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163 results on '"Suga, Michihiro"'

2. Oxygen-evolving photosystem II structures during S1–S2–S3 transitions

Author

Li, Hongjie, Nakajima, Yoshiki, Nango, Eriko, Owada, Shigeki, Yamada, Daichi, Hashimoto, Kana, Luo, Fangjia, Tanaka, Rie, Akita, Fusamichi, Kato, Koji, Kang, Jungmin, Saitoh, Yasunori, Kishi, Shunpei, Yu, Huaxin, Matsubara, Naoki, Fujii, Hajime, Sugahara, Michihiro, Suzuki, Mamoru, Masuda, Tetsuya, Kimura, Tetsunari, Thao, Tran Nguyen, Yonekura, Shinichiro, Yu, Long-Jiang, Tosha, Takehiko, Tono, Kensuke, Joti, Yasumasa, Hatsui, Takaki, Yabashi, Makina, Kubo, Minoru, Iwata, So, Isobe, Hiroshi, Yamaguchi, Kizashi, Suga, Michihiro, and Shen, Jian-Ren

Published
2024
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7. An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

Author

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, and Shen, Jian-Ren

Published
2019

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

Author

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

Published
2017
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25. Structure and function of a silicic acid channel Lsi1

Author

Saitoh, Yasunori, Suga, Michihiro, Saitoh, Yasunori, and Suga, Michihiro

Abstract

Silicon is a beneficial element for plant growth and production, especially in rice. Plant roots take up silicon in the form of silicic acid. Silicic acid channels, which belong to the NIP subfamily of aquaporins, are responsible for silicic acid uptake. Accumulated experimental results have deepened our understanding of the silicic acid channel for its uptake mechanism, physiological function, localization, and other aspects. However, how the silicic acid channel efficiently and selectively permeates silicic acid remains to be elucidated. Recently reported crystal structures of the silicic acid channel enabled us to discuss the mechanism of silicic acid uptake by plant roots at an atomic level. In this mini-review, we focus on the crystal structures of the silicic acid channel and provide a detailed description of the structural determinants of silicic acid permeation and its transport mechanism, which are crucial for the rational creation of secure and sustainable crops.

Published
2022

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

Author

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

Subjects
Structure, Observations, Methods, Photosynthesis -- Methods, Photosystem II -- Observations -- Structure
Abstract

PSII is a multi-subunit pigment-protein complex embedded in the thylakoid membranes of higher plants, green algae and cyanobacteria, and is the only molecular machine capable of oxidizing water by use [...], 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 [Mn.sub.4]Ca[O.sub.5]-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 XRD (1), EXAFS (3-7) and theoretical studies (8-14). Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanusin the [S.sub.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(m), 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.

Published
2015
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27. An oxyl/oxo mechanism for dioxygen bond formation in PSII revealed by X-ray free electron lasers

Author

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, and Shen, Jian-Ren

Abstract

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 reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

Published
2019

29. Structure of the connexin 26 gap junction channel at 3.5Å resolution

Author

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

Subjects
Research, Cell junctions -- Research, Cellular signal transduction -- Research, Junctional complexes (Epithelium) -- Research
Abstract

Intercellular signalling is one of the most essential properties of multicellular organisms. Gap junctions are specialized membrane regions containing hundreds of intercellular communication channels that allow the passage of molecules [...], 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 3.5Å 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.

Published
2009

30. Capturing structural changes of the S-1 to S-2 transition of photosystem II using time-resolved serial femtosecond crystallography

Author

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

Abstract

Photosystem II (PSII) catalyzes light-induced water oxidation through an S-i-state cycle, leading to the generation of di-oxygen, protons and electrons. Pumpprobe 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 S-1-to-S-2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S-2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S-1-to-S-2 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.

Published
2021

31. Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography

Author

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

Published
2021
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33. Capturing structural changes of photosystem II using time-resolved serial femtosecond crystallography with proper flash excitations

Author

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

Published
2020
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38. Fixed-target serial crystallography at SACLA

Author

Yamamoto, Masaki, primary, Ago, Hideo, additional, Hirata, Kunio, additional, Yamashita, Keitaro, additional, Ueno, Go, additional, Kubo, Minoru, additional, Baba, Seiki, additional, Hasegawa, Kazuya, additional, Kumasaka, Takashi, additional, Shimada, Atsuhiro, additional, Shinzawa-Itoh, Kyoko, additional, Tsukihara, Tomitake, additional, Yoshikawa, Shinya, additional, Suga, Michihiro, additional, Akita, Fusamichi, additional, and Shen, Jian-Ren, additional

Published
2017
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48. Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures.

Author

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

Abstract

Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S3 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 S3 state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn4Ca cluster. The optimized Mna(4)–Mnd(1) distance determined by QM/MM was about 5.0 Å for the S3 structure without an inserted hydroxide anion, but this is elongated by 0.2–0.3 Å 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. [ABSTRACT FROM AUTHOR]

Published
2017
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