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Narzi D, Guidoni L. Structural and dynamic insights into Mn 4Ca cluster-depleted Photosystem II. Phys Chem Chem Phys 2021; 23:27428-27436. [PMID: 34860219 DOI: 10.1039/d1cp02367e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the first steps of natural oxygenic photosynthesis, sunlight is used to oxidize water molecules to protons, electrons and molecular oxygen. This reaction takes place on the Mn4Ca cluster located in the reaction centre of Photosystem II (PSII), where the cluster is assembled and continuously repaired through a process known as photoactivation. Understanding the molecular details of such a process has important implications in different fields, in particular inspiring synthesis and repair strategies for artificial photosynthesis devices. In this regard, a detailed structural and dynamic characterization of Photosystem II lacking a Mn4Ca cluster, namely apo PSII, is a prerequisite for the full comprehension of the photoactivation. Recently, the structure of the apo PSII was resolved at 2.55 Å resolution [Zhang et al., eLife, 2017, 6, e26933], suggesting a pre-organized structure of the protein cavity hosting the cluster. Anyway, the question of whether these findings are a feature of the method used remains open. Here, by means of classical Molecular Dynamics simulations, we characterized the structural and dynamic features of the apo PSII for different protonation states of the cluster cavity. Albeit an overall conformational stability common to all investigated systems, we found significant deviations in the conformation of the side chains of the active site with respect to the X-ray positions. Our findings suggest that not all residues acting as Mn ligands are pre-organized prior to the Mn4Ca formation and previous local conformational changes are required in order to bind the first Mn ion in the high-affinity binding site.
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Affiliation(s)
- Daniele Narzi
- Department of Physical and Chemical Science, Università dellAquila, LAquila, Italy.
| | - Leonardo Guidoni
- Department of Physical and Chemical Science, Università dellAquila, LAquila, Italy.
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Sirohiwal A, Neese F, Pantazis DA. Protein Matrix Control of Reaction Center Excitation in Photosystem II. J Am Chem Soc 2020; 142:18174-18190. [PMID: 33034453 PMCID: PMC7582616 DOI: 10.1021/jacs.0c08526] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Indexed: 02/06/2023]
Abstract
Photosystem II (PSII) is a multisubunit pigment-protein complex that uses light-induced charge separation to power oxygenic photosynthesis. Its reaction center chromophores, where the charge transfer cascade is initiated, are arranged symmetrically along the D1 and D2 core polypeptides and comprise four chlorophyll (PD1, PD2, ChlD1, ChlD2) and two pheophytin molecules (PheoD1 and PheoD2). Evolution favored productive electron transfer only via the D1 branch, with the precise nature of primary excitation and the factors that control asymmetric charge transfer remaining under investigation. Here we present a detailed atomistic description for both. We combine large-scale simulations of membrane-embedded PSII with high-level quantum-mechanics/molecular-mechanics (QM/MM) calculations of individual and coupled reaction center chromophores to describe reaction center excited states. We employ both range-separated time-dependent density functional theory and the recently developed domain based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD), the first coupled cluster QM/MM calculations of the reaction center. We find that the protein matrix is exclusively responsible for both transverse (chlorophylls versus pheophytins) and lateral (D1 versus D2 branch) excitation asymmetry, making ChlD1 the chromophore with the lowest site energy. Multipigment calculations show that the protein matrix renders the ChlD1 → PheoD1 charge-transfer the lowest energy excitation globally within the reaction center, lower than any pigment-centered local excitation. Remarkably, no low-energy charge transfer states are located within the "special pair" PD1-PD2, which is therefore excluded as the site of initial charge separation in PSII. Finally, molecular dynamics simulations suggest that modulation of the electrostatic environment due to protein conformational flexibility enables direct excitation of low-lying charge transfer states by far-red light.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fakultät
für Chemie und Biochemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Narzi D, Coccia E, Manzoli M, Guidoni L. Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II. Biophys Chem 2017; 229:93-98. [DOI: 10.1016/j.bpc.2017.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 01/31/2023]
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Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
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de Jong DH, Liguori N, van den Berg T, Arnarez C, Periole X, Marrink SJ. Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex. J Phys Chem B 2015; 119:7791-803. [PMID: 26053327 DOI: 10.1021/acs.jpcb.5b00809] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and β-carotene. Parameters were also obtained for ubiquinol and ubiquinone, related cofactors involved in the respiratory chain. Parameters were derived at both atomistic and coarse grain (CG) resolutions, compatible with the building blocks of the GROMOS united-atom and Martini CG force fields, respectively. Structural and thermodynamic properties of the cofactors were compared to experimental values when available. The topologies were further tested in molecular dynamics simulations of the cofactors in their physiological environment, e.g., either in a lipid membrane environment or in complex with the heme binding protein bacterioferritin.
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Affiliation(s)
| | - Nicoletta Liguori
- ‡Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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Zhang L, Silva DA, Zhang H, Yue A, Yan Y, Huang X. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre. Nat Commun 2014; 5:4170. [PMID: 24954746 PMCID: PMC4083425 DOI: 10.1038/ncomms5170] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 05/20/2014] [Indexed: 11/11/2022] Open
Abstract
One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis. Cofactor-mediated energy and electron transfer in photosystem II occurs preferentially through one branch of the reaction centre, despite there being a symmetric path available. Here, the authors use computational methods to determine the influence of protein conformation on this selectivity.
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Affiliation(s)
- Lu Zhang
- Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Daniel-Adriano Silva
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2]
| | - Houdao Zhang
- Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Alexander Yue
- Division of Biomedical Engineering, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - YiJing Yan
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2] Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Xuhui Huang
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2] Division of Biomedical Engineering, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [3] Centre of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
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Zhang L, Silva DA, Yan Y, Huang X. Force field development for cofactors in the photosystem II. J Comput Chem 2012; 33:1969-80. [DOI: 10.1002/jcc.23016] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/05/2012] [Accepted: 04/22/2012] [Indexed: 01/03/2023]
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