Language：Japanese   Publisher：Japan Synchrotron Radiation Research Institute  

DOI： 10.18957/rr.9.4.177

Language：English  

DOI： 10.2142/biophysico.bppb-v18.021

PubMed

Language：English   Publisher：Journal of Physical Chemistry Letters  

The high-spin S2 state was investigated with photosystem II (PSII) from spinach, Thermosynechococcus vulcanus, and Cyanidioschyzon merolae. In extrinsic protein-depleted PSII, high-spin electron paramagnetic resonance (EPR) signals were not detected in either species, whereas all species showed g ∼5 signals in the presence of a high concentration of Ca2+ instead of the multiline signal. In the intact and PsbP/Q-depleted PSII from spinach, the g = 4.1 EPR signal was detected. These results show that formation of the high-spin S2 state of the manganese cluster is regulated by the extrinsic proteins through a charge located near the Mn4 atom in the Mn4CaO5 cluster but is independent of the intrinsic proteins. The shift to the g ∼5 state is caused by tilting of the z-axis in the Mn4 coordinates through hydrogen bonds or external divalent cations. The structural modification may allow insertion of an oxygen atom during the S2-to-S3 transition.

DOI： 10.1021/acs.jpclett.0c02411

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Language：Japanese   Publisher：Japanese Journal of Applied Physics  

X-ray fluorescence holography (XFH) is a technique that can directly image the 3D arrangement of atoms around an element in a sample. The holograms contain both intensity and phase information, allowing atomic reconstruction without needing prior structural information or a tentative structural model. XFH has already been used to reveal the local structures of various inorganic samples, and recently, work has begun on XFH for soft matter. In this paper, we review the progress of XFH on soft materials. First, we review the fundamental principles of XFH. Second, we review inverse mode XFH on soft materials, and the results of the experiments on hemoglobin, myoglobin, and κ-(BEDT-TTF)2Cu[N(CN)2]Br crystals. In the last section, we report the progress of the development of normal mode holography for soft materials. The new apparatus and scanning method is described, and results of the initial tests on the protein Photosystem II are discussed.

DOI： 10.7567/1347-4065/ab5d55

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Language：English   Publisher：Biochimica et Biophysica Acta - Bioenergetics  

Photosynthetic [2Fe-2S] plant-type ferredoxins have a central role in electron transfer between the photosynthetic chain and various metabolic pathways. Several genes are coding for [2Fe–2S] ferredoxins in cyanobacteria, with four in the thermophilic cyanobacterium Thermosynechococcus elongatus. The structure and functional properties of the major ferredoxin Fd1 are well known but data on the other ferredoxins are scarce. We report the structural and functional properties of a novel minor type ferredoxin, Fd2 of T. elongatus, homologous to Fed4 from Synechocystis sp. PCC 6803. Remarkably, the midpoint potential of Fd2, Em = −440 mV, is lower than that of Fd1, Em = −372 mV. However, while Fd2 can efficiently react with photosystem I or nitrite reductase, time-resolved spectroscopy shows that Fd2 has a very low capacity to reduce ferredoxin-NADP+ oxidoreductase (FNR). These unique Fd2 properties are discussed in relation with its structure, solved at 1.38 Å resolution. The Fd2 structure significantly differs from other known ferredoxins structures in loop 2, N-terminal region, hydrogen bonding networks and surface charge distributions. UV–Vis, EPR, and Mid- and Far-IR data also show that the electronic properties of the [2Fe–2S] cluster of Fd2 and its interaction with the protein differ from those of Fd1 both in the oxidized and reduced states. The structural analysis allows to propose that valine in the motif Cys53ValAsnCys56 of Fd2 and the specific orientation of Phe72, explain the electron transfer properties of Fd2. Strikingly, the nature of these residues correlates with different phylogenetic groups of cyanobacterial Fds. With its low redox potential and its discrimination against FNR, Fd2 exhibits a unique capacity to direct efficiently photosynthetic electrons to metabolic pathways not dependent on FNR.

DOI： 10.1016/j.bbabio.2019.148084

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Language：Japanese  

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Language：Japanese   Publisher：Science  

Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reve cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

DOI： 10.1126/science.aax6998

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Language：English   Publisher：Structural Dynamics  

An experimental system, SPINETT (SACLA Pump-probe INstrumEnt for Tracking Transient dynamics), dedicated for ultrafast pump-probe experiments using X-ray free-electron lasers has been developed. SPINETT consists of a chamber operated under 1 atm helium pressure, two Von Hamos spectrometers, and a large two-dimensional detector having a short work distance. This platform covers complementary X-ray techniques; one can perform time-resolved X-ray absorption spectroscopy, time-resolved X-ray emission spectroscopy, and time-resolved X-ray diffuse scattering. Two types of liquid injectors have been prepared for low-viscosity chemical solutions and for protein microcrystals embedded in a matrix. We performed a test experiment at SPring-8 Angstrom Compact free-electron LAser and demonstrated the capability of SPINETT to obtain the local electronic structure and geometrical information simultaneously.

DOI： 10.1063/1.5111795

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Language：Japanese   Publisher：Journal of the Physical Society of Japan  

The photosynthetic water oxidation reaction in photosystem II (PSII) causes the ejection of four protons (H+) and electrons from the substrate water bound to the Mn4CaO5 cluster, denoting the catalytic center of the system. Two Cl− ions, Cl1 and Cl2 sites, were found in the vicinity of the Mn4CaO5 moiety. Herein, a novel H+ transfer mechanism (amide H+ exchange-driven scheme) was identified to operate in the Cl2 pathway based on the hybrid ab initio quantum mechanics (QM) molecular dynamics (MD) simulations of PSII. The analysis revealed that H+ can be displaced across the peptide bond of the D1-His337 and D1-Asn338 backbones, interrupting the hydrogen bond network spanning to the lumenal side in the crystal structure. The estimated energy barrier was consistent with the previous kinetic data. This is the first report to address unidirectional H+ transfer through a peptide bond based on the theoretical analysis involving the environmental protein structure.

DOI： 10.7566/JPSJ.88.084802

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Language：English   Publisher：Journal of Physical Chemistry Letters  

The dynamics of the intact photosystem II core complex (PSII-CC) has been investigated extensively to elucidate its excellent photofunction. However, it is significantly difficult to observe the primary photosynthetic processes in PSII-CC because a vast number of chlorophylls (Chl) in the core complex show similar spectral features. In the present work, the dynamics of the energy transfer (ET) from β-carotene (Bcr) in intact PSII-CC followed by charge separation (CS) at the reaction center (RC) with different excitation wavelengths were compared. Upon excitation at 510 nm, which selectively excites Bcr (Bcr651) inside of the D1-D2 RC, the pheophytin anion absorption band appeared within 9.6 ps. On the other hand, upon excitation at 490 nm, mainly exciting unspecified Bcr in the antenna complex, the anion band appeared after 20 ps. These excitation wavelength dependence experiments revealed a new ET pathway of PSII-CC, which indicates that the initial CS of PSII-CC is limited by ET to the RC.

DOI： 10.1021/acs.jpclett.9b01072

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Language：English   Publisher：Science  

Diatoms are abundant photosynthetic organisms in aquatic environments and contribute 40% of its primary productivity. An important factor that contributes to the success of diatoms is their fucoxanthin chlorophyll a/c-binding proteins (FCPs), which have exceptional light-harvesting and photoprotection capabilities. Here, we report the crystal structure of an FCP from the marine diatom Phaeodactylum tricornutum, which reveals the binding of seven chlorophylls (Chls) a, two Chls c, seven fucoxanthins (Fxs), and probably one diadinoxanthin within the protein scaffold. Efficient energy transfer pathways can be found between Chl a and c, and each Fx is surrounded by Chls, enabling the energy transfer and quenching via Fx highly efficient. The structure provides a basis for elucidating the mechanisms of blue-green light harvesting, energy transfer, and dissipation in diatoms.

DOI： 10.1126/science.aav0365

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Language：Japanese  

DOI： 10.1107/S010876731909648X

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Language：Japanese   Publisher：Advances in Quantum Chemistry  

Atmospheric oxygenation and evolution of aerobic life on our earth are a result of water oxidation by oxygenic photosynthesis in photosystem II (PSII) of plants, algae, and cyanobacteria. The water oxidation in the oxygen-evolving complex (OEC) of PSII is expected to proceed through five oxidation states, known as the Si (i = 0, 1, 2, 3, and 4) states in the Kok cycle, with the S1 being the most stable state in the dark. The OEC in PSII involves the active catalytic site made of four Mn ions and one Ca ion, namely the CaMn4O5 cluster. Past decades, molecular structures of the CaMn4O5 cluster in OEC of PSII have been investigated by the extended X-ray absorption fine structure (EXAFS). The magnetostructural correlations were extensively investigated by EPR spectroscopy. Recently, Kamiya and Shen groups made a great breakthrough for determination of the S1 structure of OEC of PSII by the X-ray diffraction (XRD) and X-ray free electron laser (XFEL) experiments, providing structural foundations that are crucial for theoretical investigations of structure and reactivity of the CaMn4O5 cluster. Large-scale QM/MM calculations starting from the XRD structures elucidated geometrical, electronic, and spin structures of the CaMn4O5 cluster, indicating an important role of the Jahn–Teller (JT) effect of Mn(III) ions. This review fully examines our theoretical formulae for estimation of the Jahn–Teller deformations of the CaMn4O5 cluster in OEC of PSII. Scope and applicability of the JT deformation formulae are elucidated in relation to several different structures of the CaMn4O5 cluster proposed by XRD, XFEL, EXAFS, and other experiments. Subtle differences among XRD, XFEL, and EXAFS structures in the S1 state are examined in relation to environmental effects for the CaMn4O5 cluster in OEC of PSII. The X-ray damage of the serial femtosecond crystallography (SFX) by XFEL is also examined in relation to the damage-free low-dose (LD) XRD structure. The JT deformation formulae are also applied to theoretical analysis of the S3 structures by SFX. Implications of the computational results are discussed for further refinements of geometrical parameters of the CaMn4O5 cluster in OEC of PSII and possible mechanisms of water oxidation in OEC of PSII.

DOI： 10.1016/bs.aiq.2018.05.003

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DOI： 10.1107/S2053273314084976

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DOI： 10.1107/S2053273314096491

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DOI： 10.1107/S0108767311091082

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DOI： 10.1080/00405000.2010.498974

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Publishing type：Research paper (scientific journal)  

Energy transfer reactions are important in photosynthetic systems as natural systems and solar cells as artificial systems. Especially in the biological system, the energy transfer reaction from the phycobilisome to the photoreaction system is the essence. Femtosecond transient absorption microscopy was utilized for the phycocyanin protein in crystals. The energy transfer reactions among pigments were observed with the changes in spectral shape. The time constants of energy transfer to the respective electronic states of 760 fs, 17 ps, and 62 ps were obtained. Transient absorption microscopy is a powerful nanotool for measuring the carrier dynamics in a microcrystal.

DOI： 10.35848/1347-4065/acc3a9

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Publishing type：Research paper (scientific journal)   Publisher：The Chemical Society of Japan  

DOI： 10.1246/bcsj.20200187

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Language：English   Publishing type：Research paper (scientific journal)  

Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported. We analyzed the activities of PSII from an SQDG-deficient mutant of the cyanobacterium Thermosynechococcus elongatus by various spectroscopic methods, which showed that depletion of SQDG partially impaired the PSII activity by impairing secondary quinone (QB) exchange at the acceptor site. We further solved the crystal structure of the PSII dimer from the SQDG deletion mutant at 2.1 Å resolution and found that all of the four SQDG-binding sites were occupied by other lipids, most likely PG molecules. Replacement of SQDG at a site near the head of QB provides a possible explanation for the QB impairment. The replacement of two SQDGs located at the monomer-monomer interface by other lipids decreased the stability of the PSII dimer, resulting in an increase in the amount of PSII monomer in the mutant. The present results thus suggest that although SQDG binding in all of the PSII-binding sites is necessary to fully maintain the activity and stability of PSII, replacement of SQDG by other lipids can partially compensate for their functions.

DOI： 10.1074/jbc.RA118.004304

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society  

Photosynthetic water oxidation is performed in photosystem II (PSII) through a light-driven cycle of intermediates called S states (S0-S4) at the water oxidizing center. Time-resolved serial femtosecond crystallography (SFX) has recently been applied to the microcrystals of PSII to obtain the structural information on these intermediates. However, it remains unanswered whether the reactions efficiently proceed throughout the S-state cycle retaining the native structures of the intermediates in PSII crystals. We investigated the water oxidation reactions in the PSII microcrystals using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. In comparison with the FTIR spectra in solution, it was shown that all of the metastable intermediates in the microcrystals retained their native structures, and the efficiencies of the S-state transitions remained relatively high, although those of the S2 → S3 and S3 → S0 transitions were slightly lowered possibly due to some restriction of water movement in the crystals.

DOI： 10.1021/acs.jpclett.8b00638

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

Tanaka et al. (J. Am. Chem. Soc., 2017, 139, 1718) recently reported the three-dimensional (3D) structure of the oxygen evolving complex (OEC) of photosystem II (PSII) by X-ray diffraction (XRD) using extremely low X-ray doses of 0.03 and 0.12 MGy. They observed two different 3D structures of the CaMn4O5 cluster with different hydrogen-bonding interactions in the S1 state of OEC keeping the surrounding polypeptide frameworks of PSII the same. Our Jahn-Teller (JT) deformation formula based on large-scale quantum mechanics/molecular mechanics (QM/MM) was applied for these low-dose XRD structures, elucidating important roles of JT effects of the MnIII ion for subtle geometric distortions of the CaMn4O5 cluster in OEC of PSII. The JT deformation formula revealed the similarity between the low-dose XRD and damage-free serial femtosecond X-ray diffraction (SFX) structures of the CaMn4O5 cluster in the dark stable state. The extremely low-dose XRD structures were not damaged by X-ray irradiation. Implications of the present results are discussed in relation to recent SFX results and a blue print for the design of artificial photocatalysts for water oxidation.

DOI： 10.1002/cptc.201700162

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids. After initial light excitation, the charge separation produces an electron, which is transferred to a plastoquinone molecule (Q(A)) and then to another plastoquinone (Q(B)). PsbM is a low-molecular-weight subunit with one transmembrane helix, and is located in the monomer-monomer interface of the PSII dimer. The function of PsbM has been reported to be stabilization of the PSII dimer and maintenance of electron transfer efficiency of PSII based on previous X-ray crystal structure analysis at a resolution of 4.2 angstrom. In order to elucidate the structure-function relationships of PsbM in detail, we improved the quality of PSII crystals from a PsbM-deleted mutant (Delta PsbM-PSII) of Thermosynechococcus elongatus, and succeeded in improving the diffraction quality to a resolution of 2.2 angstrom. X-ray crystal structure analysis of Delta PsbM-PSII showed that electron densities for the PsbM subunit and neighboring carotenoid and detergent molecules were absent in the monomer-monomer interface. The overall structure of Delta PsbM-PSII was similar to wild-type PSII, but the arrangement of the hydrophobic transmembrane subunits was significantly changed by the deletion of PsbM, resulting in a slight widening of the lipid hole involving Q(B). The lipid hole-widening further induced structural changes of the bicarbonate ion coordinated to the non-heme Fe(II) atom and destabilized the polypeptide chains around the Q(B) binding site located far from the position of PsbM. The fluorescence decay measurement indicated that the electron transfer rate from Q(A) to Q(B) was decreased in DPsbM-PSII compared with wild-type PSII. The functional change in electron transfer efficiency was fully interpreted based on structural changes caused by the deletion of the PsbM subunit.

DOI： 10.1039/c6fd00213g

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the QB/non-haem iron and the Mn4CaO5 cluster. The changes around the QB/non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 Å from the Mn4CaO5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ4-oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously.

DOI： 10.1038/nature21400

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Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S205327331709475X

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Energy transfer dynamics in monomer and dimer of the photosystem II core complex (PSII-CC) was investigated by means of femtosecond transient absorption (TA) spectroscopy. There is no profound difference between the TA dynamics of the monomer and the dimer in the weak excitation intensity condition (≤21 nJ). However, the fast recovery of the ground state bleach was pronounced at higher excitation intensities, and the excitation intensity dependence of the dimer was more significant than that of the monomer. This result indicates efficient exciton-exciton annihilation taking place in the dimer due to energy transfer between the two monomer units. The annihilation dynamics was reproduced by a simple model based on binomial theorem, which indicated that although PSII-CC dimer has two reaction centers, only one charge-separated state remained after annihilation.

DOI： 10.1021/jacs.6b04316

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：OSA - The Optical Society  

Energy transfer dynamics of photosystem II monomer and dimer were compared by femtosecond transient absorption (TA) spectroscopy. Excitation energy dependence suggested more excellent quenching ability of dimer by exciton-exciton annihilation.

DOI： 10.1364/UP.2016.UTu4A.40

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

DOI： 10.1074/jbc.M115.711689

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Language：English   Publishing type：Research paper (scientific journal)  

Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

Full geometry optimizations followed by the vibrational analysis were performed for eight spin configurations of the CaMn4O4X(H2O) 3Y (X = O, OH; Y = H2O, OH) cluster in the S-1 and S-3 states of the oxygen evolution complex (OEC) of photosystem II (PSII). The energy gaps among these configurations obtained by vertical, adiabatic and adiabatic plus zero-point-energy (ZPE) correction procedures have been used for computation of the effective exchange integrals (J) in the spin Hamiltonian model. The J values are calculated by the ( 1) analytical method and the ( 2) generalized approximate spin projection (AP) method that eliminates the spin contamination errors of UB3LYP solutions. Using J values derived from these methods, exact diagonalization of the spin Hamiltonian matrix was carried out, yielding excitation energies and spin densities of the ground and lower-excited states of the cluster. The obtained results for the right (R)- and left (L)-opened structures in the S-1 and S-3 states are found to be consistent with available optical and magnetic experimental results. Implications of the computational results are discussed in relation to ( a) the necessity of the exact diagonalization for computations of reliable energy levels, (b) magneto-structural correlations in the CaMn4O5 cluster of the OEC of PSII, (c) structural symmetry breaking in the S-1 and S-3 states, and (d) the right- and left-handed scenarios for the O-O bond formation for water oxidation.

DOI： 10.1039/c4cp00282b

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The electron density map of the 3D crystal of Photosystem II from Thermosynechococcus vulcanus with a 1.9 Å resolution (PDB: 3ARC ) exhibits, in the two monomers in the asymmetric unit cell, an, until now, unidentified and uninterpreted strong difference in electron density centered at a distance of around 1.5 Å from the nitrogen Nδ of the imidazole ring of D2-His336. By MALDI-TOF/MS upon tryptic digestion, it is shown that ~20-30% of the fragments containing the D2-His336 residue of Photosystem II from both Thermosynechococcus vulcanus and Thermosynechococcus elongatus bear an extra mass of +16 Da. Such an extra mass likely corresponds to an unprecedented post-translational or chemical hydroxyl modification of histidine.

DOI： 10.1021/bi401213m

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca(2+) in this cluster and the possible location of water substrates in this process, we crystallized Sr(2+)-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 Å, and compared it with the 1.9 Å structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the Mn4CaO5-cluster relative to that of Ca(2+), resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca(2+), W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr(2+)-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 Å structure of native PSII, was found in the Sr-PSII structure.

DOI： 10.1073/pnas.1219922110

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Full geometry optimizations of mixed-valence (MV) cubane Mn(III)4-?Mn(IV)?O4 cluster (? = 04) by UB3LYP have been performed to elucidate Jahn-Teller (JT) effects for the Mn(III) ions. The optimized geometries have elucidated acute triangle for Mn(III)2 Mn(X) (X = III,IV) core in the cubane, indicating the JT effect. The JT effect is not remakable for Mn(IV)2Mn(III) cores, showing obtuse triangle and it diminishes in Mn(IV)3 core with equilateral triangle. The replacement of one of Mn ions with Ca (or Sr) ion in the cubane structure has also been examined to elucidate multiple roles of Ca(II) ion. The Ca-doping suppresses the JT effect even for Mn(III)2Mn(X) (X = III,IV) core because acute CaMnMn triangles with longer Ca-Mn distances than the Mn-Mn distance are newly formed. The suppression of the JT effect for Mn(IV)2 Mn(III) by Ca doping is also found because of the same reason. The Ca-doped cubane in the CaMn4O5 cluster (1) of oxygen evolving complex (OEC) of photosystem II (PSII) exhibits two acute CaMnMn triangles and one almost equilateral CaMnMn triangle because of the elongation of the Mn1(d)-Mn3(b) distance with the coordination of the extra Mn4(a) ion to the cubane. The Mn1(d)Mn2(c)Mn3(b) triangle becomes obtuse because of the suppression of the JT effect, indicating the Mn1(d)(III)Mn2(c)(IV)Mn3(b)(IV) valence state in the S1 state of 1. The JT distortion for Mn(III) ions modified by the Ca(or Sr) doping is coupled with the labile structural deformation for intracluster electron transfers via double exchange mechanism in 1. The structural anomalies of 1 revealed by the new XRD experiment are also crucial for derivation of several guiding principles for theoretical modeling of water splitting reaction at OEC of PSII. The hybrid DFT computational results for 1 have also supported these guiding principles that provide possible orbital and spin correlation diagrams for water splitting reactions. The Huckel-Hubbard-Hund (HHH) model has been used for qualitative understanding of these diagrams. Implications of the present computational results are discussed in relation to electronic and spin states of redox active Ca-doped Mott insulators constructed with magnetic transition metals such as Mn, Fe, Co, Ni, etc. Strongly correlated electron systems (SCES) modified by doping of Ca, Sr, Zn, etc. have been elucidated as possible candidates of bio-inspired artificial catalysts for water oxidation. (C) 2012 Wiley Periodicals, Inc.

DOI： 10.1002/qua.24280

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Several hybrid DFT methods were applied to full geometry optimizations of the CaMn4O4X(H2O)4 (X?OH1- (1) or O2- (2)) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) to elucidate Mn-Mn, Mn-Ca, and Mn-O distances on a theoretical ground. The computed Mn-Mn distances were compared with previous (London and Berlin) X-ray diffraction (XRD), and Berkeley and Berlin EXAFS results, together with the recent high-resolution XRD structure by Umena and coworkers. Present computational results by the hybrid DFT methods have elucidated several differences among these accumulated results. These DFT results led us to reassign the Mn-Mn and Mn-Ca distances by the EXAFS experiments, which became consistent with the results obtained by the high-resolution XRD structure. A characteristic feature revealed via the optimized Mn-O distances was that the degree of symmetry breaking of the Mn1-O(57)-Mn4 bond is not so remarkable under the UBHandHLYP approximation but it can be large by other hybrid DFT methods. The computational results for 2 indicated reduction of the Mn3-Mn4 distance with the deprotonation of the bridging oxo group. The hybrid DFT results for 1 are not inconsistent with an experimental proposal based on the new XRD structure, namely a protonated mu 3-oxygen at the internal O(57) site of the cluster in the S1 state. On the other hand, the reduction of Mn ions (not degradation of whole cluster structure) by the X-ray irradiation still remains an important issue for refinements of the XRD structure. The computational results are discussed in relation to those of the electron spin echo envelope modulation (ESEEM) and possible pathways for water splitting reaction. Implications of the present DFT structures are discussed in relation to the previous DFT and related computational results, together with recent XRD results for cubane-like model clusters for OEC of PSII. (C) 2012 Wiley Periodicals, Inc. DOI: 10.1002/qua.24117

DOI： 10.1002/qua.24117

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：American Institute of Physics Inc.  

Photosynthetic water-splitting takes place in photosystem II (PSII), a membrane protein complex consisting of 20 subunits with an overall molecular mass of 350 kDa. The light-induced water-splitting reaction catalyzed by PSII not only converts light energy into biologically useful chemical energy, but also provides us with oxygen indispensible for sustaining oxygenic life on the earth. We have solved the structure of PSII at a 1.9 Å resolution, from which, the detailed structure of the Mn4CaO5-cluster, the catalytic center for water-splitting, became clear. Based on the structure of PSII at the atomic resolution, possible mechanism of light-induced water-splitting was discussed.

DOI： 10.1063/1.4848085

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Scopus

Language：English   Publisher：ELSEVIER SCIENCE BV  

DOI： 10.1016/j.bbabio.2012.06.016

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The crystal structure of Photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed deformations of chlorin rings in the chlorophylls for the first time. We investigated the degrees of chlorin ring deformation and factors that contributed to them in the PSII crystal structure, using a normal-coordinate structural decomposition procedure. The out-of-plane distortion of the P(D1) chlorin ring can be described predominantly by a large "doming mode" arising from the axial ligand, D1-His198, as well as the chlorophyll side chains and PSII protein environment. In contrast, the deformation of P(D2) was caused by a "saddling mode" arising from the D2-Trp191 ring and the doming mode arising from D2-His197. Large ruffling modes, which were reported to lower the redox potential in heme proteins, were observed in P(D1) and Chl(D1), but not in P(D2) and Chl(D2). Furthermore, as P(D1) possessed the largest doming mode among the reaction center chlorophylls, the corresponding bacteriochlorophyll P(L) possessed the largest doming mode in bacterial photosynthetic reaction centers. However, the majority of the redox potential shift in the protein environment was determined by the electrostatic environment. The difference in the chlorin ring deformation appears to directly refer to the difference in "the local steric protein environment" rather than the redox potential value in PSII.

DOI： 10.1021/bi300428s

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Very recently Umena et al. have determined the X-ray diffraction (XRD) structure of the CaMn4O5 cluster in the oxygen evolution complex (OEC) of photosystem II (PSII) refined to 1.9 angstrom resolution. We have performed theoretical attempts to elucidate possible electronic and spin states of their new XRD structure of the CaMn4O5 cluster. For the purpose, hybrid density functional theory (UB3LYP and UBHandHLYP) calculations have been performed for the mixed-valence (MV) CaMn(III)(4-omega) (IV)(omega)O-5(H2O)(4) (1) and CaMn(III)(4-omega)(IV)(omega)O-4(OH)(H2O)(4) (2) clusters as active catalytic site for water splitting reaction in OEC of PSII. Full geometry optimizations of 1a (omega = 2) and 2a (omega = 2) have been performed to elucidate scope and limitation of the cluster models. Both charge and spin fluctuated structures (48 UB3LYP solutions) have been considered for the MV 1a (omega = 2). Total energies obtained by these calculations have elucidated quasi-degenerated electronic and spin states that are characterized by charge and spin density populations. The energy levels revealed by hybrid DFT are analyzed on the basis of the Heisenberg spin Hamiltonian model, providing the effective exchange integrals between manganese ions at a uniform or MV structure. The spin projections for hybrid DFT solutions are performed using the effective exchange integrals. The charge fluctuation model is introduced to analyze relative stabilities among MV structures of 1a and 2a. These computational results for 1a and 2a have explored several characteristic electronic properties of the species that are used for theoretical elucidation of possible mechanisms of water splitting reaction. Orbital and spin correlation diagrams are derived for the O-O bond formation and oxygen evolution in the reaction. Implications of the computational results are also discussed in relation to available experiments and theoretical results by other groups. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112: 321-343, 2012

DOI： 10.1002/qua.23261

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Recently, Umena et al. have revealed the X-ray diffraction structure of the CaMn4O5 cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) refined to 1.9 angstrom resolution. Their X-ray structure has first elucidated hydrogen-bonding networks and proton release pathways at OEC of PSII. Here, several working hypotheses (heuristic principles) for water splitting reaction are derived from their X-ray structure for theoretical modeling. These hypotheses suggest how water can be oxidized at OEC of PSII: namely possible reaction mechanisms for the reaction. To confirm them, we have also performed broken-symmetry (BS) UB3LYP calculations for active site models based on their XRD structure. The bond lengths of formal Mn(V)-AO with labile d pi-p pi bonds are optimized to clarify possible roles of the species that are often introduced as a key intermediate in the catalytic (Kok) cycle for water splitting reaction at OEC of PSII. Location of the transition structure for the oxygen-oxygen (O-O) bond formation is also performed by the energy optimization technique. The natural orbital (NO) analysis of the UB3LYP solutions has been performed to obtain the natural molecular orbitals and their occupation numbers that have been useful for classification of localized d-electrons, labile chemical bonds and closed-shell (valence) orbitals. The localized d-electrons characterized by the NO analysis are the origins for the magnetism revealed by ENDOR and other magnetic experiments. On the other hand, the nature of labile (soft) d pi-p pi bonds responsible for the O-O bond formation has been investigated on the basis of chemical indices such as effective bond order (b), diradical character (y), and spin density (Q) indices that are calculated using the orbital overlap between broken-symmetry orbitals. These chemical indices have been calculated for the transition structure of the O-O bond formation at OEC of PSII. Implications of present computational results are discussed in relation to the derived hypotheses and available accumulated experimental results. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112: 253-276, 2012

DOI： 10.1002/qua.23218

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

Full geometry optimizations of several inorganic model clusters, CaMn(4)O(4)XYZ(H2O)(2) (X, Y, Z = H2O, OH- or O2-), by the use of the B3LYP hybrid density functional theory (DFT) have been performed to illuminate plausible molecular structures of the catalytic site for water oxidation in the S-0, S-1, S-2 and S-3 states of the Kok cycle for the oxygen-evolving complex (OEC) of photosystem II (PSII). Optimized geometries obtained by the energy gradient method have revealed the degree of symmetry breaking of the unstable three-center Mn-a-X-Mn-d bond in CaMn(4)O(4)XYZ(H2O)(2). The right-elongated (R) Mn-a-X center dot center dot center dot Mn-d and left-elongated (L) Mn-a center dot center dot center dot X-Mn-d structures appear to occupy local minima on a double-well potential for several key intermediates in these states. The effects of insertion of one extra water molecule to the vacant coordination site, Mn-d (Mn-a), for R (L) structures have also been examined in detail. The greater stability of the L-type structure over the R-type has been concluded for key intermediates in the S-2 and S-3 states. Implications of the present DFT structures are discussed in relation to previous DFT and related results, together with recent X-ray diffraction results for model compounds of cubane-like OEC cluster of PSII.

DOI： 10.1039/c2dt31420g

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PubMed

Language：English   Publishing type：Part of collection (book)   Publisher：ELSEVIER ACADEMIC PRESS INC  

UB3LYP calculations have been performed to elucidate electronic and spin states of the CaMn(III)(4-m)Mn(IV)(m)X(H2O)(4) cluster (X=O-5 (1) and O-4(OH)) (2) as active catalytic site for water-splitting reaction in oxygen-evolving complex of PSII refined to 1.9 angstrom X-ray resolution. Both charge- and spin-fluctuated structures have been considered for the mixed-valence (MV) states of 1 and 2. Total energies obtained by these calculations have elucidated quasi-degenerated electronic and spin states that are characterized by charge and spin density populations. The energy levels revealed by UB3LYP are analyzed on the basis of the Heisenberg spin Hamiltonian model, providing the effective exchange integrals between manganese ions at an MV structure. The charge-fluctuation model is also introduced to analyze relative stabilities between MV structures of 1 and 2. The natural orbital (NO) analysis of the UB3LYP solutions has also been performed to elucidate the nature of chemical bonds of 1 and 2: classification of localized d-electrons, labile chemical bonds, and closed-shell orbitals based on their occupation numbers. The localized d-electrons characterized by the NO analysis are responsible for redox reactions, and the origins for the Heisenberg model, namely valence-bond (VB) description of the chemical bonds. On the other hand, labile d-p bonds in 1 and 2 are grasped with the molecular orbital (MO) model: occupation numbers of the NO are used for computations of effective bond order (b), diradical character (y), and spin density indices (Q). Thus, the universal MO-VB model based on the broken-symmetry (BS) calculations followed by the NO analysis is a practical and handy procedure for theoretical approaches to multinuclear transition metal complexes that are hardly investigated by the symmetry-adapted (SA) multireference approaches such as complete active space (CAS) DFT, CASPT2, and CASCC: these SA calculations for related small clusters are performed for examination of scope and applicability of UB3LYP and related DFT functions for target large systems such as 1 and 2.

DOI： 10.1016/B978-0-12-396498-4.00016-8

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The reaction center chlorophylls a (Chla) of photosystem II (PSII) are composed of six Chla molecules including the special pair Chla P(D1)/P(D2) harbored by the D1/D2 heterodimer. They serve as the ultimate electron abstractors for water oxidation in the oxygen-evolving Mn(4)CaO(5) cluster. Using the PSII crystal structure analyzed at 1.9 Å resolution, the redox potentials of P(D1)/P(D2) for one-electron oxidation (E(m)) were calculated by considering all PSII subunits and the protonation pattern of all titratable residues. The E(m)(Chla) values were calculated to be 1015-1132 mV for P(D1) and 1141-1201 mV for P(D2), depending on the protonation state of the Mn(4)CaO(5) cluster. The results showed that E(m)(P(D1)) was lower than E(m)(P(D2)), favoring localization of the charge of the cationic state more on P(D1). The P(D1)(•+)/P(D2)(•+) charge ratio determined by the large-scale QM/MM calculations with the explicit PSII protein environment yielded a P(D1)(•+)/P(D2)(•+) ratio of ~80/~20, which was found to be due to the asymmetry in electrostatic characters of several conserved D1/D2 residue pairs that cause the E(m)(P(D1))/E(m)(P(D2)) difference, e.g., D1-Asn181/D2-Arg180, D1-Asn298/D2-Arg294, D1-Asp61/D2-His61, D1-Glu189/D2-Phe188, and D1-Asp170/D2-Phe169. The larger P(D1)(•+) population than P(D2)(•+) appears to be an inevitable fate of the intact PSII that possesses water oxidation activity.

DOI： 10.1021/ja203947k

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 Å resolution. We find that chloride depletion induces formation of a salt bridge between D2-K317 and D1-D61 that could suppress the transfer of protons to the lumen.

DOI： 10.1021/bi200685w

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S(1) Mn(4)(IV,III,IV,III) state, where Ca(2+) is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 1.9 Å resolution. The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals. Our results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting.

DOI： 10.1021/bi200681q

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PubMed

Language：English   Publisher：ELSEVIER SCIENCE SA  

The catalytic center for photosynthetic water-splitting consists of 4 Mn atoms and 1 Ca atom and is located near the lumenal surface of photosystem II. So far the structure of the Mn(4)Ca-cluster has been studied by a variety of techniques including X-ray spectroscopy and diffraction, and various structural models have been proposed. However, its exact structure is still unknown due to the limited resolution of crystal structures of PSII achieved so far, as well as possible radiation damages that might have occurred. Very recently, we have succeeded in solving the structure of photosystem II at 1.9 angstrom. which yielded a detailed picture of the Mn(4)CaO(5)-cluster for the first time. In the high resolution structure, the Mn(4)CaO(5)-cluster is arranged in a distorted chair form, with a cubane-like structure formed by 3 Mn and 1 Ca, 4 oxygen atoms as the distorted base of the chair, and 1 Mn and 1 oxygen atom outside of the cubane as the back of the chair. In addition, four water molecules were associated with the cluster, among which, two are associated with the terminal Mn atom and two are associated with the Ca atom. Some of these water molecules may therefore serve as the substrates for water-splitting. The high resolution structure of the catalytic center provided a solid basis for elucidation of the mechanism of photosynthetic water splitting. We review here the structural features of the Mn(4)CaO(5)-cluster analyzed at 1.9 angstrom resolution, and compare them with the structures reported previously. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.jphotobiol.2011.03.017

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Very recently Umena et al. have determined the X-ray diffraction (XRD) structure of the CaMn4O5 cluster (1) in the oxygen-evolving complex (OEC) of photosystem II (PSII) refined to 1.9 angstrom resolution. UB3LYP calculations of 1 using this XRD structure were performed to elucidate possible mechanisms for the oxygen-oxygen (O-O) bond formation in oxygen evolution reaction of PSII. The solutions obtained were used for natural orbital (NO) analysis to obtain LUMOs of labile chemical bonds, which clearly indicated the possibilities of nucleophilic attack of hydroxide (or water molecule) to the electrophilic O(56) and/ or O(57) sites of 1. (C) 2011 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2011.06.021

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 Å. These resolutions have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting. Here we report the crystal structure of photosystem II at a resolution of 1.9 Å. From our electron density map, we located all of the metal atoms of the Mn(4)CaO(5) cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn(4)CaO(5) cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water molecules in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. The determination of the high-resolution structure of photosystem II will allow us to analyse and understand its functions in great detail.

DOI： 10.1038/nature09913

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

UB3LYP calculations were first performed to elucidate electronic and spin structures of the CaMn4O5 cluster in the oxygen-evolving-complex of the PSII system refined to the 1.9 angstrom X-ray resolution by Kamiya, Shen, and their collaborators. Eight different UB3LYP solutions with axial spin structures were constructed to obtain the energy levels of the cluster on the basis of their X-ray structure. The energy diagrams were analyzed in terms of the Heisenberg model that involves six effective-exchange integrals between manganese ions. Several characteristic features of the electronic states of the cluster are revealed from these theoretical investigations based on the UB3LYP calculations. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2011.02.030

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Language：English  

DOI： 10.1016/j.bbabio.2010.12.013

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PubMed

Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767311081293

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Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767311081256

Web of Science

Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S10_1

CiNii Research

Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S95_2

Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767311081268

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Language：English  

DOI： 10.1016/j.bbabio.2009.11.001

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PubMed

Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767310097291

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

The chloride ion, Cl(-), is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn(4)Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl(-) with a bromide ion (Br(-)) or an iodide ion (I(-)) in PSII and analyzed the crystal structures of PSII with Br(-) and I(-) substitutions. Substitution of Cl(-) with Br(-) did not inhibit oxygen evolution, whereas substitution of Cl(-) with I(-) completely inhibited oxygen evolution, indicating the efficient replacement of Cl(-) by I(-). PSII with Br(-) and I(-) substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn(4)Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn(4)Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl(-) anions are required to maintain the coordination structure of the Mn(4)Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.

DOI： 10.1073/pnas.0812797106

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PubMed

Language：English  

DOI： 10.1016/j.bbabio.2008.11.004

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PubMed

Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767308090636

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE  

L-Lactate oxidase (LOX) from Aerococcus viridans catalyzes the oxidation Of L-lactate to pyruvate by the molecular oxygen and belongs to a large family of 2-hydroxy acid-dependent flavoenzymes. To investigate the interaction of LOX with pyruvate in structural details and understand the chemical mechanism of flavin-dependent L-lactate dehydrogenation, the LOX-pyruvate complex was crystallized and the crystal structure of the complex has been solved at a resolution of 1.90 angstrom. One pyruvate molecule bound to the active site and located near N5 position of FMN for subunits, A, B, and D in the asymmetric unit, were identified. The pyruvate molecule is stabilized by the interaction of its carboxylate group with the side-chain atoms of Tyr40, Arg181, His265, and Arg268, and of its keto-oxygen atom with the side-chain atoms of Tyr146, Tyr215, and His265. The alpha-carbon of pyruvate is found to be 3.13 angstrom from the N5 atom of FMN at an angle of 105.4 degrees from the flavin N5-N10 axis. (C) 2007 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.bbrc.2007.05.021

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PubMed

Language：English   Publisher：ROYAL SOC CHEMISTRY  

Quantum mechanical (QM) and QM/molecular mechanics (MM) calculations of three different cluster models have been performed to shed light on hydrogen bonding networks and proton wires for proton release pathways (PRP) of water oxidation reactions in the oxygen evolving complex (OEC) of photosystem II (PSII). Positions of all the hydrogen atoms in an extended QM Model III including the second coordination sphere for the active-site CaMn4O5 complex of OEC of PSII have been optimized assuming the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 angstrom resolution. Full geometry optimizations of the first coordination sphere model (QM Model I) embedded in the Model III and QM (QM Model I plus seven water molecules, namely QM Model II)/MM models, together with full QM Model III, have also been conducted to elucidate confinement effects for geometrical parameters of the CaMn4O5 cluster by proteins. Computational results by these methods have elucidated the O center dot center dot center dot O(N), O center dot center dot center dot H distances and O(N)-H center dot center dot center dot O angles for hydrogen bonds in proton release paths (PRP) I and II that construct a proton wire from Asp61 toward His190. The hydrogen-bonding structures revealed have also been examined in relation to the possibilities of protonation of bridge oxygen dianions within the CaMn4O5 cluster. The optimized inter-atomic distances by QM Models I and III, together with QM(Model II)/MM, have elucidated the elongation of the Mn-Mn distances with hydrogen bonds and variations of the Mn-d-O-(5) length with confinement effects by protein. Implications of the computational results are discussed in relation to the available EXAFS experiments, and internal, semi-internal and external reductions of Mn ions and long Mn-Mn distances of the high-resolution (SP8) XRD, and rational design of artificial catalysts for water oxidation that are current topics in the field of OEC of PSII.

DOI： 10.1039/c3cy00051f

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

Photosystem II (PSII) is a membrane-protein complex consisting of 17 trans-membrane subunits and 3 peripheral, extrinsic subunits with a total molecular mass of 350 kDa for a monomer. PSII performs a series of light-induced electron transfer reactions, leading to the conversion of light energy into biologically useful chemical energy, coupled with this is the splitting of water and generation of molecular oxygen. Both the chemical energy converted and molecular oxygen generated by PSII are indispensible for sustaining life on the earth; thus PSII is an extremely important protein complex. We have succeeded in crystallizing the PSII complex at a resolution of 1.9 Å, and analyzed its structure. Here we describe the structure of PSII, in particular the Mn₄CaO₅-cluster, which is the catalytic center of water-splitting, analyzed at the atomic resolution. Based on these, we discuss the possible mechanisms of light-induced water-splitting and its implications in artificial photosynthesis.<br>

DOI： 10.2142/biophys.52.140

CiNii Books

CiNii Research

Other Link： https://jlc.jst.go.jp/DN/JALC/10000488562?from=CiNii

Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

CiNii Books

Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

CiNii Books

Language：English   Publishing type：Research paper, summary (international conference)   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767311098035

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767311081335

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767308092544

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767308089447

Web of Science

Language：Japanese   Publisher：日本ビタミン学会  

CiNii Books

Language：Japanese  

DOI： 10.18957/rr.8.1.1

CiNii Research

Language：Japanese  

DOI： 10.18957/rr.9.4.177

CiNii Research

Language：Japanese  

DOI： 10.18957/rr.10.2.108

CiNii Research

Language：Japanese  

Photosystem II (PSII) is a multi-subunit membrane protein complex. PSII performs a series of light-induced electron transfer reactions leading to the splitting of water and generation of molecular oxygen, the latter of which is essential for almost all life on the earth. The catalytic center is a Mn₄CaO₅-cluster, whose detailed structure has been successfully resolved in the 1.9 Å structure of PSII from <i>Thermosynechococcus vulcanus</i>. This structure also revealed the presence of nearly 2,800 water molecules, some of which are directly associated with the Mn₄CaO₅-cluster and thus may serve as the substrate water molecules for the oxygen-evolving reaction.

DOI： 10.5940/jcrsj.54.247

CiNii Research

Language：Japanese  

DOI： 10.11316/jpsgaiyo.66.1.2.0_378_2

CiNii Research

CiNii Research

CiNii Research

Ycf12 is a recently identified low-molecular mass trans-membrane protein of photosystem II (PSII), and its location is unknown in the current crystal structure. We purified PSII dimers from a Ycf12-deletion mutant of <I>Thermosynechococcus elongatus</I>, crystallized, and analyzed the structure of the mutant PSII. Our result showed that Ycf12 is located in the periphery of PSII close to PsbK and PsbZ, and corresponded to an unassigned helix X1 in the 3.0 Å structure reported by the Berlin group. Combining our previous results that X2 is PsbY, it is strongly suggested that the remaining unassigned helix X3 in the 3.0 Å structure corresponds to PsbX. We also purified PSII from a PsbZ deletion mutant, and crystallized PSII from the mutant. The crystals obtained had significantly different unit cell constants than those of wild type, indicating the participation of this subunit in joining the two PSII dimers within the wild type crystals

DOI： 10.14841/jspp.2009.0.0047.0

CiNii Research

Language：Japanese  

<p>‘Softcrystals’ is the name of a group of new functional materials that can cause changes in luminescence properties and crystal phase-transitions by applying relatively weak external fields such as light irradiation, vapor exposure, and mechanical stimuli. The time-scale of these structural transitions are very widely. In this paper, we will introduce various time-resolved measurement systems using synchrotron radiation as structure-tracking methods for external field-responsive softcrystals.</p>

DOI： 10.5940/jcrsj.63.24

CiNii Research

Although the central part of photosystem II (PSII) is highly conserved from prokaryotic cyanobacteria to eukaryotes, there are some differences in the extrinsic proteins involved in oxygen evolution among different organisms. The crystal structure of PSII from cyanobacteria has been reported; however, no reports have been published on the structure of any eukaryotic PSII. Red alga is one of the eukaryotic algae closely related to cyanobacteria, but its PSII differs from that of cyanobacteria in that the former contains a 20 kDa protein, the fourth extrinsic protein. In order to elucidate the structure of red algal PSII, we have purified and crystallized PSII from a red alga <I>Cyanidium caldarium</I>. We improved the crystallization conditions which yielded crystals that diffracted to a higher resolution than we reported previously. The crystals obtained in the present study will allow us to analyze the structure of red algal PSII.

DOI： 10.14841/jspp.2008.0.0557.0

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