise nature of primary excitation and the factors that control asymmetric charge transfer remaining under investigation. Here we present a detailed atomistic description for both. We combine large-scale simulations of membrane-embedded PSII with high-level quantum-mechanics/molecular-mechanics (QM/MM) calculations of individual and coupled reaction center chromophores to describe reaction center excited states. We employ both range-separated time-dependent density functional theory and the recently developed domain based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD), the first coupled cluster QM/MM calculations of the reaction center. We find that the protein matrix is exclusively responsible for both transverse (chlorophylls versus pheophytins) and lateral (D1 versus D2 branch) excitation asymmetry, making ChlD1 the chromophore with the lowest site energy. Multipigment calculations show that the protein matrix renders the ChlD1 → PheoD1 charge-transfer the lowest energy excitation globally within the reaction center, lower than any pigment-centered local excitation. Remarkably, no low-energy charge transfer states are located within the "special pair" PD1-PD2, which is therefore excluded as the site of initial charge separation in PSII. Finally, molecular dynamics simulations suggest that modulation of the electrostatic environment due to protein conformational flexibility enables direct excitation of low-lying charge transfer states by far-red light.
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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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12
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Kavanagh MA, Karlsson JKG, Colburn JD, Barter LMC, Gould IR. A TDDFT investigation of the Photosystem II reaction center: Insights into the precursors to charge separation. Proc Natl Acad Sci U S A 2020; 117:19705-19712. [PMID: 32747579 PMCID: PMC7443915 DOI: 10.1073/pnas.1922158117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Photosystem II (PS II) captures solar energy and directs charge separation (CS) across the thylakoid membrane during photosynthesis. The highly oxidizing, charge-separated state generated within its reaction center (RC) drives water oxidation. Spectroscopic studies on PS II RCs are difficult to interpret due to large spectral congestion, necessitating modeling to elucidate key spectral features. Herein, we present results from time-dependent density functional theory (TDDFT) calculations on the largest PS II RC model reported to date. This model explicitly includes six RC chromophores and both the chlorin phytol chains and the amino acid residues <6 Å from the pigments' porphyrin ring centers. Comparing our wild-type model results with calculations on mutant D1-His-198-Ala and D2-His-197-Ala RCs, our simulated absorption-difference spectra reproduce experimentally observed shifts in known chlorophyll absorption bands, demonstrating the predictive capabilities of this model. We find that inclusion of both nearby residues and phytol chains is necessary to reproduce this behavior. Our calculations provide a unique opportunity to observe the molecular orbitals that contribute to the excited states that are precursors to CS. Strikingly, we observe two high oscillator strength, low-lying states, in which molecular orbitals are delocalized over ChlD1 and PheD1 as well as one weaker oscillator strength state with molecular orbitals delocalized over the P chlorophylls. Both these configurations are a match for previously identified exciton-charge transfer states (ChlD1+PheD1-)* and (PD2+PD1-)*. Our results demonstrate the power of TDDFT as a tool, for studies of natural photosynthesis, or indeed future studies of artificial photosynthetic complexes.
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Affiliation(s)
- Maeve A Kavanagh
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
| | - Joshua K G Karlsson
- Molecular Photonics Laboratory, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - Jonathan D Colburn
- School of Chemistry, University of St. Andrews, St. Andrews KY16 9ST, Scotland
| | - Laura M C Barter
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom;
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
| | - Ian R Gould
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom;
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
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Polyakov IV, Khrenova MG, Moskovsky AA, Shabanov BM, Nemukhin AV. Towards first-principles calculation of electronic excitations in the ring of the protein-bound bacteriochlorophylls. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Gelzinis A, Abramavicius D, Ogilvie JP, Valkunas L. Spectroscopic properties of photosystem II reaction center revisited. J Chem Phys 2017; 147:115102. [DOI: 10.1063/1.4997527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Andrius Gelzinis
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Jennifer P. Ogilvie
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Leonas Valkunas
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
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15
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Baker LA, Habershon S. Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport. Proc Math Phys Eng Sci 2017; 473:20170112. [PMID: 28588417 PMCID: PMC5454362 DOI: 10.1098/rspa.2017.0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/04/2017] [Indexed: 02/01/2023] Open
Abstract
Photosynthetic pigment-protein complexes (PPCs) are a vital component of the light-harvesting machinery of all plants and photosynthesizing bacteria, enabling efficient transport of the energy of absorbed light towards the reaction centre, where chemical energy storage is initiated. PPCs comprise a set of chromophore molecules, typically bacteriochlorophyll species, held in a well-defined arrangement by a protein scaffold; this relatively rigid distribution leads to a viewpoint in which the chromophore subsystem is treated as a network, where chromophores represent vertices and inter-chromophore electronic couplings represent edges. This graph-based view can then be used as a framework within which to interrogate the role of structural and electronic organization in PPCs. Here, we use this network-based viewpoint to compare excitation energy transfer (EET) dynamics in the light-harvesting complex II (LHC-II) system commonly found in higher plants and the Fenna-Matthews-Olson (FMO) complex found in green sulfur bacteria. The results of our simple network-based investigations clearly demonstrate the role of network connectivity and multiple EET pathways on the efficient and robust EET dynamics in these PPCs, and highlight a role for such considerations in the development of new artificial light-harvesting systems.
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Affiliation(s)
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK
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16
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Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1627-1640. [PMID: 27372198 DOI: 10.1016/j.bbabio.2016.06.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 01/09/2023]
Abstract
While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
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Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
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Guo Y, Sivalingam K, Valeev EF, Neese F. SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory. J Chem Phys 2016; 144:094111. [DOI: 10.1063/1.4942769] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yang Guo
- Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Kantharuban Sivalingam
- Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24014, USA
| | - Frank Neese
- Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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