1
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Chiariello MG, Zarmiento-Garcia R, Marrink SJ. Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis. Int J Mol Sci 2024; 25:7947. [PMID: 39063190 PMCID: PMC11277265 DOI: 10.3390/ijms25147947] [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: 06/20/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
As a critical step in advancing the simulation of photosynthetic complexes, we present the Martini 3 coarse-grained (CG) models of key cofactors associated with light harvesting (LHCII) proteins and the photosystem II (PSII) core complex. Our work focuses on the parametrization of beta-carotene, plastoquinone/quinol, violaxanthin, lutein, neoxanthin, chlorophyll A, chlorophyll B, and heme. We derived the CG parameters to match the all-atom reference simulations, while structural and thermodynamic properties of the cofactors were compared to experimental values when available. To further assess the reliability of the parameterization, we tested the behavior of these cofactors within their physiological environments, specifically in a lipid bilayer and bound to photosynthetic complexes. The results demonstrate that our CG models maintain the essential features required for realistic simulations. This work lays the groundwork for detailed simulations of the PSII-LHCII super-complex, providing a robust parameter set for future studies.
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Affiliation(s)
| | | | - Siewert-Jan Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; (M.G.C.); (R.Z.-G.)
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2
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Wilson S, Clarke CD, Carbajal MA, Buccafusca R, Fleck RA, Daskalakis V, Ruban AV. Hydrophobic Mismatch in the Thylakoid Membrane Regulates Photosynthetic Light Harvesting. J Am Chem Soc 2024; 146:14905-14914. [PMID: 38759103 PMCID: PMC11140739 DOI: 10.1021/jacs.4c05220] [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: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
The ability to harvest light effectively in a changing environment is necessary to ensure efficient photosynthesis and crop growth. One mechanism, known as qE, protects photosystem II (PSII) and regulates electron transfer through the harmless dissipation of excess absorbed photons as heat. This process involves reversible clustering of the major light-harvesting complexes of PSII (LHCII) in the thylakoid membrane and relies upon the ΔpH gradient and the allosteric modulator protein PsbS. To date, the exact role of PsbS in the qE mechanism has remained elusive. Here, we show that PsbS induces hydrophobic mismatch in the thylakoid membrane through dynamic rearrangement of lipids around LHCII leading to observed membrane thinning. We found that upon illumination, the thylakoid membrane reversibly shrinks from around 4.3 to 3.2 nm, without PsbS, this response is eliminated. Furthermore, we show that the lipid digalactosyldiacylglycerol (DGDG) is repelled from the LHCII-PsbS complex due to an increase in both the pKa of lumenal residues and in the dipole moment of LHCII, which allows for further conformational change and clustering in the membrane. Our results suggest a mechanistic role for PsbS as a facilitator of a hydrophobic mismatch-mediated phase transition between LHCII-PsbS and its environment. This could act as the driving force to sort LHCII into photoprotective nanodomains in the thylakoid membrane. This work shows an example of the key role of the hydrophobic mismatch process in regulating membrane protein function in plants.
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Affiliation(s)
- Sam Wilson
- Department
of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Charlea D. Clarke
- Department
of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - M. Alejandra Carbajal
- Centre
for Ultrastructural Imaging, King’s
College London, London SE1 1UL, United Kingdom
| | - Roberto Buccafusca
- Department
of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Roland A. Fleck
- Centre
for Ultrastructural Imaging, King’s
College London, London SE1 1UL, United Kingdom
| | - Vangelis Daskalakis
- Department
of Chemical Engineering, School of Engineering, University of Patras, Patras 26504, Greece
| | - Alexander V. Ruban
- Department
of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
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3
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Marulanda Valencia W, Pandit A. Photosystem II Subunit S (PsbS): A Nano Regulator of Plant Photosynthesis. J Mol Biol 2024; 436:168407. [PMID: 38109993 DOI: 10.1016/j.jmb.2023.168407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
Light is required for photosynthesis, but plants are often exposed to excess light, which can lead to photodamage and eventually cell death. To prevent this, they evolved photoprotective feedback mechanisms that regulate photosynthesis and trigger processes that dissipate light energy as heat, called non-photochemical quenching (NPQ). In excess light conditions, the light reaction and activity of Photosystem II (PSII) generates acidification of the thylakoid lumen, which is sensed by special pH-sensitive proteins called Photosystem II Subunit S (PsbS), actuating a photoprotective "switch" in the light-harvesting antenna. Despite its central role in regulating photosynthetic energy conversion, the molecular mechanism of PsbS as well as its interaction with partner proteins are not well understood. This review summarizes the current knowledge on the molecular structure and mechanistic aspects of the light-stress sensor PsbS and addresses open questions and challenges in the field regarding a full understanding of its functional mechanism and role in NPQ.
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Affiliation(s)
| | - Anjali Pandit
- Leiden Inst. of Chemistry, Gorlaeus Laboratory, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
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4
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Manna P, Hoffmann M, Davies T, Richardson KH, Johnson MP, Schlau-Cohen GS. Energetic driving force for LHCII clustering in plant membranes. SCIENCE ADVANCES 2023; 9:eadj0807. [PMID: 38134273 PMCID: PMC10745693 DOI: 10.1126/sciadv.adj0807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Plants capture and convert solar energy in a complex network of membrane proteins. Under high light, the luminal pH drops and induces a reorganization of the protein network, particularly clustering of the major light-harvesting complex (LHCII). While the structures of the network have been resolved in exquisite detail, the thermodynamics that control the assembly and reorganization had not been determined, largely because the interaction energies of membrane proteins have been inaccessible. Here, we describe a method to quantify these energies and its application to LHCII. Using single-molecule measurements, LHCII proteoliposomes, and statistical thermodynamic modeling, we quantified the LHCII-LHCII interaction energy as ~-5 kBT at neutral pH and at least -7 kBT at acidic pH. These values revealed an enthalpic thermodynamic driving force behind LHCII clustering. Collectively, this work captures the interactions that drive the organization of membrane protein networks from the perspective of equilibrium statistical thermodynamics, which has a long and rich tradition in biology.
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Affiliation(s)
- Premashis Manna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Madeline Hoffmann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Davies
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | - Matthew P. Johnson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
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5
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Li DH, Wilson S, Mastroianni G, Ruban AV. Altered lipid acyl chain length controls energy dissipation in light-harvesting complex II proteoliposomes by hydrophobic mismatch. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 246:112758. [PMID: 37531665 DOI: 10.1016/j.jphotobiol.2023.112758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023]
Abstract
In plants, the major light-harvesting antenna complex (LHCII) is vital for both light harvesting and photoprotection in photosystem II. Previously, we proposed that the thylakoid membrane itself could switch LHCII into the photoprotective state, qE, via a process known as hydrophobic mismatch. The decrease in the membrane thickness that followed the formation of ΔpH was a key fact that prompted this idea. To test this, we made proteoliposomes from lipids with altered acyl chain length (ACL). Here, we show that ACL regulates the average chlorophyll fluorescence lifetime of LHCII. For liposomes made of lipids with an ACL of 18 carbons, the lifetime was ∼2 ns, like that for the thylakoid membrane. Furthermore, LHCII appears to be quenched in proteoliposomes with an ACL both shorter and longer than 18 carbons. The proteoliposomes made of short ACL lipids display structural heterogeneity revealing two quenched conformations of LHCII, each having characteristic 77 K fluorescence spectra. One conformation spectrally resembles isolated LHCII aggregates, whilst the other resembles LHCII immobilized in polyacrylamide gels. Overall, the decrease in the ACL appears to produce quenched conformations of LHCII, which renders plausible the idea that the trigger of qE is the hydrophobic mismatch.
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Affiliation(s)
- Dan-Hong Li
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
| | - Sam Wilson
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
| | - Giulia Mastroianni
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
| | - Alexander V Ruban
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
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6
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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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7
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Maity S, Kleinekathöfer U. Recent progress in atomistic modeling of light-harvesting complexes: a mini review. PHOTOSYNTHESIS RESEARCH 2023; 156:147-162. [PMID: 36207489 PMCID: PMC10070314 DOI: 10.1007/s11120-022-00969-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.
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Affiliation(s)
- 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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8
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Ptushenko VV, Bondarenko GN, Vinogradova EN, Glagoleva ES, Karpova OV, Ptushenko OS, Shibzukhova KA, Solovchenko AE, Lobakova ES. Chilling Upregulates Expression of the PsbS and LhcSR Genes in the Chloroplasts of the Green Microalga Lobosphaera incisa IPPAS C-2047. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1699-1706. [PMID: 36717458 DOI: 10.1134/s0006297922120240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Non-photochemical quenching (NPQ) of excited chlorophyll states is essential for protecting the photosynthetic apparatus (PSA) from the excessive light-induced damage in all groups of oxygenic photosynthetic organisms. The key component of the NPQ mechanism in green algae and some other groups of algae and mosses is the LhcSR protein of the light harvesting complex (LHC) protein superfamily. In vascular plants, LhcSR is replaced by PsbS, another member of the LHC superfamily and a subunit of photosystem II (PSII). PsbS also performs the photoprotective function in mosses. For a long time, PsbS had been believed to be nonfunctional in green algae, although the corresponding gene was discovered in the genome of these organisms. The first evidence of the PsbS accumulation in the model green alga Chlamydomonas reinhardtii in response to the increase in irradiance was obtained only six years ago. However, the observed increase in the PsbS content was short-termed (on an hour-timescale). Here, we report a significant (more than three orders of magnitude) and prolonged (four days) upregulation of PsbS expression in response to the chilling-induced high-light stress followed by a less significant (~ tenfold) increase in the PsbS expression for nine days. This is the first evidence for the long-term upregulation of the PsbS expression in green alga (Chlorophyta) in response to stress. Our data indicate that the role of PsbS in the PSA of Chlorophyta is not limited to the first-line defense against stress, as it was previously assumed, but includes full-scale participation in the photoprotection of PSA from the environmental stress factors.
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Affiliation(s)
- Vasily V Ptushenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | | | - Elizaveta N Vinogradova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Kurchatov Institute National Research Center, 123182 Moscow Russia
| | - Elena S Glagoleva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga V Karpova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Oxana S Ptushenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Karina A Shibzukhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexei E Solovchenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Pskov State University, Pskov, 128000, Russia
| | - Elena S Lobakova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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9
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Arshad R, Saccon F, Bag P, Biswas A, Calvaruso C, Bhatti AF, Grebe S, Mascoli V, Mahbub M, Muzzopappa F, Polyzois A, Schiphorst C, Sorrentino M, Streckaité S, van Amerongen H, Aro EM, Bassi R, Boekema EJ, Croce R, Dekker J, van Grondelle R, Jansson S, Kirilovsky D, Kouřil R, Michel S, Mullineaux CW, Panzarová K, Robert B, Ruban AV, van Stokkum I, Wientjes E, Büchel C. A kaleidoscope of photosynthetic antenna proteins and their emerging roles. PLANT PHYSIOLOGY 2022; 189:1204-1219. [PMID: 35512089 PMCID: PMC9237682 DOI: 10.1093/plphys/kiac175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/17/2022] [Indexed: 05/17/2023]
Abstract
Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.
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Affiliation(s)
- Rameez Arshad
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc 783 71, Czech Republic
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Francesco Saccon
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Pushan Bag
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå 901 87, Sweden
| | - Avratanu Biswas
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Claudio Calvaruso
- Institute for Molecular Biosciences, Goethe University of Frankfurt, Frankfurt 60438, Germany
| | - Ahmad Farhan Bhatti
- Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands
| | - Steffen Grebe
- Department of Life Technologies, MolecularPlant Biology, University of Turku, Turku FI–20520, Finland
| | - Vincenzo Mascoli
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Moontaha Mahbub
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Fernando Muzzopappa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette 1198, France
| | - Alexandros Polyzois
- Université de Paris, Faculté de Pharmacie de Paris, CiTCoM UMR 8038 CNRS, Paris 75006, France
| | | | - Mirella Sorrentino
- Photon Systems Instruments, spol. s.r.o., Drásov, Czech Republic
- Department of Agricultural Sciences, University of Naples Federico II, Naples 80138, Italy
| | - Simona Streckaité
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette 1198, France
| | | | - Eva-Mari Aro
- Department of Life Technologies, MolecularPlant Biology, University of Turku, Turku FI–20520, Finland
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Verona, Italy
| | - Egbert J Boekema
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Roberta Croce
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Jan Dekker
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Rienk van Grondelle
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Stefan Jansson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå 901 87, Sweden
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette 1198, France
| | - Roman Kouřil
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc 783 71, Czech Republic
| | - Sylvie Michel
- Université de Paris, Faculté de Pharmacie de Paris, CiTCoM UMR 8038 CNRS, Paris 75006, France
| | - Conrad W Mullineaux
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Klára Panzarová
- Photon Systems Instruments, spol. s.r.o., Drásov, Czech Republic
| | - Bruno Robert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette 1198, France
| | - Alexander V Ruban
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ivo van Stokkum
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Emilie Wientjes
- Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands
| | - Claudia Büchel
- Institute for Molecular Biosciences, Goethe University of Frankfurt, Frankfurt 60438, Germany
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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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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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12
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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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13
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Ruban AV, Wilson S. The Mechanism of Non-Photochemical Quenching in Plants: Localization and Driving Forces. PLANT & CELL PHYSIOLOGY 2021; 62:1063-1072. [PMID: 33351147 DOI: 10.1093/pcp/pcaa155] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/25/2020] [Indexed: 05/20/2023]
Abstract
Non-photochemical chlorophyll fluorescence quenching (NPQ) remains one of the most studied topics of the 21st century in photosynthesis research. Over the past 30 years, profound knowledge has been obtained on the molecular mechanism of NPQ in higher plants. First, the largely overlooked significance of NPQ in protecting the reaction center of photosystem II (RCII) against damage, and the ways to assess its effectiveness are highlighted. Then, the key in vivo signals that can monitor the life of the major NPQ component, qE, are presented. Finally, recent knowledge on the site of qE and the possible molecular events that transmit ΔpH into the conformational change in the major LHCII [the major trimeric light harvesting complex of photosystem II (PSII)] antenna complex are discussed. Recently, number of reports on Arabidopsis mutants lacking various antenna components of PSII confirmed that the in vivo site of qE rests within the major trimeric LHCII complex. Experiments on biochemistry, spectroscopy, microscopy and molecular modeling suggest an interplay between thylakoid membrane geometry and the dynamics of LHCII, the PsbS (PSII subunit S) protein and thylakoid lipids. The molecular basis for the qE-related conformational change in the thylakoid membrane, including the possible onset of a hydrophobic mismatch between LHCII and lipids, potentiated by PsbS protein, begins to unfold.
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Affiliation(s)
- Alexander V Ruban
- Department of Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, Fogg Building, Mile End Road, London E1 4NS, UK
| | - Sam Wilson
- Department of Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, Fogg Building, Mile End Road, London E1 4NS, UK
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14
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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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15
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Montero O, Velasco M, Miñón J, Marks EAN, Sanz-Arranz A, Rad C. Differential Membrane Lipid Profiles and Vibrational Spectra of Three Edaphic Algae and One Cyanobacterium. Int J Mol Sci 2021; 22:11277. [PMID: 34681936 PMCID: PMC8538821 DOI: 10.3390/ijms222011277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
The membrane glycerolipids of four phototrophs that were isolated from an edaphic assemblage were determined by UPLC-MS after cultivation in a laboratory growth chamber. Identification was carried out by 18S and 16S rDNA sequencing. The algal species were Klebsormidium flaccidum (Charophyta), Oocystis sp. (Chlorophyta), and Haslea spicula (Bacillariophyta), and the cyanobacterium was Microcoleus vaginatus (Cyanobacteria). The glycerolipid profile of Oocystis sp. was dominated by monogalactosyldiacylglycerol (MGDG) species, with MGDG(18:3/16:4) accounting for 68.6%, whereas MGDG(18:3/16:3) was the most abundant glycerolipid in K. flaccidum (50.1%). A ratio of digalactosyldiacylglycerol (DGDG) species to MGDG species (DGDG/MGDG) was shown to be higher in K. flaccidum (0.26) than in Oocystis sp. (0.14). This ratio increased under high light (HL) as compared to low light (LL) in all the organisms, with its highest value being shown in cyanobacterium (0.38-0.58, LL-HL). High contents of eicosapentaenoic acid (EPA, C20:5) and hexadecenoic acid were observed in the glycerolipids of H. spicula. Similar Fourier transform infrared (FTIR) and Raman spectra were found for K. flaccidum and Oocystis sp. Specific bands at 1629.06 and 1582.78 cm-1 were shown by M. vaginatus in the Raman spectra. Conversely, specific bands in the FTIR spectrum were observed for H. spicula at 1143 and 1744 cm-1. The results of this study point out differences in the membrane lipid composition between species, which likely reflects their different morphology and evolutionary patterns.
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Affiliation(s)
- Olimpio Montero
- Institute of Biology and Molecular Genetics (IBGM), Spanish Council for Scientific Research (CSIC), Sanz y Forés Str. 3, 47003 Valladolid, Spain;
| | - Marta Velasco
- Institute of Biology and Molecular Genetics (IBGM), Spanish Council for Scientific Research (CSIC), Sanz y Forés Str. 3, 47003 Valladolid, Spain;
| | - Jorge Miñón
- Composting Research Group UBUCOMP, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain; (J.M.); (C.R.)
| | - Evan A. N. Marks
- BETA Technological Center, University of Vic-University of Central Catalonia, Edifici Can Baumann, Crta. de Roda 70, 08500 Vic, Spain;
| | - Aurelio Sanz-Arranz
- Department of Fisica de la Materia Condensada, University of Valladolid, 47002 Valladolid, Spain;
| | - Carlos Rad
- Composting Research Group UBUCOMP, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain; (J.M.); (C.R.)
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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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Welc R, Luchowski R, Kluczyk D, Zubik-Duda M, Grudzinski W, Maksim M, Reszczynska E, Sowinski K, Mazur R, Nosalewicz A, Gruszecki WI. Mechanisms shaping the synergism of zeaxanthin and PsbS in photoprotective energy dissipation in the photosynthetic apparatus of plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:418-433. [PMID: 33914375 DOI: 10.1111/tpj.15297] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 05/20/2023]
Abstract
Safe operation of photosynthesis is vital to plants and is ensured by the activity of processes protecting chloroplasts against photo-damage. The harmless dissipation of excess excitation energy is considered to be the primary photoprotective mechanism and is most effective in the combined presence of PsbS protein and zeaxanthin, a xanthophyll accumulated in strong light as a result of the xanthophyll cycle. Here we address the problem of specific molecular mechanisms underlying the synergistic effect of zeaxanthin and PsbS. The experiments were conducted with Arabidopsis thaliana, using wild-type plants, mutants lacking PsbS (npq4), and mutants affected in the xanthophyll cycle (npq1), with the application of molecular spectroscopy and imaging techniques. The results lead to the conclusion that PsbS interferes with the formation of densely packed aggregates of thylakoid membrane proteins, thus allowing easy exchange and incorporation of xanthophyll cycle pigments into such structures. It was found that xanthophylls trapped within supramolecular structures, most likely in the interfacial protein region, determine their photophysical properties. The structures formed in the presence of violaxanthin are characterized by minimized dissipation of excitation energy. In contrast, the structures formed in the presence of zeaxanthin show enhanced excitation quenching, thus protecting the system against photo-damage.
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Affiliation(s)
- Renata Welc
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, 20-290, Poland
| | - Rafal Luchowski
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
| | - Dariusz Kluczyk
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Maria Curie-Sklodowska University, Lublin, 20-033, Poland
| | - Monika Zubik-Duda
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
| | - Wojciech Grudzinski
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
| | - Magdalena Maksim
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, 20-290, Poland
| | - Emilia Reszczynska
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Maria Curie-Sklodowska University, Lublin, 20-033, Poland
| | - Karol Sowinski
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
| | - Radosław Mazur
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, 02-096, Poland
| | - Artur Nosalewicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, 20-290, Poland
| | - Wieslaw I Gruszecki
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, 20-031, Poland
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19
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Krishnan-Schmieden M, Konold PE, Kennis JTM, Pandit A. The molecular pH-response mechanism of the plant light-stress sensor PsbS. Nat Commun 2021; 12:2291. [PMID: 33863895 PMCID: PMC8052336 DOI: 10.1038/s41467-021-22530-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/12/2021] [Indexed: 11/12/2022] Open
Abstract
Plants need to protect themselves from excess light, which causes photo-oxidative damage and lowers the efficiency of photosynthesis. Photosystem II subunit S (PsbS) is a pH sensor protein that plays a crucial role in plant photoprotection by detecting thylakoid lumen acidification in excess light conditions via two lumen-faced glutamates. However, how PsbS is activated under low-pH conditions is unknown. To reveal the molecular response of PsbS to low pH, here we perform an NMR, FTIR and 2DIR spectroscopic analysis of Physcomitrella patens PsbS and of the E176Q mutant in which an active glutamate has been replaced. The PsbS response mechanism at low pH involves the concerted action of repositioning of a short amphipathic helix containing E176 facing the lumen and folding of the luminal loop fragment adjacent to E71 to a 310-helix, providing clear evidence of a conformational pH switch. We propose that this concerted mechanism is a shared motif of proteins of the light-harvesting family that may control thylakoid inter-protein interactions driving photoregulatory responses.
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Affiliation(s)
| | - Patrick E Konold
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
| | - Anjali Pandit
- Dept. of Solid-State NMR, Leiden Inst. of Chemistry, Leiden University, Leiden, The Netherlands.
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20
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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: 22] [Impact Index Per Article: 7.3] [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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21
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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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22
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Kaňa R, Steinbach G, Sobotka R, Vámosi G, Komenda J. Fast Diffusion of the Unassembled PetC1-GFP Protein in the Cyanobacterial Thylakoid Membrane. Life (Basel) 2020; 11:life11010015. [PMID: 33383642 PMCID: PMC7823997 DOI: 10.3390/life11010015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 01/08/2023] Open
Abstract
Biological membranes were originally described as a fluid mosaic with uniform distribution of proteins and lipids. Later, heterogeneous membrane areas were found in many membrane systems including cyanobacterial thylakoids. In fact, cyanobacterial pigment-protein complexes (photosystems, phycobilisomes) form a heterogeneous mosaic of thylakoid membrane microdomains (MDs) restricting protein mobility. The trafficking of membrane proteins is one of the key factors for long-term survival under stress conditions, for instance during exposure to photoinhibitory light conditions. However, the mobility of unbound 'free' proteins in thylakoid membrane is poorly characterized. In this work, we assessed the maximal diffusional ability of a small, unbound thylakoid membrane protein by semi-single molecule FCS (fluorescence correlation spectroscopy) method in the cyanobacterium Synechocystis sp. PCC6803. We utilized a GFP-tagged variant of the cytochrome b6f subunit PetC1 (PetC1-GFP), which was not assembled in the b6f complex due to the presence of the tag. Subsequent FCS measurements have identified a very fast diffusion of the PetC1-GFP protein in the thylakoid membrane (D = 0.14 - 2.95 µm2s-1). This means that the mobility of PetC1-GFP was comparable with that of free lipids and was 50-500 times higher in comparison to the mobility of proteins (e.g., IsiA, LHCII-light-harvesting complexes of PSII) naturally associated with larger thylakoid membrane complexes like photosystems. Our results thus demonstrate the ability of free thylakoid-membrane proteins to move very fast, revealing the crucial role of protein-protein interactions in the mobility restrictions for large thylakoid protein complexes.
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Affiliation(s)
- Radek Kaňa
- Center ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic; (R.S.); (J.K.)
- Correspondence:
| | - Gábor Steinbach
- Institute of Biophysics, Biological Research Center, 6726 Szeged, Hungary;
| | - Roman Sobotka
- Center ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic; (R.S.); (J.K.)
| | - György Vámosi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Josef Komenda
- Center ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic; (R.S.); (J.K.)
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23
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Saccon F, Durchan M, Bína D, Duffy CD, Ruban AV, Polívka T. A Protein Environment-Modulated Energy Dissipation Channel in LHCII Antenna Complex. iScience 2020; 23:101430. [PMID: 32818906 PMCID: PMC7452274 DOI: 10.1016/j.isci.2020.101430] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
The major light-harvesting complex of photosystem II (LHCII) is the main contributor to sunlight energy harvesting in plants. The flexible design of LHCII underlies a photoprotective mechanism whereby this complex switches to a dissipative state in response to high light stress, allowing the rapid dissipation of excess excitation energy (non-photochemical quenching, NPQ). In this work, we locked single LHCII trimers in a quenched conformation after immobilization of the complexes in polyacrylamide gels to impede protein interactions. A comparison of their pigment excited-state dynamics with quenched LHCII aggregates in buffer revealed the presence of a new spectral band at 515 nm arising after chlorophyll excitation. This is suggested to be the signature of a carotenoid excited state, linked to the quenching of chlorophyll singlet excited states. Our data highlight the marked sensitivity of pigment excited-state dynamics in LHCII to structural changes induced by the environment.
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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
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - David Bína
- University of South Bohemia, Institute of Chemistry, Faculty of Science, České Budějovice, Czech Republic
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Christopher D.P. Duffy
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, E1 4NS London, UK
| | - Alexander V. Ruban
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, E1 4NS London, UK
| | - Tomáš Polívka
- University of South Bohemia, Institute of Physics, Faculty of Science, České Budějovice, Czech Republic
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24
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Saccon F, Giovagnetti V, Shukla MK, Ruban AV. Rapid regulation of photosynthetic light harvesting in the absence of minor antenna and reaction centre complexes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3626-3637. [PMID: 32149343 PMCID: PMC7307847 DOI: 10.1093/jxb/eraa126] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/02/2020] [Indexed: 05/25/2023]
Abstract
Plants are subject to dramatic fluctuations in the intensity of sunlight throughout the day. When the photosynthetic machinery is exposed to high light, photons are absorbed in excess, potentially leading to oxidative damage of its delicate membrane components. A photoprotective molecular process called non-photochemical quenching (NPQ) is the fastest response carried out in the thylakoid membranes to harmlessly dissipate excess light energy. Despite having been intensely studied, the site and mechanism of this essential regulatory process are still debated. Here, we show that the main NPQ component called energy-dependent quenching (qE) is present in plants with photosynthetic membranes largely enriched in the major trimeric light-harvesting complex (LHC) II, while being deprived of all minor LHCs and most photosystem core proteins. This fast and reversible quenching depends upon thylakoid lumen acidification (ΔpH). Enhancing ΔpH amplifies the extent of the quenching and restores qE in the membranes lacking PSII subunit S protein (PsbS), whereas the carotenoid zeaxanthin modulates the kinetics and amplitude of the quenching. These findings highlight the self-regulatory properties of the photosynthetic light-harvesting membranes in vivo, where the ability to switch reversibly between the harvesting and dissipative states is an intrinsic property of the major LHCII.
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Affiliation(s)
- Francesco Saccon
- Queen Mary University of London, School of Biological and Chemical Sciences, London, UK
| | - Vasco Giovagnetti
- Queen Mary University of London, School of Biological and Chemical Sciences, London, UK
| | - Mahendra K Shukla
- Queen Mary University of London, School of Biological and Chemical Sciences, London, UK
| | - Alexander V Ruban
- Queen Mary University of London, School of Biological and Chemical Sciences, London, UK
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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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Murchie EH, Ruban AV. Dynamic non-photochemical quenching in plants: from molecular mechanism to productivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:885-896. [PMID: 31686424 DOI: 10.1111/tpj.14601] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/18/2019] [Accepted: 10/28/2019] [Indexed: 05/02/2023]
Abstract
Photoprotection refers to a set of well defined plant processes that help to prevent the deleterious effects of high and excess light on plant cells, especially within the chloroplast. Molecular components of chloroplast photoprotection are closely aligned with those of photosynthesis and together they influence productivity. Proof of principle now exists that major photoprotective processes such as non-photochemical quenching (NPQ) directly determine whole canopy photosynthesis, biomass and yield via prevention of photoinhibition and a momentary downregulation of photosynthetic quantum yield. However, this phenomenon has neither been quantified nor well characterized across different environments. Here we address this problem by assessing the existing literature with a different approach to that taken previously, beginning with our understanding of the molecular mechanism of NPQ and its regulation within dynamic environments. We then move to the leaf and the plant level, building an understanding of the circumstances (when and where) NPQ limits photosynthesis and linking to our understanding of how this might take place on a molecular and metabolic level. We argue that such approaches are needed to fine tune the relevant features necessary for improving dynamic NPQ in important crop species.
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Affiliation(s)
- Erik H Murchie
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Alexander V Ruban
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Daskalakis V, Papadatos S, Stergiannakos T. The conformational phase space of the photoprotective switch in the major light harvesting complex II. Chem Commun (Camb) 2020; 56:11215-11218. [DOI: 10.1039/d0cc04486e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Extensive conformational sampling of the major light harvesting complex II defines the collective variables of the photoprotective switch.
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Affiliation(s)
- Vangelis Daskalakis
- Department of Chemical Engineering
- Cyprus University of Technology
- 3603 Limassol
- Cyprus
| | - Sotiris Papadatos
- Department of Chemical Engineering
- Cyprus University of Technology
- 3603 Limassol
- Cyprus
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28
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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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