1
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Gritsi CS, Sarmas E, Daskalakis V, Kotzabasis K. Acclimation mechanism of microalgal photosynthetic apparatus under low atmospheric pressures - new astrobiological perspectives in a Mars-like atmosphere. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24058. [PMID: 38902906 DOI: 10.1071/fp24058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/25/2024] [Indexed: 06/22/2024]
Abstract
This study reveals a new acclimation mechanism of the eukaryotic unicellular green alga Chlorella vulgaris in terms of the effect of varying atmospheric pressures on the structure and function of its photosynthetic apparatus using fluorescence induction measurements (JIP-test). The results indicate that low (400mbar) and extreme low (2 atmosphere (simulating the Mars atmosphere), reveals that the impact of extremely low atmospheric pressure on PQ mobility within the photosynthetic membrane, coupled with the low density of an almost 100% CO2 Mars-like atmosphere, results to a similar photosynthetic efficiency to that on Earth. These findings pave the way for the identification of novel functional acclimation mechanisms of microalgae to extreme environments that are vastly distinct from those found on Earth.
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Affiliation(s)
| | - Evangelos Sarmas
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Crete GR 70013, Greece
| | - Vangelis Daskalakis
- Department of Chemical Engineering, School of Engineering, University of Patras, Patras GR 26504, Greece
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Crete GR 70013, Greece
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2
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Gray C, Kailas L, Adams PG, Duffy CDP. Unravelling the fluorescence kinetics of light-harvesting proteins with simulated measurements. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149004. [PMID: 37699505 DOI: 10.1016/j.bbabio.2023.149004] [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: 02/21/2023] [Revised: 08/24/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
The plant light-harvesting pigment-protein complex LHCII is the major antenna sub-unit of PSII and is generally (though not universally) accepted to play a role in photoprotective energy dissipation under high light conditions, a process known Non-Photochemical Quenching (NPQ). The underlying mechanisms of energy trapping and dissipation within LHCII are still debated. Various models have been proposed for the underlying molecular detail of NPQ, but they are often based on different interpretations of very similar transient absorption measurements of isolated complexes. Here we present a simulated measurement of the fluorescence decay kinetics of quenched LHCII aggregates to determine whether this relatively simple measurement can discriminate between different potential NPQ mechanisms. We simulate not just the underlying physics (excitation, energy migration, quenching and singlet-singlet annihilation) but also the signal detection and typical experimental data analysis. Comparing this to a selection of published fluorescence decay kinetics we find that: (1) Different proposed quenching mechanisms produce noticeably different fluorescence kinetics even at low (annihilation free) excitation density, though the degree of difference is dependent on pulse width. (2) Measured decay kinetics are consistent with most LHCII trimers becoming relatively slow excitation quenchers. A small sub-population of very fast quenchers produces kinetics which do not resemble any observed measurement. (3) It is necessary to consider at least two distinct quenching mechanisms in order to accurately reproduce experimental kinetics, supporting the idea that NPQ is not a simple binary switch.
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Affiliation(s)
- Callum Gray
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End, London E1 4NS, United Kingdom
| | - Lekshmi Kailas
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter G Adams
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Christopher D P Duffy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End, London E1 4NS, United Kingdom.
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3
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Ruan M, Li H, Zhang Y, Zhao R, Zhang J, Wang Y, Gao J, Wang Z, Wang Y, Sun D, Ding W, Weng Y. Cryo-EM structures of LHCII in photo-active and photo-protecting states reveal allosteric regulation of light harvesting and excess energy dissipation. NATURE PLANTS 2023; 9:1547-1557. [PMID: 37653340 DOI: 10.1038/s41477-023-01500-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/26/2023] [Indexed: 09/02/2023]
Abstract
The major light-harvesting complex of photosystem II (LHCII) has a dual regulatory function in a process called non-photochemical quenching to avoid the formation of reactive oxygen. LHCII undergoes reversible conformation transitions to switch between a light-harvesting state for excited-state energy transfer and an energy-quenching state for dissipating excess energy under full sunshine. Here we report cryo-electron microscopy structures of LHCII in membrane nanodiscs, which mimic in vivo LHCII, and in detergent solution at pH 7.8 and 5.4, respectively. We found that, under low pH conditions, the salt bridges at the lumenal side of LHCII are broken, accompanied by the formation of two local α-helices on the lumen side. The formation of α-helices in turn triggers allosterically global protein conformational change, resulting in a smaller crossing angle between transmembrane helices. The fluorescence decay rates corresponding to different conformational states follow the Dexter energy transfer mechanism with a characteristic transition distance of 5.6 Å between Lut1 and Chl612. The experimental observations are consistent with the computed electronic coupling strengths using multistate density function theory.
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Affiliation(s)
- Meixia Ruan
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Ying Zhang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruoqi Zhao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yingjie Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Jiali Gao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Zhuan Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yumei Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Dapeng Sun
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Wei Ding
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yuxiang Weng
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Songshan Lake Materials Laboratory, Dongguan, China.
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4
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Navakoudis E, Stergiannakos T, Daskalakis V. A perspective on the major light-harvesting complex dynamics under the effect of pH, salts, and the photoprotective PsbS protein. PHOTOSYNTHESIS RESEARCH 2023; 156:163-177. [PMID: 35816266 PMCID: PMC10070230 DOI: 10.1007/s11120-022-00935-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The photosynthetic apparatus is a highly modular assembly of large pigment-binding proteins. Complexes called antennae can capture the sunlight and direct it from the periphery of two Photosystems (I, II) to the core reaction centers, where it is converted into chemical energy. The apparatus must cope with the natural light fluctuations that can become detrimental to the viability of the photosynthetic organism. Here we present an atomic scale view of the photoprotective mechanism that is activated on this line of defense by several photosynthetic organisms to avoid overexcitation upon excess illumination. We provide a complete macroscopic to microscopic picture with specific details on the conformations of the major antenna of Photosystem II that could be associated with the switch from the light-harvesting to the photoprotective state. This is achieved by combining insight from both experiments and all-atom simulations from our group and the literature in a perspective article.
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Affiliation(s)
- Eleni Navakoudis
- Department of Chemical Engineering, Cyprus University of Technology, 95 Eirinis Street, 3603, Limassol, Cyprus
| | - Taxiarchis Stergiannakos
- Department of Chemical Engineering, Cyprus University of Technology, 95 Eirinis Street, 3603, Limassol, Cyprus
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 95 Eirinis Street, 3603, Limassol, Cyprus.
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5
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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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6
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Panagiotopoulos AA, Kalyvianaki K, Tsodoulou PK, Darivianaki MN, Dellis D, Notas G, Daskalakis V, Theodoropoulos PA, Panagiotidis CΑ, Castanas E, Kampa M. Recognition motifs for importin 4 [(L)PPRS(G/P)P] and importin 5 [KP(K/Y)LV] binding, identified by bio-informatic simulation and experimental in vitro validation. Comput Struct Biotechnol J 2022; 20:5952-5961. [PMID: 36382187 PMCID: PMC9646746 DOI: 10.1016/j.csbj.2022.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/21/2023] Open
Abstract
Nuclear translocation of large proteins is mediated through karyopherins, carrier proteins recognizing specific motifs of cargo proteins, known as nuclear localization signals (NLS). However, only few NLS signals have been reported until now. In the present work, NLS signals for Importins 4 and 5 were identified through an unsupervised in silico approach, followed by experimental in vitro validation. The sequences LPPRS(G/P)P and KP(K/Y)LV were identified and are proposed as recognition motifs for Importins 4 and 5 binding, respectively. They are involved in the trafficking of important proteins into the nucleus. These sequences were validated in the breast cancer cell line T47D, which expresses both Importins 4 and 5. Elucidating the complex relationships of the nuclear transporters and their cargo proteins is very important in better understanding the mechanism of nuclear transport of proteins and laying the foundation for the development of novel therapeutics, targeting specific importins.
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Affiliation(s)
| | - Konstantina Kalyvianaki
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece
| | - Paraskevi K. Tsodoulou
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Maria N. Darivianaki
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Dimitris Dellis
- National Infrastructures for Research and Technology, Athens 11523, Greece
| | - George Notas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
| | | | - Christos Α. Panagiotidis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Elias Castanas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece,Corresponding authors.
| | - Marilena Kampa
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece,Corresponding authors.
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7
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Daskalakis V. Deciphering the QR Code of the CRISPR-Cas9 System: Synergy between Gln768 (Q) and Arg976 (R). ACS PHYSICAL CHEMISTRY AU 2022; 2:496-505. [PMID: 36855610 PMCID: PMC9955204 DOI: 10.1021/acsphyschemau.2c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 10/14/2022]
Abstract
Markov state models (MSMs) and machine learning (ML) algorithms can extrapolate the long-time-scale behavior of large biomolecules from molecular dynamics (MD) trajectories. In this study, an MD-MSM-ML scheme has been applied to probe the large endonuclease (Cas9) in the bacterial adaptive immunity CRISPR-Cas9 system. CRISPR has become a programmable and state-of-the-art powerful genome editing tool that has already revolutionized life sciences. CRISPR-Cas9 is programmed to process specific DNA sequences in the genome. However, human/biomedical applications are compromised by off-target DNA damage. Characterization of Cas9 at the structural and biophysical levels is a prerequisite for the development of efficient and high-fidelity Cas9 variants. The Cas9 wild type and two variants (R63A-R66A-R70A, R69A-R71A-R74A-R78A) are studied herein. The configurational space of Cas9 is provided with a focus on the conformations of the side chains of two residues (Gln768 and Arg976). A model for the synergy between those two residues is proposed. The results are discussed within the context of experimental literature. The results and methodology can be exploited for the study of large biomolecules in general and for the engineering of more efficient and safer Cas9 variants for applications.
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8
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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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9
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Pirintsos S, Panagiotopoulos A, Bariotakis M, Daskalakis V, Lionis C, Sourvinos G, Karakasiliotis I, Kampa M, Castanas E. From Traditional Ethnopharmacology to Modern Natural Drug Discovery: A Methodology Discussion and Specific Examples. Molecules 2022; 27:molecules27134060. [PMID: 35807306 PMCID: PMC9268545 DOI: 10.3390/molecules27134060] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
Ethnopharmacology, through the description of the beneficial effects of plants, has provided an early framework for the therapeutic use of natural compounds. Natural products, either in their native form or after crude extraction of their active ingredients, have long been used by different populations and explored as invaluable sources for drug design. The transition from traditional ethnopharmacology to drug discovery has followed a straightforward path, assisted by the evolution of isolation and characterization methods, the increase in computational power, and the development of specific chemoinformatic methods. The deriving extensive exploitation of the natural product chemical space has led to the discovery of novel compounds with pharmaceutical properties, although this was not followed by an analogous increase in novel drugs. In this work, we discuss the evolution of ideas and methods, from traditional ethnopharmacology to in silico drug discovery, applied to natural products. We point out that, in the past, the starting point was the plant itself, identified by sustained ethnopharmacological research, with the active compound deriving after extensive analysis and testing. In contrast, in recent years, the active substance has been pinpointed by computational methods (in silico docking and molecular dynamics, network pharmacology), followed by the identification of the plant(s) containing the active ingredient, identified by existing or putative ethnopharmacological information. We further stress the potential pitfalls of recent in silico methods and discuss the absolute need for in vitro and in vivo validation as an absolute requirement. Finally, we present our contribution to natural products’ drug discovery by discussing specific examples, applying the whole continuum of this rapidly evolving field. In detail, we report the isolation of novel antiviral compounds, based on natural products active against influenza and SARS-CoV-2 and novel substances active on a specific GPCR, OXER1.
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Affiliation(s)
- Stergios Pirintsos
- Department of Biology, School of Sciences and Technology, University of Crete, 71409 Heraklion, Greece;
- Botanical Garden, University of Crete, 74100 Rethymnon, Greece
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Correspondence: (S.P.); (E.C.)
| | - Athanasios Panagiotopoulos
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71409 Heraklion, Greece;
| | - Michalis Bariotakis
- Department of Biology, School of Sciences and Technology, University of Crete, 71409 Heraklion, Greece;
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, Limassol 3603, Cyprus;
| | - Christos Lionis
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Clinic of Social and Family Medicine, School of Medicine, University of Crete, 71409 Heraklion, Greece
| | - George Sourvinos
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71409 Heraklion, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, School of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Marilena Kampa
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71409 Heraklion, Greece;
| | - Elias Castanas
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71409 Heraklion, Greece;
- Correspondence: (S.P.); (E.C.)
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10
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Pandit A. Structural dynamics of light harvesting proteins, photosynthetic membranes and cells observed with spectral editing solid-state NMR. J Chem Phys 2022; 157:025101. [DOI: 10.1063/5.0094446] [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
Photosynthetic light-harvesting complexes have a remarkable capacity to perform robust photo physics at ambient temperatures and in fluctuating environments. Protein conformational dynamics and membrane mobility are processes that contribute to the light-harvesting efficiencies and control photoprotective responses. This short review describes the application of Magic Angle Spinning (MAS) NMR spectroscopy for characterizing the structural dynamics of pigment, protein and thylakoid membrane components related to light harvesting and photoprotection. I will discuss the use of dynamics-based spectral editing solid-state NMR for distinguishing rigid and mobile components and assessing protein, pigment and lipid dynamics on sub-nanosecond to millisecond timescales. Dynamic spectral editing NMR has been applied to investigate Light-Harvesting Complex II (LHCII) protein conformational dynamics inside lipid bilayers and in native membranes. Furthermore, we used the NMR approach to assess thylakoid membrane dynamics. Finally, it is shown that dynamics-based spectral editing NMR, for reducing spectral complexity, by filtering motion-dependent signals, enabled us to follow processes in live photosynthetic cells.
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11
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Cignoni E, Cupellini L, Mennucci B. A fast method for electronic couplings in embedded multichromophoric systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:304004. [PMID: 35552268 DOI: 10.1088/1361-648x/ac6f3c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Electronic couplings are key to understanding exciton delocalization and transport in natural and artificial light harvesting processes. We develop a method to compute couplings in multichromophoric aggregates embedded in complex environments without running expensive quantum chemical calculations. We use a transition charge approximation to represent the quantum mechanical transition densities of the chromophores and an atomistic and polarizable classical model to describe the environment atoms. We extend our framework to estimate transition charges directly from the chromophore geometry, i.e., bypassing completely the quantum mechanical calculations using a regression approach. The method allows to rapidly compute accurate couplings for a large number of geometries along molecular dynamics trajectories.
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Affiliation(s)
- Edoardo Cignoni
- 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
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
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12
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Cignoni E, Slama V, Cupellini L, Mennucci B. The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol. J Chem Phys 2022; 156:120901. [DOI: 10.1063/5.0086275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Slama
- 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
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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13
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Azadi-Chegeni F, Thallmair S, Ward ME, Perin G, Marrink SJ, Baldus M, Morosinotto T, Pandit A. Protein dynamics and lipid affinity of monomeric, zeaxanthin-binding LHCII in thylakoid membranes. Biophys J 2022; 121:396-409. [PMID: 34971616 PMCID: PMC8822613 DOI: 10.1016/j.bpj.2021.12.039] [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] [Received: 09/01/2021] [Revised: 12/02/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
The xanthophyll cycle in the antenna of photosynthetic organisms under light stress is one of the most well-known processes in photosynthesis, but its role is not well understood. In the xanthophyll cycle, violaxanthin (Vio) is reversibly transformed to zeaxanthin (Zea) that occupies Vio binding sites of light-harvesting antenna proteins. Higher monomer/trimer ratios of the most abundant light-harvesting protein, the light-harvesting complex II (LHCII), usually occur in Zea accumulating membranes and have been observed in plants after prolonged illumination and during high-light acclimation. We present a combined NMR and coarse-grained simulation study on monomeric LHCII from the npq2 mutant that constitutively binds Zea in the Vio binding pocket. LHCII was isolated from 13C-enriched npq2 Chlamydomonas reinhardtii (Cr) cells and reconstituted in thylakoid lipid membranes. NMR results reveal selective changes in the fold and dynamics of npq2 LHCII compared with the trimeric, wild-type and show that npq2 LHCII contains multiple mono- or digalactosyl diacylglycerol lipids (MGDG and DGDG) that are strongly protein bound. Coarse-grained simulations on npq2 LHCII embedded in a thylakoid lipid membrane agree with these observations. The simulations show that LHCII monomers have more extensive lipid contacts than LHCII trimers and that protein-lipid contacts are influenced by Zea. We propose that both monomerization and Zea binding could have a functional role in modulating membrane fluidity and influence the aggregation and conformational dynamics of LHCII with a likely impact on photoprotection ability.
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Affiliation(s)
- Fatemeh Azadi-Chegeni
- Leiden Institute of Chemistry, Department of Solid-State NMR, Leiden University, Leiden, the Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
| | - Meaghan E Ward
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Giorgio Perin
- Department of Biology, University of Padua, Padua, Italy
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Anjali Pandit
- Leiden Institute of Chemistry, Department of Solid-State NMR, Leiden University, Leiden, the Netherlands.
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14
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A different perspective for nonphotochemical quenching in plant antenna complexes. Nat Commun 2021; 12:7152. [PMID: 34887401 PMCID: PMC8660843 DOI: 10.1038/s41467-021-27526-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Light-harvesting complexes of plants exert a dual function of light-harvesting (LH) and photoprotection through processes collectively called nonphotochemical quenching (NPQ). While LH processes are relatively well characterized, those involved in NPQ are less understood. Here, we characterize the quenching mechanisms of CP29, a minor LHC of plants, through the integration of two complementary enhanced-sampling techniques, dimensionality reduction schemes, electronic calculations and the analysis of cryo-EM data in the light of the predicted conformational ensemble. Our study reveals that the switch between LH and quenching state is more complex than previously thought. Several conformations of the lumenal side of the protein occur and differently affect the pigments' relative geometries and interactions. Moreover, we show that a quenching mechanism localized on a single chlorophyll-carotenoid pair is not sufficient but many chlorophylls are simultaneously involved. In such a diffuse mechanism, short-range interactions between each carotenoid and different chlorophylls combined with a protein-mediated tuning of the carotenoid excitation energies have to be considered in addition to the commonly suggested Coulomb interactions.
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15
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Panagiotopoulos AA, Karakasiliotis I, Kotzampasi DM, Dimitriou M, Sourvinos G, Kampa M, Pirintsos S, Castanas E, Daskalakis V. Natural Polyphenols Inhibit the Dimerization of the SARS-CoV-2 Main Protease: The Case of Fortunellin and Its Structural Analogs. Molecules 2021; 26:6068. [PMID: 34641612 PMCID: PMC8512273 DOI: 10.3390/molecules26196068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
3CL-Pro is the SARS-CoV-2 main protease (MPro). It acts as a homodimer to cleave the large polyprotein 1ab transcript into proteins that are necessary for viral growth and replication. 3CL-Pro has been one of the most studied SARS-CoV-2 proteins and a main target of therapeutics. A number of drug candidates have been reported, including natural products. Here, we employ elaborate computational methods to explore the dimerization of the 3CL-Pro protein, and we formulate a computational context to identify potential inhibitors of this process. We report that fortunellin (acacetin 7-O-neohesperidoside), a natural flavonoid O-glycoside, and its structural analogs are potent inhibitors of 3CL-Pro dimerization, inhibiting viral plaque formation in vitro. We thus propose a novel basis for the search of pharmaceuticals as well as dietary supplements in the fight against SARS-CoV-2 and COVID-19.
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Affiliation(s)
- Athanasios A. Panagiotopoulos
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (A.A.P.); (D.-M.K.); (M.K.)
| | - Ioannis Karakasiliotis
- Laboratory of Biology, School of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.K.); (M.D.)
| | - Danai-Maria Kotzampasi
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (A.A.P.); (D.-M.K.); (M.K.)
| | - Marios Dimitriou
- Laboratory of Biology, School of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.K.); (M.D.)
| | - George Sourvinos
- Laboratory of Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece;
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece;
| | - Marilena Kampa
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (A.A.P.); (D.-M.K.); (M.K.)
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece;
| | - Stergios Pirintsos
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece;
- Department of Biology, University of Crete, 71409 Heraklion, Greece
- Botanical Garden, University of Crete, 74100 Rethymnon, Greece
| | - Elias Castanas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (A.A.P.); (D.-M.K.); (M.K.)
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece;
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 3603 Limassol, Cyprus
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16
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Chrysafoudi A, Maity S, Kleinekathöfer U, Daskalakis V. Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study. J Phys Chem Lett 2021; 12:9626-9633. [PMID: 34585934 DOI: 10.1021/acs.jpclett.1c02498] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Diatoms generate a large portion of the oxygen produced on earth due to their exceptional light-harvesting properties involving fucoxanthin and chlorophyll-binding proteins (FCP). At the same time, an efficient adaptation of these complexes to fluctuating light conditions is necessary to protect the diatoms against photodamage. So far, structural and dynamic data for the interaction between FCP and the photoprotective LHCX family of proteins in diatoms are lacking. In this computational study, we provide a structural basis for a remarkable pH-dependent adaptation at the molecular level. Upon binding of the LHCX1 protein to the FCP complex together with a change in pH, conformational changes within the FCP protein result in a variation of the electronic coupling in a specific chlorophyll-fucoxanthin pair, leading to a change in the exciton transfer rate by almost an order of magnitude. A common strategy for photoprotection between diatoms and higher plants is identified and discussed.
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Affiliation(s)
- Anthi Chrysafoudi
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - 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
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3603 Limassol, Cyprus
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17
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Maity S, Sarngadharan P, Daskalakis V, Kleinekathöfer U. Time-dependent atomistic simulations of the CP29 light-harvesting complex. J Chem Phys 2021; 155:055103. [PMID: 34364345 DOI: 10.1063/5.0053259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II, which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional-based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results, the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, time-dependent and time-independent excitonic Hamiltonians of the system have been constructed and applied to the determination of absorption spectra as well as exciton dynamics.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str. 3603, Limassol, Cyprus
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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18
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Hydrogen gas as a central on-off functional switch of reversible metabolic arrest - New perspectives for biotechnological applications. J Biotechnol 2021; 335:9-18. [PMID: 34090950 DOI: 10.1016/j.jbiotec.2021.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/09/2021] [Accepted: 06/01/2021] [Indexed: 11/23/2022]
Abstract
Metabolism is the sum of all chemical reactions that sustain life. There is an ongoing effort to control metabolic rate, which correlates with the maximum lifespan potential and constitutes one of the oldest scientific questions. Herein, we report on the complete reversible arrest of cellular metabolism and cell growth in a series of organisms, from microalgae to yeast upon exposure to a 100 % hydrogen atmosphere. We also report a tolerance of the microalgae under these conditions against extreme stress conditions, like high salt concentrations. The addition of oxygen or air almost completely restores the metabolic rate and cell growth. Molecular dynamics simulations are employed to decipher this phenomenon at atomic scale. Various proteins, including photosynthetic and respiratory complexes (LHCII, cytochrome c5) are probed in the interaction with hydrogen. Exposure to hydrogen, as opposed to oxygen, decreases the fluctuations of protein residues indicating thermostability. According to the above mechanism, an absolute hydrogen atmosphere can preserve biological products (e.g. fruits) for a long time without consuming any energy. By combining biological, chemical and computational methods, in this research we provide the basis for future innovative studies and advances in the field of biotechnology.
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19
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Mascoli V, Liguori N, Cupellini L, Elias E, Mennucci B, Croce R. Uncovering the interactions driving carotenoid binding in light-harvesting complexes. Chem Sci 2021; 12:5113-5122. [PMID: 34163750 PMCID: PMC8179543 DOI: 10.1039/d1sc00071c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/14/2021] [Indexed: 11/25/2022] Open
Abstract
Carotenoids are essential constituents of plant light-harvesting complexes (LHCs), being involved in protein stability, light harvesting, and photoprotection. Unlike chlorophylls, whose binding to LHCs is known to require coordination of the central magnesium, carotenoid binding relies on weaker intermolecular interactions (such as hydrogen bonds and van der Waals forces), whose character is far more elusive. Here we addressed the key interactions responsible for carotenoid binding to LHCs by combining molecular dynamics simulations and polarizable quantum mechanics/molecular mechanics calculations on the major LHC, LHCII. We found that carotenoid binding is mainly stabilized by van der Waals interactions with the surrounding chlorophyll macrocycles rather than by hydrogen bonds to the protein, the latter being more labile than predicted from structural data. Furthermore, the interaction network in the binding pockets is relatively insensitive to the chemical structure of the embedded carotenoid. Our results are consistent with a number of experimental data and challenge the role played by specific interactions in the assembly of pigment-protein complexes.
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Affiliation(s)
- Vincenzo Mascoli
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Nicoletta Liguori
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Lorenzo Cupellini
- Department of Chemistry, University of Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Eduard Elias
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Benedetta Mennucci
- Department of Chemistry, University of Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Roberta Croce
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
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20
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Gray C, Wei T, Polívka T, Daskalakis V, Duffy CDP. Trivial Excitation Energy Transfer to Carotenoids Is an Unlikely Mechanism for Non-photochemical Quenching in LHCII. FRONTIERS IN PLANT SCIENCE 2021; 12:797373. [PMID: 35095968 PMCID: PMC8792765 DOI: 10.3389/fpls.2021.797373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/20/2021] [Indexed: 05/04/2023]
Abstract
Higher plants defend themselves from bursts of intense light via the mechanism of Non-Photochemical Quenching (NPQ). It involves the Photosystem II (PSII) antenna protein (LHCII) adopting a conformation that favors excitation quenching. In recent years several structural models have suggested that quenching proceeds via energy transfer to the optically forbidden and short-lived S 1 states of a carotenoid. It was proposed that this pathway was controlled by subtle changes in the relative orientation of a small number of pigments. However, quantum chemical calculations of S 1 properties are not trivial and therefore its energy, oscillator strength and lifetime are treated as rather loose parameters. Moreover, the models were based either on a single LHCII crystal structure or Molecular Dynamics (MD) trajectories about a single minimum. Here we try and address these limitations by parameterizing the vibronic structure and relaxation dynamics of lutein in terms of observable quantities, namely its linear absorption (LA), transient absorption (TA) and two-photon excitation (TPE) spectra. We also analyze a number of minima taken from an exhaustive meta-dynamical search of the LHCII free energy surface. We show that trivial, Coulomb-mediated energy transfer to S 1 is an unlikely quenching mechanism, with pigment movements insufficiently pronounced to switch the system between quenched and unquenched states. Modulation of S 1 energy level as a quenching switch is similarly unlikely. Moreover, the quenching predicted by previous models is possibly an artifact of quantum chemical over-estimation of S 1 oscillator strength and the real mechanism likely involves short-range interaction and/or non-trivial inter-molecular states.
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Affiliation(s)
- Callum Gray
- Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom
| | - Tiejun Wei
- Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom
| | - Tomáš Polívka
- Department of Physics, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
| | - Christopher D. P. Duffy
- Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom
- *Correspondence: Christopher D. P. Duffy
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