Updated on 2022/04/06

写真a

 
SUGA Michi
 
Organization
Research Institute for Interdisciplinary Science Professor
Position
Professor
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Degree

  • 博士(理学) ( 大阪大学 )

Research Areas

  • Life Science / Structural biochemistry

Education

  • 大阪大学理学研究科    

    2006 - 2009

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Research History

  • Okayama University   Research Institute for Interdisciplinary Science   Professor

    2022.4

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  • Japan Science and Technology Agency

    2018.10 - 2022.3

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Professional Memberships

  • THE JAPANESE SOCIETY OF PLANT PHYSIOLOGISTS

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  • THE BIOPHYSICAL SOCIETY OF JAPAN

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  • PROTEIN SCIENCE SOCIETY OF JAPAN

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  • THE CRYSTALLOGRAPHIC SOCIETY OF JAPAN

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  • THE JAPANESE SOCIETY OF PHOTOSYNTHESIS RESEARCH

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  • 国際光合成学会

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Committee Memberships

  • 岡山大学   自然生命科学研究支援センター 光放射線情報解析部門 津島施設長  

    2022.4   

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  • 岡山大学   放射線同位元素等安全管理委員会委員  

    2022.4   

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  • 量子生命科学会   2022年会プログラム委員  

    2021.12 - 2022.12   

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    Committee type:Academic society

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Papers

  • Structural basis for high selectivity of a rice silicon channel Lsi1 Reviewed

    Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jian-Ren Shen, Jian Feng Ma, Michihiro Suga

    Nature Communications   12 ( 1 )   2021.10

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    Authorship:Last author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    <title>Abstract</title>Silicon (Si), the most abundant mineral element in the earth’s crust, is taken up by plant roots in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1 at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity filter (SF) composed of five residues. Our structural, functional, and theoretical investigations provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to secure and sustainable rice production by manipulating Lsi1 selectivity for different metalloids.

    DOI: 10.1038/s41467-021-26535-x

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    Other Link: https://www.nature.com/articles/s41467-021-26535-x

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

    Suga M, Akita F, Yamashita K, Nakajima Y, Ueno G, Li H, Yamane T, Hirata K, Umena Y, Yonekura S, Yu LJ, 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 JR

    Science (New York, N.Y.)   366 ( 6463 )   334 - 338   2019.10

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER ASSOC ADVANCEMENT SCIENCE  

    Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S-0 to S-4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S-1, S-2, and S-3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S-2, but flipping of D1 Glu(189) upon transition to S-3 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 reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

    DOI: 10.1126/science.aax6998

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  • Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL Reviewed

    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   543 ( 7643 )   131 - +   2017.3

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

    Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC)(1-3). The structure of PSII has been analysed at 1.9 angstrom resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, `distorted-chair' form(4). This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the `radiation damage-free'(5) 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 angstrom using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 angstrom 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 angstrom 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 mu 4-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 angstrom between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously(6,7.)

    DOI: 10.1038/nature21400

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  • Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex Reviewed

    Xiaochun Qin, Michihiro Suga, Tingyun Kuang, Jian-Ren Shen

    SCIENCE   348 ( 6238 )   989 - 995   2015.5

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER ASSOC ADVANCEMENT SCIENCE  

    Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors-especially within LHCI-as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.

    DOI: 10.1126/science.aab0214

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  • Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses Reviewed

    Michihiro Suga, Fusamichi Akita, Kunio Hirata, Go Ueno, Hironori Murakami, Yoshiki Nakajima, Tetsuya Shimizu, Keitaro Yamashita, Masaki Yamamoto, Hideo Ago, Jian-Ren Shen

    NATURE   517 ( 7532 )   99 - U265   2015.1

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

    Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 angstrom resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment(1). However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation(2), and slight differences were found in the Mn-Mn distances determined by XRD1, EXAFS(3-7) and theoretical studies(8-14). Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S-1 state at a resolution of 1.95 angstroms using femtosecond X-ray pulses of the SPring-8 angstrom compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 angstroms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.

    DOI: 10.1038/nature13991

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  • Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography. Reviewed International journal

    Hongjie Li, Yoshiki Nakajima, Takashi Nomura, Michihiro Sugahara, Shinichiro Yonekura, Siu Kit Chan, Takanori Nakane, Takahiro Yamane, Yasufumi Umena, Mamoru Suzuki, Tetsuya Masuda, Taiki Motomura, Hisashi Naitow, Yoshinori Matsuura, Tetsunari Kimura, Kensuke Tono, Shigeki Owada, Yasumasa Joti, Rie Tanaka, Eriko Nango, Fusamichi Akita, Minoru Kubo, So Iwata, Jian-Ren Shen, Michihiro Suga

    IUCrJ   8 ( Pt 3 )   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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  • Structural variations of photosystem I-antenna supercomplex in response to adaptations to different light environments. Invited Reviewed International journal

    Michihiro Suga, Jian-Ren Shen

    Current opinion in structural biology   63   10 - 17   2020.8

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    Photosystem I (PSI) is one of the two photosystems in photosynthesis, and generates reducing power required for carbon dioxide fixation. PSI exists as a reaction center core in cyanobacteria but is surrounded by light-harvesting antenna complexes (LHCI) to form PSI-LHCI supercomplexes in eukaryotic organisms. The structures of PSI core and PSI-LHCI have been reported from various organisms. We compare these structures and highlight the differences among different organisms. While the PSI core is more conserved, there are differences in its subunit composition and organization. Larger differences are found in the subunit composition, organization, and pigment binding in LHCI. All these changes can be explained in the framework of better adaptation to different light environment that each photosynthetic organism inhabits.

    DOI: 10.1016/j.sbi.2020.02.005

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  • Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Reviewed International journal

    Michihiro Suga, Atsuhiro Shimada, Fusamichi Akita, Jian-Ren Shen, Takehiko Tosha, Hiroshi Sugimoto

    Biochimica et biophysica acta. General subjects   1864 ( 2 )   129466 - 129466   2020.2

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    BACKGROUND: The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach. SCOPE OF REVIEW: Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described. MAJOR CONCLUSIONS: XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data. GENERAL SIGNIFICANCE: XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.

    DOI: 10.1016/j.bbagen.2019.129466

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  • Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography Reviewed

    Shoji Mitsuo, Isobe Hiroshi, Shen Jian-Ren, Suga Michihiro, Akita Fusamichi, Miyagawa Koichi, Shigeta Yasuteru, Yamaguchi Kizashi

    CHEMICAL PHYSICS LETTERS   730   416 - 425   2019.9

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

    The fully optimized geometrical structures of the CaMn4Ox (x = 5, 6) clusters in the Si (i = 0-3) states of the Kok cycle of photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics (QM/MM) calculations were compared to recent experimental results based on serial femtosecond crystallography (SFX). The Mn-Mn and Ca-Mn distances obtained by the QM/MM calculations were found to be totally comparable to the SFX experiments, elucidating the entire Kok cycle involving the S-4 transition state during the O-O bond formation for water oxidation in the oxygen evolving complex (OEC) of photosystem II (PSII).

    DOI: 10.1016/j.cplett.2019.06.026

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  • Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I Reviewed

    Suga Michihiro, Ozawa Shin-Ichiro, Yoshida-Motomura Kaori, Akita Fusamichi, Miyazaki Naoyuki, Takahashi Yuichiro

    NATURE PLANTS   5 ( 6 )   626 - 636   2019.6

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  • Structural basis for blue-green light harvesting and energy dissipation in diatoms Reviewed

    Wang Wenda, Yu Long-Jiang, Xu Caizhe, Tomizaki Takashi, Zhao Songhao, Umena Yasufumi, Chen Xiaobo, Qin Xiaochun, Xin Yueyong, Suga Michihiro, Han Guangye, Kuang Tingyun, Shen Jian-Ren

    SCIENCE   363 ( 6427 )   eaav0365 - +   2019.2

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    DOI: 10.1126/science.aav0365

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  • Novel features of LH1-RC from Thermochromatium tepidum revealed from its atomic resolution structure

    Long-Jiang Yu, Michihiro Suga, Zheng-Yu Wang-Otomo, Jian-Ren Shen

    FEBS JOURNAL   285 ( 23 )   4359 - 4366   2018.12

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

    Light-harvesting-1 (LH1)-reaction center (RC) super-complex is a membrane protein-pigment complex existing in purple photosynthetic bacteria, where LH1 absorbs light energy and transfers them rapidly and efficiently to RC to initiate the charge separation and electron transfer reactions. The structure of LH1-RC has been reported at relatively low resolutions from several different species of bacteria previously, but was solved at an atomic resolution recently from a thermophilic photosynthetic bacterium Thermochromatium tepidum. This high-resolution structure revealed the detailed organization of the super-complex including a number of unique features that are important for its functioning, such as a more intact RC structure, transporting routes for quinones to replace the bound Q(B) as well as for the in-and-out of the closed LH1 ring, detailed coordinating environment of the Ca2+ ions in LH1 important for the remarkable red shift of the absorption spectrum, as well as for the enhanced thermostability. These results thus greatly advance our understanding on the mechanisms of energy transfer, quinone exchange, the red shift in the LH1-Qy transition and the enhanced thermal stability, in this super-complex.

    DOI: 10.1111/febs.14679

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

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   293 ( 38 )   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.

    DOI: 10.1074/jbc.RA118.004304

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  • Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II Reviewed

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

    Journal of Physical Chemistry Letters   9 ( 9 )   2121 - 2126   2018.5

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

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

    DOI: 10.1021/acs.jpclett.8b00638

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  • Structure of photosynthetic LH1-RC supercomplex at 1.9 Å resolution Reviewed

    Long-Jiang Yu, Michihiro Suga, Zheng-Yu Wang-Otomo, Jian-Ren Shen

    Nature   556 ( 7700 )   209 - 213   2018.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Nature Publishing Group  

    Light-harvesting complex 1 (LH1) and the reaction centre (RC) form a membrane-protein supercomplex that performs the primary reactions of photosynthesis in purple photosynthetic bacteria. The structure of the LH1-RC complex can provide information on the arrangement of protein subunits and cofactors
    however, so far it has been resolved only at a relatively low resolution. Here we report the crystal structure of the calcium-ion-bound LH1-RC supercomplex of Thermochromatium tepidum at a resolution of 1.9 Å. This atomic-resolution structure revealed several new features about the organization of protein subunits and cofactors. We describe the loop regions of RC in their intact states, the interaction of these loop regions with the LH1 subunits, the exchange route for the bound quinone QB with free quinone molecules, the transport of free quinones between the inside and outside of the LH1 ring structure, and the detailed calcium-ion-binding environment. This structure provides a solid basis for the detailed examination of the light reactions that occur during bacterial photosynthesis.

    DOI: 10.1038/s41586-018-0002-9

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  • Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain Reviewed

    Taiki Motomura, Michihiro Suga, Rainer Hienerwadel, Akiko Nakagawa, Thanh-Lan Lai, Wolfgang Nitschke, Takahiro Kuma, Miwa Sugiura, Alain Boussac, Jian-Ren Shen

    JOURNAL OF BIOLOGICAL CHEMISTRY   292 ( 23 )   9599 - 9612   2017.6

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

    Photosystem II catalyzes light-induced water oxidation leading to the generation of dioxygen indispensable for sustaining aerobic life on Earth. The Photosystem II reaction center is composed of D1 and D2 proteins encoded by psbA and psbD genes, respectively. In cyanobacteria, different psbA genes are present in the genome. The thermophilic cyanobacterium Thermosynechococcus elongatus contains three psbA genes: psbA1, psbA2, and psbA3, and a new c-type heme protein, Tll0287, was found to be expressed in a strain expressing the psbA2 gene only, but the structure and function of Tll0287 are unknown. Here we solved the crystal structure of Tll0287 at a 2.0 angstrom resolution. The overall structure of Tll0287 was found to be similar to some kinases and sensor proteins with a Per-Arnt-Sim-like domain rather than to other c-type cytochromes. The fifth and sixth axial ligands for the heme were Cys and His, instead of the His/Met or His/His ligand pairs observed for most of the c-type hemes. The redox potential, E-1/2, of Tll0287 was -255 +/- 20 mV versus normal hydrogen electrode at pH values above 7.5. Below this pH value, the E1/2 increased by approximate to 57 mV/pH unit at 15 degrees C, suggesting the involvement of a protonatable group with a pK(red) = 7.2 +/- 0.3. Possible functions of Tll0287 as a redox sensor under microaerobic conditions or a cytochrome subunit of an H2S-oxidizing system are discussed in view of the environmental conditions in which psbA2 is expressed, as well as phylogenetic analysis, structural, and sequence homologies.

    DOI: 10.1074/jbc.M116.746263

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  • Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures Reviewed

    Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi

    FARADAY DISCUSSIONS   198   83 - 106   2017.6

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

    Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S-3 state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened structure was found to be stable under the assumption of no hydroxide anion insertion in the S-3 state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn4Ca cluster. The optimized Mn-a(4)-Mn-d(1) distance determined by QM/MM was about 5.0 angstrom for the S-3 structure without an inserted hydroxide anion, but this is elongated by 0.2-0.3 angstrom after insertion. These computational results are discussed in relation to the possible mechanisms of O-O bond formation in water oxidation by the OEC of PSII.

    DOI: 10.1039/c6fd00230g

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  • Structure and energy transfer pathways of the plant photosystem I-LHCI supercomplex Invited Reviewed

    Michihiro Suga, Xiaochun Qin, Tingyun Kuang, Jian-Ren Shen

    CURRENT OPINION IN STRUCTURAL BIOLOGY   39   46 - 53   2016.8

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:CURRENT BIOLOGY LTD  

    Photosystem I (PSI) is one of the two photosystems in oxygenic photosynthesis, and absorbs light energy to generate reducing power for the reduction of NADP+ to NADPH with a quantum efficiency close to 100%. The plant PSI core forms a supercomplex with light-harvesting complex I (LHCI) with a total molecular weight of over 600 kDa. Recent X-ray structure analysis of the PSI-LHCI membrane-protein supercomplex has revealed detailed arrangement of the light-harvesting pigments and other cofactors especially within LHCI. Here we introduce the overall structure of the PSI-LHCI supercomplex, and then focus on the excited energy transfer (EET) pathways from LHCI to the PSI core and photoprotection mechanisms based on the structure obtained.

    DOI: 10.1016/j.sbi.2016.04.004

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  • On the guiding principles for lucid understanding of the damage-free S-1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II Reviewed

    Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi

    CHEMICAL PHYSICS LETTERS   627   44 - 52   2015.5

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    Several key concepts and geometrical rules for the Mn-Mn and Mn-O distances of the CaMn4O5 cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by previous and present theoretical calculations were examined for a clear understanding of the damage-free Si structure revealed by X-ray free electron laser (XFEL). A simple equation to estimate the Mn-a-Mn-b distance in relation to the Mn-a-O(5) distance was derived taking into consideration the Jahn-Teller (JT) effects for Mn centers, indicating that the XFEL structure is regarded as a slightly right-elongated quasi-central structure in contradiction to a right-opened structure proposed by the EXAFS measurements. (C) 2015 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cplett.2015.03.033

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  • Theoretical studies of the damage- free S-1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II Reviewed

    Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi

    CHEMICAL PHYSICS LETTERS   623   1 - 7   2015.3

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    The structure of the oxygen evolving complex (OEC) of photosystem II (PSII) was recently analyzed by crystallography at 1.95 angstrom resolution using X-ray free electron laser (XFEL), but the positions of hydrogen atoms were not determined. We have examined the XFEL structure theoretically under the assumption off our protonation cases. The spin densities obtained by the high-spin UB3LYP revealed that a partial internal reduction of the high-valent Mn ions in the CaMn4O4X(H2O)(3)Y cluster occurs for the O-(5)(=X) = O2- case, entailing its protonation (X = OH-) in the XFEL structure. (C) 2015 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cplett.2015.01.030

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  • Crystal structure at 1.5 angstrom resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus Reviewed

    Michihiro Suga, Thanh-Lan Lai, Miwa Sugiura, Jian-Ren Shen, Alain Boussac

    FEBS LETTERS   587 ( 19 )   3267 - 3272   2013.10

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    PsbV2 is a c-type cytochrome present in a very low abundance in the thermophilic cyanobacterium Thermosynechococcus elongatus. We purified this cytochrome and solved its crystal structure at a resolution of 1.5 angstrom. The protein existed as a dimer in the crystal, and has an overall structure similar to other c-type cytochromes like Cytc(6) and Cytc(550), for example. However, the 5th and 6th heme iron axial ligands were found to be His51 and Cys101, respectively, in contrast to the more common bis-His or His/Met ligands found in most cytochromes. Although a few other c-type cytochromes were suggested to have this axial coordination, this is the first crystal structure reported for a c-type heme with this unusual His/Cys axial coordination. Previous spectroscopic characterizations of PsbV2 are discussed in relation to its structural properties. (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

    DOI: 10.1016/j.febslet.2013.08.023

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  • Crystal Structure of Psb31, a Novel Extrinsic Protein of Photosystem II from a Marine Centric Diatom and Implications for Its Binding and Function Reviewed

    Ryo Nagao, Michihiro Suga, Ayako Niikura, Akinori Okumura, Faisal Hammad Mekky Koua, Takehiro Suzuki, Tatsuya Tomo, Isao Enami, Jian-Ren Shen

    BIOCHEMISTRY   52 ( 38 )   6646 - 6652   2013.9

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    Psb31 is a fifth extrinsic protein found in photosystem II (PSII) of a centric diatom, Chaetoceros gracilis. The protein has been shown to bind directly to PSII in the absence of other extrinsic proteins and serves in part as a substitute for PsbO in supporting oxygen evolution. We report here the crystal structure of Psb31 at a resolution of 1.55 angstrom. The structure of Psb31 was composed of two domains, one major, N-terminal four helical domain and one minor, flexible C-terminal domain. The four helices in the N-terminal domain were arranged in an up down-up-down-fold, which appeared unexpectedly to be similar to the structure of spinach PsbQ in spite of their low sequence homology. This suggests that the centric diatom PSII contains another PsbQ- type extrinsic protein in addition to the original PsbQ protein found in the organism. On the other hand, the C-terminal domain of Psb31 has a unique structure composed of one loop and one short helix. Based on these structural analysis and chemical cross-linking experiments, residues responsible for the binding of Psb31 to PSII intrinsic proteins were suggested. The results are discussed in relation to the copy number of extrinsic proteins in higher plant PSII.

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  • Distinguishing between Cl- and O-2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase Reviewed

    Michihiro Suga, Naomine Yano, Kazumasa Muramoto, Kyoko Shinzawa-Itoh, Tomoko Maeda, Eiki Yamashita, Tomitake Tsukihara, Shinya Yoshikawa

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   67   742 - 744   2011.8

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    Fully oxidized cytochrome c oxidase (CcO) under enzymatic turnover is capable of pumping protons, while fully oxidized CcO as isolated is not able to do so upon one-electron reduction. The functional difference is expected to be a consequence of structural differences: [Fe3+-OH-] under enzymatic turnover versus [Fe3+-O-2(2-)-Cu2+] for the as-isolated CcO. However, the electron density for O-2(2-) is equally assignable to Cl-. An anomalous dispersion analysis was performed in order to conclusively demonstrate the absence of Cl- between the Fe3+ and Cu2+. Thus, the peroxide moiety receives electron equivalents from cytochrome c without affecting the oxidation states of the metal sites. The metal-site reduction is coupled to the proton pump.

    DOI: 10.1107/S0907444911022803

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  • Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1) Reviewed

    Kohei Takeshita, Isao Suetake, Eiki Yamashita, Michihiro Suga, Hirotaka Narita, Atsushi Nakagawa, Shoji Tajima

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   108 ( 22 )   9055 - 9059   2011.5

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    Methylation of cytosine in DNA plays a crucial role in development through inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation patterns to the next generation via its preferential methylation of hemimethylated CpG sites in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here we report the crystal structure of the large fragment (291-1620) of mouse Dnmt1 and its complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein. Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to replication foci is inserted into the DNA-binding pocket, indicating that this domain must be removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic cysteine residue undergoes a conformation transition to a catalytically competent position. For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance methylation is a multistep process accompanied by structural changes.

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  • A description of the structural determination procedures of a gap junction channel at 3.5 angstrom resolution Reviewed

    Michihiro Suga, Shoji Maeda, So Nakagawa, Eiki Yamashita, Tomitake Tsukihara

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   65   758 - 766   2009.8

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    Intercellular signalling is an essential characteristic of multicellular organisms. Gap junctions, which consist of arrays of intercellular channels, permit the exchange of ions and small molecules between adjacent cells. Here, the structural determination of a gap junction channel composed of connexin 26 (Cx26) at 3.5 angstrom resolution is described. During each step of the purification process, the protein was examined using electron microscopy and/or dynamic light scattering. Dehydration of the crystals improved the resolution limits. Phase refinement using multi-crystal averaging in conjunction with noncrystallographic symmetry averaging based on strictly determined noncrystallographic symmetry operators resulted in an electron-density map for model building. The amino-acid sequence of a protomer structure consisting of the amino-terminal helix, four transmembrane helices and two extracellular loops was assigned to the electron-density map. The amino-acid assignment was confirmed using six selenomethionine (SeMet) sites in the difference Fourier map of the SeMet derivative and three intramolecular disulfide bonds in the anomalous difference Fourier map of the native crystal.

    DOI: 10.1107/S0907444909014711

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  • Structure of the connexin 26 gap junction channel at 3.5 A resolution. Reviewed International journal

    Shoji Maeda, So Nakagawa, Michihiro Suga, Eiki Yamashita, Atsunori Oshima, Yoshinori Fujiyoshi, Tomitake Tsukihara

    Nature   458 ( 7238 )   597 - 602   2009.4

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    Gap junctions consist of arrays of intercellular channels between adjacent cells that permit the exchange of ions and small molecules. Here we report the crystal structure of the gap junction channel formed by human connexin 26 (Cx26, also known as GJB2) at 3.5 A resolution, and discuss structural determinants of solute transport through the channel. The density map showed the two membrane-spanning hemichannels and the arrangement of the four transmembrane helices of the six protomers forming each hemichannel. The hemichannels feature a positively charged cytoplasmic entrance, a funnel, a negatively charged transmembrane pathway, and an extracellular cavity. The pore is narrowed at the funnel, which is formed by the six amino-terminal helices lining the wall of the channel, which thus determines the molecular size restriction at the channel entrance. The structure of the Cx26 gap junction channel also has implications for the gating of the channel by the transjunctional voltage.

    DOI: 10.1038/nature07869

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  • Structure of Physarum polycephalum cytochrome b5 reductase at 1.56Åresolution. Reviewed

    Acta Cryst

    Sangwoo Kim, Michihiro Suga, Kyoko Ogasahara, Terumi Ikegami, Yoshiko Minami, Toshitsugu Yubisui and Tomitake Tsukihara   63   274 - 279   2007

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    DOI: 10.1107/S1744309107010731

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Books

  • Structure, Electron Transfer Chain of Photosystem II and the Mechanism of Water Splitting

    Jian-Ren Shen, Yoshiki Nakajima, Fusamichi Akita, Michihiro Suga( Role: Contributor)

    Springer, Cham  2021.9 

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  • 光エネルギー変換における分子触媒の新展開 : 天然光合成を凌駕する反応系の構築を目指して

    日本化学会( Role: Joint author ,  光合成光化学系IIの構造と触媒機能)

    化学同人  2020.9  ( ISBN:9784759813982

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MISC

  • Current and Future Demands in Structural Biology Invited Reviewed

    Michihiro SUGA

    Nihon Kessho Gakkaishi   62 ( 4 )   238 - 240   2020.12

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    DOI: 10.5940/jcrsj.62.238

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  • Structural basis for the photosynthetic water-splitting/oxygenevolving reaction Reviewed

    Fusamichi Akita, Michihiro Suga, Jian-Ren Shen

    Seikagaku   89 ( 5 )   699 - 709   2017

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    Language:Japanese   Publishing type:Book review, literature introduction, etc.   Publisher:Japanese Biochemical Society  

    DOI: 10.14952/SEIKAGAKU.2017.890699

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  • X線自由電子レーザーを利用した光化学系IIの原子構造と水分解反応機構の解明 Invited Reviewed

    菅 倫寛, 秋田 総理, 沈 建仁

    レーザー学会誌「レーザー研究」   45 ( 8 )   475 - 479   2017

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  • 植物光化学系I-集光性アンテナI 超複合体におけるエネルギー伝達の構造基盤 Invited Reviewed

    菅 倫寛, 沈 建仁

    SPring-8/SACLA利用者情報   22 ( 3 )   233 - 237   2017

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  • 光合成の構造生物学 Invited Reviewed

    沈 建仁, 秋田 総理, 菅 倫寛

    生物物理   56 ( 2 )   79 - 86   2016

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    DOI: 10.2142/biophys.56.079

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  • フェムト秒X線レーザーを用いて決定した光化学系II複合体の無損傷構造 Invited Reviewed

    菅 倫寛, 秋田 総理, 沈 建仁, 山本 雅貴, 吾郷 日出夫

    日本結晶学会誌   58 ( 3 )   126 - 132   2016

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    DOI: 10.5940/jcrsj.58.126

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  • X線自由電子レーザーで決定した光化学系Ⅱ複合体の無損傷結晶構造と水分解反応機構 Invited Reviewed

    菅 倫寛, 秋田 総理, 山本 雅貴

    放射光 : 日本放射光学会誌   28 ( 4 )   177 - 182   2015.7

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Presentations

  • An open-cubane oxyl/oxo mechanism for O=O bond formation in photosystem II revealed by X-ray free electron laser pulses

    菅倫寛, 秋田総理, 山本雅貴, 吾郷日出夫, 沈建仁

    第61回日本植物生理学会年会(新型コロナウイルスにより中止)  2020.3.19 

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    Presentation type:Poster presentation  

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  • X-ray free electron lasers reveal the molecular mechanism for water oxidation in photosystem II Invited

    Michi Suga, Yoshiki Naiajima, Hongjie Li, Jian-Ren Shen

    2021.11.25 

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  • X線自由電子レーザーによって明らかになった光合成光化学系IIの水分解反応 Invited

    MBSJ2020 (online)  2020.12.4 

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  • X-ray free electron lasers reveal the molecular mechanism for water oxidation in photosystem II Invited

    Michihiro Suga

    11th International workshop on X-ray radiation damage to biological samples – RD11, online  2020.10.14 

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  • 結晶構造から紐解く光合成の酸素発生の反応機構 Invited

    菅倫寛

    第60回生物物理若手の会夏の学会(オンライン)、メインセミナーIII  2020.8.25 

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  • Intermediate Si-state structures of photosystem II reveal the nature’s molecular mechanism for water oxidation. Invited International conference

    Michi Suga

    The 11th Inthernational workshop on X-ray damage to biological samples (RD11): Postponed due to Covid-2019  2020.3.25 

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  • An open-cubane oxyl/oxo mechanism for O=O bond formation in photosynthetic photosystem II revealed by X-ray free laser pulses. Invited International conference

    Michi Suga

    16th Conference of the Asian Crystallographic Association  2019.12.17 

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  • Structure of the green algal Photosystem I-Light hearvesting complex I supercomplex Invited

    Michi Suga

    NIPS EM Workshop  2019.11.26 

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  • Intermediate Si-state structures of photosystem II reveal the molecular mechanism for water oxidation in nature Invited

    Michi Suga

    3rd International Solar Fuels Conference (keynote lecture)  2019.11.24 

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  • X-ray free electron laser reveals the molecular mechanism for water oxidation in nature Invited

    Michi Suga

    International Workshop on Frontier of Science and Technology for Solar Energy Conversion  2019.11.5 

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  • Structural changes of oxygen-evoving PSII during S-state transitions and a possible mechaniism for oxygen evolving reaction revealed by X-ray free electron laser pulses Invited

    Michi Suga

    2019 ESP-IUPB world congress  2019.8.25 

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  • Structural changes of oxygen-evolving PSII during S-state transitions revealed by XFEL Invited

    Michi Suga

    Joint Annual Meeting of 71st JSCB & 19th PSSJ  2019.6.24 

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  • Crystal structure of PSII in the intermediate states and possible mechanism for the O=O bond formation. Invited

    Michi Suga

    Crystal structure of PSII in the intermediate states and possible mechanism for the O=O bond formation.  2018.9.17 

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  • Structure of oxygen evolving photosystem II and possible mechanism for the O=O bond formation. Invited

    Michi Suga

    SACLA Users' Meeting 2018 (Invited talk)  2018.9.7 

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  • The 1st SACLA Workshop on Femtosecond Crystallography Invited

    Michi Suga

    The 1st SACLA Workshop on Femtosecond Crystallography  2015.3.26 

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Awards

  • Young Scientist Award from the Photobiology Association of Japan

    2020.8   Photobiology Association of Japan  

    Michi Suga

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  • The Japanese Society of Plant Physiology Young Investigator Award

    2017.3   The Japanese Society of Plant Physiology  

    Michi Suga

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  • 岡山大学若手トップリサーチャー学長表彰

    2017  

    菅 倫寛

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  • The Young Scientists’ Prize of the Commendation for Science and Technology by the Ministry of Education, Culture, Sports, Science and Technology

    2016.4   the Ministry of Education, Culture, Sports, Science and Technology  

    Michi Suga

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  • 岡山大学学長奨励賞

    2016  

    菅 倫寛

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  • Young Scientist Award from the Crystallographic Society of Japan

    2015   the Crystallographic Society of Japan  

    Michi Suga

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  • Early Career Award in Biophysics

    2015   The Biophysical Society of Japan  

    Michi Suga

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  • Young Scientist Award from Protein Science Society of Japan

    2015   Protein Science Society of Japan  

    Michi Suga

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  • Rising star award from the Asian Crystallographic Association

    2009   the Asian Crystallographic Association  

    Michi Suga

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Research Projects

  • 土壌環境変動に応答する植物のミネラル輸送システムの可塑性の解明

    Grant number:21H05034  2021.07 - 2026.03

    日本学術振興会  科学研究費助成事業 基盤研究(S)  基盤研究(S)

    馬 建鋒

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    Grant amount:\189280000 ( Direct expense: \145600000 、 Indirect expense:\43680000 )

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  • Structural analysis of the oxygen evolving center of photosystem II to gain insights into the water splitting reaction

    Grant number:20H03226  2020.04 - 2023.03

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

    菅 倫寛, 中島 芳樹

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    Grant amount:\17810000 ( Direct expense: \13700000 、 Indirect expense:\4110000 )

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  • Ultrafast structural dynamics of light-harvesting complex I and the photosynthetic reaction center supercomplex

    Grant number:20H05446  2020.04 - 2022.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    菅 倫寛

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    Grant amount:\10400000 ( Direct expense: \8000000 、 Indirect expense:\2400000 )

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  • 量子ビームが拓く光合成膜タンパク質のマルチモーダル構造解析

    2018.10 - 2022.03

    JST  さきがけ研究 

    菅倫寛

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  • 光合成膜タンパク質のフェムト秒時間分解能での構造ダイナミクス

    Grant number:17H05884  2017.04 - 2019.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    菅 倫寛

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    Grant amount:\13000000 ( Direct expense: \10000000 、 Indirect expense:\3000000 )

    光化学系IIは光駆動の水分子の分解反応とそれに伴う分子状酸素の発生を行う,分子量70万にもおよぶ巨大な膜タンパク質複合体である。本研究では光化学系IIを中心とする巨大な光合成膜タンパク質複合体を対象として、光による励起後の構造変化をフェムト秒時間分解能で明らかにすることを目指している。研究代表者らはとくに光化学系IIの水分解・酸素発生の反応機構における原子基盤を明らかにすることを目的としてX線自由電子レーザーを用いた構造解析を行ってきた。これまでに反応開始状態に相当するS1状態および反応中間体に相当するS3状態を構造解析することに成功したので、この研究基盤を用いて光励起後の時間経過に伴う構造変化を捉えることを試みている。H30年度は結晶サンプルの調製方法を改良し大型化することで比較的簡便に結晶サンプルを供給する方法を確立することをめざした。なお、結晶化されたサンプルの観察およびその品質を迅速に評価する方法が必要であることを実感したので、新たに結晶観察装置などを購入した。最終的に,4点の多点測定が可能な量の結晶サンプルが供給できるようになったが,この方法で調製した結晶サンプルは分解能および同型性ともに従来の方法と比べて良くないことが判明している。従って,サンプルの供給方法は継続して改善する必要がある。研究課題は最終年度ではあるが,これからも根気強く精製スケールの大型化と回折データの改善を行って詳細な構造解析を完結させ、反応機構の詳細を明らかにして論文発表したい。さらに本研究課題で開発された構造解析手法を今後は他の光合成膜タンパク質にもこの手法を適用して構造解析を行うことを予定している。本年度は他の光合成膜タンパク質の一つであるFCPタンパク質の精製,結晶化,構造解析に成功したのでこれを論文発表した。

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  • Integrated analysis of mineral transport system in crops

    Grant number:16H06296  2016.04 - 2021.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Specially Promoted Research  Grant-in-Aid for Specially Promoted Research

    馬 建鋒, 山地 直樹, 宮地 孝明, 三谷 奈見季, 横正 健剛, 菅 倫寛, 櫻井 玄

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    Grant amount:\536250000 ( Direct expense: \412500000 、 Indirect expense:\123750000 )

    独自な膜小胞アッセイ法を用いて、幾つかミネラル輸送体の輸送基質を同定した。イネのアルミニウム耐性に関わる転写因子ART2を同定した。ART2を破壊すると、イネのアルミニウム耐性が低下したが、そのアルミニウム耐性への寄与はART1ほど大きくなかった。またART2はART1による制御を受けず、下流に異なる遺伝子を制御していた。オオムギのアルミニウム耐性遺伝子HvAACT1の発現制御機構を調べたところ、上流に少なくとも15.5kbの挿入が関与していることが分かった。またこの挿入の脱メチル化が遺伝子発現の向上に関与することを突き止めた。さらにアルミニウム耐性遺伝子OsFRDL4の発現制御に転写因子WRKY 22が関与することを突き止めた。
    輸送体遺伝子OsNIP1;1とOsNIP3;3をイネに過剰発現させると、イネのヒ素集積が大幅に低下した。また節で発現するABCC1遺伝子を特異的なプロモーター制御下に発現させると、種子中のヒ素濃度が有意に減少した。
    ソバからアルミニウム耐性に関わる輸送体遺伝子FeSTAR1とFeSTAR2を同定した。両遺伝によってコードされたタンパク質は複合体を形成し、ABC輸送体として機能することを明らかにした。
    作物のミネラル輸送体(ケイ酸輸送体、カドミウム輸送体、亜鉛輸送体、アニオン性小分子輸送体)の昆虫細胞を用いた大量発現・精製・結晶化と機能解析を行った。ケイ酸輸送体は昨年度に得られた結晶の条件を改善してX線結晶構造解析により立体構造を決定できた。得られた結晶構造からケイ酸輸送に関わる構造基盤を変異導入と機能解析によって明らかにした。重原子輸送体とアニオン性小分子輸送体について結晶化に十分な量と純度の試料を得ることができた。
    去年度までに完成させたミネラルの輸送に関する細胞スケールの3次元モデルと作物全体スケールのモデルを融合させ、ハイブリッドスケールモデルを開発した。

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  • Structural analysis for photosystem II in the intermediate Si-state by using X-ray free electron laser pulses

    Grant number:16H06162  2016.04 - 2019.03

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

    Suga Michihiro, Shen Jian-Ren

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    Grant amount:\24570000 ( Direct expense: \18900000 、 Indirect expense:\5670000 )

    Photosystem II (PSII) catalyzes photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been analyzed at resolutions higher than 2.0A by using X-ray as well as XFEL. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures determined at atomic resolution. We prepared PSII in the S3 state by providing two-flash illumination into micro-sized crystals at room temperature and determined the structure at 2.35A resolution by using an XFEL. An isomorphous difference Fourier map between the two-flash-illuminated and dark-adapted states revealed apparent structural changes. Among them, the insertion of a new oxygen atom O6 close to the putative substrate oxo-bridge O5 was observed. We proposed the mechanism of O=O bond formation between O5 and O6. The findings provide a structural basis for the mechanism of oxygen evolution.

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  • 時分割シリアルフェムト秒構造解析法の開発と光化学系II複合体への適用

    Grant number:15H01642  2015.04 - 2017.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    菅 倫寛

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    Grant amount:\5980000 ( Direct expense: \4600000 、 Indirect expense:\1380000 )

    光化学系IIは光駆動の水分子の酸化と酸素分子の発生を担う、分子量70万の巨大な膜タンパク質複合体である。この水分解・酸素発生の反応機構における原子基盤を明らかにすることは、生物の基本現象を明らかにするのみでなく、エネルギー問題や環境問題を解決する可能性があり、人工光合成研究にも大きく貢献することが期待される。
    初年度より光化学系IIの水分解の反応の解明をめざし、反応中間体状態を解析可能なX線自由電子レーザーをもちいたシリアルフェムト秒結晶学の開発と光化学系IIのサンプルの条件検討を行ってきた。本年度はサンプルかの回折分解能を大幅に改善する事に成功した。その結果、X線自由電子レーザー施設SACLAを用いて、サイズが100um程度の非凍結の小さな結晶に対し室温にて閃光を二発照射してS3状態へと励起させた回折データを収集して、2.35A分解能で構造解析した。構造解析の結果、S1状態からS3状態への遷移にともない、Mn原子の動きと周辺の配位子の構造変化がみられた。さらにMnクラスターからの水分子を含む水素結合ネットワークが分断されるとともに、酸素発生する触媒部分に新たな水分子に相当する電子密度の挿入が確認された。これにより酸素が発生する直前の構造を明らかにし、この新たな水分子が基質となる反応機構を提唱した。またMnクラスターだけでなく、電子授与体側においても構造変化を確認した。これらの成果は論文発表した。

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  • Radiation damage free structure of photosystem II revealed by X-ray free electron laser.

    Grant number:26840023  2014.04 - 2016.03

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

    Suga Michi

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    Grant amount:\4160000 ( Direct expense: \3200000 、 Indirect expense:\960000 )

    The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700 kDa membrane protein complex that catalyzes water-splitting reaction through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by XRD at 1.9 A resolution, which revealed that the OEC is a Mn4CaO5 cluster. However, the manganese atoms in the OEC are easily reduced by X-ray irradiation.
    Recently, it was demonstrated that radiation damage free structure can be obtainable using X-ray free electron lasers (XFEL). We determined a radiation damage free structure of PSII in the S1 state at a resolution of 1.95 A using XFEL pulses. Compared with the structure from XRD, the OEC in the XFEL structure has Mn-Mn distances that are shorter by 0.1-0.2A. Based on the XFEL structure, the valences of each manganese atom were assigned as Mn1(+3), Mn2(+4), Mn3(+4) and Mn4(+3) in the S1 state. These findings provide a structural basis for the mechanism of oxygen evolution.

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  • 生体超分子チトクロム酸化酵素のプロトンポンプ機構と酸化還元機構の解明

    Grant number:08J06358  2008 - 2009

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows  Grant-in-Aid for JSPS Fellows

    菅 倫寛

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    Grant amount:\1200000 ( Direct expense: \1200000 )

    チトクロム酸化酵素活性中心には完全酸化型状態において電子密度が存在することがわかっており、この電子密度をめぐっては20年以上も論争が続いている。この電子密度の決定は酸化還元機構を議論する上でも特に重要である。研究代表者らは昨年度にこの電子密度がハーオキサイドであることを発表したが、それに対し多くの反響と反論を得た。そこで本年度、研究代表者らは新たに回折実験を計画した。この実験はX線による異常分散効果を利用して、パーオキサイドに対する反論の矛盾点を指摘するものであった。実験には精度良い回折実験が必要であったが、これを様々な工夫により克服した。得られた結果はパーオキサイド説に対する反論を完全に否定するものであった。また研究代表者は前年度に得た1.4A分解能のX線回折データを用いて高分解能の構造解析を進めた。前年度から実施してきた、精度の高いFcを求めることを目的とした構造精密化を導入することで、原子モデルの結晶学的freeRを0.20から0.15に改善させた。この結晶系ではチトクロム酸化酵素は単量体の状態でパッキングしていたため、これまで得られていた二量体の構造と比較を行った。この比較から脂質がチトクロム酸化酵素の単量体と二量体の構造変化を制御していて、脂質分子が膜蛋白質の機能において特別な役割を果たすという、新しいモデルを提案することができた。さらに研究代表者は構造精密化後の座標中のカルボン酸の炭素原子-酸素原子間の距離からプロトン化状態を判別する方法を検討した。実験誤差をまったく含まないテストデータを用意し、このデータに対して構造精密化を行ってプロトン化状態の再現性を調べた。その結果、freeRが0.10を切る精度の高いFcのもとでは1.7A分解能でもプロトン化状態の判別が可能であることを示した。

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  • Basic Biology (2021academic year) Third semester  - 木3~4

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    日経バイオテク  2021.11

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    山陽新聞  2019.10

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