1
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Fan JJ, Ou ZY, Zhang Z. Entangled photons enabled ultrafast stimulated Raman spectroscopy for molecular dynamics. LIGHT, SCIENCE & APPLICATIONS 2024; 13:163. [PMID: 39004616 PMCID: PMC11247098 DOI: 10.1038/s41377-024-01492-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 07/16/2024]
Abstract
Quantum entanglement has emerged as a great resource for studying the interactions between molecules and radiation. We propose a new scheme of stimulated Raman scattering with entangled photons. A quantum ultrafast Raman spectroscopy is developed for condensed-phase molecules, to monitor the exciton populations and coherences. Analytic results are obtained, showing an entanglement-enabled time-frequency scale not attainable by classical light. The Raman signal presents an unprecedented selectivity of molecular correlation functions, as a result of the Hong-Ou-Mandel interference. Our work suggests a new paradigm of using an unconventional interferometer as part of spectroscopy, with the potential to unveil advanced information about complex materials.
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Affiliation(s)
- Jiahao Joel Fan
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Zhe-Yu Ou
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
| | - Zhedong Zhang
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen, Guangdong, China.
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2
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Saraceno P, Sardar S, Caferri R, Camargo FVA, Dall'Osto L, D'Andrea C, Bassi R, Cupellini L, Cerullo G, Mennucci B. Probing the Effect of Mutations on Light Harvesting in CP29 by Transient Absorption and First-Principles Simulations. J Phys Chem Lett 2024; 15:6398-6408. [PMID: 38861672 DOI: 10.1021/acs.jpclett.4c01040] [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: 06/13/2024]
Abstract
Natural light harvesting is exceptionally efficient thanks to the local energy funnel created within light-harvesting complexes (LHCs). To understand the design principles underlying energy transport in LHCs, ultrafast spectroscopy is often complemented by mutational studies that introduce perturbations into the excitonic structure of the natural complexes. However, such studies may fall short of identifying all excitation energy transfer (EET) pathways and their changes upon mutation. Here, we show that a synergistic combination of first-principles calculations and ultrafast spectroscopy can give unprecedented insight into the EET pathways occurring within LHCs. We measured the transient absorption spectra of the minor CP29 complex of plants and of two mutants, systematically mapping the kinetic components seen in experiments to the simulated exciton dynamics. With our combined strategy, we show that EET in CP29 is surprisingly robust to the changes in the exciton states induced by mutations, explaining the versatility of plant LHCs.
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Affiliation(s)
- Piermarco Saraceno
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy
| | - Samim Sardar
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy
| | - Roberto Caferri
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Franco V A Camargo
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Luca Dall'Osto
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Cosimo D'Andrea
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy
| | - Giulio Cerullo
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza L. da Vinci 32, 20133 Milano, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy
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3
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Betti E, Saraceno P, Cignoni E, Cupellini L, Mennucci B. Insights into Energy Transfer in Light-Harvesting Complex II Through Machine-Learning Assisted Simulations. J Phys Chem B 2024; 128:5188-5200. [PMID: 38761151 DOI: 10.1021/acs.jpcb.4c01494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Light-harvesting complex II (LHCII) is the major antenna of higher plants. Energy transfer processes taking place inside its aggregate of chlorophylls have been experimentally investigated with time-resolved techniques, but a complete understanding of the most relevant energy transfer pathways and relative characteristic times remains elusive. Theoretical models to disentangle experimental data in LHCII have long been challenged by the large size and complex nature of the system. Here, we show that a fully first-principles approach combining molecular dynamics and machine learning can be successfully used to reproduce transient absorption spectra and characterize the EET pathways and the involved times.
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Affiliation(s)
- Elena Betti
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Piermarco Saraceno
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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4
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Sarngadharan P, Holtkamp Y, Kleinekathöfer U. Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex. J Phys Chem B 2024; 128:5201-5217. [PMID: 38756003 PMCID: PMC11145653 DOI: 10.1021/acs.jpcb.4c01637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
In this study, the site energy fluctuations, energy transfer dynamics, and some spectroscopic properties of the minor light-harvesting complex CP24 in a membrane environment were determined. For this purpose, a 3 μs-long classical molecular dynamics simulation was performed for the CP24 complex. Furthermore, using the density functional tight binding/molecular mechanics molecular dynamics (DFTB/MM MD) approach, we performed excited state calculations for the chlorophyll a and chlorophyll b molecules in the complex starting from five different positions of the MD trajectory. During the extended simulations, we observed variations in the site energies of the different sets as a result of the fluctuating protein environment. In particular, a water coordination to Chl-b 608 occurred only after about 1 μs in the simulations, demonstrating dynamic changes in the environment of this pigment. From the classical and the DFTB/MM MD simulations, spectral densities and the (time-dependent) Hamiltonian of the complex were determined. Based on these results, three independent strongly coupled chlorophyll clusters were revealed within the complex. In addition, absorption and fluorescence spectra were determined together with the exciton relaxation dynamics, which reasonably well agrees with experimental time scales.
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Affiliation(s)
- Pooja Sarngadharan
- School of Science, Constructor
University, Campus Ring
1, 28759 Bremen, Germany
| | - Yannick Holtkamp
- School of Science, Constructor
University, Campus Ring
1, 28759 Bremen, Germany
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5
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Zheng M, Pang X, Chen M, Tian L. Ultrafast energy quenching mechanism of LHCSR3-dependent photoprotection in Chlamydomonas. Nat Commun 2024; 15:4437. [PMID: 38789432 PMCID: PMC11126702 DOI: 10.1038/s41467-024-48789-x] [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: 11/07/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Photosynthetic organisms have evolved an essential energy-dependent quenching (qE) mechanism to avoid any lethal damages caused by high light. While the triggering mechanism of qE has been well addressed, candidates for quenchers are often debated. This lack of understanding is because of the tremendous difficulty in measuring intact cells using transient absorption techniques. Here, we have conducted femtosecond pump-probe measurements to characterize this photophysical reaction using micro-sized cell fractions of the green alga Chlamydomonas reinhardtii that retain physiological qE function. Combined with kinetic modeling, we have demonstrated the presence of an ultrafast excitation energy transfer (EET) pathway from Chlorophyll a (Chl a) Qy to a carotenoid (car) S1 state, therefore proposing that this carotenoid, likely lutein1, is the quencher. This work has provided an easy-to-prepare qE active thylakoid membrane system for advanced spectroscopic studies and demonstrated that the energy dissipation pathway of qE is evolutionarily conserved from green algae to land plants.
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Affiliation(s)
- Mengyuan Zheng
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojie Pang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Chen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Lijin Tian
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Zhao S, Shen L, Li X, Tao Q, Li Z, Xu C, Zhou C, Yang Y, Sang M, Han G, Yu LJ, Kuang T, Shen JR, Wang W. Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana. Nat Commun 2023; 14:8164. [PMID: 38071196 PMCID: PMC10710467 DOI: 10.1038/s41467-023-44055-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.
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Affiliation(s)
- Songhao Zhao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lili Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Xiaoyi Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Qiushuang Tao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Zhenhua Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Caizhe Xu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Mechanical Engineering, Tsinghua University, Beijing, China
| | - Cuicui Zhou
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Yanyan Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Min Sang
- China National Botanical Garden, Beijing, China
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
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7
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Saraceno P, Sláma V, Cupellini L. First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex. J Chem Phys 2023; 159:184112. [PMID: 37962444 DOI: 10.1063/5.0170295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The dynamics of delocalized excitons in light-harvesting complexes (LHCs) can be investigated using different experimental techniques, and transient absorption (TA) spectroscopy is one of the most valuable methods for this purpose. A careful interpretation of TA spectra is essential for the clarification of excitation energy transfer (EET) processes occurring during light-harvesting. However, even in the simplest LHCs, a physical model is needed to interpret transient spectra as the number of EET processes occurring at the same time is very large to be disentangled from measurements alone. Physical EET models are commonly built by fittings of the microscopic exciton Hamiltonians and exciton-vibrational parameters, an approach that can lead to biases. Here, we present a first-principles strategy to simulate EET and transient absorption spectra in LHCs, combining molecular dynamics and accurate multiscale quantum chemical calculations to obtain an independent estimate of the excitonic structure of the complex. The microscopic parameters thus obtained are then used in EET simulations to obtain the population dynamics and the related spectroscopic signature. We apply this approach to the CP29 minor antenna complex of plants for which we follow the EET dynamics and transient spectra after excitation in the chlorophyll b region. Our calculations reproduce all the main features observed in the transient absorption spectra and provide independent insight on the excited-state dynamics of CP29. The approach presented here lays the groundwork for the accurate simulation of EET and unbiased interpretation of transient spectra in multichromophoric systems.
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Affiliation(s)
- Piermarco Saraceno
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Sláma
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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8
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Li Z, Zhou C, Zhao S, Zhang J, Liu X, Sang M, Qin X, Yang Y, Han G, Kuang T, Shen JR, Wang W. Structural and functional properties of different types of siphonous LHCII trimers from an intertidal green alga Bryopsis corticulans. Structure 2023; 31:1247-1258.e3. [PMID: 37633266 DOI: 10.1016/j.str.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/27/2023] [Accepted: 08/01/2023] [Indexed: 08/28/2023]
Abstract
Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms.
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Affiliation(s)
- Zhenhua Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Science, Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Cuicui Zhou
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Science, Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Songhao Zhao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Science, Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jinyang Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Science, Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xueyang Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Science, Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Min Sang
- China National Botanical Garden, Beijing 100093, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Yanyan Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China.
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9
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Novoderezhkin VI. Excitation energy equilibration in a trimeric LHCII complex involves unusual pathways. Phys Chem Chem Phys 2023; 25:26360-26369. [PMID: 37750240 DOI: 10.1039/d3cp02836d] [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: 09/27/2023]
Abstract
We explore the energy equilibration within the LHCII trimer using various approaches, including the Redfield-Förster method (with different compartmentalization schemes) and the exact hierarchical equation of motion (HEOM). We demonstrate that the inter-monomeric migration in the trimeric LHCII complex is not limited to direct transfers between quasi-equilibrated chlorophylls (Chls) a, but also involves additional pathways with uphill transfers from Chls a to the stromal-side Chls b (connecting the Chls a clusters from different monomeric subunits). Although these uphill transfers are slow they still can increase the total rate of inter-monomeric transfers by a factor of 1.5. The same stromal-side Chls b also promote a depopulation of the Chl a604 long-lived state (blue-shifted and mixed with the lumenal-side Chls b). Due to the connection between the stromal- and lumenal-side Chls b clusters the intra- and inter-monomeric transfers from a604 to the main Chls a become faster by a factor of 1.6 and 1.75, respectively.
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Affiliation(s)
- Vladimir I Novoderezhkin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119992, Moscow, Russia.
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10
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Novoderezhkin VI. Resonant vibrations produce quantum bridge over high-energy states in heterogeneous antenna. PHOTOSYNTHESIS RESEARCH 2023; 158:13-21. [PMID: 37584896 DOI: 10.1007/s11120-023-01042-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/29/2023] [Indexed: 08/17/2023]
Abstract
Photosynthetic light-harvesting complexes usually contain several pools of molecules with a big difference in transition energies, for example, chlorophylls a and b in plant antennas. Some pathways of the excitation energy transfer may include pigments from the low-energy pool separated by a site occupied by a high-energy molecule. We demonstrate that such pathways may be functional if high-frequency intramolecular vibrations fall in resonance with the energy gap between the neighboring molecules belonging to different pools. In this case, a vibration-assisted mixing of the excited states can produce delocalized vibronic states playing a role of 'quantum bridge' that facilitates a passage over high-energy barrier. We perform calculations of the excitation dynamics in the model three-state system with the parameters emerging from our previous studies of real antennas. Simulation of the dynamics in an explicit electron-vibrational basis demonstrates that the rate of transfer between the two chlorophylls a through the chlorophyll b intermediate is increased by a factor of 1.7-2 in the presence of resonant vibration. A possible influence of energetic disorder and other (non-resonant) vibrations on this effect is discussed.
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Affiliation(s)
- Vladimir I Novoderezhkin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119992, Moscow, Russia.
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11
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Novoderezhkin VI, Croce R. The location of the low-energy states in Lhca1 favors excitation energy transfer to the core in the plant PSI-LHCI supercomplex. PHOTOSYNTHESIS RESEARCH 2023; 156:59-74. [PMID: 36374368 DOI: 10.1007/s11120-022-00979-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Lhca1 is one of the four pigment-protein complexes composing the outer antenna of plant Photosystem I-light-havesting I supercomplex (PSI-LHCI). It forms a functional dimer with Lhca4 but, differently from this complex, it does not contain 'red-forms,' i.e., pigments absorbing above 700 nm. Interestingly, the recent PSI-LHCI structures suggest that Lhca1 is the main point of delivering the energy harvested by the antenna to the core. To identify the excitation energy pathways in Lhca1, we developed a structure-based exciton model based on the simultaneous fit of the low-temperature absorption, linear dichroism, and fluorescence spectra of wild-type Lhca1 and two mutants, lacking chlorophylls contributing to the long-wavelength region of the absorption. The model enables us to define the locations of the lowest energy pigments in Lhca1 and estimate pathways and timescales of energy transfer within the complex and to the PSI core. We found that Lhca1 has a particular energy landscape with an unusual (compared to Lhca4, LHCII, and CP29) configuration of the low-energy states. Remarkably, these states are located near the core, facilitating direct energy transfer to it. Moreover, the low-energy states of Lhca1 are also coupled to the red-most state (red forms) of the neighboring Lhca4 antenna, providing a pathway for effective excitation energy transfer from Lhca4 to the core.
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Affiliation(s)
- Vladimir I Novoderezhkin
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia.
| | - Roberta Croce
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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12
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Caspy I, Fadeeva M, Mazor Y, Nelson N. Structure of Dunaliella photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes. eLife 2023; 12:e81150. [PMID: 36799903 PMCID: PMC9949808 DOI: 10.7554/elife.81150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
Photosystem II (PSII) generates an oxidant whose redox potential is high enough to enable water oxidation , a substrate so abundant that it assures a practically unlimited electron source for life on earth . Our knowledge on the mechanism of water photooxidation was greatly advanced by high-resolution structures of prokaryotic PSII . Here, we show high-resolution cryogenic electron microscopy (cryo-EM) structures of eukaryotic PSII from the green alga Dunaliella salina at two distinct conformations. The conformers are also present in stacked PSII, exhibiting flexibility that may be relevant to the grana formation in chloroplasts of the green lineage. CP29, one of PSII associated light-harvesting antennae, plays a major role in distinguishing the two conformations of the supercomplex. We also show that the stacked PSII dimer, a form suggested to support the organisation of thylakoid membranes , can appear in many different orientations providing a flexible stacking mechanism for the arrangement of grana stacks in thylakoids. Our findings provide a structural basis for the heterogenous nature of the eukaryotic PSII on multiple levels.
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Affiliation(s)
- Ido Caspy
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
| | - Maria Fadeeva
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
| | - Yuval Mazor
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
- Biodesign Center for Applied Structural Discovery, Arizona State UniversityTempeUnited States
| | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
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13
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Elias E, Liguori N, Croce R. The origin of pigment-binding differences in CP29 and LHCII: the role of protein structure and dynamics. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023:10.1007/s43630-023-00368-7. [PMID: 36740636 DOI: 10.1007/s43630-023-00368-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/13/2023] [Indexed: 02/07/2023]
Abstract
The first step of photosynthesis in plants is performed by the light-harvesting complexes (LHC), a large family of pigment-binding proteins embedded in the photosynthetic membranes. These complexes are conserved across species, suggesting that each has a distinct role. However, they display a high degree of sequence homology and their static structures are almost identical. What are then the structural features that determine their different properties? In this work, we compared the two best-characterized LHCs of plants: LHCII and CP29. Using molecular dynamics simulations, we could rationalize the difference between them in terms of pigment-binding properties. The data also show that while the loops between the helices are very flexible, the structure of the transmembrane regions remains very similar in the crystal and the membranes. However, the small structural differences significantly affect the excitonic coupling between some pigment pairs. Finally, we analyzed in detail the structure of the long N-terminus of CP29, showing that it is structurally stable and it remains on top of the membrane even in the absence of other proteins. Although the structural changes upon phosphorylation are minor, they can explain the differences in the absorption properties of the pigments observed experimentally.
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Affiliation(s)
- Eduard Elias
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Nicoletta Liguori
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Roberta Croce
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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14
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Lin ZH, Chen CS, Zhao SQ, Liu Y, Zhong QS, Ruan QC, Chen ZH, You XM, Shan RY, Li XL, Zhang YZ. Molecular and physiological mechanisms of tea (Camellia sinensis (L.) O. Kuntze) leaf and root in response to nitrogen deficiency. BMC Genomics 2023; 24:27. [PMID: 36650452 PMCID: PMC9847173 DOI: 10.1186/s12864-023-09112-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND As an economically important crop, tea is strongly nitrogen (N)-dependent. However, the physiological and molecular mechanisms underlying the response of N deficiency in tea are not fully understood. Tea cultivar "Chunlv2" [Camellia sinensis (L.) O. Kuntze] were cultured with a nutrient solution with 0 mM [N-deficiency] or 3 mM (Control) NH4NO3 in 6 L pottery pots containing clean river sands. RESULTS N deficiency significantly decreased N content, dry weight, chlorophyll (Chl) content, L-theanine and the activities of N metabolism-related enzymes, but increased the content of total flavonoids and polyphenols in tea leaves. N deficiency delayed the sprouting time of tea buds. By using the RNA-seq technique and subsequent bioinformatics analysis, 3050 up-regulated and 2688 down-regulated differentially expressed genes (DEGs) were isolated in tea leaves in response to N deficiency. However, only 1025 genes were up-regulated and 744 down-regulated in roots. Gene ontology (GO) term enrichment analysis showed that 205 DEGs in tea leaves were enriched in seven GO terms and 152 DEGs in tea roots were enriched in 11 GO items based on P < 0.05. In tea leaves, most GO-enriched DEGs were involved in chlorophyll a/b binding activities, photosynthetic performance, and transport activities. But most of the DEGs in tea roots were involved in the metabolism of carbohydrates and plant hormones with regard to the GO terms of biological processes. N deficiency significantly increased the expression level of phosphate transporter genes, which indicated that N deficiency might impair phosphorus metabolism in tea leaves. Furthermore, some DEGs, such as probable anion transporter 3 and high-affinity nitrate transporter 2.7, might be of great potential in improving the tolerance of N deficiency in tea plants and further study could work on this area in the future. CONCLUSIONS Our results indicated N deficiency inhibited the growth of tea plant, which might be due to altered N metabolism and expression levels of DEGs involved in the photosynthetic performance, transport activity and oxidation-reduction processes.
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Affiliation(s)
- Zheng-He Lin
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Chang-Song Chen
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Shui-Qing Zhao
- Laixi Bureau of Agriculture and Rural Affairs of Shandong Province, Laixi, 266699 China
| | - Yuan Liu
- Laixi Bureau of Agriculture and Rural Affairs of Shandong Province, Laixi, 266699 China
| | - Qiu-Sheng Zhong
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Qi-Chun Ruan
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Zhi-Hui Chen
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Xiao-Mei You
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Rui-Yang Shan
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Xin-Lei Li
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
| | - Ya-Zhen Zhang
- grid.418033.d0000 0001 2229 4212Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu’an, 355000 China
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15
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Kim E, Kubota-Kawai H, Kawai F, Yokono M, Minagawa J. Conformation of Light-Harvesting Complex II Trimer Depends upon Its Binding Site. J Phys Chem B 2022; 126:5855-5865. [PMID: 35920883 DOI: 10.1021/acs.jpcb.2c04061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The light-harvesting complex II (LHCII) trimer in plants functions as a major antenna complex and a quencher to protect it from photooxidative damage. Theoretical studies on the structure of an LHCII trimer have demonstrated that excitation energy transfer between chlorophylls (Chls) in LHCII can be modulated by its exquisite conformational fluctuation. However, conformational changes depending on its binding location have not yet been investigated, even though reorganization of protein complexes occurs by physiological regulations. In this study, we investigated conformational differences in LHCII by comparing published structures of an identical LHCII trimer in the three different photosystem supercomplexes from the green alga Chlamydomonas reinhardtii. Our results revealed distinct differences in Chl configurations as well as polypeptide conformations of the LHCII trimers depending on its binding location. We propose that these configurational differences readily modulate the function of LHCII and possibly lead to a change in excitation-energy flow over the photosynthetic supercomplex.
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Affiliation(s)
- Eunchul Kim
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | | | - Fumihiro Kawai
- Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Makio Yokono
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan
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16
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Li J, Olevano V. Bethe-Salpeter equation insights into the photo-absorption function and exciton structure of chlorophyll a and b in light-harvesting complex II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112475. [PMID: 35644069 DOI: 10.1016/j.jphotobiol.2022.112475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
Abstract
The photo-absorption process and the excitation of chlorophyll (Chl) is the primary and essential step of photosynthesis in green plants. By solving the Bethe-Salpeter equation (BSE) on top of the GW approximation within ab initio many-body perturbation theory, we calculate the photo-absorption function and the excitons structure of Chl a and b in their in vivo conformations as measured by X-ray diffraction in the light-harvesting complex (LHC) II. BSE optical absorption spectra are in good agreement with the experiment and we discuss residual discrepancies. The experimental evidence of multiple Chla forms in vivo is explained by BSE. The Chla and Chlb BSE exciton wavefunctions present important charge-transfer differences on the Soret band. Q excitons are almost identical, apart from charge (both electron and hole) localization on the Chlb C7 aldheide formyl group, absent on the Chla methyl C7, that is exactly the group where the two chlorophylls differ.
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Affiliation(s)
- Jing Li
- Univ. Grenoble Alpes, Grenoble 38000, France; CEA, Leti, Minatec Campus, Grenoble 38054, France; CNRS, Institut Néel, Grenoble 38042, France; ETSF, Nano-Bio-Pharma Spectroscopy group, Grenoble 38000, France.
| | - Valerio Olevano
- Univ. Grenoble Alpes, Grenoble 38000, France; CNRS, Institut Néel, Grenoble 38042, France; ETSF, Nano-Bio-Pharma Spectroscopy group, Grenoble 38000, France.
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17
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Mikalčiūtė A, Gelzinis A, Mačernis M, Büchel C, Robert B, Valkunas L, Chmeliov J. Structure-based model of fucoxanthin-chlorophyll protein complex: Calculations of chlorophyll electronic couplings. J Chem Phys 2022; 156:234101. [PMID: 35732526 DOI: 10.1063/5.0092154] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Diatoms are a group of marine algae that are responsible for a significant part of global oxygen production. Adapted to life in an aqueous environment dominated by the blue-green light, their major light-harvesting antennae-fucoxanthin-chlorophyll protein complexes (FCPs)-exhibit different pigment compositions than of plants. Despite extensive experimental studies, until recently the theoretical description of excitation energy dynamics in these complexes was limited by the lack of high-resolution structural data. In this work, we use the recently resolved crystallographic information of the FCP complex from Phaeodactylum tricornutum diatom [Wang et al., Science 363, 6427 (2019)] and quantum chemistry-based calculations to evaluate the chlorophyll transition dipole moments, atomic transition charges from electrostatic potential, and the inter-chlorophyll couplings in this complex. The obtained structure-based excitonic couplings form the foundation for any modeling of stationary or time-resolved spectroscopic data. We also calculate the inter-pigment Förster energy transfer rates and identify two quickly equilibrating chlorophyll clusters.
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Affiliation(s)
- Austėja Mikalčiūtė
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Andrius Gelzinis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Mindaugas Mačernis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Jevgenij Chmeliov
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
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18
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Sarngadharan P, Maity S, Kleinekathöfer U. Spectral densities and absorption spectra of the core antenna complex CP43 from photosystem II. J Chem Phys 2022; 156:215101. [DOI: 10.1063/5.0091005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities, and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/molecular mechanics molecular dynamics simulations are performed employing the parameterized density functional tight binding (DFTB) while the time-dependent long-range-corrected DFTB scheme is applied for the excited state calculations. The obtained average spectral density of the CP43 complex shows a very good agreement with experimental results. Moreover, the excitonic Hamiltonian of the system along with the computed site-dependent spectral densities was used to determine the linear absorption. While a Redfield-like approximation has severe shortcomings in dealing with the CP43 complex due to quasi-degenerate states, the non-Markovian full second-order cumulant expansion formalism is able to overcome the drawbacks. Linear absorption spectra were obtained, which show a good agreement with the experimental counterparts at different temperatures. This study once more emphasizes that by combining diverse techniques from the areas of molecular dynamics simulations, quantum chemistry, and open quantum systems, it is possible to obtain first-principle results for photosynthetic complexes, which are in accord with experimental findings.
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Affiliation(s)
- Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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19
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Do TN, Nguyen HL, Akhtar P, Zhong K, Jansen TLC, Knoester J, Caffarri S, Lambrev PH, Tan HS. Ultrafast Excitation Energy Transfer Dynamics in the LHCII-CP29-CP24 Subdomain of Plant Photosystem II. J Phys Chem Lett 2022; 13:4263-4271. [PMID: 35522529 DOI: 10.1021/acs.jpclett.2c00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We measure the two-dimensional electronic spectra of the LHCII(M)-CP29-CP24 complex in photosystem II (PSII) and provide the first study of the ultrafast excitation energy transfer (EET) processes of an asymmetric and native light-harvesting assembly of the antenna of PSII. With comparisons to LHCII, we observe faster energy equilibrations in the intermediate levels of the LHCII(M)-CP29-CP24 complex at 662 and 670 nm. Notably, the putative "bottleneck" states in LHCII exhibit faster effective dynamics in the LHCII(M)-CP24-CP29 complex, with the average lifetime shortening from 2.5 ps in LHCII to 1.2 ps in the bigger assembly. The observations are supported by high-level structure-based calculations, and the accelerated dynamics can be attributed to the structural change of LHCII(M) in the bigger complex. This study shows that the biological functioning structures of the complexes are important to understand the overall EET dynamics of the PSII supercomplex.
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Affiliation(s)
- Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Parveen Akhtar
- Biological Research Center, Szeged, Temesvári körút 62, Szeged 6726, Hungary
- ELI-ALPS, ELI-HU Nonprofit Limited, Wolfgang Sandner utca 3, Szeged 6728, Hungary
| | - Kai Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Jasper Knoester
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Stefano Caffarri
- Aix Marseille Université, CEA, CNRS, BIAM, LGBP, 13009 Marseille, France
| | - Petar H Lambrev
- Biological Research Center, Szeged, Temesvári körút 62, Szeged 6726, Hungary
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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20
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Violaxanthin and Zeaxanthin May Replace Lutein at the L1 Site of LHCII, Conserving the Interactions with Surrounding Chlorophylls and the Capability of Triplet-Triplet Energy Transfer. Int J Mol Sci 2022; 23:ijms23094812. [PMID: 35563202 PMCID: PMC9105099 DOI: 10.3390/ijms23094812] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
Carotenoids represent the first line of defence of photosystems against singlet oxygen (1O2) toxicity, because of their capacity to quench the chlorophyll triplet state (3Chl) through a physical mechanism based on the transfer of triplet excitation (triplet-triplet energy transfer, TTET). In previous works, we showed that the antenna LHCII is characterised by a robust photoprotective mechanism, able to adapt to the removal of individual chlorophylls while maintaining a remarkable capacity for 3Chl quenching. In this work, we investigated the effects on this quenching induced in LHCII by the replacement of the lutein bound at the L1 site with violaxanthin and zeaxanthin. We studied LHCII isolated from the Arabidopsis thaliana mutants lut2-in which lutein is replaced by violaxanthin-and lut2 npq2, in which all xanthophylls are replaced constitutively by zeaxanthin. We characterised the photophysics of these systems via optically detected magnetic resonance (ODMR) and time-resolved electron paramagnetic resonance (TR-EPR). We concluded that, in LHCII, lutein-binding sites have conserved characteristics, and ensure efficient TTET regardless of the identity of the carotenoid accommodated.
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21
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Zhu R, Ruan M, Li H, Leng X, Zou J, Wang J, Chen H, Wang Z, Weng Y. Vibrational and vibronic coherences in the energy transfer process of light-harvesting complex II revealed by two-dimensional electronic spectroscopy. J Chem Phys 2022; 156:125101. [DOI: 10.1063/5.0082280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The presence of quantum coherence in light-harvesting complex II (LHCII) as a mechanism to understand the efficiency of the light-harvesting function in natural photosynthetic systems is still debated due to its structural complexity and weak-amplitude coherent oscillations. Here, we revisit the coherent dynamics and clarify different types of coherences in the energy transfer processes of LHCII using a joint method of the high-S/N transient grating and two-dimensional electronic spectroscopy. We find that the electronic coherence decays completely within 50 fs at room temperature. The vibrational coherences of chlorophyll a dominate over oscillations within 1 ps, whereas a low-frequency mode of 340 cm−1 with a vibronic mixing character may participate in vibrationally assisted energy transfer between chlorophylls a. Our results may suggest that vibronic mixing is relevant for rapid energy transfer processes among chlorophylls in LHCII.
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Affiliation(s)
- Ruidan Zhu
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meixia Ruan
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Li
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Leng
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiading Zou
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayu Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailong Chen
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Zhuan Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuxiang Weng
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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22
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ZHU ZHE, Higashi M, Saito S. Excited states of chlorophyll a and b in solution by time-dependent density functional theory. J Chem Phys 2022; 156:124111. [DOI: 10.1063/5.0083395] [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
The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in functionals. Here, we optimize the range-separated parameter, µ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of µ for Chl a and Chl b are smaller than the default value of µ and that for bacteriochlorophyll a, indicating the change in electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.
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Affiliation(s)
| | - Masahiro Higashi
- Department of Molecular Engineering, Kyoto University - Katsura Campus, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
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23
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Ruban A, Saccon F. Chlorophyll a De-Excitation Pathways in the LHCII antenna. J Chem Phys 2022; 156:070902. [DOI: 10.1063/5.0073825] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alexander Ruban
- SBBS, Queen Mary University of London - Mile End Campus, United Kingdom
| | - Francesco Saccon
- School of Biological and Chemical Sciences, Queen Mary University of London - Mile End Campus, United Kingdom
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24
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Son M, Moya R, Pinnola A, Bassi R, Schlau-Cohen GS. Protein-Protein Interactions Induce pH-Dependent and Zeaxanthin-Independent Photoprotection in the Plant Light-Harvesting Complex, LHCII. J Am Chem Soc 2021; 143:17577-17586. [PMID: 34648708 DOI: 10.1021/jacs.1c07385] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plants use energy from the sun yet also require protection against the generation of deleterious photoproducts from excess energy. Photoprotection in green plants, known as nonphotochemical quenching (NPQ), involves thermal dissipation of energy and is activated by a series of interrelated factors: a pH drop in the lumen, accumulation of the carotenoid zeaxanthin (Zea), and formation of arrays of pigment-containing antenna complexes. However, understanding their individual contributions and their interactions has been challenging, particularly for the antenna arrays, which are difficult to manipulate in vitro. Here, we achieved systematic and discrete control over the array size for the principal antenna complex, light-harvesting complex II, using near-native in vitro membranes called nanodiscs. Each of the factors had a distinct influence on the level of dissipation, which was characterized by measurements of fluorescence quenching and ultrafast chlorophyll-to-carotenoid energy transfer. First, an increase in array size led to a corresponding increase in dissipation; the dramatic changes in the chlorophyll dynamics suggested that this is due to an allosteric conformational change of the protein. Second, a pH drop increased dissipation but exclusively in the presence of protein-protein interactions. Third, no Zea dependence was identified which suggested that Zea regulates a distinct aspect of NPQ. Collectively, these results indicate that each factor provides a separate type of control knob for photoprotection, which likely enables a flexible and tunable response to solar fluctuations.
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Affiliation(s)
- Minjung Son
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Raymundo Moya
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alberta Pinnola
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Roberto Bassi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy.,Accademia Nazionale di Lincei, 00165 Rome, Italy
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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25
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Arsenault EA, Schile AJ, Limmer DT, Fleming GR. Vibronic coupling in light-harvesting complex II revisited. J Chem Phys 2021; 155:096101. [PMID: 34496581 DOI: 10.1063/5.0056478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eric A Arsenault
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Addison J Schile
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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26
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Elias E, Liguori N, Saga Y, Schäfers J, Croce R. Harvesting Far-Red Light with Plant Antenna Complexes Incorporating Chlorophyll d. Biomacromolecules 2021; 22:3313-3322. [PMID: 34269578 PMCID: PMC8356222 DOI: 10.1021/acs.biomac.1c00435] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/28/2021] [Indexed: 11/28/2022]
Abstract
Increasing the absorption cross section of plants by introducing far-red absorbing chlorophylls (Chls) has been proposed as a strategy to boost crop yields. To make this strategy effective, these Chls should bind to the photosynthetic complexes without altering their functional architecture. To investigate if plant-specific antenna complexes can provide the protein scaffold to accommodate these Chls, we have reconstituted the main light-harvesting complex (LHC) of plants LHCII in vitro and in silico, with Chl d. The results demonstrate that LHCII can bind Chl d in a number of binding sites, shifting the maximum absorption ∼25 nm toward the red with respect to the wild-type complex (LHCII with Chl a and b) while maintaining the native LHC architecture. Ultrafast spectroscopic measurements show that the complex is functional in light harvesting and excitation energy transfer. Overall, we here demonstrate that it is possible to obtain plant LHCs with enhanced far-red absorption and intact functional properties.
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Affiliation(s)
- Eduard Elias
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Nicoletta Liguori
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Yoshitaka Saga
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
- Department
of Chemistry, Faculty of Science and Engineering, Kindai University, Higashi-Osaka 577-8502, Osaka, Japan
| | - Judith Schäfers
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Roberta Croce
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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27
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Pan X, Tokutsu R, Li A, Takizawa K, Song C, Murata K, Yamasaki T, Liu Z, Minagawa J, Li M. Structural basis of LhcbM5-mediated state transitions in green algae. NATURE PLANTS 2021; 7:1119-1131. [PMID: 34239095 DOI: 10.1038/s41477-021-00960-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/03/2021] [Indexed: 05/10/2023]
Abstract
In green algae and plants, state transitions serve as a short-term light-acclimation process in the regulation of the light-harvesting capacity of photosystems I and II (PSI and PSII, respectively). During the process, a portion of light-harvesting complex II (LHCII) is phosphorylated, dissociated from PSII and binds with PSI to form the supercomplex PSI-LHCI-LHCII. Here, we report high-resolution structures of PSI-LHCI-LHCII from Chlamydomonas reinhardtii, revealing the mechanism of assembly between the PSI-LHCI complex and two phosphorylated LHCII trimers containing all four types of LhcbM protein. Two specific LhcbM isoforms, namely LhcbM1 and LhcbM5, directly interact with the PSI core through their phosphorylated amino terminal regions. Furthermore, biochemical and functional studies on mutant strains lacking either LhcbM1 or LhcbM5 indicate that only LhcbM5 is indispensable in supercomplex formation. The results unravel the specific interactions and potential excitation energy transfer routes between green algal PSI and two phosphorylated LHCIIs.
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Affiliation(s)
- Xiaowei Pan
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Science, Capital Normal University, Beijing, China
| | - Ryutaro Tokutsu
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Department of Basic Biology, School of Life Science, the Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
| | - Anjie Li
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kenji Takizawa
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Astrobiology Centre, National Institutes of Natural Sciences, Mitaka, Japan
| | - Chihong Song
- Exploratory Research Centre on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuyoshi Murata
- Exploratory Research Centre on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Tomohito Yamasaki
- Science and Technology Department, Natural Science Cluster, Kochi University, Kochi, Japan
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Jun Minagawa
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.
- Department of Basic Biology, School of Life Science, the Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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28
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Maity S, Daskalakis V, Elstner M, Kleinekathöfer U. Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II. Phys Chem Chem Phys 2021; 23:7407-7417. [PMID: 33876100 DOI: 10.1039/d1cp01011e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light-Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born-Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. To the best of our knowledge, this is the first theoretical attempt on this large complex system is ever made to accurately simulate the spectral density. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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29
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Ishizaki A, Fleming GR. Insights into Photosynthetic Energy Transfer Gained from Free-Energy Structure: Coherent Transport, Incoherent Hopping, and Vibrational Assistance Revisited. J Phys Chem B 2021; 125:3286-3295. [PMID: 33724833 DOI: 10.1021/acs.jpcb.0c09847] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Giant strides in ultrashort laser pulse technology have enabled real-time observation of dynamical processes in complex molecular systems. Specifically, the discovery of oscillatory transients in the two-dimensional electronic spectra of photosynthetic systems stimulated a number of theoretical investigations exploring the possible physical mechanisms of the remarkable quantum efficiency of light harvesting processes. In this work, we revisit the elementary aspects of environment-induced fluctuations in the involved electronic energies and present a simple way to understand energy flow with the intuitive picture of relaxation in a funnel-type free-energy landscape. The presented free-energy description of energy transfer reveals that typical photosynthetic systems operate in an almost barrierless regime. The approach also provides insights into the distinction between coherent and incoherent energy transfer and the criteria by which the necessity of the vibrational assistance is considered.
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Affiliation(s)
- Akihito Ishizaki
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan.,School of Physical Sciences, Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Kavli Energy NanoSciences Institute at Berkeley, Berkeley, California 94720, United States
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30
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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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31
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Nguyen HL, Do TN, Akhtar P, Jansen TLC, Knoester J, Wang W, Shen JR, Lambrev PH, Tan HS. An Exciton Dynamics Model of Bryopsis corticulans Light-Harvesting Complex II. J Phys Chem B 2021; 125:1134-1143. [PMID: 33478222 DOI: 10.1021/acs.jpcb.0c10634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bryopsis corticulans is a marine green macroalga adapted to the intertidal environment. It possesses siphonaxanthin-binding light-harvesting complexes of photosystem II (LHCII) with spectroscopic properties markedly different from the LHCII in plants. By applying a phenomenological fitting procedure to the two-dimensional electronic spectra of the LHCII from B. corticulans measured at 77 K, we can extract information about the excitonic states and energy-transfer processes. The fitting method results in well-converged parameters, including excitonic energy levels with their respective transition dipole moments, spectral widths, energy-transfer rates, and coupling properties. The 2D spectra simulated from the fitted parameters concur very well with the experimental data, showing the robustness of the fitting method. An excitonic energy-transfer scheme can be constructed from the fitting parameters. It shows the rapid energy transfer from chlorophylls (Chls) b to a at subpicosecond time scales and a long-lived state in the Chl b region at around 659 nm. Three weakly connected terminal states are resolved at 671, 675, and 677 nm. The lowest state is higher in energy than that in plant LHCII, which is probably because of the fewer number of Chls a in a B. corticulans LHCII monomer. Modeling based on existing Hamiltonians for the plant LHCII structure with two Chls a switched to Chls b suggests several possible Chl a-b replacements in comparison with those of plant LHCII. The adaptive changes result in a slower energy equilibration in the complex, revealed by the longer relaxation times of several exciton states compared to those of plant LHCII. The strength of our phenomenological fitting method for obtaining excitonic energy levels and energy-transfer network is put to the test in systems such as B. corticulans LHCII, where prior knowledge on exact assignment and spatial locations of pigments are lacking.
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Affiliation(s)
- Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371.,University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Parveen Akhtar
- Biological Research Center, Szeged, Temesvári Körút 62, Szeged 6726, Hungary.,ELI-ALPS, ELI-HU Nonprofit Ltd., Budapesti út 5, Szeged 6728, Hungary
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jasper Knoester
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.,Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8350, Japan
| | - Petar H Lambrev
- Biological Research Center, Szeged, Temesvári Körút 62, Szeged 6726, Hungary
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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32
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Gelzinis A, Augulis R, Büchel C, Robert B, Valkunas L. Confronting FCP structure with ultrafast spectroscopy data: evidence for structural variations. Phys Chem Chem Phys 2021; 23:806-821. [PMID: 33427836 DOI: 10.1039/d0cp05578f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diatoms are a major group of algae, responsible for a quarter of the global primary production on our planet. Their adaptation to marine environments is ensured by their light-harvesting antenna - the fucoxanthin-chlorophyll protein (FCP) complex, which absorbs strongly in the blue-green spectral region. Although these essential proteins have been the subject of many studies, for a long time their comprehensive description was not possible in the absence of structural data. Last year, the 3D structures of several FCP complexes were revealed. The structure of an FCP dimer was resolved by crystallography for the pennate diatom Phaeodactylum tricornutum [W. Wang et al., Science, 2019, 363, 6427] and the structure of the PSII supercomplex from the centric diatom Chaetoceros gracilis, containing several FCPs, was obtained by electron microscopy [X. Pi et al., Science, 2019, 365, 6452; R. Nagao et al., Nat. Plants, 2019, 5, 890]. In this Perspective article, we evaluate how precisely these structures may account for previously published ultrafast spectroscopy results, describing the excitation energy transfer in the FCP from another centric diatom Cyclotella meneghiniana. Surprisingly, we find that the published FCP structures cannot explain several observations obtained from ultrafast spectroscopy. Using the available structures, and results from electron microscopy, we construct a trimer-based FCP model for Cyclotella meneghiniana, consistent with ultrafast experimental data. As a whole, our observations suggest that the structures from the proteins belonging to the FCP family display larger variations than the equivalent LHC proteins in plants, which may reflect species-specific adaptations or original strategies for adapting to rapidly changing marine environments.
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Affiliation(s)
- Andrius Gelzinis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania. and Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
| | - Ramūnas Augulis
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straβe 9, 60438 Frankfurt, Germany
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania. and Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
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33
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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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34
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The role of mixed vibronic Q y-Q x states in green light absorption of light-harvesting complex II. Nat Commun 2020; 11:6011. [PMID: 33243997 PMCID: PMC7691517 DOI: 10.1038/s41467-020-19800-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/27/2020] [Indexed: 11/24/2022] Open
Abstract
The importance of green light for driving natural photosynthesis has long been underappreciated, however, under the presence of strong illumination, green light actually drives photosynthesis more efficiently than red light. This green light is absorbed by mixed vibronic Qy-Qx states, arising from chlorophyll (Chl)-Chl interactions, although almost nothing is known about these states. Here, we employ polarization-dependent two-dimensional electronic-vibrational spectroscopy to study the origin and dynamics of the mixed vibronic Qy-Qx states of light-harvesting complex II. We show the states in this region dominantly arise from Chl b and demonstrate how it is possible to distinguish between the degree of vibronic Qy versus Qx character. We find that the dynamics for states of predominately Chl b Qy versus Chl b Qx character are markedly different, as excitation persists for significantly longer in the Qx states and there is an oscillatory component to the Qx dynamics, which is discussed. Our findings demonstrate the central role of electronic-nuclear mixing in efficient light-harvesting and the different functionalities of Chl a and Chl b. The green component of the solar spectrum can efficiently drive natural photosynthesis, but the process has been little investigated due to the complexity of the excited states involved. Here the authors utilize polarization-dependent two-dimensional electronic-vibrational spectroscopy to define the origin and dynamics of these states in light-harvesting complex II.
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35
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Saccon F, Durchan M, Polívka T, Ruban AV. The robustness of the terminal emitter site in major LHCII complexes controls xanthophyll function during photoprotection. Photochem Photobiol Sci 2020; 19:1308-1318. [PMID: 32815966 DOI: 10.1039/d0pp00174k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Xanthophylls in light harvesting complexes perform a number of functions ranging from structural support to light-harvesting and photoprotection. In the major light harvesting complex of photosystem II in plants (LHCII), the innermost xanthophyll binding pockets are occupied by lutein molecules. The conservation of these sites within the LHC protein family suggests their importance in LHCII functionality. In the present work, we induced the photoprotective switch in LHCII isolated from the Arabidopsis mutant npq1lut2, where the lutein molecules are exchanged with violaxanthin. Despite the differences in the energetics of the pigments and the impairment of chlorophyll fluorescence quenching in vivo, we show that isolated complexes containing violaxanthin are still able to induce the quenching switch to a similar extent to wild type LHCII monomers. Moreover, the same spectroscopic changes take place, which suggest the involvement of the terminal emitter site (L1) in energy dissipation in both complexes. These results indicate the robust nature of the L1 xanthophyll binding domain in LHCII, where protein structural cues are the major determinant of the function of the bound carotenoid.
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Affiliation(s)
- Francesco Saccon
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road E1 4NS, London, UK.
| | - Milan Durchan
- University of South Bohemia, Institute of Physics, Faculty of Science, České Budějovice, Czech Republic
| | - Tomáš Polívka
- University of South Bohemia, Institute of Physics, Faculty of Science, České Budějovice, Czech Republic
| | - Alexander V Ruban
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road E1 4NS, London, UK.
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36
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Cupellini L, Lipparini F, Cao J. Absorption and Circular Dichroism Spectra of Molecular Aggregates With the Full Cumulant Expansion. J Phys Chem B 2020; 124:8610-8617. [PMID: 32901476 PMCID: PMC7901647 DOI: 10.1021/acs.jpcb.0c05180] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The exciton Hamiltonian of multichromophoric aggregates can be probed by spectroscopic
techniques such as linear absorption and circular dichroism. To compare calculated
Hamiltonians to experiments, a lineshape theory is needed, which takes into account the
coupling of the excitons with inter- and intramolecular vibrations. This coupling is
normally introduced in a perturbative way through the cumulant expansion formalism and
further approximated by assuming a Markovian exciton dynamics, for example with the
modified Redfield theory. Here, we present the implementation of the full cumulant
expansion (FCE) formalism (142, 2015, 09410625747060) to
efficiently compute absorption and circular dichroism spectra of molecular aggregates
beyond the Markov approximation, without restrictions on the form of
exciton–phonon coupling. By employing the LH2 system of purple bacteria as a
challenging test case, we compare the FCE lineshapes with the Markovian lineshapes
obtained with the modified Redfield theory, showing that the latter presents a less
satisfying agreement with experiments. The FCE approach instead accurately describes the
lineshapes, especially in the vibronic sideband of the B800 peak. We envision that the
FCE approach will become a valuable tool for accurately comparing model exciton
Hamiltonians with optical spectroscopy experiments.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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37
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Agostini A, Büchel C, Di Valentin M, Carbonera D. A distinctive pathway for triplet-triplet energy transfer photoprotection in fucoxanthin chlorophyll-binding proteins from Cyclotella meneghiniana. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148310. [PMID: 32991847 DOI: 10.1016/j.bbabio.2020.148310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 11/29/2022]
Abstract
Fucoxanthin chlorophyll-binding proteins (FCPs) are the major light-harvesting complexes of diatoms. In this work, FCPs isolated from Cyclotella meneghiniana have been studied by means of optically detected magnetic resonance (ODMR) and time-resolved electron paramagnetic resonance (TR-EPR), with the aim to characterize the photoprotective mechanism based on triplet-triplet energy transfer (TTET). The spectroscopic properties of the chromophores carrying the triplet state have been interpreted on the basis of a delved analysis of the recently solved crystallographic structures of FCP. The results point toward a photoprotective role for two fucoxanthin molecules exposed to the exterior of the FCP monomers. This shows that FCP has adopted a structural strategy different from that of related light-harvesting complexes from plants and other microalgae, in which the photoprotective role is carried out by two highly conserved carotenoids in the interior of the complex.
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Affiliation(s)
- Alessandro Agostini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
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Artes Vivancos JM, van Stokkum IHM, Saccon F, Hontani Y, Kloz M, Ruban A, van Grondelle R, Kennis JTM. Unraveling the Excited-State Dynamics and Light-Harvesting Functions of Xanthophylls in Light-Harvesting Complex II Using Femtosecond Stimulated Raman Spectroscopy. J Am Chem Soc 2020; 142:17346-17355. [PMID: 32878439 PMCID: PMC7564077 DOI: 10.1021/jacs.0c04619] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Photosynthesis
in plants starts with the capture of photons by
light-harvesting complexes (LHCs). Structural biology and spectroscopy
approaches have led to a map of the architecture and energy transfer
pathways between LHC pigments. Still, controversies remain regarding
the role of specific carotenoids in light-harvesting and photoprotection,
obligating the need for high-resolution techniques capable of identifying
excited-state signatures and molecular identities of the various pigments
in photosynthetic systems. Here we demonstrate the successful application
of femtosecond stimulated Raman spectroscopy (FSRS) to a multichromophoric
biological complex, trimers of LHCII. We demonstrate the application
of global and target analysis (GTA) to FSRS data and utilize it to
quantify excitation migration in LHCII trimers. This powerful combination
of techniques allows us to obtain valuable insights into structural,
electronic, and dynamic information from the carotenoids of LHCII
trimers. We report spectral and dynamical information on ground- and
excited-state vibrational modes of the different pigments, resolving
the vibrational relaxation of the carotenoids and the pathways of
energy transfer to chlorophylls. The lifetimes and spectral characteristics
obtained for the S1 state confirm that lutein 2 has a distorted conformation
in LHCII and that the lutein 2 S1 state does not transfer to chlorophylls,
while lutein 1 is the only carotenoid whose S1 state plays a significant
energy-harvesting role. No appreciable energy transfer takes place
from lutein 1 to lutein 2, contradicting recent proposals regarding
the functions of the various carotenoids (Son et al. Chem.2019, 5 (3), 575–584). Also, our results demonstrate that FSRS can be used in combination
with GTA to simultaneously study the electronic and vibrational landscapes
in LHCs and pave the way for in-depth studies of photoprotective conformations
in photosynthetic systems.
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Affiliation(s)
- Juan M Artes Vivancos
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.,Department of Chemistry, Kennedy College of Science, University of Massachusetts-Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Ivo H M van Stokkum
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Francesco Saccon
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road/E1 4NS London, U.K
| | - Yusaku Hontani
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Miroslav Kloz
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Alexander Ruban
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road/E1 4NS London, U.K
| | - Rienk van Grondelle
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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39
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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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40
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Bhattacharyya P, Fleming GR. The role of resonant nuclear modes in vibrationally assisted energy transport: The LHCII complex. J Chem Phys 2020; 153:044119. [DOI: 10.1063/5.0012420] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Pallavi Bhattacharyya
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
- Kavli Energy Nanosciences Institute at Berkeley, Berkeley, California 94720, USA
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41
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Sláma V, Cupellini L, Mennucci B. Exciton properties and optical spectra of light harvesting complex II from a fully atomistic description. Phys Chem Chem Phys 2020; 22:16783-16795. [PMID: 32662461 DOI: 10.1039/d0cp02492a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a fully atomistic simulation of linear optical spectra (absorption, fluorescence and circular dichroism) of the Light Harvesting Complex II (LHCII) trimer using a hybrid approach, which couples a quantum chemical description of the chlorophylls with a classical model for the protein and the external environment (membrane and water). The classical model uses a polarizable Molecular Mechanics force field, thus allowing mutual polarization effects in the calculations of the excitonic properties. The investigation is performed both on the crystal structure and on structures generated by a μs long classical molecular dynamics simulation of the complex within a solvated membrane. The results show that this integrated approach not only provides a good description of the excitonic properties and optical spectra without the need for additional refinements of the excitonic parameters, but it also allows an atomistic investigation of the relative importance of electronic, structural and environment effects in determining the optical spectra.
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Affiliation(s)
- Vladislav Sláma
- Department of Chemistry and Industrial Chemistry, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy.
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42
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Leng X, Do TN, Akhtar P, Nguyen HL, Lambrev PH, Tan H. Hierarchical Equations of Motion Simulation of Temperature‐Dependent Two‐Dimensional Electronic Spectroscopy of the ChlorophyllaManifold in LHCII. Chem Asian J 2020; 15:1996-2004. [DOI: 10.1002/asia.202000467] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/11/2020] [Indexed: 01/12/2023]
Affiliation(s)
- Xuan Leng
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Parveen Akhtar
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
- Biological Research Centre Szeged Temesvári körút 62 Szeged 6726 Hungary
- ELI-ALPS, ELI-HU Nonprofit Ltd. Wolfgang Sandner utca 3 Szeged 6728 Hungary
| | - Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Petar H. Lambrev
- Biological Research Centre Szeged Temesvári körút 62 Szeged 6726 Hungary
| | - Howe‐Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
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43
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Ostroumov EE, Götze JP, Reus M, Lambrev PH, Holzwarth AR. Characterization of fluorescent chlorophyll charge-transfer states as intermediates in the excited state quenching of light-harvesting complex II. PHOTOSYNTHESIS RESEARCH 2020; 144:171-193. [PMID: 32307623 DOI: 10.1007/s11120-020-00745-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/31/2020] [Indexed: 05/20/2023]
Abstract
Light-harvesting complex II (LHCII) is the major antenna complex in higher plants and green algae. It has been suggested that a major part of the excited state energy dissipation in the so-called "non-photochemical quenching" (NPQ) is located in this antenna complex. We have performed an ultrafast kinetics study of the low-energy fluorescent states related to quenching in LHCII in both aggregated and the crystalline form. In both sample types the chlorophyll (Chl) excited states of LHCII are strongly quenched in a similar fashion. Quenching is accompanied by the appearance of new far-red (FR) fluorescence bands from energetically low-lying Chl excited states. The kinetics of quenching, its temperature dependence down to 4 K, and the properties of the FR-emitting states are very similar both in LHCII aggregates and in the crystal. No such FR-emitting states are found in unquenched trimeric LHCII. We conclude that these states represent weakly emitting Chl-Chl charge-transfer (CT) states, whose formation is part of the quenching process. Quantum chemical calculations of the lowest energy exciton and CT states, explicitly including the coupling to the specific protein environment, provide detailed insight into the chemical nature of the CT states and the mechanism of CT quenching. The experimental data combined with the results of the calculations strongly suggest that the quenching mechanism consists of a sequence of two proton-coupled electron transfer steps involving the three quenching center Chls 610/611/612. The FR-emitting CT states are reaction intermediates in this sequence. The polarity-controlled internal reprotonation of the E175/K179 aa pair is suggested as the switch controlling quenching. A unified model is proposed that is able to explain all known conditions of quenching or non-quenching of LHCII, depending on the environment without invoking any major conformational changes of the protein.
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Affiliation(s)
- Evgeny E Ostroumov
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim a. d. Ruhr, Germany
- Quantum Matter Institute, University of British Columbia, 2355 East Mall, Vancouver, V6T 1Z1, Canada
| | - Jan P Götze
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim a. d. Ruhr, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Michael Reus
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim a. d. Ruhr, Germany
| | - Petar H Lambrev
- Biological Research Centre, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Alfred R Holzwarth
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim a. d. Ruhr, Germany.
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44
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Liguori N, Croce R, Marrink SJ, Thallmair S. Molecular dynamics simulations in photosynthesis. PHOTOSYNTHESIS RESEARCH 2020; 144:273-295. [PMID: 32297102 PMCID: PMC7203591 DOI: 10.1007/s11120-020-00741-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.
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Affiliation(s)
- Nicoletta Liguori
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Roberta Croce
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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45
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Arsenault EA, Yoneda Y, Iwai M, Niyogi KK, Fleming GR. Vibronic mixing enables ultrafast energy flow in light-harvesting complex II. Nat Commun 2020; 11:1460. [PMID: 32193383 PMCID: PMC7081214 DOI: 10.1038/s41467-020-14970-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/12/2020] [Indexed: 11/09/2022] Open
Abstract
Since the discovery of quantum beats in the two-dimensional electronic spectra of photosynthetic pigment-protein complexes over a decade ago, the origin and mechanistic function of these beats in photosynthetic light-harvesting has been extensively debated. The current consensus is that these long-lived oscillatory features likely result from electronic-vibrational mixing, however, it remains uncertain if such mixing significantly influences energy transport. Here, we examine the interplay between the electronic and nuclear degrees of freedom (DoF) during the excitation energy transfer (EET) dynamics of light-harvesting complex II (LHCII) with two-dimensional electronic-vibrational spectroscopy. Particularly, we show the involvement of the nuclear DoF during EET through the participation of higher-lying vibronic chlorophyll states and assign observed oscillatory features to specific EET pathways, demonstrating a significant step in mapping evolution from energy to physical space. These frequencies correspond to known vibrational modes of chlorophyll, suggesting that electronic-vibrational mixing facilitates rapid EET over moderately size energy gaps.
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Affiliation(s)
- Eric A Arsenault
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Yoneda
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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46
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Excitation dynamics and relaxation in the major antenna of a marine green alga Bryopsis corticulans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148186. [PMID: 32171793 DOI: 10.1016/j.bbabio.2020.148186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/24/2020] [Accepted: 03/09/2020] [Indexed: 11/20/2022]
Abstract
The light-harvesting complexes II (LHCIIs) of spinach and Bryopsis corticulans as a green alga are similar in structure, but differ in carotenoid (Car) and chlorophyll (Chl) compositions. Carbonyl Cars siphonein (Spn) and siphonaxanthin (Spx) bind to B. corticulans LHCII likely in the sites as a pair of lutein (Lut) molecules bind to spinach LHCII in the central domain. To understand the light-harvesting and photoprotective properties of the algal LHCII, we compared its excitation dynamics and relaxation to those of spinach LHCII been well documented. It was found that B. corticulans LHCII exhibited a substantially longer chlorophyll (Chl) fluorescence lifetime (4.9 ns vs 4.1 ns) and a 60% increase of the fluorescence quantum yield. Photoexcitation populated 3Car* equally between Spn and Spx in B. corticulans LHCII, whereas predominantly at Lut620 in spinach LHCII. These results prove the functional differences of the LHCIIs with different Car pairs and Chl a/b ratios: B. corticulans LHCII shows the enhanced blue-green light absorption, the alleviated quenching of 1Chl*, and the dual sites of quenching 3Chl*, which may facilitate its light-harvesting and photoprotection functions. Moreover, for both types of LHCIIs, the triplet excitation profiles revealed the involvement of extra 3Car* formation mechanisms besides the conventional Chl-to-Car triplet transfer, which are discussed in relation to the ultrafast processes of 1Chl* quenching. Our experimental findings will be helpful in deepening the understanding of the light harvesting and photoprotection functions of B. corticulans living in the intertidal zone with dramatically changing light condition.
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Mascoli V, Novoderezhkin V, Liguori N, Xu P, Croce R. Design principles of solar light harvesting in plants: Functional architecture of the monomeric antenna CP29. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148156. [DOI: 10.1016/j.bbabio.2020.148156] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/13/2019] [Accepted: 01/22/2020] [Indexed: 11/16/2022]
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48
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Do TN, Huerta-Viga A, Akhtar P, Nguyen HL, Nowakowski PJ, Khyasudeen MF, Lambrev PH, Tan HS. Revealing the excitation energy transfer network of Light-Harvesting Complex II by a phenomenological analysis of two-dimensional electronic spectra at 77 K. J Chem Phys 2019; 151:205101. [DOI: 10.1063/1.5125744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Adriana Huerta-Viga
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Parveen Akhtar
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
- Biological Research Centre, Szeged, Temesvári Körút 62, Szeged 6726, Hungary
- ELI-ALPS, ELI-HU Nonprofit Ltd., Budapesti út 5, Szeged, Hungary
| | - Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Paweł J. Nowakowski
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - M. Faisal Khyasudeen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Petar H. Lambrev
- Biological Research Centre, Szeged, Temesvári Körút 62, Szeged 6726, Hungary
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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49
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Macroorganisation and flexibility of thylakoid membranes. Biochem J 2019; 476:2981-3018. [DOI: 10.1042/bcj20190080] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
Abstract
The light reactions of photosynthesis are hosted and regulated by the chloroplast thylakoid membrane (TM) — the central structural component of the photosynthetic apparatus of plants and algae. The two-dimensional and three-dimensional arrangement of the lipid–protein assemblies, aka macroorganisation, and its dynamic responses to the fluctuating physiological environment, aka flexibility, are the subject of this review. An emphasis is given on the information obtainable by spectroscopic approaches, especially circular dichroism (CD). We briefly summarise the current knowledge of the composition and three-dimensional architecture of the granal TMs in plants and the supramolecular organisation of Photosystem II and light-harvesting complex II therein. We next acquaint the non-specialist reader with the fundamentals of CD spectroscopy, recent advances such as anisotropic CD, and applications for studying the structure and macroorganisation of photosynthetic complexes and membranes. Special attention is given to the structural and functional flexibility of light-harvesting complex II in vitro as revealed by CD and fluorescence spectroscopy. We give an account of the dynamic changes in membrane macroorganisation associated with the light-adaptation of the photosynthetic apparatus and the regulation of the excitation energy flow by state transitions and non-photochemical quenching.
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50
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Daskalakis V, Maity S, Hart CL, Stergiannakos T, Duffy CDP, Kleinekathöfer U. Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II. J Phys Chem B 2019; 123:9609-9615. [DOI: 10.1021/acs.jpcb.9b09767] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vangelis Daskalakis
- Department of Environmental Science and Technology, Cyprus University of Technology, 30 Archbishop Kyprianou Street, 3603, Limassol, Cyprus
| | - Sayan Maity
- Department of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Cameron Lewis Hart
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Taxiarchis Stergiannakos
- Department of Environmental Science and Technology, Cyprus University of Technology, 30 Archbishop Kyprianou Street, 3603, Limassol, Cyprus
| | - Christopher D. P. Duffy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Ulrich Kleinekathöfer
- Department of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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