2022/05/06 更新

写真a

ナカジマ ヨシキ
中島 芳樹
NAKAJIMA Yoshiki
所属
異分野基礎科学研究所 助教(特任)
職名
助教(特任)
外部リンク

学位

  • 理学博士 ( 岡山大学 )

研究キーワード

  • 光化学系II

  • 構造生物学

  • 光合成

研究分野

  • ライフサイエンス / 構造生物化学

所属学協会

 

論文

  • Excitation-energy transfer in heterocysts isolated from the cyanobacterium Anabaena sp. PCC 7120 as studied by time-resolved fluorescence spectroscopy. 査読 国際誌

    Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Yoshiki Nakajima, Takehiro Suzuki, Ka-Ho Kato, Naoki Tsuboshita, Naoshi Dohmae, Jian-Ren Shen, Shigeki Ehira, Seiji Akimoto

    Biochimica et biophysica acta. Bioenergetics   148509 - 148509   2021年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Heterocysts are formed in filamentous heterocystous cyanobacteria under nitrogen-starvation conditions, and possess a very low amount of photosystem II (PSII) complexes than vegetative cells. Molecular, morphological, and biochemical characterizations of heterocysts have been investigated; however, excitation-energy dynamics in heterocysts are still unknown. In this study, we examined excitation-energy-relaxation processes of pigment-protein complexes in heterocysts isolated from the cyanobacterium Anabaena sp. PCC 7120. Thylakoid membranes from the heterocysts showed no oxygen-evolving activity under our experimental conditions and no thermoluminescence-glow curve originating from charge recombination of S2QA-. Two dimensional blue-native/SDS-PAGE analysis exhibits tetrameric, dimeric, and monomeric PSI complexes but almost no dimeric and monomeric PSII complexes in the heterocyst thylakoids. The steady-state fluorescence spectrum of the heterocyst thylakoids at 77 K displays both characteristic PSI fluorescence and unusual PSII fluorescence different from the fluorescence of PSII dimer and monomer complexes. Time-resolved fluorescence (TRF) spectra at 77 K, followed by fluorescence decay-associated spectra, showed different PSII and PSI fluorescence bands between heterocysts and vegetative thylakoids. Based on these findings, we discuss the excitation-energy-transfer mechanism in the heterocysts.

    DOI: 10.1016/j.bbabio.2021.148509

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  • Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer. 査読 国際誌

    Huaxin Yu, Tasuku Hamaguchi, Yoshiki Nakajima, Koji Kato, Keisuke Kawakami, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

    Biochimica et biophysica acta. Bioenergetics   1862 ( 10 )   148471 - 148471   2021年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.

    DOI: 10.1016/j.bbabio.2021.148471

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  • Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography 査読 国際誌

    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 ( 3 )   431 - 443   2021年5月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:International Union of Crystallography (IUCr)  

    Photosystem II (PSII) catalyzes light-induced water oxidation through an S<italic>
    i
    </italic>-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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  • High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. 査読 国際誌

    Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

    Communications biology   4 ( 1 )   382 - 382   2021年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

    DOI: 10.1038/s42003-021-01919-3

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  • Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins. 査読 国際誌

    Fusamichi Akita, Ryo Nagao, Koji Kato, Yoshiki Nakajima, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Naoshi Dohmae, Jian-Ren Shen, Seiji Akimoto, Naoyuki Miyazaki

    Communications biology   3 ( 1 )   232 - 232   2020年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-Å resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex.

    DOI: 10.1038/s42003-020-0949-6

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  • FTIR Microspectroscopic Analysis of the Water Oxidation Reaction in a Single Photosystem II Microcrystal. 査読 国際誌

    Kato Y, Haniu S, Nakajima Y, Akita F, Shen JR, Noguchi T

    The journal of physical chemistry. B   124 ( 1 )   121 - 127   2019年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/acs.jpcb.9b10154

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

    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年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1126/science.aax6998

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  • Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II in Thermosynechococcus elongatus. 査読 国際誌

    Nakajima Y, Umena Y, Nagao R, Endo K, Kobayashi K, Akita F, Suga M, Wada H, Noguchi T, Shen JR

    The Journal of biological chemistry   293 ( 38 )   14786 - 14797   2018年9月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    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 査読

    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年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元: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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  • Structured near-infrared Magnetic Circular Dichroism spectra of the Mn4CaO5 cluster of PSII in T. vulcanus are dominated by Mn(IV) d-d ‘spin-flip’ transitions 査読

    Jennifer Morton, Maria Chrysina, Vincent S. J. Craig, Fusamichi Akita, Yoshiki Nakajima, Wolfgang Lubitz, Nicholas Cox, Jian-Ren Shen, Elmars Krausz

    Biochimica et Biophysica Acta - Bioenergetics   1859 ( 2 )   88 - 98   2018年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier B.V.  

    Photosystem II passes through four metastable S-states in catalysing light-driven water oxidation. Variable temperature variable field (VTVH) Magnetic Circular Dichroism (MCD) spectra in PSII of Thermosynochococcus (T.) vulcanus for each S-state are reported. These spectra, along with assignments, provide a new window into the electronic and magnetic structure of Mn4CaO5. VTVH MCD spectra taken in the S2 state provide a clear g = 2, S = 1/2 paramagnetic characteristic, which is entirely consistent with that known by EPR. The three features, seen as positive (+) at 749 nm, negative (−) at 773 nm and (+) at 808 nm are assigned as 4A → 2E spin-flips within the d3 configuration of the Mn(IV) centres present. This assignment is supported by comparison(s) to spin-flips seen in a range of Mn(IV) materials. S3 exhibits a more intense (−) MCD peak at 764 nm and has a stronger MCD saturation characteristic. This S3 MCD saturation behaviour can be accurately modelled using parameters taken directly from analyses of EPR spectra. We see no evidence for Mn(III) d-d absorption in the near-IR of any S-state. We suggest that Mn(IV)-based absorption may be responsible for the well-known near-IR induced changes induced in S2 EPR spectra of T. vulcanus and not Mn(III)-based, as has been commonly assumed. Through an analysis of the nephelauxetic effect, the excitation energy of S-state dependent spin-flips seen may help identify coordination characteristics and changes at each Mn(IV). A prospectus as to what more detailed S-state dependent MCD studies promise to achieve is outlined.

    DOI: 10.1016/j.bbabio.2017.10.004

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

    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年3月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元: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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  • Proton Matrix ENDOR Studies on Ca2+-depleted and Sr2+-substituted Manganese Cluster in Photosystem II 査読

    Hiroki Nagashinna, Yoshiki Nakajima, Jian-Ren Shen, Hiroyuki Mino

    JOURNAL OF BIOLOGICAL CHEMISTRY   290 ( 47 )   28166 - 28174   2015年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

    Proton matrix ENDOR spectra were measured for Ca2+-depleted and Sr2+-substituted photosystem II (PSII) membrane samples from spinach and core complexes from Theymosynechococcus vulcanus in the S-2 state. The ENDOR spectra obtained were similar for untreated PSII from T. vulcanus and spinach, as well as for Ca2+-containing and Sr2+-substituted PSII, indicating that the proton arrangements around the manganese cluster in cyanobacterial and higher plant PSII and Ca2+-containing and Sr2+-substituted are similar in the S-2 state, in agreement with the similarity of the crystal structure of both Ca2+-containing and Sr2+-substituted PSII in the Si state. Nevertheless, slightly different hyperfine separations were found between Ca2+-containing and Sr2+-substituted PSII because of modifications of the water protons ligating to the Sr2+ ion. Importantly, Ca2+ depletion caused the loss of ENDOR signals with a 1.36-MHz separation because of the loss of the water proton W4 connecting Ca2+ and Y, directly. With respect to the crystal structure and the functions of Ca2+ in oxygen evolution, it was concluded that the roles of Ca2+ and Sr2+ involve the maintenance of the hydrogen bond network near the Ca2+ site and electron transfer pathway to the manganese cluster.

    DOI: 10.1074/jbc.M115.675496

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  • Optical identification of the long-wavelength (700-1700 nm) electronic excitations of the native reaction centre, Mn4CaO5 cluster and cytochromes of photosystem II in plants and cyanobacteria. 査読

    Morton J, Akita F, Nakajima Y, Shen JR, Krausz E

    Biochimica et biophysica acta   1847 ( 2 )   153 - 161   2015年2月

  • Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses. 査読

    Suga M, Akita F, Hirata K, Ueno G, Murakami H, Nakajima Y, Shimizu T, Yamashita K, Yamamoto M, Ago H, Shen JR

    Nature   517 ( 7532 )   99 - U265   2015年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/nature13991

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  • Optical identification of the long-wavelength (700-1700 nm) electronic excitations of the native reaction centre, Mn4CaO5 cluster and cytochromes of photosystem II in plants and cyanobacteria 査読

    Jennifer Morton, Fusamichi Akita, Yoshiki Nakajima, Jian-Ren Shen, Elmars Krausz

    Biochimica et Biophysica Acta - Bioenergetics   1847 ( 2 )   153 - 161   2015年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier B.V.  

    Visible/UV absorption in PS II core complexes is dominated by the chl-a absorptions, which extend to ~ 700 nm. A broad 700-730 nm PS II core complex absorption in spinach has been assigned [1] to a charge transfer excitation between ChlD1 and ChlD2. Emission from this state, which peaks at 780 nm, has been seen [2] for both plant and cyanobacterial samples. We show that Thermosynechococcus vulcanus PS II core complexes have parallel absorbance in the 700-730 nm region and similar photochemical behaviour to that seen in spinach. This establishes the low energy charge transfer state as intrinsic to the native PS II reaction centre. High-sensitivity MCD measurements made in the 700-1700 nm region reveal additional electronic excitations at ~ 770 nm and ~ 1550 nm. The temperature and field dependence of MCD spectra establish that the system peaking near 1550 nm is a heme-to-Fe(III) charge transfer excitation. These transitions have not previously been observed for cyt b559 or cyt c550. The distinctive characteristics of the MCD signals seen at 770 nm allow us to assign absorption in this region to a dz2 → dx2 - y2 transition of Mn(III) in the Ca-Mn4O5 cluster of the oxygen evolving centre. Current measurements were performed in the S1 state. Detailed analyses of this spectral region, especially in higher S states, promise to provide a new window on models of water oxidation.

    DOI: 10.1016/j.bbabio.2014.11.003

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▼全件表示

書籍等出版物

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

    Jian-Ren Shen, Yoshiki Nakajima, Fusamichi Akita, Michihiro Suga( 担当: 分担執筆)

    Springer  2021年9月 

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MISC

  • 光化学系IIによる水分解・酸素発生機構研究の歩み

    中島 芳樹

    CanAppleニュース 第205号   2021年10月

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    掲載種別:記事・総説・解説・論説等(その他)  

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  • 水分解反応のしくみを観測ー人工光合成触媒開発へ前進ー

    久保稔, 菅原道泰, 中島芳樹

    Chem-station   2017年5月

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    掲載種別:記事・総説・解説・論説等(その他)  

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講演・口頭発表等

  • X線自由電子レーザーが明らかにする光化学系IIの水分解反応の分子機構

    〇菅倫寛, 中島芳樹, Hongjie Li, 沈建仁

    第59回日本生物物理学会年会  2021年11月25日 

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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

    〇菅倫寛, 中島芳樹, 秋田総理, 沈建仁

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共同研究・競争的資金等の研究

  • ゆがんだイス型の触媒の立体構造が紐解く光化学系IIの水分解反応

    研究課題/領域番号:20H03226  2020年04月 - 2023年03月

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

    菅 倫寛, 中島 芳樹

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    担当区分:研究分担者 

    配分額:17810000円 ( 直接経費:13700000円 、 間接経費:4110000円 )

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