Faculty Profiles - SHEN Jian-Ren

MISC - SHEN Jian-Ren

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Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations

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

COORDINATION CHEMISTRY REVIEWS 471 2022.11

Language：English Publishing type：Book review, literature introduction, etc. Publisher：ELSEVIER SCIENCE SA

The aim of this review is to elucidate geometric structures of the catalytic CaMn4Ox (x = 5, 6) cluster in the Kok cycle for water oxidation in the oxygen evolving complex (OEC) of photosystem II (PSII) based on the high-resolution (HR) X-ray diffraction (XRD) and serial femtosecond crystallography (SFX) experiments using the X-ray free-electron laser (XFEL). Quantum mechanics (QM) and QM/molecular mechanics (MM) computations are performed to elucidate the electronic and spin structures of the CaMn4Ox (x = 5, 6) cluster in five states S-i (i = 0 similar to 4) on the basis of the X-ray spectroscopy, electron paramagnetic resonance (EPR) and related experiments. Interplay between the experiments and theoretical computations has been effective to elucidate the coordination structures of the CaMn4Ox (x = 5, 6) cluster ligated by amino acid residues of the protein matrix of PSII, valence states of the four Mn ions and total spin states by their exchange-couplings, and proton-shifted isomers of the CaMn4Ox (x = 5, 6) cluster. The HR XRD and SFX XFEL experiments have also elucidated the biomolecular systems structure of OEC of PSII and the hydrogen bonding networks consisting of water molecules, chloride anions, etc., for water inlet and proton release pathways in PSII. Large-scale QM/MM computations have been performed for elucidation of the hydrogen bonding distances and angles by adding invisible hydrogen atoms to the HR XRD structure. Full geometry optimizations by the QM and QM/MM methods have been effective for elucidation of the molecular systems structure around the CaMn4Ox (x = 5, 6) cluster in OEC. DLPNO-CCSD(T-0) method has been applied to elucidate relative energies of possible intermediates in each state of the Kok cycle for water oxidation. Implications of these results are discussed in relation to the blueprint for developments of artificial catalysts for water oxidation. (C) 2022 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.ccr.2022.214742

Web of Science

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Structural basis for silicic acid permeation mechanism by rice silicic acid channel

齊藤恭紀, 三谷(上野)奈見季, 斉藤圭亮, 斉藤圭亮, 松木謙悟, HUANG Sheng, YANG Lingli, 山地直樹, 石北央, 石北央, SHEN Jian-Ren, SHEN Jian-Ren, MA Jian Feng, 菅倫寛, 菅倫寛, 菅倫寛

日本分子生物学会年会プログラム・要旨集(Web) 44th 2021

クライオ電子顕微鏡単粒子解析による光合成超分子複合体の構造解析 Reviewed

宮崎直幸, 長尾遼, 加藤公児, 沈建仁, 秋田総理

光合成研究 28 112 - 118 2018

The crystal structure of Deg9 reveals a novel octameric-type HtrA protease. International journal

Min Ouyang, Xiaoyi Li, Shun Zhao, Hua Pu, Jianren Shen, Zach Adam, Tim Clausen, Lixin Zhang

Nature plants 3 ( 12 ) 973 - 982 2017.12

Language：English Publisher：NATURE PUBLISHING GROUP

The high temperature requirement A (HtrA) proteases (also termed Deg proteases) play important roles in diverse organisms by regulating protein quality and quantity. One of the 16 Arabidopsis homologs, Deg9, is located in the nucleus where it modulates cytokinin- and light-mediated signalling via degrading the ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). To uncover the structural features underlying the proteolytic activity of Deg9, we determined its crystal structure. Unlike the well-established trimeric building block of HtrAs, Deg9 displays a novel octameric structure consisting of two tetrameric rings that have distinct conformations. Based on the structural architecture, we generated several mutant variants of Deg9, determined their structure and tested their proteolytic activity towards ARR4. The results of the structural and biochemical analyses allowed us to propose a model for a novel mechanism of substrate recognition and activity regulation of Deg9. In this model, protease activation of one tetramer is mediated by en-bloc reorientation of the protease domains to open an entrance for the substrate in the opposite (inactive) tetramer. This study provides the structural basis for understanding how the levels of nuclear signal components are regulated by a plant protease.

DOI： 10.1038/s41477-017-0060-2

Web of Science

PubMed

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Molecular mechanism of photosynthetic water-splitting reaction

262 400 - 406 2017

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

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

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

菅倫寛, 沈建仁

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

Structural basis for the photosynthetic water-splitting/oxygenevolving reaction

Fusamichi Akita, Michihiro Suga, Jian-Ren Shen

Seikagaku 89 ( 5 ) 699 - 709 2017

シリアルフェムト秒結晶解析により明らかにした光化学系IIの反応中間体の構造と酸素発生機構

菅倫寛, 秋田総理, 菅原道泰, 久保稔, 岩田想, 沈建仁

日本放射光学会誌 30 ( 5 ) 228 - 234 2017

光合成水分解反応の分子機構

沈建仁

医学のあゆみ 262 400 - 406 2017

放射光X 線結晶構造解析による光合成・光化学系IIの水分解・酸素発生機構の解明

神谷信夫, 沈建仁

日本結晶学会誌 59 ( 2 ) 1 - 8 2017

Elucidation of the water-splitting and oxygen evolution mechanism of photosynthetic photosystem II by synchrotron radiation X-ray crystallography

Journal of the Japanese Crystallography Society 59 1 - 8 2017

Structural basis for the photosynthetic water-splitting/oxygen-evolving reaction

Journal of the Japanese Biochemical Society 89 699 - 709 2017

Toward artificial photosynthesis -- Synthesis of model compounds of photosynthetic water-splitting catalyst

Chemistry 72 46 - 50 2016

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

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

Structural biology of photosynthesis

Biophysics 56 ( 2 ) 79 - 86 2016

Structural Biology of Photosynthetic Systems

SHEN Jian-Ren, AKITA Fusamichi, SUGA Michihiro

Seibutsu Butsuri 56 ( 2 ) 79 - 86 2016

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

Oxygenic photosynthesis synthesizes sugars from water and carbon dioxide using light energy from the sun, thereby converts light energy into chemical energy and provides oxygen for aerobic life on the earth. The light-harvesting, electron transfer, and water-splitting reactions of photosynthesis are catalyzed by two large membrane-protein complexes photosystem II (PSII) and photosystem I (PSI). Through high-resolution crystal structural analysis by synchrotron X-rays as well as femtosecond X-ray free electron lasers, the mechanisms of these reactions have become understandable at the atomic level. Here we review the recent progresses in analyzing the structures of PSII and PSI as well as their functional implications.

DOI： 10.2142/biophys.56.079

CiNii Article

CiNii Books

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Other Link： https://jlc.jst.go.jp/DN/JLC/20021928091?from=CiNii

SACLAが解き明かす光合成の仕組み

沈建仁

月刊 OPTRONICS 409 31 - 35 2016

光合成水分解触媒のモデル化合物の合成ー人工光合成の実現に向けて

沈建仁

化学 72 46 - 50 2016

Damage-free structure of photosystem II determined by femtosecond X-ray free electron laser

Journal of the Japanese Crystallography Society 58 ( 3 ) 126 - 132 2016

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