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Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

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PHOTOSYNTHESIS RESEARCH 2023年第1期156卷 89-100页

作者： Amin, Muhamed Univ Groningen Univ Coll Groningen Dept Sci Hoendiepskade 23-24 NL-9718 BG Groningen Netherlands Univ Groningen Groningen Biomol Sci & Biotechnol Inst Rijksuniv Groningen Netherlands Deutsch Elektronen Synchrotron DESY Ctr Free Electron Laser Sci Notkestr 85 D-22607 Hamburg Germany

Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn's oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S-1 state. However, significant discrepancies are observed for the excited XFEL states (S-2, S-3,S- and S-0) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

关键词： Serial femtosecond crystallography oxygen-evolving complex Machine learning

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High-efficiency oxygen evolution by photosystem II oxygen-evolving complex containing 3Mn per reaction center

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JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY 2023年第4期28卷 393-401页

作者： Semin, Boris K. Davletshina, Lira N. Moscow MV Lomonosov State Univ Fac Biol Dept Biophys Moscow 119234 Russia

Ca-depleted photosystem II membranes obtained by treatment with acidic buffer do not contain Ca2+ in the Mn4CaO5 cluster but contain all extrinsic proteins protecting this cluster (PSII(-Ca/low pH)). However, unlike native photosystem II, Mn cluster in PSII(-Ca/low pH) samples is available for small-sized reductants. Using this property, we investigated the substitution possibility of Mn cation(s) with Fe cation(s) to obtain a chimeric cluster in PSII(-Ca/low pH) samples containing extrinsic proteins. We found that Fe(II) cation replaces Mn cation at pH 6.5, however, PSII(-Ca/low pH) membranes with the 3Mn1Fe chimeric cluster in the oxygen-evolving complex evolve O-2 with high intensity in the presence of exogenous Ca2+. The O-2 evolution rate is about 80% of the same rate in PSII(-Ca/low pH) membranes. [GRAPHICS]

关键词： Photosystem II oxygen-evolving complex Manganese Ferrous iron Extrinsic proteins Calcium

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Current analysis of cations substitution in the oxygen-evolving complex of photosystem II

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BIOPHYSICAL REVIEWS 2024年第2期16卷 237-247页

作者： Semin, Boris Loktyushkin, Aleksey Lovyagina, Elena Lomonosov Moscow State Univ Fac Biol Dept Biophys Moscow 119234 Russia

Water oxidation in photosystem II (PSII) is performed by the oxygen-evolving complex Mn4CaO5 which can be extracted from PSII and then reconstructed using exogenous cations Mn(II) and Ca2+. The binding efficiency of other cations to the Mn-binding sites in Mn-depleted PSII was investigated without any positive results. At the same time, a study of the Fe cations interaction with Mn-binding sites showed that it binds at a level comparable with the binding of Mn cations. Binding of Fe(II) cations first requires its light-dependent oxidation. In general, the interaction of Fe(II) with Mn-depleted PSII has a number of features similar to the two-quantum model of photoactivation of the complex with the release of oxygen. Interestingly, incubation of Ca-depleted PSII with Fe(II) cations under certain conditions is accompanied by the formation of a chimeric cluster Mn/Fe in the oxygen-evolving complex. PSII with the cluster 2Mn2Fe was found to be capable of water oxidation, but only to the H2O2 intermediate. However, the cluster 3Mn1Fe can oxidize water to O2 with an efficiency about 25% of the original in the absence of extrinsic proteins PsbQ and PsbP. In the presence of these proteins, the efficiency of O2 evolution can reach 80% of the original when adding exogenous Ca2+. In this review, we summarized information on the formation of chimeric Mn-Fe clusters in the oxygen-evolving complex. The data cited may be useful for detailing the mechanism of water oxidation.

关键词： Photosystem II oxygen-evolving complex Iron Manganese Manganese replacement Calcium

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Chloride facilitates Mn(III) formation during photoassembly of the Photosystem II oxygen-evolving complex

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PHOTOSYNTHESIS RESEARCH 2022年第3期152卷 283-288页

作者： Russell, Brandon P. Vinyard, David J. Louisiana State Univ Dept Biol Sci Baton Rouge LA 70803 USA

The Mn4Ca oxygen-evolving complex (OEC) in Photosystem II (PSII) is assembled in situ from free Mn2+, Ca2+, and water. In an early light-driven step, Mn2+ in a protein high-affinity site is oxidized to Mn3+. Using dual-mode electron paramagnetic resonance spectroscopy, we observed that Mn3+ accumulation increases as chloride concentration increases in spinach PSII membranes depleted of all extrinsic subunits. At physiologically relevant pH values, this effect requires the presence of calcium. When combined with pH studies, we conclude that the first Mn2+ oxidation event in OEC assembly requires a deprotonation that is facilitated by chloride.

关键词： Photosystem II oxygen-evolving complex Assembly Electron paramagnetic resonance spectroscopy

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Mechanism of Inhibition of the oxygen-evolving complex of Photosystem II by Lanthanide Cations

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Biophysics (Russian Federation) 2023年第4期68卷 519-524页

作者： Lovyagina, E.R. Loktyushkin, A.V. Vasiliev, N.S. Semin, B.K. Faculty of Biology Moscow State University Moscow 119234 Russian Federation

Abstract: The interaction of La3+ and Tb3+ cations with the Ca-binding site of the oxygen-evolving complex of photosystem II samples depleted of calcium has been studied. The binding of cations to the Ca-binding site ... 详细信息

Abstract: The interaction of La³⁺ and Tb³⁺ cations with the Ca-binding site of the oxygen-evolving complex of photosystem II samples depleted of calcium has been studied. The binding of cations to the Ca-binding site is irreversible and the bound cations cannot be washed out or replaced by Ca²⁺ cations. The feature of lanthanides to bind strongly to the Ca-binding site was used to investigate whether the bound Ln³⁺ cation has an effect on the high-affinity Mn-binding site of the oxygen-evolving complex. For this purpose, hydroquinone was used to extract manganese cations from the oxygen-evolving complex of the calcium-depleted photosystem II membranes with the Ca-binding site blocked by La³⁺ or Tb³⁺, and the activity of the high-affinity site was then examined using exogenous electron donors (Mn²⁺ + H₂O₂) and 1,5-diphenylcarbazide. It was found that lanthanide cations bound to the Ca-binding site significantly inhibited oxidation of electron donors through the high-affinity Mn-binding site. The mechanism of the observed effect is discussed. © 2023, Pleiades Publishing, Inc.

关键词： calcium high-affinity Mn-binding site lanthanides oxygen-evolving complex photosystem II

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Peculiarities of Mn(II) Cation Oxidation in the Photosystem II without an oxygen-evolving complex: Evolutionary Aspect

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Moscow University Biological Sciences Bulletin 2022年第2期77卷 92-97页

作者： Lovyagina, E.R. Davletshina, L.N. Semin, B.K. Department of Biophysics School of Biology Moscow State University Moscow 119234 Russian Federation

Abstract: One of the main reactions in the process of light energy transformation in oxygenic organisms is the extraction of electrons from water, which are necessary for the light stage of photosynthesis. The light-dependent oxidation of water is carried out by an oxygen-evolving complex (OEC), the catalytic center of which is the cluster Mn₄CaO₅. OEC is located in photosystem II (PSII) on the lumen side of the thylakoid membrane. The evolutionary origin of the PSII is unclear, as is the origin of the manganese cluster in the OEC. Recently, Johnson et al. (2013) suggested that, in the primary PSII in the Archean period, the cluster Mn₄CaO₅ was absent, and PSII oxidized not water but Mn (II) cations, i.e., manganese cations were the source of electrons. In the presented work, the authors investigated the possibility of the influence of some environmental factors (citrate and hydrogen peroxide) on the oxidation rate of Mn(II) cations by a PSII that does not contain OEC. It was found that citrate inhibit the oxidation of Mn(II) cations binding them but does not extract Mn cations from OEC. Hydrogen peroxide, on the contrary, significantly increases the oxidation rate of manganese (from 28 ± 2 to 145 ± 7 µmol 2,6-dichlorophenolindophenol mg Chl^–1 h^–1 in the presence of H₂O₂). Such effects should be taken into account when investigating the oxidation of manganese cations by the photosystem as a possible source of electrons in the early stages of evolution. © 2022, Allerton Press, Inc.

关键词： citrate evolution of photosystems hydrogen peroxide manganese oxygen-evolving complex photosystem II

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CaMn₃₍IV)O4 Cubane Models of the oxygen-evolving complex: Spin Ground States S9/2 and the Effect of Oxo Protonation

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ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2021年第32期60卷 17671-17679页

作者： Lee, Heui Beom Shiau, Angela A. Marchiori, David A. Oyala, Paul H. Yoo, Byung-Kuk Kaiser, Jens T. Rees, Douglas C. Britt, R. David Agapie, Theodor CALTECH Dept Chem & Chem Engn 1200 E Calif Blvd MC 127-72 Pasadena CA 91125 USA Univ Calif Davis Dept Chem One Shields Ave Davis CA 95616 USA

We report the single crystal XRD and MicroED structure, magnetic susceptibility, and EPR data of a series of (CaMn3O4)-O-IV and (YMn3O4)-O-IV complexes as structural and spectroscopic models of the cuboidal subunit of the oxygen-evolving complex (OEC). The effect of changes in heterometal identity, cluster geometry, and bridging oxo protonation on the spin-state structure was investigated. In contrast to previous computational models, we show that the spin ground state of (CaMn3O4)-O-IV complexes and variants with protonated oxo moieties need not be S=9/2. Desymmetrization of the pseudo-C-3-symmetric Ca(Y)(Mn3O4)-O-IV core leads to a lower S=5/2 spin ground state. The magnitude of the magnetic exchange coupling is attenuated upon oxo protonation, and an S=3/2 spin ground state is observed in (CaMn3O3)-O-IV(OH). Our studies complement the observation that the interconversion between the low-spin and high-spin forms of the S-2 state is pH-dependent, suggesting that the (de)protonation of bridging or terminal oxygen atoms in the OEC may be connected to spin-state changes.

关键词： electronic structure magnetic susceptibility model complexes oxygen-evolving complex spin states

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Conformational changes in a Photosystem II hydrogen bond network stabilize the oxygen-evolving complex

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BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2024年第1期1865卷 149020页

作者： Russell, Brandon P. Vinyard, David J. Louisiana State Univ Dept Biol Sci 202 Life Sci Bldg Baton Rouge LA 70803 USA

The Mn4CaO5 oxygen-evolving complex (OEC) in Photosystem II (PSII) is assembled in situ and catalyzes water oxidation. After OEC assembly, the PsbO extrinsic subunit docks to the lumenal face of PSII and both stabilizes the OEC and facilitates efficient proton transfer to the lumen. D1 residue R334 is part of a hydrogen bond network involved in proton release during catalysis and interacts directly with PsbO. D1-R334 has recently been observed in different conformations in apo-and holo-OEC PSII structures. We generated a D1-R334G point mutant in Synechocystis sp. PCC 6803 to better understand this residue's function. D1-R334G PSII is active under continuous light, but the OEC is unstable in darkness. Isolated D1-R334G core complexes have little bound PsbO and less manganese as the wild type control. The S2 intermediate is stabilized in D1-R334G indicating that the local environment around the OEC has been altered. These results suggest that the hydrogen bond network that includes D1-R334 exists in a different functional conformation during PSII biogenesis in the absence of PsbO.

关键词： Photosystem II oxygen-evolving complex Water oxidation Hydrogen-bonding network Proton transport

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Physiological Role of pH-Dependent Structural Transition in oxygen-evolving complex of PSII

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RUSSIAN JOURNAL OF PLANT PHYSIOLOGY 2023年第1期70卷 1-1页

作者： Semin, B. K. Davletshina, L. N. Loktyushkin, A. V. Lovyagina, E. R. Moscow MV Lomonosov State Univ Moscow Russia

Photosystem II (PSII) of the photosynthetic apparatus in oxygenic organisms contains a catalytic center that performs one of the most important reactions in bioenergetics: light-dependent water oxidation to molecular oxygen. The catalytic center is a Mn4CaO5 cluster consisting of four cations of manganese and one calcium cation linked by oxygen bridges. The authors reported earlier that a structural transition occurs at pH 5.7 in the cluster resulting in changes in manganese cation(s) redox potential and elevation of the Mn-clus-ter resistance to reducing agents. The discovered effect was examined in a series of investigations that are reviewed in this work. It was found that, at pH 5.7, Fe(II) cations replace not two manganese cations as it happens at pH 6.5 but only one cation;as a result, a chimeric Mn3Fe1 cluster is produced. In the presence of exogenous calcium ions, membrane preparations of PSII with such a chimeric cluster are capable of evolving oxygen in the light (at a rate of approximately 25% of the rate in native PSII). It was found that photoinhibition that greatly depends on the processes of oxidation or reduction at pH 5.7 slows down as compared with pH 6.5. PSII preparations were also more resistant to thermal inactivation at pH 5.7 than at pH 6.5. However, in PSII preparations lacking manganese cations in the oxygen-evolving complex, the rates of photoinhibition at pH 6.5 and 5.7 did not differ. In thylakoid membranes, protonophores that abolish the proton gradient and increase pH in the lumen (where the manganese cluster is located) from 5.7 to 7.0 considerably elevated the rate of PSII photoinhibition. It is assumed that the structural transition in the Mn-cluster at pH 5.7 is involved in the mechanisms of PSII defense against photoinhibition.

关键词： pH dependence iron calcium oxygen oxygen-evolving complex manganese thylakoid photoinhibition photosystem II

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The Thermal Stability of Electron Transfer in Membrane Preparations of Photosystem II with a Ca ²⁺ -Depleted oxygen-evolving complex

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Biophysics (Russian Federation) 2021年第1期66卷 65-69页

作者： Lovyagina, E.R. Semin, B.K. Department of Biology Moscow State University Moscow 119234 Russian Federation

The temperature stability of electron transfer to the artificial electron acceptor 2,6-dichlorophenolindophenol in preparations of native photosystem II and photosystem II without the calcium cation in an oxygen-evolving complex was studied. The thermal stability of the processes of oxygen evolution and electron transfer from the oxygen-evolving complex to 2,6-dichlorophenolindophenol in photosystem II were significantly different: the reduction of 2,6-dichlorophenolindophenol was more resistant to temperature than oxygen evolution. The reaction of 2,6-dichlorophenolindophenol reduction in the Ca²⁺-depleted preparations of photosystem II was less resistant to heating than in the preparations of native photosystem II. The thermal inactivation of the photosystem II in the Ca²⁺-depleted membrane preparations was inhibited by cytochrome c at a concentration of 50 cytochrome c molecules per a photosystem II reaction center. The activity of this preparation (the rate of the 2,6-dichlorophenolindophenol reduction) increased by 19%, approaching the activity of the native photosystem II. The protective effect of cytochrome c appears to be determined by its protein nature, rather than its redox activity, since an equal protective effect was observed upon the addition of albumin at a similar concentration. Almost complete inactivation of the 2,6-dichlorophenolindophenol reduction reaction in the native and Ca²⁺-depleted preparations of photosystem II was observed at the same temperature (50°C). According to the EPR data, photosystem II in the Ca²⁺-depleted preparation after incubation at this temperature lacked a manganese cluster, while a peripheral protein of 33 kDa was present. © 2021, Pleiades Publishing, Inc.

关键词： calcium Keywords: photosystem II oxygen-evolving complex temperature stability

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