Updated on 2024/03/29

写真a

 
UMENA Yasufumi
 
Organization
Synchrotron Radiation Research Center Division of Synchrotron Radiation Associate professor
Graduate School
Graduate School of Engineering
Title
Associate professor
External link

Degree 1

  1. 博士(理学) ( 2007.6   大阪大学 ) 

Research Interests 6

  1. Biochemistry

  2. Protein crystallography

  3. Structure biology

  4. X-ray Crystallography

  5. Photosynthesis

  6. Molecular biology

Research Areas 1

  1. Life Science / Structural biochemistry  / Protein Crystallography

Research History 8

  1. Nagoya University   Synchrotron Radiation Research Center   Associate professor

    2021.4

  2. Jichi Medical University

    2020.4 - 2021.3

  3. Okayama University   The Research Institute for Interdisciplinary Science

    2016.4 - 2020.3

  4. Okayama University

    2015.1 - 2016.3

  5. Japan Society for Promotion of Science

    2011.10 - 2015.3

  6. Osaka City University   Advanced Research Institute for Natural Science and Technology   Designated associate professor

    2011.10 - 2014.12

  7. Osaka University   Institute for Protein Research

    2010.4 - 2011.9

  8. Osaka City University   Graduate School of Science

    2007.7 - 2010.3

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Education 2

  1. 大阪大学大学院   理学研究科   高分子科学専攻 博士課程

    2004.4 - 2007.3

  2. 京都大学大学院   理学研究科 原子炉実験所   特別研究学生

    2004.4 - 2007.3

Professional Memberships 4

  1. THE JAPANESE SOCIETY OF PHOTOSYNTHESIS RESEARCH

  2. THE BIOPHYSICAL SOCIETY OF JAPAN

  3. THE CRYSTALLOGRAPHIC SOCIETY OF JAPAN

  4. PROTEIN SCIENCE SOCIETY OF JAPAN

Committee Memberships 3

  1. SPring-8シンポジウム2019   現地実行委員  

    2019.2 - 2019.9   

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    Committee type:Academic society

  2. SPring-8ユーザー共同体 放射光構造生物学研究会   幹事  

    2016.4   

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    Committee type:Academic society

  3. 第56回日本生物物理学会年会   実行委員  

    2016.4 - 2018.9   

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    Committee type:Academic society

Awards 3

  1. Outstanding Poster Award

    2014.9   15th International Conference on the Crystallization of Biological Macromolecules   "New approach in photosystem II crystal handlings: characterization using near-infrared imaging, dehydration of the glue coating crystals using humid gas and laser-processing to cylinder-shaped crystals"

    Yasufumi Umena

  2. 特別賞 光と緑の賞

    2012.6   日本光合成学会   「酸素発生光化学系IIの1.9Å分解能における結晶構造」

    梅名 泰史, 川上恵典, 神谷信夫, 沈建仁

  3. 進歩賞

    2011.11   日本結晶学会   「酸素発生光化学系IIの構造と機能に関する結晶学的研究」

    梅名 泰史

 

Papers 65

  1. The Blinking of Small-Angle X-ray Scattering Reveals the Degradation Process of Protein Crystals at Microsecond Timescale Reviewed

    Arai, T; Mio, K; Onoda, H; Chavas, LMG; Umena, Y; Sasaki, YC

    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES   Vol. 24 ( 23 )   2023.12

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  2. Biological Advantage of the Arrangements of C-Phycocyanin Chromophores in Phycobilisome from the Electronic Energy Transfer Viewpoint Reviewed

    Mishima, K; Shoj, M; Umena, Y; Shigeta, Y

    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN   Vol. 96 ( 4 ) page: 381 - 393   2023.4

  3. Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals

    Ang, AKR; Umena, Y; Sato-Tomita, A; Shibayama, N; Happo, N; Marumi, R; Yamamoto, Y; Kimura, K; Kawamura, N; Takano, Y; Matsushita, T; Sasaki, YC; Shen, JR; Hayashi, K

    JOURNAL OF SYNCHROTRON RADIATION   Vol. 30 ( Pt 2 ) page: 368 - 378   2023.3

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    X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter–scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

    DOI: 10.1107/S1600577522011833

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  4. Dynamic interactions in the l-lactate oxidase active site facilitate substrate binding at pH4.5. Reviewed

    Furubayashi N, Inaka K, Kamo M, Umena Y, Matsuoka T, Morimoto Y

    Biochemical and biophysical research communications   Vol. 568   page: 131 - 135   2021.9

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    DOI: 10.1016/j.bbrc.2021.06.078

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  5. Capturing structural changes of the S<sub>1</sub> to S<sub>2</sub> transition of photosystem II using time-resolved serial femtosecond crystallography Reviewed

    Li, HJ; Nakajima, Y; Nomura, T; Sugahara, M; Yonekura, S; Chan, SK; Nakane, T; Yamane, T; Umena, Y; Suzuki, M; Masuda, T; Motomura, T; Naitow, H; Matsuura, Y; Kimura, T; Tono, K; Owada, S; Joti, Y; Tanaka, R; Nango, E; Akita, F; Kubo, M; Iwata, S; Shen, JR; Suga, M

    IUCRJ   Vol. 8 ( Pt 3 ) page: 431 - 443   2021.5

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    Photosystem II (PSII) catalyzes light-induced water oxidation through an S i-state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.

    DOI: 10.1107/S2052252521002177

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  6. Improvement Method by Laser-processing of Photosystem II Crystals for Valence Analysis of Mn-cluster Reviewed

    Umena Yasufumi, Kawakami Keisuke, Kawano Yoshiaki, Yamamoto Masaki, Kamiya Nobuo, Shen Jian-Ren

    SPring-8/SACLA Research Report   Vol. 9 ( 4 ) page: 177 - 181   2021

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    Language:Japanese   Publisher:Japan Synchrotron Radiation Research Institute  

    DOI: 10.18957/rr.9.4.177

  7. Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores. Reviewed

    Mishima K, Shoji M, Umena Y, Boero M, Shigeta Y

    Biophysics and physicobiology   Vol. 18   page: 196 - 214   2021

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    DOI: 10.2142/biophysico.bppb-v18.021

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  8. Formation of the High-Spin S<sub>2</sub> State Related to the Extrinsic Proteins in the Oxygen Evolving Complex of Photosystem II Reviewed

    Taguchi, S; Shen, LL; Han, GY; Umena, Y; Shen, JR; Noguchi, T; Mino, H

    JOURNAL OF PHYSICAL CHEMISTRY LETTERS   Vol. 11 ( 20 ) page: 8908 - 8913   2020.10

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    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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  9. X-ray fluorescence holography for soft matter Reviewed

    Ang, AKR; Sato-Tomita, A; Shibayama, N; Umena, Y; Happo, N; Marumi, R; Kimura, K; Matsushita, T; Akagi, K; Sasaki, T; Sasaki, YC; Hayashi, K

    JAPANESE JOURNAL OF APPLIED PHYSICS   Vol. 59 ( 1 )   2020.1

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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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  10. An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties Reviewed

    Motomura, T; Zuccarello, L; Sétif, P; Boussac, A; Umena, Y; Lemaire, D; Tripathy, JN; Sugiura, M; Hienerwadel, R; Shen, JR; Berthomieu, C

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS   Vol. 1860 ( 11 ) page: 148084   2019.11

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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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  11. An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser Reviewed

    Suga Michihiro, Akita Fusamichi, Yamashita Keitaro, Nakajima Yoshiki, Ueno Go, Li Hongjie, Yamane Takahiro, Hirata Kunio, Umena Yasufumi, Yonekura Shinichiro, Yu Long-Jiang, Murakami Hironori, Nomura Takashi, Kimura Tetsunari, Kubo Minoru, Baba Seiki, Kumasaka Takashi, Tono Kensuke, Yabashi Makina, Isobe Hiroshi, Yamaguchi Kizashi, Yamamoto Masaki, Ago Hideo, Shen Jian-Ren

    SCIENCE   Vol. 366 ( 6463 ) page: 334 - +   2019.10

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  12. An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

    Suga M., Akita F., Yamashita K., Nakajima Y., Ueno G., Li H., Yamane T., Hirata K., Umena Y., Yonekura S., Yu L.J., Murakami H., Nomura T., Kimura T., Kubo M., Baba S., Kumasaka T., Tono K., Yabashi M., Isobe H., Yamaguchi K., Yamamoto M., Ago H., Shen J.R.

    Science   Vol. 366 ( 6463 ) page: 334 - 338   2019.10

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    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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  13. A versatile experimental system for tracking ultrafast chemical reactions with X-ray free-electron lasers Reviewed

    Katayama, T; Nozawa, S; Umena, Y; Lee, S; Togashi, T; Owada, S; Yabashi, M

    STRUCTURAL DYNAMICS-US   Vol. 6 ( 5 ) page: 054302   2019.9

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    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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  14. Novel Mechanism of Cl-Dependent Proton Dislocation in Photosystem II (PSII): Hybrid Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation Reviewed

    Nakamura, A; Kang, J; Terada, R; Kino, H; Umena, Y; Kawakami, K; Shen, JR; Kamiya, N; Tateno, M

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   Vol. 88 ( 8 )   2019.8

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    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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  15. β-Carotene Probes the Energy Transfer Pathway in the Photosystem II Core Complex Reviewed

    Yoneda, Y; Nagasawa, Y; Umena, Y; Miyasaka, H

    JOURNAL OF PHYSICAL CHEMISTRY LETTERS   Vol. 10 ( 13 ) page: 3710 - 3714   2019.7

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    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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  16. Structural basis for blue-green light harvesting and energy dissipation in diatoms

    Wang, WD; Yu, LJ; Xu, CZ; Tomizaki, T; Zhao, SH; Umena, Y; Chen, XB; Qin, XC; Xin, YY; Suga, M; Han, GY; Kuang, TY; Shen, JR

    SCIENCE   Vol. 363 ( 6427 ) page: 598 - +   2019.2

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    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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  17. Crystallographic study on estimation of the valence of each of the four Mn atoms in Photosystem II using anomalous diffraction techniques

    Umena, Y; Kawakami, K; Kamiya, N; Kawano, Y; Yamashita, K; Ago, H; Yamamoto, M; Shen, JR

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 75   page: A363 - A363   2019

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    DOI: 10.1107/S010876731909648X

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  18. Theoretical Elucidation of Geometrical Structures of the CaMn<sub>4</sub>O<sub>5</sub> Cluster in Oxygen Evolving Complex of Photosystem II Scope and Applicability of Estimation Formulae of Structural Deformations via the Mixed-Valence and Jahn-Teller Effects Reviewed

    Shoji, M; Isobe, H; Yamanaka, S; Umena, Y; Kawakami, K; Kamiya, N; Yamaguchi, K

    QUANTUM SYSTEMS IN PHYSICS, CHEMISTRY AND BIOLOGY - THEORY, INTERPRETATION, AND RESULTS   Vol. 78   page: 307 - 451   2019

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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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  19. High-resolution and low-dose X-ray crystal structure of Photosytem II Reviewed

    Tanaka, A; Kawakami, K; Umena, Y; Kamiya, N

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 70   page: C1502 - C1502   2014.8

  20. Crystallographic studies on Mn atoms in Photosystem II using K-edge wavelength Reviewed

    Umena, Y; Kawakami, K; Shen, J; Kamiya, N

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 70   page: C350 - C350   2014.8

  21. SR Beamline for macromolecular assemblies by the institute for protein research Reviewed

    Nakagawa, A; Yamashita, E; Umena, Y; Yoshimura, M; Suzuki, M; Hasegawa, K; Furukawa, Y; Ohata, T; Kumasaka, T; Ueno, G; Yamamoto, M; Yoshikawa, S; Tsukihara, T

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 67   page: C354 - C354   2011

  22. Friction characteristics of fabrics in the presence of air Reviewed

    Bao, LM; Umena, Y; Kemmochi, K

    JOURNAL OF THE TEXTILE INSTITUTE   Vol. 102 ( 7 ) page: 598 - 603   2011

  23. Observation of energy transfer dynamics in a phycocyanin protein crystal by utilizing femtosecond transient absorption microscopy Reviewed

    Tetsuro Katayama, Shuto Ueda, Yuma Fujita, Yuichiro Akagi, Pankaj Koinkar, Yasufumi Umena, Akihiro Furube

    Japanese Journal of Applied Physics   Vol. 62 ( SG )   2023.6

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    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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  24. Role of the Propionic Acid Side-Chain of C-Phycocyanin Chromophores in the Excited States for the Photosynthesis Process Reviewed

    Kenji Mishima, Mitsuo Shoji, Yasufumi Umena, Mauro Boero, Yasuteru Shigeta

    Bulletin of the Chemical Society of Japan   Vol. 93 ( 12 ) page: 1509 - 1519   2020.12

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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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  25. Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II in Thermosynechococcus elongatus. Reviewed International journal

    Yoshiki Nakajima, Yasufumi Umena, Ryo Nagao, Kaichiro Endo, Koichi Kobayashi, Fusamichi Akita, Michihiro Suga, Hajime Wada, Takumi Noguchi, Jian-Ren Shen

    The Journal of biological chemistry   Vol. 293 ( 38 ) page: 14786 - 14797   2018.9

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    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.

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  26. Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II. Reviewed International journal

    Yuki Kato, Fusamichi Akita, Yoshiki Nakajima, Michihiro Suga, Yasufumi Umena, Jian-Ren Shen, Takumi Noguchi

    The journal of physical chemistry letters   Vol. 9 ( 9 ) page: 2121 - 2126   2018.5

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    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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  27. Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem II: Applicability of the Jahn-Teller Deformation Formula. Reviewed International journal

    Mitsuo Shoji, Hiroshi Isobe, Ayako Tanaka, Yoshimasa Fukushima, Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Takahito Nakajima, Kizashi Yamaguchi

    ChemPhotoChem   Vol. 2 ( 3 ) page: 257 - 270   2018.3

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    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.

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  28. Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II Reviewed

    S. Uto, K. Kawakami, Y. Umena, M. Iwai, M. Ikeuchi, J. -R. Shen, N. Kamiya

    FARADAY DISCUSSIONS   Vol. 198   page: 107 - 120   2017.6

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    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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  29. Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. Reviewed International journal

    Michihiro Suga, Fusamichi Akita, Michihiro Sugahara, Minoru Kubo, Yoshiki Nakajima, Takanori Nakane, Keitaro Yamashita, Yasufumi Umena, Makoto Nakabayashi, Takahiro Yamane, Takamitsu Nakano, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Tetsunari Kimura, Takashi Nomura, Shinichiro Yonekura, Long-Jiang Yu, Tomohiro Sakamoto, Taiki Motomura, Jing-Hua Chen, Yuki Kato, Takumi Noguchi, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Eriko Nango, Rie Tanaka, Hisashi Naitow, Yoshinori Matsuura, Ayumi Yamashita, Masaki Yamamoto, Osamu Nureki, Makina Yabashi, Tetsuya Ishikawa, So Iwata, Jian-Ren Shen

    Nature   Vol. 543 ( 7643 ) page: 131 - 135   2017.3

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    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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  30. Proton transfer inhibition by molecular anion substitutions in Photosystem II Reviewed

    Yasufumi Umena, Shouya Tamaru, Jian-Ren Shen

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 73   page: C96 - C96   2017

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    DOI: 10.1107/S205327331709475X

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  31. Dynamics of Excitation Energy Transfer Between the Subunits of Photosystem II Dimer. Reviewed International journal

    Yusuke Yoneda, Tetsuro Katayama, Yutaka Nagasawa, Hiroshi Miyasaka, Yasufumi Umena

    Journal of the American Chemical Society   Vol. 138 ( 36 ) page: 11599 - 605   2016.9

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    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.

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  32. Energy transfer between subunits of photosystem II dimer observed by femtosecond transient absorption Reviewed

    Yusuke Yoneda, Tetsuro Katayama, Yutaka Nagasawa, Hiroshi Miyasaka, Yasufumi Umena

    Optics InfoBase Conference Papers     2016.7

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    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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  33. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga. Reviewed International journal

    Hideo Ago, Hideyuki Adachi, Yasufumi Umena, Takayoshi Tashiro, Keisuke Kawakami, Nobuo Kamiya, Lirong Tian, Guangye Han, Tingyun Kuang, Zheyi Liu, Fangjun Wang, Hanfa Zou, Isao Enami, Masashi Miyano, Jian-Ren Shen

    The Journal of biological chemistry   Vol. 291 ( 11 ) page: 5676 - 5687   2016.3

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    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.

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  34. Subunit arrangement of a 2-ketoisovalerate ferredoxin oxidoreductase from Thermococcus profundus revealed by a low resolution X-ray analysis Reviewed

    Y. Ozawa, Y. Umena, T. Imai, Y. Morimoto

    Advances in Enzyme Research     2015.10

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  35. Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S-1 and S-3 states of the oxygen evolving complex of photosystem II Reviewed

    H. Isobe, M. Shoji, S. Yamanaka, H. Mino, Y. Umena, K. Kawakami, N. Kamiya, J. -R. Shen, K. Yamaguchi

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   Vol. 16 ( 24 ) page: 11911 - 11923   2014

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    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.

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  36. Evidence for an unprecedented histidine hydroxyl modification on D2-His336 in Photosystem II of Thermosynechoccocus vulcanus and Thermosynechoccocus elongatus. Reviewed International journal

    Miwa Sugiura, Kazumi Koyama, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Alain Boussac

    Biochemistry   Vol. 52 ( 52 ) page: 9426 - 31   2013.12

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    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.

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  37. Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation. Reviewed International journal

    Faisal Hammad Mekky Koua, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 110 ( 10 ) page: 3889 - 94   2013.3

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    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.

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  38. The nature of chemical bonds of the CaMn4O5 cluster in oxygen evolving complex of photosystem II: Jahn-Teller distortion and its suppression by Ca doping in cubane structures Reviewed

    K. Yamaguchi, S. Yamanaka, H. Isobe, T. Saito, K. Kanda, Y. Umena, K. Kawakami, J. -R. Shen, N. Kamiya, M. Okumura, H. Nakamura, M. Shoji, Y. Yoshioka

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   Vol. 113 ( 4 ) page: 453 - 473   2013.2

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    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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  39. Full geometry optimizations of the mixed-valence CaMn4O4X(H2O)(4) (X=OH or O) cluster in OEC of PS II: Degree of symmetry breaking of the labile Mn-X-Mn bond revealed by several hybrid DFT calculations Reviewed

    K. Yamaguchi, H. Isobe, S. Yamanaka, T. Saito, K. Kanda, M. Shoji, Y. Umena, K. Kawakami, J. -R. Shen, N. Kamiya, M. Okumura

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   Vol. 113 ( 4 ) page: 525 - 541   2013.2

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    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

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  40. Structural basis of photosynthetic water-splitting Reviewed

    Jian-Ren Shen, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya

    AIP Conference Proceedings   Vol. 1568   page: 31 - 34   2013

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    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.

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  41. High resolution structure of photosystem II and the mechanism of water-splitting Reviewed

    Jian-Ren Shen, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS   Vol. 1817   page: S2 - S3   2012.10

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    DOI: 10.1016/j.bbabio.2012.06.016

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  42. Deformation of chlorin rings in the Photosystem II crystal structure. Reviewed International journal

    Keisuke Saito, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Hiroshi Ishikita

    Biochemistry   Vol. 51 ( 21 ) page: 4290 - 9   2012.5

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    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.

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  43. Structure and Reactivity of the Mixed-Valence CaMn4O5(H2O)(4) and CaMn4O4(OH)(H2O)(4) Clusters at Oxygen Evolution Complex of Photosystem II. Hybrid DFT (UB3LYP and UBHandHLYP) Calculations Reviewed

    S. Yamanaka, T. Saito, K. Kanda, H. Isobe, Y. Umena, K. Kawakami, J-R Shen, N. Kamiya, M. Okumura, H. Nakamura, K. Yamaguchi

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   Vol. 112 ( 1 ) page: 321 - 343   2012.1

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    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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  44. Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathways Revealed for CaMn4O5 Cluster of PSII Refined to 1.9 angstrom X-Ray Resolution Reviewed

    T. Saito, S. Yamanaka, K. Kanda, H. Isobe, Y. Takano, Y. Shigeta, Y. Umena, K. Kawakami, J-R Shen, N. Kamiya, M. Okumura, M. Shoji, Y. Yoshioka, K. Yamaguchi

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   Vol. 112 ( 1 ) page: 253 - 276   2012.1

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    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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  45. Theoretical illumination of water-inserted structures of the CaMn4O5 cluster in the S-2 and S-3 states of oxygen-evolving complex of photosystem II: full geometry optimizations by B3LYP hybrid density functional Reviewed

    H. Isobe, M. Shoji, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J. -R. Shen, K. Yamaguchi

    DALTON TRANSACTIONS   Vol. 41 ( 44 ) page: 13727 - 13740   2012

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    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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  46. Electronic and Spin Structures of the CaMn4O5(H2O)(4) Cluster in OEC of PSII Refined to 1.9 angstrom X-ray Resolution Reviewed

    S. Yamanaka, K. Kanda, T. Saito, Y. Umena, K. Kawakami, J. -R. Shen, N. Kamiya, M. Okumura, H. Nakamura, K. Yamaguchi

    ADVANCES IN QUANTUM CHEMISTRY, VOL 64   Vol. 64   page: 121 - 187   2012

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    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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  47. Distribution of the cationic state over the chlorophyll pair of the photosystem II reaction center. Reviewed International journal

    Keisuke Saito, Toyokazu Ishida, Miwa Sugiura, Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Jian-Ren Shen, Hiroshi Ishikita

    Journal of the American Chemical Society   Vol. 133 ( 36 ) page: 14379 - 88   2011.9

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    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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  48. Structural-functional role of chloride in photosystem II. Reviewed International journal

    Ivan Rivalta, Muhamed Amin, Sandra Luber, Serguei Vassiliev, Ravi Pokhrel, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Doug Bruce, Gary W Brudvig, M R Gunner, Victor S Batista

    Biochemistry   Vol. 50 ( 29 ) page: 6312 - 5   2011.7

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    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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  49. S1-state model of the O2-evolving complex of photosystem II. Reviewed International journal

    Sandra Luber, Ivan Rivalta, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Gary W Brudvig, Victor S Batista

    Biochemistry   Vol. 50 ( 29 ) page: 6308 - 11   2011.7

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    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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  50. Structure of the catalytic, inorganic core of oxygen-evolving photosystem II at 1.9 angstrom resolution Reviewed

    Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Jian-Ren Shen

    JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY   Vol. 104 ( 1-2 ) page: 9 - 18   2011.7

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    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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  51. Possible mechanisms for the O-O bond formation in oxygen evolution reaction at the CaMn4O5(H2O)(4) cluster of PSII refined to 1.9 angstrom X-ray resolution Reviewed

    S. Yamanaka, H. Isobe, K. Kanda, T. Saito, Y. Umena, K. Kawakami, J. -R. Shen, N. Kamiya, M. Okumura, H. Nakamura, K. Yamaguchi

    CHEMICAL PHYSICS LETTERS   Vol. 511 ( 1-3 ) page: 138 - 145   2011.7

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    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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  52. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Reviewed International journal

    Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya

    Nature   Vol. 473 ( 7345 ) page: 55 - 60   2011.5

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    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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  53. Labile electronic and spin states of the CaMn4O5 cluster in the PSII system refined to the 1.9 angstrom X-ray resolution. UB3LYP computational results Reviewed

    Keita Kanda, Shusuke Yamanaka, Tohru Saito, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Mitsutaka Okumura, Haruki Nakamura, Kizashi Yamaguchi

    CHEMICAL PHYSICS LETTERS   Vol. 506 ( 1-3 ) page: 98 - 103   2011.4

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    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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  54. Roles of PsbI and PsbM in photosystem II dimer formation and stability studied by deletion mutagenesis and X-ray crystallography. Reviewed

    Kawakami K, Umena Y, Iwai M, Kawabata Y, Ikeuchi M, Kamiya N, Shen JR

    Biochimica et biophysica acta   Vol. 1807 ( 3 ) page: 319 - 325   2011.3

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  55. Hydrogen-bond networks and channels revealed in the 1.9 angstrom structure of PSII Reviewed

    Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya, Jian-Ren Shen

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 67   page: C741 - C741   2011

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    DOI: 10.1107/S0108767311081293

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  56. Crystallization and structure analysis of a PsbM-deletion mutant of PSII Reviewed

    Sayaka Uto, Keisuke Kawakami, Yasufumi Umena, Masako Iwai, Masahiko Ikeuchi, Jian-Ren Shen, Nobuo Kamiya

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 67   page: C743 - C743   2011

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    DOI: 10.1107/S0108767311081256

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  57. 1SL-02 Atomic structure of photosystem II that enables photosynthetic water-splitting(1SL The leading edge of photosynthesis research and energy creation,The 49th Annual Meeting of the Biophysical Society of Japan)

    Shen Jian-Ren, Umena Yasufumi, Kawakami Keisuke, Kamiya Nobuo

    Seibutsu Butsuri   Vol. 51 ( supplement ) page: S10   2011

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

    DOI: 10.2142/biophys.51.S10_1

    CiNii Research

  58. 2L1412 Crystal structure of oxygen evolving Photosystem II complex at an atomic resolution(Photobiology: Photosynthesis,The 48th Annual Meeting of the Biophysical Society of Japan) Reviewed

    Umena Yasufumi, Kawakami Keisuke, Kamiya Nobuo, Shen Jian-Ren

    Seibutsu Butsuri   Vol. 51   page: S95   2011

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    DOI: 10.2142/biophys.51.S95_2

  59. Crystal structures of photosystem II complexed with electron-transfer inhibitors Reviewed

    Satoshi Suzuri, Keisuke Kawakami, Takayoshi Tashiro, Yasufumi Umena, Jian-Ren Shen, Nobuo Kamiya

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 67   page: C742 - C742   2011

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    DOI: 10.1107/S0108767311081268

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  60. Structural and functional studies on Ycf12 (Psb30) and PsbZ-deletion mutants from a thermophilic cyanobacterium. Reviewed

    Takasaka K, Iwai M, Umena Y, Kawakami K, Ohmori Y, Ikeuchi M, Takahashi Y, Kamiya N, Shen JR

    Biochimica et biophysica acta   Vol. 1797 ( 2 ) page: 278 - 284   2010.2

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  61. Crystal structure of oxygen evolving Photosystem II at atomic resolution. Reviewed

    Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 66   page: S124 - S125   2010

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    DOI: 10.1107/S0108767310097291

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  62. Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography Reviewed

    Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Jian-Ren Shen

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   Vol. 106 ( 21 ) page: 8567 - 8572   2009.5

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    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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  63. Towards structural elucidation of eukaryotic photosystem II: Purification, crystallization and preliminary X-ray diffraction analysis of photosystem II from a red alga. Reviewed

    Adachi H, Umena Y, Enami I, Henmi T, Kamiya N, Shen JR

    Biochimica et biophysica acta   Vol. 1787 ( 2 ) page: 121 - 128   2009.2

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  64. Crystal structural analysis of photosystem II with the novel method to reduce X-ray radiation damage Reviewed

    Yasufumi Umena, Keisuke Kawakami, Akio Ohkuma, Shinya Saijyou, Hisashi Naitow, Jian-Ren Shen, Nobuo Kamiya

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 64   page: C293 - C293   2008

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    DOI: 10.1107/S0108767308090636

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  65. Crystallographic study on the interaction of L-lactate oxidase with pyruvate at 1.9 angstrom resolution Reviewed

    Shu Jie Li, Yasufumi Umena, Kazuko Yorita, Takeshi Matsuoka, Akiko Kita, Kiyoshi Fukui, Yukio Morimoto

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   Vol. 358 ( 4 ) page: 1002 - 1007   2007.7

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    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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MISC 15

  1. Structural analysis of ligand binding mechanism of L-lactate oxidase from Aerococcus viridans by use of ligand soaking crystals

    Y. Morimoto, N. Furubayashi, M. Kamo, Y. Umena, A. Kita, T. Matsuoka, K. Inaka

    16th Conference of the Asian Crystallographic Association (AsCA2019)     2019.12

  2. On the guiding principles for understanding of geometrical structures of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Proposal of estimation formula of structural deformations via the Jahn-Teller effects

    K. Yamaguchi, M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya

    MOLECULAR PHYSICS   Vol. 115 ( 5 ) page: 636 - 666   2017

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    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) in PSII is expected to proceed through five oxidation states, known as the S-i (i = 0, 1, 2, 3 and 4) states in the Kok cycle, with the S-1 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 in PSII have been investigated by the extended X-ray absorption fine structure (EXAFS). The magneto-structural correlations were extensively investigated by electron paramagnetic resonance (EPR) spectroscopy. Recently, Kamiya and Shen groups made great breakthrough for determination of the S-1 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 the CaMn4O5 cluster. Large-scale quantum mechanics/molecular mechanics 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 paper presents theoretical formulas for estimation of the JT deformations of the CaMn4O5 cluster in OEC of PSII. Scope and applicability of the formulas are examined in relation to several different structures of the CaMn4O5 cluster proposed by XRD, XFEL, EXAFS and other experiments. Implications of the computational results are discussed for further refinements of geometrical parameters of the CaMn4O5 cluster.

    DOI: 10.1080/00268976.2016.1278476

    Web of Science

  3. Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II

    Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya, Jian-Ren Shen, Takahito Nakajima, Kizashi Yamaguchi

    MOLECULAR PHYSICS   Vol. 113 ( 3-4 ) page: 359 - 384   2015.2

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    Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 angstrom resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O center dot center dot center dot O(N) and O center dot center dot center dot H distances and O(N)-H center dot center dot center dot O angles in PRP, together with the Cl-O(N) and Cl center dot center dot center dot H distances and O(N)-H center dot center dot center dot Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes.

    DOI: 10.1080/00268976.2014.960021

    Web of Science

  4. Large-Scale QM/MM Calculations of Hydrogen Bonding Networks for Proton Transfer and Water Inlet Channels for Water Oxidation-Theoretical System Models of the Oxygen-Evolving Complex of Photosystem II

    M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J-R Shen, T. Nakajima, K. Yamaguchi

    ADVANCES IN QUANTUM CHEMISTRY, VOL 70   Vol. 70   page: 325 - 413   2015

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    Language:English   Publisher:ELSEVIER ACADEMIC PRESS INC  

    In order to confirm theoretical system models of photosystem II (PSII), quantum mechanics (QM)/molecular mechanics (MM) calculations using a large-scale QM model (QM Model V) have been performed to elucidate hydrogen bonding networks and proton wires for proton release pathways (PRPs) of water oxidation reaction in the oxygen-evolving complex (OEC) of PSII. Full geometry optimizations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment on PSII refined to 1.9 angstrom resolution. The optimized Mn-Mn and Ca-Mn distances by largescale QM/MM are consistent with the EXAFS results, removing out the discrepancy between the refined XRD and EXAFS. Computational results from QM/MM calculations have demonstrated the labile nature of the Mn-a-O-(5)-dMn(d) bond of the CaMn4O5 cluster in the OEC of PSII which allows left (L)-opened, quasi-central (C-o)-, and right (R)-opened structures. This confirms the feasibility of the left-and right-hand scenarios for water oxidation in the OEC of PSII that are dependent on the hydrogen bonding networks. The QM/MM computations have elucidated the networks structures: hydrogen bonding O center dot center dot center dot O(N) and O center dot center dot center dot H distances and O(N)-H center dot center dot center dot O angles in PRP, together with the Cl-O(N) and Cl center dot center dot center dot H distances and O(N)-H center dot center dot center dot Cl angles for chloride anions. The obtained hydrogen bonding networks are fully consistent with the results from XRD and available experiments such as EXAFS, showing the reliability of our theoretical system model that is crucial for investigations of functions of PSII such as water oxidation. The QM/MM computations have elucidated possible roles of chloride anions in OEC of PSII for proton transfers. The QM/MM computational results have provided useful information for the understanding and explanation of several experimental results obtained with mutants of the OEC of PSII. The possible implications of the present results are discussed in relation to our theoretical system models of PSII, strong or weak perturbations of the system structures by mutations, damage-free X-ray free-electron laser structure of PSII, and bioinspired working hypotheses for the development of artificial water oxidation systems which use 3d transition metal complexes.

    DOI: 10.1016/bs.aiq.2014.10.001

    Web of Science

  5. Identification of β-Cryptoxanthin in Oxygen-Evolving Photosystem II from Thermosynechococcus vulcanus Reviewed

    Keisuke Kawakami, Ritsuko Fujii, Yasufumi Umena, Shin-ichiro Ozawa, Yuichiro Takahashi, Hideki Hashimoto, Jian-Ren Shen, Nobuo Kamiya

    CAROTENOID SCIENCE   Vol. 19   page: 48 - 51   2015

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    Language:English   Publishing type:Article, review, commentary, editorial, etc. (other)  

  6. 光合成の水分解・酸素発生機構の解明に向けて

    神谷信夫, 川上恵典, 梅名泰史, 沈 建仁

    放射光学会誌   Vol. 26   page: 3 - 10   2013

  7. Theoretical insight in to hydrogen-bonding networks and proton wire for the CaMn4O5 cluster of photosystem II. Elongation of Mn-Mn distances with hydrogen bonds

    M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J. -R. Shen, K. Yamaguchi

    CATALYSIS SCIENCE & TECHNOLOGY   Vol. 3 ( 7 ) page: 1831 - 1848   2013

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    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

    Web of Science

  8. Mechanism of photosynthetic water-splitting based on high resolution structure of photosystem II

    Jian-Ren Shen, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya

    Biophysics   Vol. 52 ( 3 ) page: 140 - 143   2012

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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 Mn<sub>4</sub>CaO<sub>5</sub>-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

  9. 25pGP-7 Densily functional study of electronic structures of the manganese cluster in photosystem II

    Yamanaka S., Kanda K., Umena Y., Kawakami K., Shen J.-R., Kamiya N., Okumura M., Nakamura H., Yamaguchi K.

    Meeting abstracts of the Physical Society of Japan   Vol. 66 ( 1 ) page: 378 - 378   2011.3

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

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  10. 25pGP-2 Atomic resolution structure of photosystem II that enables photosynthetic oxygen evolution

    Shen Jian-Ren, Umena Yasufumi, Kawakami Keisuke, Kamiya Nobuo

    Meeting abstracts of the Physical Society of Japan   Vol. 66 ( 1 ) page: 376 - 376   2011.3

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

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  11. Mechanism of PSII oxygen evolution predicted from its 1.9 angstrom resolution structure

    Nobuo Kamiya, Keisuke Kawakami, Yasufumi Umena, Jian-Ren Shen

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 67   page: C80 - C81   2011

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

    DOI: 10.1107/S0108767311098035

    Web of Science

  12. How iodide ions inhibit the oxygen evolution of photosystem II?

    Keisuke Kawakami, Daisuke Hagiwara, Yasufumi Umena, Jian-Ren Shen, Nobuo Kamiya

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 67   page: C739 - C740   2011

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

    DOI: 10.1107/S0108767311081335

    Web of Science

  13. Purification, crystallization and preliminary X-ray analysis of photosystem II dimer from a red alga

    Hideyuki Adachi, Yasufumi Umena, Isao Enami, Nobuo Kamiya, Jian-Ren Shen

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 64   page: C232 - C232   2008

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

    DOI: 10.1107/S0108767308092544

    Web of Science

  14. Coordination structure of two Cl--binding sites in oxygen-evolving photosystem II

    Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Jian-Ren Shen

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 64   page: C330 - C330   2008

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

    DOI: 10.1107/S0108767308089447

    Web of Science

  15. 1-II-4 X線結晶構造解析に基づいたL-乳酸酸化酵素の基質結合様式(ビタミン学の原点・栄養学への21世紀的回帰, 日本ビタミン学会第59回大会)

    頼田 和子, 梅名 泰史, 森本 幸生, 福井 清

    ビタミン   Vol. 81 ( 4 ) page: 147 - 147   2007.4

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

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Presentations 26

  1. 光合成アンテナ蛋白質フィコシアニンにおける光エネルギー移動の構造研究 Invited

    梅名泰史, 片山哲郎, 高山 友理子, 中根 崇智

    第61回生物物理学会年会  2023.11.15 

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    Event date: 2023.11

    Language:English   Presentation type:Symposium, workshop panel (nominated)  

  2. 光合成アンテナ蛋白質フィコシアニンにおける光エネルギー移動の構造研究 Invited

    梅名泰史, 片山哲郎, 高山 友理子, 中根 崇智

    第61回生物物理学会年会  2023.11.16 

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    Event date: 2023.11

    Language:English   Presentation type:Symposium, workshop panel (nominated)  

  3. 光合成アンテナ蛋白質フィコシアニンにおける光エネルギー移動の構造研究

    第13回日本光合成学会年会  2023.6.3 

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    Event date: 2023.6

    Language:Japanese   Presentation type:Poster presentation  

  4. 人工光合成のお手本となる天然の光合成タンパク質の構造を見る Invited

    梅名泰史

    SAT テクノロジー・ショーケース   2023.1.26 

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    Event date: 2023.1

    Language:Japanese   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

  5. Novel Mechanism of Cl-Dependent Proton Dislocation in Photosystem Ⅱ (PSⅡ) : Hybrid Ab initio Quantum Mechanics Molecular Mechanics Molecular Dynamics Simulation

    Nakamura Atsushi, Kang Jiyoung, Terada Ryu-ichiro, Kino Hiori, Umena Yasufumi, Kawakami Keisuke, Shen Jian-Ren, Kamiya Nobuo, Tateno Masaru

    Journal of the Physical Society of Japan  2019.8  Physical Society of Japan

  6. Determination of the Mn Valence in Oxygen-Evolving Photosystem II

    Umena Yasufumi, Kawakami Keisuke, Shen Jian-Ren, Kamiya Nobuo

    SPring-8/SACLA Research Report  2020.3.26  Japan Synchrotron Radiation Research Institute

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    Language:Japanese  

    DOI: 10.18957/rr.8.1.1

    CiNii Research

  7. Improvement Method by Laser-processing of Photosystem II Crystals for Valence Analysis of Mn-cluster

    Umena Yasufumi, Kawakami Keisuke, Kawano Yoshiaki, Yamamoto Masaki, Kamiya Nobuo, Shen Jian-Ren

    SPring-8/SACLA Research Report  2021.6.30  Japan Synchrotron Radiation Research Institute

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    Language:Japanese  

    DOI: 10.18957/rr.9.4.177

    CiNii Research

  8. Improvement of Photosystem II Crystals by Dehydration Treatment

    Umena Yasufumi, Kawakami Keisuke, Shen Jian-Ren, Kamiya Nobuo

    SPring-8/SACLA Research Report  2022.4.28  Japan Synchrotron Radiation Research Institute

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    Language:Japanese  

    DOI: 10.18957/rr.10.2.108

    CiNii Research

  9. Crystal Structural and Functional Analysis of Oxygen-Evolving Photosystem II Complex

    UMENA Yasufumi

    Nihon Kessho Gakkaishi  2012  The Crystallographic Society of Japan

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    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 Mn<sub>4</sub>CaO<sub>5</sub>-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 Mn<sub>4</sub>CaO<sub>5</sub>-cluster and thus may serve as the substrate water molecules for the oxygen-evolving reaction.

    DOI: 10.5940/jcrsj.54.247

    CiNii Research

  10. Improvement of X-ray diffraction resolution of photosystem II crystal from a red alga <I>Cyanidium caldarium</I>.

    Adachi Hideyuki, Umena Yasufumi, Enami Isao, Kamiya Nobuo, Shen Jian-Ren

    Plant and Cell Physiology Supplement  2008  The Japanese Society of Plant Physiologists

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    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

    CiNii Research

  11. Time-Resolved X-ray Crystallography Using Synchrotron Radiation

    SATO-TOMITA Ayana, UMENA Yasufumi, ICHIYANAGI Kouhei, FUKAYA Ryo, HIKTA Masahide, MATSUGAKI Naohiro, MUTAI Toshiki

    Nihon Kessho Gakkaishi  2021.2.28  The Crystallographic Society of Japan

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    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

  12. 25pGP-7 Densily functional study of electronic structures of the manganese cluster in photosystem II

    Yamanaka S., Kanda K., Umena Y., Kawakami K., Shen J.-R., Kamiya N., Okumura M., Nakamura H., Yamaguchi K.

    Meeting Abstracts of the Physical Society of Japan  2011  The Physical Society of Japan

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  13. Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography

    梅名 泰史, 沈 建仁

    PNAS 106  2009 

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  14. Structura an nctiona studies on Ycf12 (Psb30) and PsbZ deletion mutants from a thermophilic cyanobacterium

    梅名 泰史, 沈 建仁

    BBA 1797  2010 

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  15. X-ray crystallographic analysis of PSII from Ycf12 (Psb30) and PsbZ deletion mutants of thermophilic cyanobacteria

    Takasaka Kenji, Iwai Masako, Umena Yasufumi, Kamiya Nobuo, Kawakami Keisuke, Shen Jian-Ren

    Plant and Cell Physiology Supplement  2009  The Japanese Society of Plant Physiologists

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    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

  16. あいちSRの名古屋大学硬X線回折ビームラインBL2S1

    第37回日本放射光学会年会  2024.1.12 

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    Event date: 2024.1

    Language:Japanese   Presentation type:Poster presentation  

  17. 光合成活性中心の構造解析 Invited

    3. 第二回量子技術研究テーマの交流会  2023.11.17 

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    Event date: 2023.11

    Language:Japanese   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

  18. フェムト秒顕微過渡吸収分光法を用いた単一結晶中フィコシアニン三量体間のエネルギー移動反応の観測 Invited

    片山哲郎, 上田柊斗, 古部昭広, 梅名泰史,

    第61回生物物理学会年会  2023.11.15 

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    Event date: 2023.11

    Language:English   Presentation type:Symposium, workshop panel (nominated)  

  19. あいちSR の名古屋大学X 線回折ビームラインBL2S1

    第61回生物物理学会年会  2023.11.16 

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    Event date: 2023.11

    Language:English   Presentation type:Poster presentation  

  20. タンパク質結晶高速解析のための音響細胞整列技術の開発

    檜垣僚冶, 梅名泰史, 片山哲郎, 磯崎瑛宏

    第48回化学とマイクロ・ナノシステム学会研究会  2023.11.6 

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    Event date: 2023.11

    Language:Japanese   Presentation type:Poster presentation  

  21. あいちSR の名古屋大学ビームラインBL2S1 における高圧セルを使ったX 線回折測定の研究支援

    第64回高圧討論会  2023.11.2 

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    Event date: 2023.11

    Language:Japanese   Presentation type:Poster presentation  

  22. あいちSRの名古屋大学X線回折ビームラインBL2S1の即応性と多様性

    令和5年度日本結晶学会年会  2023.10.27 

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    Event date: 2023.10

    Language:Japanese   Presentation type:Poster presentation  

  23. The in vivo macromolecular crystallization platform at Nagoya University

    2023.10.28 

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    Event date: 2023.10

    Language:Japanese   Presentation type:Oral presentation (general)  

  24. 夏休み体験学習 ータンパク質と水の結晶を作る、観る、調べるー

    2023.7.24 

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    Event date: 2023.7

    Language:Japanese   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

  25. あいちSRの名古屋大学X線回折ビームラインBL2S1の即応性と多様性の利用支援

    第23回日本蛋白質科学年会  2023.7.6 

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    Event date: 2023.7

    Language:Japanese   Presentation type:Poster presentation  

  26. 名古屋大学ビームラインBL2S1 におけるX 線回折測定支援と現状

    シンクロトロン光研究センターシンポジウム2023  2023.1.15 

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    Event date: 2023.1

    Language:Japanese   Presentation type:Poster presentation  

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Research Project for Joint Research, Competitive Funding, etc. 1

  1. 有害金属環境の改良手法における光合成タンパク質の金属阻害作用の解明

    2022.4 - 2023.3

    公益財団法人 日比科学技術振興財団  研究助成 

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\862000

KAKENHI (Grants-in-Aid for Scientific Research) 15

  1. 光化学系II蛋白質における金属阻害機構の構造化学的解明

    Grant number:22K06100  2022.4 - 2025.3

    日本学術振興会  科学研究費助成事業  基盤研究(C)

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    Authorship:Principal investigator 

    Grant amount:\4160000

  2. Structural analysis of various light-driven reaction mechanisms of light-sensitive proteins.

    Grant number:19H05779  2019.6 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

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    Authorship:Coinvestigator(s) 

  3. Structural study on the function of chloride ion in photosystem II

    Grant number:18K06158  2018.4 - 2021.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    Umena Yasufumi

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    Authorship:Principal investigator 

    Grant amount:\4420000 ( Direct Cost: \3400000 、 Indirect Cost:\1020000 )

    In order to elucidate the role of chloride ion, which is an essential cofactor for water splitting in photosystem II (PSII) in photosynthesis reaction, we studied the inhibition mechanism from the crystal structure of PSII bound with molecular anions, which reduced PSII activity and to understand the original role of chloride ion from structural chemistry.
    This study succeeded in analyzing PSII crystals substituted with molecular anions azide, nitrate, and nitrite ions at 2-2.1 angstrom resolution. The inhibition mechanism was clarified from the common structural changes associated with these substitutions compared with the original structure. We concluded that the role of the chlorine ion in PSII is for supporting the proton transfer mechanism and for sustaining the structure of the active center of the Mn-cluster.

  4. X線ホログラフィーによる光学系II蛋白質の活性サイトMnクラスターの構造研究

    Grant number:17H05219  2017.4 - 2019.3

    科学研究費助成事業  新学術領域研究(研究領域提案型)

    梅名 泰史

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    Authorship:Principal investigator 

    Grant amount:\6500000 ( Direct Cost: \5000000 、 Indirect Cost:\1500000 )

    光合成の水分解・酸素発生反応を担う光化学系II蛋白質(PSII)には、活性中心にMn4Caクラスターが触媒中心として存在する。Mn4Caクラスターは価数が異なるMnで構成される混合原子価状態であることが知られているが、各Mnの価数はまだ未解決である。また、反応サイクルにおいて、4つのMnのうちで酸化還元を行っているMnを特定することも課題となっている。本研究では、散乱X線を3次元的に計測してホログラフィーによる像再生を行うことで、金属間の位置情報と価数情報を解析する蛍光X線ホログラフィー法により、Mn4Caクラスターの個々のMnの位置と価数の分析を行い、励起前後の比較から、酸化還元反応を行うMnを特定する研究である。
    これまで、蛍光X線ホログラフィーは金属合金結晶や低分子の金属錯体結晶等を対象としていたが、本研究期間により、生体試料の高分子量蛋白質結晶であるPSIIも実験対象とすることができた。また、X線損傷に鋭敏なPSIIを自然状態で測定するための、ラスタースキャンによるノーマルモードでの測定条件を開発し、X線による還元作用を受けずにデータ収集を行うことができた。これまでの測定により、PSII結晶のMn4Caクラスターに由来するホログラムパターンを得ることに成功した。また1段階遷移試料で同様の測定を行い、遷移による違いを確認できるホログラムパターンも得ることができた。生体試料の成果はミオグロビンなど僅かな例しか報告されていない。
    PSII結晶のMn4Caクラスターの構造情報から計算されるシミュレーションのホログラムと実験結果の比較から、Mn4CaクラスターのMn1に対応する部分に差異が確認されたことから、Mn1が酸化還元に関与している可能性が示唆された。しかし、まだ、金属合金等の蛍光X線ホログラフィー分析と比較すると、信頼性が劣るため、精度の点で課題が残っている。
    平成30年度が最終年度であるため、記入しない。
    平成30年度が最終年度であるため、記入しない。

  5. Crystal structural analysis of photosystem II in pH dependence for trapping S2 intermediate state

    Grant number:15H05588  2015.4 - 2018.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Young Scientists (A)

    Umena Yasufumi, Furutani Yuji

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    Authorship:Principal investigator 

    Grant amount:\23530000 ( Direct Cost: \18100000 、 Indirect Cost:\5430000 )

    Crystal structures of cyanobacterium Photosystem II (PSII) in pH4 or pH9 condition were solved at 2.0-angstrom resolution. These acidic or basic PSII crystals changed from the neutral state were obtained by using the mixture solution of three kinds of buffers for the linear pH gradient without changing the composition of crystal mother liquid. Whole structures were no differences among neutral, acidic and basic structure. However, the pH-dependant structure changes were observed on the proton pathways from the active site of water-oxidation. The each of structural change was in the different locations between acidic and basic structure, respectively. We concluded that these parts were essential for proton transfer from the water-splitting reaction in PSII.

  6. Elucidation of the mechanism controlling the formation of photosystem II complex by means of structural analysis of various mutants

    Grant number:20570038  2008 - 2010

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    SIN Kenjin, KAMIYA Nobuo, UMENA Yasufumi, KAWAKAMI Keisuke, TAKASAKA Kenji, IWAI Masako, IKEUCHI Masahiko

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    Authorship:Other 

    In order to elucidate the mechanism controlling the formation of the photosystem II complex, studies on the structures and functions of various low molecular weight subunit-deletion mutants of PSII were carried out. The crystal structure of Ycf12 (Psb30)-deletion mutant confirmed the location of Ycf12, and PSII isolated from a PsbZ-deletion mutant lacked both Ycf12 and PsbK, suggesting the requirement of PsbZ for the stable binding of these two subunits to PSII. In addition, PsbM was shown to be required for maintaining the stability of PSII dimer, while PsbI was required for the formation of PSII dimer but not required for the stability of the dimer.

  7. Structural analysis of various light-driven reaction mechanisms of light-sensitive proteins.

    2019 - 2024

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    Grant type:Competitive

  8. 光化学系IIにおける塩素イオンの構造化学的な機能解明

    2018.4 - 2021.3

    日本学術振興会  基盤研究(C) 

    梅名 泰史

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\4420000 ( Direct Cost: \3400000 、 Indirect Cost:\1020000 )

    光合成の酸素発生は光化学系II蛋白質(PSII)による水分解反応に由来している.PSIIの水分解反応には塩素イオン(Cl-)が必須であることは知られ,水分解に伴うプロトンの放出や構造安定化などが議論されてきた.これらの塩素イオンは擬ハロゲンなどの分子アニオンで置き換えられ,反応が抑制されることは知られている.申請者は2011年に反応中心の近傍に2箇所の塩素イオン結合サイトを見出したが,塩素イオンの構造的な役割はまだよく分かっていない.本研究は,塩素イオンを擬ハロゲンのアジ化物イオン(N3-)と硝酸イオン(NO3-)や亜硝酸イオン(NO2-)などの分子アニオンに置き換えた結晶構造を解析し,構造様式の変化から阻害機構を解明し,塩素イオンの構造化学的な役割を解明することを目的とする.

  9. X線ホログラフィーによる光学系II蛋白質の活性サイトMnクラスターの構造研究

    2017.4 - 2019.3

    日本学術振興会  新学術領域研究(研究領域提案型) 

    梅名 泰史

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\6500000 ( Direct Cost: \5000000 、 Indirect Cost:\1500000 )

    地球の好気的な環境は光合成による水分解・酸素発生反応によって支えられており,この反応は植物や藻類に存在する光化学系IIタンパク質(PSII)の酵素反応に起因している.PSIIの水分解反応の活性サイトにはMn4CaO5クラスター(Mnクラスター)が触媒として存在し,申請者は2011年に初めてその分子構造をPSIIの結晶構造で特定した.しかし,蛋白質結晶構造は位相情報を新たに導入する必要があり,また座標精度が低いことが反応を理解する上で課題となっている.これまでのX線吸収分光などの研究からMnクラスターはIII価とIV価の混合原子価状態にあることが知られており,4つのMn原子それぞれが酸化・還元することで水分解反応が触媒されている.このことから,PSIIで起こる水分解反応を理解するためには,Mnクラスターの精密な構造と4つのMn原子それぞれの価数を理解する必要がある.本申請はPSII結晶のX線ホログラフィー法により,位相問題によるバイアスのないMnクラスターの精密な構造とMn原子の価数を特定し,PSIIで起こる水分解反応の理解を目指すものである.

  10. Crystallographic study of water-spilitting reaction in photosystem II

    Grant number:16KT0058  2016.7 - 2020.3

    Umena Yasufumi

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    Authorship:Principal investigator 

    Grant amount:\18200000 ( Direct Cost: \14000000 、 Indirect Cost:\4200000 )

    Oxygen-evolving Photosystem II (PSII) protein in photosynthetic organisms has a Mn4CaO5 cluster as the reaction center of catalyzing a water-splitting reaction. In this study, the oxidation state in each of four Mn atoms in the cluster was investigated as well as the crystal structure of PSII in the four intermediate states of the reaction. To understand the detailed process of the water-splitting reaction in PSII, we developed a novel crystallographic analysis method using the wavelength of the absorption inflection point of a target metal atom. We prepared a lot of tinny PSII crystal, excited by pulse-laser, and then cryo-fixed. Both redox properties of each Mn atom in the cluster and crystal structure of PSII were simultaneously analyzed. As a result, we observed the redox changes in each Mn atom in the process of water-splitting reaction. Simultaneously with this redox analysis, we also captured the movements of water and proteins in PSII in the process of PSII.

  11. 構造化学的手法による光化学系IIの水分解反応の機構解明

    2016.4 - 2019.3

    日本学術振興会  基盤研究(B) 特設分野 遷移状態制御 

    梅名 泰史

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\18200000 ( Direct Cost: \14000000 、 Indirect Cost:\4200000 )

    本研究は、光合成で働く光化学系II蛋白質 (PSII)(図1A)が行っている水分解・酸素発生反応を解明するため、これまでの溶液試料による1次元のスペクトル分析ではなく、立体構造情報を基軸とした複合的な分析による、活性中心Mn4CaO5クラスター(OEC)(図1B)で起こる化学反応を構造化学的に理解することを目的とする。反応中間状態の結晶試料は、閃光照射と低温トラップによって調製し、以下の3つの独自の構造化学的なアプローチで遷移状態を分析する:1)金属の価数に応じたX線吸収の差異を利用した結晶構造解析(XRD)による4つのMn原子の価数を個別に分析、2)結晶試料と放射光の高輝度光源を用いた顕微赤外振動分光(FT-IR)によるMn-酸素間の微細な局所構造の変化を分析、3)多原子間の情報を含むFT-IRスペクトルのシミュレーション解析、活性中心を取り囲む水と蛋白質を含む広域な量子科学計算。それぞれが相補的な分析を統合し、OECの触媒作用を「現象の記述」ではなく、「化学反応として理解」することを目指す。

  12. 光化学系II膜蛋白質のpHトラップによるS2反応中間体の結晶構造解析

    2015.4 - 2018.3

    日本学術振興会  若手研究(A) 

    梅名 泰史

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\23530000 ( Direct Cost: \18100000 、 Indirect Cost:\5430000 )

    光合成の水分解・酸素発生を担う光化学系II膜蛋白質(PSII)のpH4とpH9の結晶構造解析に混合緩衝液を使うことで2.0Å分解能で成功した。酸性と塩基性条件では、それぞれ異なる部位のプロトン輸送に関係する構造が変化しており、pHにより活性が低下する構造上の要因が明らかになった。一方、反応中間S2状態のPSIIの結晶構造解析はこのpH条件では困難なため、結晶の凍結温度を変える方法を試みた。PSII結晶をフィルム状になる粘性液体で保護することで、100Kから200Kに温度を上げても結晶性は劣化せず、また結晶に光を照射するとX線吸収分光分析から、励起状態を保ったPSII結晶であることが確認された

  13. Studies on the oxygen-evolving reaction mechanism of photosystem II at an atomic resolution

    Grant number:24227002  2012.5 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (S)

    Kamiya Nobuo, KAWAKAMI KEISUKE, UMENA YASUFUMI, Fukushima Yoshimasa, Noji Tomoyasu, KAWAKAMI KEISUKE, UMENA YASUFUMI, Fukushima Yoshimasa, Noji Tomoyasu

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    Authorship:Collaborating Investigator(s) (not designated on Grant-in-Aid) 

    We have reported the high-resolution structure of photosystem II (PSII), which is evolving oxygen from water molecules in photosynthesis, at 1.9 A in 2011. The structure involves the oxygen-evolving Mn-cluster at the most stable Kok’s S1 state. In order to understand the oxygen-evolving mechanism of PSII, activated structures of PSII should be resolved. In this study, we determined many structures of PSII crystals; four of complexes with herbicides, one of PsbM-subunit deleted mutant, two of ion-substituted derivatives from chloride to bromide or iodide, and so on. By studying intermediate states, S0 and S2, in the Kok cycle, new knowledge on the oxygen-evolving mechanism of PSII was obtained.

  14. 光化学系II複合体の酸素発生反応の構造化学的な手法による原理解明

    2011.10 - 2015.3

    日本科学技術振興機構  さきがけ研究「光エネルギーと物質変換」 

    梅名 泰史

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    Authorship:Principal investigator  Grant type:Competitive

  15. X-ray Crystallographic Studies on Mechanism of Photosystem II Membrane Protein Complex

    Grant number:16087102  2004 - 2009

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Priority Areas

    KAMIYA Nobuo, SHIN Kenjin, IKEUCHI Akihiko, NAKAZATO Katsuyoshi, UMENA Yasufumi, SHIN Kenjin, IKEUCHI Akihiko, NAKAZATO Katsuyoshi, UMENA Yasufumi

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    Authorship:Collaborating Investigator(s) (not designated on Grant-in-Aid) 

    Photosystem II (PSII) catalyzes the oxygen evolution from water in the photosynthesis utilizing solar light energy. We succeeded to determine, first in the world, the three-dimensional structure of the oxygen-evolving Mn4Ca cluster at atomic resolution, including the whole structure of PSII. Because PSII also provides chemical energy for CO2 condensation, our results serve structural strict-bases for efficient use of solar energy in the green chemistry.

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Industrial property rights 2

  1. 光合成関連蛋白質のX線回折測定用結晶試料の選別方法およびそれに用いる装置

    梅名 泰史

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    Applicant:公立大学法人大阪市立大学

    Application no:特願2013-209199  Date applied:2013.10

    Announcement no:特開2015-071576  Date announced:2015.4

    J-GLOBAL

  2. スクリーニング用溶液の作製方法及び装置

    森本 幸生, 阿部 真琴, 鈴木 雅洋, 梅名 泰史

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    Applicant:国立大学法人京都大学

    Application no:特願2003-308422  Date applied:2003.9

    Announcement no:特開2005-077255  Date announced:2005.3

    Patent/Registration no:特許第4314364号  Date issued:2009.5

    J-GLOBAL

 

Teaching Experience (On-campus) 1

  1. 令和4年度名古屋大学グローバルサイエンスキャンパス

    2023

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    令和4年度グローバルサイエンスキャンパス(プロジェクトコード:0122G2906c)の第二ステージの高校生2名の研究の指導教官とした1年間従事した。

 

Social Contribution 2

  1. 1. 名古屋大学シンクロトロン光研究センター「休み体験学習 タンパク質と水の結晶を作る、観る、調べる」

    Role(s):Lecturer, Advisor, Planner, Organizing member, Demonstrator

    名古屋大学シンクロトロン光研究センター  2023.7

  2. 名古屋大学グローバルサイエンスキャンパス「名大 MIRAI GSC」

    Role(s):Lecturer, Advisor

    2023.4 - 2024.3

Academic Activities 2

  1. 日本結晶学会 編集委員

    Role(s):Planning, management, etc., Supervision (editorial), Review, evaluation, Peer review

    日本結晶学会  2023.4 - 2024.3

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    Type:Peer review 

  2. 日本結晶学会2024年度年会 実行委員

    Role(s):Planning, management, etc.

    日本結晶学会  2023.4 - 2023.11

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    Type:Academic society, research group, etc.