研究者詳細 - 磯部　寛

論文 - 磯部　寛

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Conformational Flexibility of D1-Glu189: A Crucial Determinant in Substrate Water Selection, Positioning, and Stabilization within the Oxygen-Evolving Complex of Photosystem II

Hiroshi Isobe, Takayoshi Suzuki, Michihiro Suga, Jian-Ren Shen, Kizashi Yamaguchi

ACS OMEGA 9 ( 50 ) 50041 - 50048 2024年12月

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 CHEMICAL SOC

Photosynthetic water oxidation is a vital process responsible for producing dioxygen and supplying the energy necessary to sustain life on Earth. This fundamental reaction is catalyzed by the oxygen-evolving complex (OEC) of photosystem II, which houses the Mn4CaO5 cluster as its catalytic core. In this study, we specifically focus on the D1-Glu189 amino acid residue, which serves as a direct ligand to the Mn4CaO5 cluster. Our primary goal is to explore, using density functional theory (DFT), how the conformational flexibility of the D1-Glu189 side chain influences crucial catalytic processes, particularly the selection, positioning, and stabilization of a substrate water molecule within the OEC. Our investigation is based on a hypothesis put forth by Li et al. (Nature, 2024, 626, 670), which suggests that during the transition from the S2 to S3 state, a specific water molecule temporarily coordinating with the Ca ion, referred to as O6*, may exist as a hydroxide ion (OH-). Our results demonstrate a key mechanism by which the detachment of the D1-Glu189 carboxylate group from its coordination with the Ca ion allows the creation of a specialized microenvironment within the OEC that enables the selective attraction of O6* in its deprotonated form (OH-) and stabilizes it at the catalytic metal (MnD) site. Our findings indicate that D1-Glu189 is not only a structural ligand for the Ca ion but may also play an active and dynamic role in the catalytic process, positioning O6* optimally for its subsequent participation in the oxidation sequence during the water-splitting cycle.

DOI： 10.1021/acsomega.4c09981

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Roles of the Flexible Primary Coordination Sphere of the Mn4CaOx Cluster: What Are the Immediate Decay Products of the S3 State? 国際誌

Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

The journal of physical chemistry. B 126 ( 38 ) 7212 - 7228 2022年9月

記述言語：英語掲載種別：研究論文（学術雑誌）

The primary coordination sphere of the multinuclear cofactor (Mn4CaOx) in the oxygen-evolving complex (OEC) of photosystem II is absolutely conserved to maintain its structure and function. Recent time-resolved serial femtosecond crystallography identified large reorganization of the primary coordination sphere in the S2 to S3 transition, which elicits a cascade of events involving Mn oxidation and water molecule binding to a putative catalytic Mn site. We examined how the crystallographic fields, created by transient conformational states of the OEC at various time points, affect the thermodynamics of various isomers of the Mn cluster using DFT calculations, with an aim of comprehending the functional roles of the flexible primary coordination sphere in the S2 to S3 transition and in the recovery of the S2 state. The results show that the relative movements of surrounding residues change the size and shape of the cavity of the cluster and thereby affect the thermodynamics of various catalytic intermediates as well as the ability to capture a new water molecule at a coordinatively unsaturated site. The implication of these findings is that the protein dynamics may serve to gate the catalytic reaction efficiently by controlling the sequence of Mn oxidation/reduction and water binding/release. This interpretation is consistent with EPR experiments; g ∼ 5 and g ∼ 3 signals obtained after near-infrared (NIR) excitation of the S3 state at 4 K and a g ∼ 5 only signal produced after prolonged incubation of the S3 state at 77 K can be best explained as originating from water-bound S2 clusters (Stotal = 7/2) under a S3 ligand field, i.e., the immediate one-electron reduction products of the oxyl-oxo (Stotal = 6) and hydroxo-oxo (Stotal = 3) species in the S3 state.

DOI： 10.1021/acs.jpcb.2c02596

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Elucidation of a multiple S3 intermediates model for water oxidation in the oxygen evolving complex of photosystem II. Calcium-assisted concerted O-O bond formation 査読

K. Yamaguchi, K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami

Chem. Phys. Lett. 806 140042-1 - 140042-12 2022年9月

Relative energies among S3 intermediates in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Possible pathways of water insertion in the S2 to S3 transition 査読

K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami, T. Nakajima, K. Yamaguchi

Chem. Phys. Lett. 793 139439-1 - 139439-12 2022年2月

Relative energies among proton-shifted S2 isomers in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Proton transfer coupled spin transitions of the CaMn4Ox cluster in OEC of PSII 査読

K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami, T. Nakajima, K. Yamaguchi

Chem. Phys. Lett. 790 139357-1 - 139357-11 2022年1月

Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S3 state of the oxygen evolving complex of photosystem II 査読

Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

Journal of Photochemistry and Photobiology A: Chemistry 405 112905 - 112905 2021年1月

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

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

Science 366 ( 6463 ) 334 - 338 2019年10月

掲載種別：研究論文（学術雑誌）出版者・発行元：American Association for the Advancement of Science (AAAS)

Inspecting S states in photosynthesis

Oxygenic photosynthesis uses a Mn ₄ CaO ₅ cluster in the oxygen-evolving complex to extract electrons from water and produce dioxygen. Visualizing each of the chemical states in this process, S ₀ to S ₄ , and assigning chemical identities and mechanisms on the basis of structures has been a challenge addressed recently by work at x-ray free-electron lasers. Suga et al. used serial crystallography at cryogenic temperatures to trap and determine the structures of several stable states during photosystem II water oxidation (see the Perspective by Britt and Marchiori). Changes around the water cluster already happen in the S ₂ state and set the stage for water insertion that occurs during transition to the S ₃ state. A short 1.9-angstrom distance between the two oxygen atoms in the S ₃ state is consistent with theoretical studies supporting an oxyl/oxo mechanism for oxygen-oxygen coupling.

Science , this issue p. 334 ; see also p. 305

DOI： 10.1126/science.aax6998

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Spin, Valence, and Structural Isomerism in the S3 State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity 査読

Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

Journal of Chemical Theory and Computation 15 ( 4 ) 2375 - 2391 2019年4月

Geometric and electronic structures of the synthetic Mn4CaO4 model compound mimicking the photosynthetic oxygen-evolving complex 国際誌

Mitsuo Shoji, Hiroshi Isobe, Jian-Ren Shen, Kizashi Yamaguchi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 ( 16 ) 11330 - 11340 2016年4月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ROYAL SOC CHEMISTRY

Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(ButCOO)(8)(py)(ButCOOH)(2)] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S-2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1.

DOI： 10.1039/c5cp07226c

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Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II 査読

Hiroshi Isobe, Mitsuo Shoji, Jian-Ren Shen, Kizashi Yamaguchi

Inorganic Chemistry 55 ( 2 ) 502 - 511 2016年1月

Strong Coupling between the Hydrogen Bonding Environment and Redox Chemistry during the S2 to S3 Transition in the Oxygen-Evolving Complex of Photosystem II 査読

Hiroshi Isobe, Mitsuo Shoji, Jian-Ren Shen, Kizashi Yamaguchi

The Journal of Physical Chemistry B 119 ( 43 ) 13922 - 13933 2015年10月

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

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

MOLECULAR PHYSICS 113 ( 3-4 ) 359 - 384 2015年2月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：TAYLOR & FRANCIS LTD

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

DOI： 10.1080/00268976.2014.960021

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Water Oxidation Chemistry of a Synthetic Dinuclear Ruthenium Complex Containing Redox-Active Quinone Ligands 査読

Hiroshi Isobe, Koji Tanaka, Jian-Ren Shen, Kizashi Yamaguchi

Inorganic Chemistry 53 ( 8 ) 3973 - 3984 2014年4月

Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S1 and S3 states of the oxygen evolving complex of photosystem II 査読

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

Phys. Chem. Chem. Phys. 16 ( 24 ) 11911 - 11923 2014年

担当区分：筆頭著者掲載種別：研究論文（学術雑誌）出版者・発行元：Royal Society of Chemistry (RSC)

<p>Broken-symmetry UB3LYP calculations have elucidated structural symmetry-breaking in the S₁ and S₃ states of the oxygen evolution complex (OEC) of photosystem II (PSII), providing the right (RO)- and left (LO)-opened structures.</p>

DOI： 10.1039/c4cp00282b

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2P257 光合成酸素発生中心(PSII-OEC)の立体構造と電荷状態変化についての理論的研究(18B. 光生物:光合成,ポスター,第52回日本生物物理学会年会(2014年度))

Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Shen Jian-Ren, Yamaguchi Kizashi

生物物理 54 ( 1 ) S237 2014年

Electronic structure of the CaMn4O5 cluster in the PSII system refined to the 1.9 Å X-ray resolution. Possible mechanisms of photosynthetic water splitting

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

Advanced Topics in Science and Technology in China 250 - 254 2013年

記述言語：英語掲載種別：論文集(書籍)内論文出版者・発行元：Springer

Broken-symmetry (BS) UB3LYP calculations have been performed for the CaMn4O5 cluster (1) in the oxygen-evolving complex (OEC) of the PSII system refined to 1.9 Å resolution by Umena, Kawakami, Kamiya, Shen to elucidate its electronic structure that is crucial for consideration of possible mechanisms of photosynthetic water splitting. Our UB3LYP computations have elucidated the position of protonated oxygen of the CaMn(III)2Mn(IV)2O4(OH) cluster (1a) at the S1 stage of Kok cycle. Starting from the newly elucidated S1 structure of 1a, we have calculated the electronic structure of proton and electron released CaMn(IV)4O5 cluster (1b) that mimics the S4 stage of the cycle. The LUMOs of 1b are depicted for pictorial understanding of electrophilic oxygen sites that are responsible for nucleophilic attack of hydroxide anion (or water) for the O-O bond formation. Implications of present computational results are discussed in relation to possible mechanisms of photosynthetic water splitting.

DOI： 10.1007/978-3-642-32034-7_52

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Tanaka Koji, Isobe Hiroshi, Yamanaka Shusuke, Yamaguchi Kizashi

Proceedings of the National Academy of Sciences of the United States of America 109 ( 39 ) 15600 - 15605 2012年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：National Academy of Sciences

The nature of chemical bonds of ruthenium(Ru)-quinine(Q) complexes, mononuclear [Ru(trpy)(3, 5-t-Bu(2)Q)(OH(2))](ClO(4))(2) (trpy = 2, 2('):6('), 2('')-terpyridine, 3, 5-di-tert-butyl-1, 2-benzoquinone) (1), and binuclear [Ru(2)(btpyan)(3, 6-di-Bu(2)Q)(2)(OH(2))](2+) (btpyan = 1, 8-bis(2, 2('):6('), 2('')-terpyrid-4(')-yl)anthracene, 3, 6-t-Bu(2)Q = 3, 6-di-tert-butyl-1, 2-benzoquinone) (2), has been investigated by broken-symmetry (BS) hybrid density functional (DFT) methods. BS DFT computations for the Ru complexes have elucidated that the closed-shell structure (2b) Ru(II)-Q complex is less stable than the open-shell structure (2bb) consisting of Ru(III) and semiquinone (SQ) radical fragments. These computations have also elucidated eight different electronic and spin structures of tetraradical intermediates that may be generated in the course of water splitting reaction. The Heisenberg spin Hamiltonian model for these species has been derived to elucidate six different effective exchange interactions (J) for four spin systems. Six J values have been determined using total energies of the eight (or seven) BS solutions for different spin configurations. The natural orbital analyses of these BS DFT solutions have also been performed in order to obtain natural orbitals and their occupation numbers, which are useful for the lucid understanding of the nature of chemical bonds of the Ru complexes. Implications of the computational results are discussed in relation to the proposed reaction mechanisms of water splitting reaction in artificial photosynthesis systems and the similarity between artificial and native water splitting systems.

DOI： 10.1073/pnas.1120705109

CiNii Article

CiNii Books

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Role of Perferryl–Oxo Oxidant in Alkane Hydroxylation Catalyzed by Cytochrome P450: A Hybrid Density Functional Study 査読

Hiroshi Isobe, Kizashi Yamaguchi, Mitsutaka Okumura, Jiro Shimada

The Journal of Physical Chemistry B 116 ( 16 ) 4713 - 4730 2012年4月

Theoretical illumination of water-inserted structures of the CaMn4O5 cluster in the S2 and S3 states of oxygen-evolving complex of photosystem II: full geometry optimizations by B3LYP hybrid density functional 査読

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

Dalton Transactions 41 ( 44 ) 13727 - 13727 2012年

Symmetry and broken symmetry in molecular orbital description of unstable molecules IV: comparison between single- and multi-reference computational results for antiaromtic molecules 査読

Toru Saito, Satomichi Nishihara, Shusuke Yamanaka, Yasutaka Kitagawa, Takashi Kawakami, Satoru Yamada, Hiroshi Isobe, Mitsutaka Okumura, Kizashi Yamaguchi

THEORETICAL CHEMISTRY ACCOUNTS 130 ( 4-6 ) 749 - 763 2011年12月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：SPRINGER

First principle calculations of the effective exchange integrals (J) in the Heisenberg model for diradical species are presented for both symmetry-adapted multi-reference (MR) and single-reference broken-symmetry (BS) methods. The Mukherjee-type state-specific MR coupled cluster singles and doubles (MkCCSD) method with several different reference orbitals including BS natural orbitals is used to calculate the singlet-triplet energy gaps (S-T energy gap or 2J) and diradical characters for the antiaromatic molecules [a cyclopropenyl anion (CPA), b cyclobutadiene (CBD), and c cyclopentadienyl cation (CPC)], the cyclobutadiene derivatives with polar substitutents [d aminocyclobutadiene (ACBD), e formylcyclobutadiene (FCBD), and f 1-amino-2-formyl-cyclobutadiene (AFCBD)] and finally the cyclobutadine derivatives with radical substitutents [g 1,2-bis(methylene)cyclobutadiene (1,2-BMCBD) and h 1,3-bis(methylene)cyclobutadiene (1,3-BMCBD)]. For the BS methods, the spin-unrestricted Hartree-Fock based CCSD (UHF-CCSD), the CCD with the spin-unrestricted Brueckner determinant (UBD), and BS density functional theory (UDFT) computations are performed. Comparison between MkCCSD and the UHF-CCSD results indicates that spin-contamination of UHF-CCSD solutions still remains. In comparison with UHF-CCSD, the UBD results show that spin-contamination involved in BS solutions is greatly suppressed. To eliminate the spin contamination, an approximate spin-projection (AP) scheme is applied to the BS solutions. The AP procedure with the use of the expectation value of the total-spin operator corresponding to UHF-CCSD and UBD results yields good agreement with the MkCCSD results. As for the AP correction of the UDFT methods, three different computational schemes for predicting the expectation value of the total-spin operator are examined. Systematic comparisons between these methods are presented for the S-T energy gaps (2J). Implications of the present computational results have been discussed in relation to the design of magnetic oligomers and polymers.

DOI： 10.1007/s00214-011-0941-9

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