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

Acaryochloris species belong to a special category of cyanobacteria possessing chlorophyll (Chl) d. One of the photosynthetic characteristics of Acaryochloris marina MBIC11017 is that the absorption spectra of photosystem I (PSI) showed almost no bands and shoulders of low-energy Chls d over 740 nm. In contrast, the absorption spectra of other Acaryochloris species showed a shoulder around 740 nm, suggesting that low-energy Chls d within PSI are diversified among Acaryochloris species. In this study, we purified PSI trimer and monomer cores from Acaryochloris sp. NBRC 102871 and examined their protein and pigment compositions and spectral properties. The protein bands and pigment compositions of the PSI trimer and monomer of NBRC102871 were virtually identical to those of MBIC11017. The absorption spectra of the NBRC102871 PSIs exhibited a shoulder around 740 nm, whereas the fluorescence spectra of PSI trimer and monomer displayed maximum peaks at 754 and 767 nm, respectively. These spectral properties were different from those of MBIC11017, indicating the presence of low-energy Chls d within the NBRC102871 PSIs. Moreover, we analyzed the NBRC102871 genome to identify amino acid sequences of PSI proteins and compared them with those of the A. marina MBIC11017 and MBIC10699 strains whose genomes are available. The results showed that some of the sequences in NBRC102871 were distinct from those in MBIC11017 and MBIC10699. These findings provide insights into the variety of low-energy Chls d with respect to the protein environments of PSI cores among the three Acaryochloris strains.

DOI： 10.1007/s11120-024-01108-3

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Diatoms, a group of prevalent marine algae, contribute significantly to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, facilitated by fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs), which exhibit oligomeric diversity across diatom species. Using mild clear native PAGE analysis of solubilized thylakoid membranes, we displayed monomeric, dimeric, trimeric, tetrameric, and pentameric FCPs in diatoms. Mass spectrometry analysis revealed that each oligomeric FCP has a specific protein composition, and together they constitute a large Lhcf family of FCP antennas. In addition, we resolved the structures of the Thalassiosira pseudonana FCP (Tp-FCP) homotrimer and the Chaetoceros gracilis FCP (Cg-FCP) pentamer by cryoelectron microscopy at 2.73-Å and 2.65-Å resolution, respectively. The distinct pigment compositions and organizations of various oligomeric FCPs affect their blue-green light-harvesting, excitation energy transfer pathways. Compared with dimeric and trimeric FCPs, the Cg-FCP tetramer and Cg-FCP pentamer exhibit stronger absorption by Chl c, redshifted and broader Chl a fluorescence emission, and more robust circular dichroism signals originating from Chl a-carotenoid dimers. These spectroscopic characteristics indicate that Chl a molecules in the Cg-FCP tetramer and Cg-FCP pentamer are more heterogeneous than in both dimers and the Tp-FCP trimer. The structural and spectroscopic insights provided by this study contribute to a better understanding of the mechanisms that empower diatoms to adapt to fluctuating light environments.

DOI： 10.1016/j.xplc.2024.101041

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DOI： 10.17912/micropub.biology.001183

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Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from A. marina at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.

DOI： 10.1126/sciadv.adk7140

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Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) a/c-peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate Amphidinium carterae are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate Symbiodinium species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls a and c and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.

DOI： 10.1073/pnas.2315476121

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Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0-4) at the Mn4CaO5 cluster1-3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4-7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.

DOI： 10.1038/s41586-023-06987-5

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The spatial separation of photosystems I and II (PSI and PSII) is thought to be essential for efficient photosynthesis by maintaining a balanced flow of excitation energy between them. Unlike the thylakoid membranes of plant chloroplasts, cyanobacterial thylakoids do not form tightly appressed grana stacks that enforce strict lateral separation. The coexistence of the two photosystems provides a ground for spillover-excitation energy transfer from PSII to PSI. Spillover has been considered as a pathway of energy transfer from the phycobilisomes to PSI and may also play a role in state transitions as means to avoid overexcitation of PSII. Here, we demonstrate a significant degree of energy spillover from PSII to PSI in reconstituted membranes and isolated thylakoid membranes of Thermosynechococcus (Thermostichus) vulcanus and Synechocystis sp. PCC 6803 by steady-state and time-resolved fluorescence spectroscopy. The quantum yield of spillover in these systems was determined to be up to 40%. Spillover was also found in intact cells but to a considerably lower degree (20%) than in isolated thylakoid membranes. The findings support a model of coexistence of laterally separated microdomains of PSI and PSII in the cyanobacterial cells as well as domains where the two photosystems are energetically connected. The methodology presented here can be applied to probe spillover in other photosynthetic organisms.

DOI： 10.1093/pcp/pcad127

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Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.

DOI： 10.1038/s41467-023-44055-8

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Publisher：Cold Spring Harbor Laboratory  

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Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and their structural variety in photosystem I-LHC (PSI-LHCI) supercomplexes has been shown. However, structural and evolutionary correlations of red-lineage LHCs are unknown. Here we determined a 1.92-Å resolution cryo-electron microscopic structure of a PSI-LHCI supercomplex isolated from the red algaCyanidium caldariumRK-1 (NIES-2137) which is an important taxon in the Cyanidiophyceae, and subsequently investigated these correlations through structural comparisons and phylogenetic analysis. The PSI-LHCI structure shows five LHCI subunits together with a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in red-lineage algae showed clear orthology of LHCs betweenC. caldariumandCyanidioschyzon merolae, whereas no orthologous relationships were found betweenC. caldariumLhcr1–3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

DOI： 10.1101/2023.10.25.563911

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Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from Thalassiosira pseudonana at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls a/c is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms.

DOI： 10.1126/sciadv.adi8446

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Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms.

DOI： 10.1016/j.str.2023.08.001

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Phycobilisomes (PBSs), which are huge pigment-protein complexes displaying distinctive color variations, bind to photosystem cores for excitation-energy transfer. It is known that the isolation of supercomplexes consisting of PBSs and photosystem I (PSI) or PBSs and photosystem II (PSII) is challenging due to weak interactions between PBSs and the photosystem cores. In this study, we succeeded in purifying PSI-monomer-PBS and PSI-dimer-PBS supercomplexes from the cyanobacterium Anabaena sp. PCC 7120 grown under iron-deficient conditions by anion-exchange chromatography, followed by trehalose density gradient centrifugation. The absorption spectra of the two types of supercomplexes showed apparent bands originating from PBSs, and their fluorescence-emission spectra exhibited characteristic peaks of PBSs. Two-dimensional blue-native (BN)/SDS-PAGE of the two samples showed a band of CpcL, which is a linker protein of PBS, in addition to PsaA/B subunits. Since interactions of PBSs with PSI are easily dissociated during BN-PAGE using thylakoids from this cyanobacterium grown under iron-replete conditions, it is suggested that iron deficiency for Anabaena induces tight associations of CpcL with PSI, resulting in the formation of PSI-monomer-PBS and PSI-dimer-PBS supercomplexes. Based on these findings, we discuss interactions of PBSs with PSI in Anabaena in response to growth conditions.

DOI： 10.1016/j.bbabio.2023.148993

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Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to QB, a plastoquinone molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with molecular structures similar to that of plastoquinone can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95 to 2.10 Å resolution. Our results show that all AEAs substitute for QB and are bound to the QB-binding site (QB site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the QB site and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone-binding site, designated the QD site, was discovered, which is located in the vicinity of QB site and close to QC site, a binding site reported previously. This QD site is expected to play a role as a channel or a storage site for quinones to be transported to the QB site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of QB in PSII and also provide information for the design of more efficient electron acceptors.

DOI： 10.1016/j.jbc.2023.104839

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s11120-023-01025-x

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Other Link： https://link.springer.com/article/10.1007/s11120-023-01025-x/fulltext.html

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Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that diverged from aquatic green algae and evolved into land plants. The moss Physcomitrium patens (P. patens) has a light-harvesting complex (LHC) superfamily more diverse than those of green algae and higher plants. Here, we solved the structure of a PSI-LHCI-LHCII-Lhcb9 supercomplex from P. patens at 2.68 Å resolution using cryo-electron microscopy. This supercomplex contains one PSI-LHCI, one phosphorylated LHCII trimer, one moss-specific LHC protein, Lhcb9, and one additional LHCI belt with four Lhca subunits. The complete structure of PsaO was observed in the PSI core. One Lhcbm2 in the LHCII trimer interacts with PSI core through its phosphorylated N terminus, and Lhcb9 mediates assembly of the whole supercomplex. The complicated pigment arrangement provided important information for possible energy-transfer pathways from the peripheral antennae to the PSI core.

DOI： 10.1038/s41477-023-01401-4

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X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

DOI： 10.1107/S1600577522011833

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Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.

DOI： 10.1038/s41467-023-36504-1

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Light-harvesting complexes (LHCs) have been diversified in oxygenic photosynthetic organisms, and play an essential role in capturing light energy which is transferred to two types of photosystem cores to promote charge-separation reactions. Red algae are one of the groups of photosynthetic eukaryotes, and their chlorophyll (Chl) a-binding LHCs are specifically associated with photosystem I (PSI). In this study, we purified three types of preparations, PSI-LHCI supercomplexes, PSI cores, and isolated LHCIs, from the red alga Cyanidium caldarium, and examined their properties. The polypeptide bands of PSI-LHCI showed characteristic PSI and LHCI components without contamination by other proteins. The carotenoid composition of LHCI displayed zeaxanthins, β-cryptoxanthins, and β-carotenes. Among the carotenoids, zeaxanthins were enriched in LHCI. On the contrary, both zeaxanthins and β-cryptoxanthins could not be detected from PSI, suggesting that zeaxanthins and β-cryptoxanthins are bound to LHCI but not PSI. A Qy peak of Chl a in the absorption spectrum of LHCI was shifted to a shorter wavelength than those in PSI and PSI-LHCI. This tendency is in line with the result of fluorescence-emission spectra, in which the emission maxima of PSI-LHCI, PSI, and LHCI appeared at 727, 719, and 677 nm, respectively. Time-resolved fluorescence spectra of LHCI represented no 719 and 727-nm fluorescence bands from picoseconds to nanoseconds. These results indicate that energy levels of Chls around/within LHCIs and within PSI are changed by binding LHCIs to PSI. Based on these findings, we discuss the expression, function, and structure of red algal PSI-LHCI supercomplexes.

DOI： 10.1007/s11120-023-00999-y

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The light-harvesting complex II of Bryopsis corticulans (B-LHCII), a green alga, differs from that of spinach (S-LHCII) in chlorophyll (Chl) and carotenoid (Car) compositions. We investigated ultrafast excitation dynamics of B-LHCII with visible-to-near infrared time-resolved absorption spectroscopy. Absolute fluorescence quantum yield (Φ FL) of LHCII and spectroelectrochemical (SEC) spectra of Chl a and b were measured to assist the spectral analysis. Red-light excitation at Chl Qy-band, but not Car-band, induced transient features resembling the characteristic SEC spectra of Chl a ⋅+ and Chl b ⋅-, indicating ultrafast photogeneration of Chl-Chl charge transfer (CT) species; Φ FL and 3Car∗ declined whereas CT species increased upon prolonging excitation wavelength, showing positive correlation of 1Chl∗ deactivation with Chl-Chl CT formation. Moreover, ultrafast Chl b-to-Chl a and Car-to-Chl singlet excitation transfer were illustrated. The red-light induction of Chl-Chl CT species, as also observed for S-LHCII, is considered a general occurrence for LHCIIs in light-harvesting form.

DOI： 10.1016/j.isci.2022.105761

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The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.

DOI： 10.1111/jipb.13367

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Rate-limiting steps in the dark-to-light transition of Photosystem II (PSII) were discovered by measuring the variable chlorophyll-a fluorescence transients elicited by single-turnover saturating flashes (STSFs). It was shown that in diuron-treated samples: (i) the first STSF, despite fully reducing the QA quinone acceptor molecule, generated only an F1(<Fm) fluorescence level; (ii) to produce the maximum (Fm) level, additional excitations were required, which, however, (iii) were effective only with sufficiently long Δτ waiting times between consecutive STSFs. Detailed studies revealed the gradual formation of the light-adapted charge-separated state, PSIIL. The data presented here substantiate this assignment: (i) the Δτ1/2 half-increment rise (or half-waiting) times of the diuron-treated isolated PSII core complexes (CCs) of Thermostichus vulcanus and spinach thylakoid membranes displayed similar temperature dependences between 5 and −80 °C, with substantially increased values at low temperatures; (ii) the Δτ1/2 values in PSII CC were essentially invariant on the Fk−to-Fk+1 (k = 1−4) increments both at 5 and at −80 °C, indicating the involvement of the same physical mechanism during the light-adaptation process of PSIIL. These data are in harmony with the earlier proposed role of dielectric relaxation processes in the formation of the light-adapted charge-separated state and in the variable chlorophyll-a fluorescence of PSII.

DOI： 10.3390/ijms24010094

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Photosystem I (PSI) is one of the two photosystems functioning in light-energy harvesting, transfer, and electron transfer in photosynthesis. However, the oligomerization state of PSI is variable among photosynthetic organisms. We present a 3.8-Å resolution cryo-electron microscopic structure of tetrameric PSI isolated from the glaucophyte alga Cyanophora paradoxa, which reveals differences with PSI from other organisms in subunit composition and organization. The PSI tetramer is organized in a dimer of dimers with a C2 symmetry. Unlike cyanobacterial PSI tetramers, two of the four monomers are rotated around 90°, resulting in a completely different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and excitation-energy transfer in the Cyanophora PSI tetramer, suggesting that the Cyanophora PSI could represent a turning point in the evolution of PSI from prokaryotes to eukaryotes.

DOI： 10.1038/s41467-022-29303-7

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as light harvesters in diatoms. The structure of a diatom photosystem II-FCPII (PSII-FCPII) supercomplex have been solved by cryo-electron microscopy (cryo-EM) previously; however, the FCPII subunits that constitute the FCPII tetramers and monomers are not identified individually due to their low resolutions. Here, we report a 2.5 Å resolution structure of the PSII-FCPII supercomplex using cryo-EM. Two types of tetrameric FCPs, S-tetramer, and M-tetramer, are identified as different types of hetero-tetrameric complexes. In addition, three FCP monomers, m1, m2, and m3, are assigned to different gene products of FCP. The present structure also identifies the positions of most Chls c and diadinoxanthins, which form a complicated pigment network. Excitation-energy transfer from FCPII to PSII is revealed by time-resolved fluorescence spectroscopy. These structural and spectroscopic findings provide insights into an assembly model of FCPII and its excitation-energy transfer and quenching processes.

DOI： 10.1038/s41467-022-29294-5

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DOI： 10.1007/s11120-022-00982-z

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The light-harvesting complex II of a green alga Bryopsis corticulans (B-LHCII) is peculiar in that it contains siphonein and siphonaxathin as carotenoid (Car). Since the S1 state of siphonein and siphonaxathin lies substantially higher than the Qy state of chlorophyll a (Chl a), the Chl a(Qy)-to-Car(S1) excitation energy transfer is unfeasible. To understand the photoprotective mechanism of algal photosynthesis, we investigated the influence of temperature on the excitation dynamics of B-LHCII in trimeric and aggregated forms. At room temperature, the aggregated form showed a 10-fold decrease in fluorescence intensity and lifetime than the trimeric form. Upon lowering the temperature, the characteristic 680 nm fluorescence (F-680) of B-LHCII in both forms exhibited systematic intensity enhancement and spectral narrowing; however, only the aggregated form showed a red emission extending over 690-780 nm (F-RE) with pronounced blueshift, lifetime prolongation, and intensity boost. The remarkable T-dependence of F-RE is ascribed to the Chl-Chl charge transfer (CT) species involved directly in the aggregation-induced Chl deactivation. The CT-quenching mechanism, which is considered to be crucial for B. corticulans photoprotection, draws strong support from the positive correlation of the Chl deactivation rate with the CT state population, as revealed by comparing the fluorescence dynamics of B-LHCII with that of the plant LHCII.

DOI： 10.1021/acs.jpcb.2c05823

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Three psbA genes (psbA1, psbA2, and psbA3) encoding the D1 subunit of photosystem II (PSII) are present in the thermophilic cyanobacterium Thermosynechococcus elongatus and are expressed differently in response to changes in the growth environment. To clarify the functional differences of the D1 protein expressed from these psbA genes, PSII dimers from two strains, each expressing only one psbA gene (psbA2 or psbA3), were crystallized, and we analyzed their structures at resolutions comparable to previously studied PsbA1-PSII. Our results showed that the hydrogen bond between pheophytin/D1 (PheoD1) and D1-130 became stronger in PsbA2- and PsbA3-PSII due to change of Gln to Glu, which partially explains the increase in the redox potential of PheoD1 observed in PsbA3. In PsbA2, one hydrogen bond was lost in PheoD1 due to the change of D1-Y147F, which may explain the decrease in stability of PheoD1 in PsbA2. Two water molecules in the Cl-1 channel were lost in PsbA2 due to the change of D1-P173M, leading to the narrowing of the channel, which may explain the lower efficiency of the S-state transition beyond S2 in PsbA2-PSII. In PsbA3-PSII, a hydrogen bond between D1-Ser270 and a sulfoquinovosyl-diacylglycerol molecule near QB disappeared due to the change of D1-Ser270 in PsbA1 and PsbA2 to D1-Ala270. This may result in an easier exchange of bound QB with free plastoquinone, hence an enhancement of oxygen evolution in PsbA3-PSII due to its high QB exchange efficiency. These results provide a structural basis for further functional examination of the three PsbA variants.

DOI： 10.1016/j.jbc.2022.102668

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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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Low-temperature, metastable electrochromism has been used as a tool to assign pigments in Photosystem I (PS I) from Thermosynechococcus vulcanus and both the white light and far-red light (FRL) forms of Chroococcidiopsis thermalis. We find that a minimum of seven pigments is required to satisfactorily model the electrochromism of PS I. Using our model, we provide a short list of candidates for the chlorophyll f pigment in FRL C. thermalis that absorbs at 756 nm, whose identity, to date, has proven to be controversial. Specifically, we propose the linker pigments A40 and B39 and two antenna pigments A26 and B24 as defined by crystal structure 1JB0. The pros and cons of these assignments are discussed, and we propose further experiments to better understand the functioning of FRL C. thermalis.

DOI： 10.1063/5.0100431

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One of the primary objectives in chemistry research is to observe atomic motions during reactions in real time. Although X-ray free-electron lasers (XFELs) have facilitated the capture of reaction intermediates using time-resolved serial femtosecond crystallography (TR-SFX), only a few natural photoactive proteins have been investigated using this method, mostly due to the lack of suitable phototriggers. Here we report the genetic encoding of a xanthone amino acid (FXO), as an efficient phototrigger, into a rationally designed human liver fatty-acid binding protein mutant (termed XOM), which undergoes photo-induced C-H bond transformation with high selectivity and quantum efficiency. We solved the structures of XOM before and 10-300 ns after flash illumination, at 1.55-1.70 Å resolutions, and captured the elusive excited-state intermediates responsible for precise C-H bond activation. We expect that most redox enzymes can now be investigated by TR-SFX, using our method, to reveal reaction intermediates key for their efficiency and selectivity.

DOI： 10.1038/s41557-022-00992-3

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s11120-022-00948-1

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Other Link： https://link.springer.com/article/10.1007/s11120-022-00948-1/fulltext.html

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s11120-022-00944-5

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Other Link： https://link.springer.com/article/10.1007/s11120-022-00944-5/fulltext.html

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

Photosystem II (PSII) has a number of hydrogen-bonding networks connecting the manganese cluster with the lumenal bulk solution. The structure of PSII from Thermosynechococcus vulcanus (T. vulcanus) showed that D1-R323, D1-N322, D1-D319 and D1-H304 are involved in one of these hydrogen-bonding networks located in the interfaces between the D1, CP43 and PsbV subunits. In order to investigate the functions of these residues in PSII, we generated seven site-directed mutants D1-R323A, D1-R323E, D1-N322R, D1-D319L, D1-D319R, D1-D319Y and D1-H304D of T. vulcanus and examined the effects of these mutations on the growth and functions of the oxygen-evolving complex. The photoautotrophic growth rates of these mutants were similar to that of the wild type, whereas the oxygen-evolving activities of the mutant cells were decreased differently to 63-91% of that of the wild type at pH 6.5. The mutant cells showed a higher relative activity at higher pH region than the wild type cells, suggesting that higher pH facilitated proton egress in the mutants. In addition, oxygen evolution of thylakoid membranes isolated from these mutants showed an apparent decrease compared to that of the cells. This is due to the loss of PsbU during purification of the thylakoid membranes. Moreover, PsbV was also lost in the PSII core complexes purified from the mutants. Taken together, D1-R323, D1-N322, D1-D319 and D1-H304 are vital for the optimal function of oxygen evolution and functional binding of extrinsic proteins to PSII core, and may be involved in the proton egress pathway mediated by YZ.

DOI： 10.1007/s11120-022-00920-z

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

Photosystem II (PSII) is the pigment-protein complex driving the photoinduced oxidation of water and reduction of plastoquinone in all oxygenic photosynthetic organisms. Excitations in the antenna chlorophylls are photochemically trapped in the reaction center (RC) producing the chlorophyll-pheophytin radical ion pair P+ Pheo-. When electron donation from water is inhibited, the oxidized RC chlorophyll P+ acts as an excitation quencher, but knowledge on the kinetics of quenching is limited. Here, we used femtosecond transient absorption spectroscopy to compare the excitation dynamics of PSII with neutral and oxidized RC (P+). We find that equilibration in the core antenna has a major lifetime of about 300 fs, irrespective of the RC redox state. Two-dimensional electronic spectroscopy revealed additional slower energy equilibration occurring on timescales of 3-5 ps, concurrent with excitation trapping. The kinetics of PSII with open RC can be described well with previously proposed models according to which the radical pair P+ Pheo- is populated with a main lifetime of about 40 ps, which is primarily determined by energy transfer between the core antenna and the RC chlorophylls. Yet, in PSII with oxidized RC (P+), fast excitation quenching was observed with decay lifetimes as short as 3 ps and an average decay lifetime of about 90 ps, which is shorter than the excited-state lifetime of PSII with open RC. The underlying mechanism of this extremely fast quenching prompts further investigation.

DOI： 10.1063/5.0086046

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Publishing type：Research paper (scientific journal)   Publisher：eLife Sciences Publications, Ltd  

Photosystem I (PSI) is a multi-subunit pigment-protein complex that functions in light-harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO₂ fixation in photosynthetic organisms. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the sites of low-energy Chls are still under debate. Here, we solved a 2.04-Å resolution structure of a PSI trimer by cryo-electron microscopy from a primordial cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure shows the absence of some subunits commonly found in other cyanobacteria, confirming the primordial nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the Gloeobacter PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 is missing in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. These findings provide insights into not only the identity of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls in oxyphototrophs.

DOI： 10.7554/elife.73990

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Other Link： https://cdn.elifesciences.org/articles/73990/elife-73990-v1.xml

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

Photosystem I (PSI) is a protein complex functioning in light-induced charge separation, electron transfer, and reduction reactions of ferredoxin in photosynthesis, which finally results in the reduction of NAD(P)- to NAD(P)H required for the fixation of carbon dioxide. In eukaryotic algae, PSI is associated with light-harvesting complex I (LHCI) subunits, forming a PSI-LHCI supercomplex. LHCI harvests and transfers light energy to the PSI core, where charge separation and electron transfer reactions occur. During the course of evolution, the number and sequences of protein subunits and the pigments they bind in LHCI change dramatically depending on the species of organisms, which is a result of adaptation of organisms to various light environments. In this chapter, I will describe the structure of various PSI-LHCI supercomplexes from different organisms solved so far either by X-ray crystallography or by cryo-electron microscopy, with emphasis on the differences in the number, structures, and association patterns of LHCI subunits associated with the PSI core found in different organisms.

DOI： 10.1007/978-3-031-00793-4_11

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The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET)1-3. The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.

DOI： 10.1038/s41586-021-04277-6

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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

Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1111/ppl.13598

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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 photosystem I (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 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 excitation-energy-transfer mechanisms in the heterocysts.

DOI： 10.1016/j.bbabio.2021.148509

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

Water splitting will become important to store excess renewable electrical energy into hydrogen. Although the oxygen-evolution reaction (OER) by water oxidation is a critical reaction for water splitting, further investigations are needed to find the details of the OER mechanism for various electrocatalysts. More in particular for homogeneous electrocatalysts, the Randles-Sevcik equation has been extensively applied to determine the turnover frequency (TOF). Herein, using vitamin B12 as a case study, we show that the dynamical deposition/dissolution of the heterogeneous catalyst during OER makes the Randles-Sevcik equation too complicated to be used for calculating the TOF. Indeed, the conventionally applied post-characterization methods do not provide sufficient accuracy to prove the homogeneity of OER mechanisms
thus, using the Randles-Sevcik equation to calculate the TOF is not necessarily correct.

DOI： 10.1016/j.ijhydene.2021.09.039

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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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Publisher：Cold Spring Harbor Laboratory  

Abstract

Photosystem I (PSI) of photosynthetic organisms is a multi-subunit pigment-protein complex and functions in light harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO₂ fixation. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the site of low-energy Chls is still under debate. Here, we solved a 2.04-Å resolution structure of a PSI trimer by cryo-electron microscopy from a primitive cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure showed absence of some subunits commonly found in other cyanobacteria, confirming the primitive nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the Gloeobacter PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 does not exist in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. Since Gloeobacter is susceptible to light, this indicates that Low1 serves as a main photoprotection site in most oxyphototrophs, whereas Low2 is involved in either energy transfer or energy quenching in some of the oxyphototrophs. Thus, these findings provide insights into not only the functional significance of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls responsible for the photoprotection machinery from photosynthetic prokaryotes to eukaryotes.

DOI： 10.1101/2021.09.29.462462

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Phycobilisomes (PBSs) are huge, water-soluble light-harvesting complexes used by oxygenic photosynthetic organisms. The structures of some subunits of the PBSs, including allophycocyanin (APC) and phycocyanin (PC), have been solved by X-ray crystallography previously. However, there are few reports on the overall structures of PBS complexes in photosynthetic organisms. Here, we report the overall structure of the PBS complex isolated from the cyanobacterium Thermosynechococcus vulcanus, determined by negative-staining electron microscopy (EM). Intact PBS complexes were purified by trehalose density gradient centrifugation with a high-concentration phosphate buffer and then subjected to a gradient-fixation preparation using glutaraldehyde. The final map constructed by the single-particle analysis of EM images showed a hemidiscoidal structure of the PBS, consisting of APC cores and peripheral PC rods. The APC cores are composed of five cylinders: A1, A2, B, C1, and C2. Each of the cylinders is composed of three (A1 and A2), four (B), or two (C1 and C2) APC trimers. In addition, there are eight PC rods in the PBS: one bottom pair (Rb and Rb'), one top pair (Rt and Rt'), and two side pairs (Rs1/Rs1' and Rs2/Rs2'). Comparison with the overall structures of PBSs from other organisms revealed structural characteristics of T. vulcanus PBS.

DOI： 10.1016/j.bbabio.2021.148458

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Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. We analysed the structures of two Psb28-bound PSII intermediates, Psb28-RC47 and Psb28-PSII, purified from a psbV-deletion strain of the thermophilic cyanobacterium Thermosynechococcus vulcanus, using cryo-electron microscopy. Both Psb28-RC47 and Psb28-PSII bind one Psb28, one Tsl0063 and an unknown subunit. Psb28 is located at the cytoplasmic surface of PSII and interacts with D1, D2 and CP47, whereas Tsl0063 is a transmembrane subunit and binds at the side of CP47/PsbH. Substantial structural perturbations are observed at the acceptor side, which result in conformational changes of the quinone (QB) and non-haem iron binding sites and thus may protect PSII from photodamage during assembly. These results provide a solid structural basis for understanding the assembly process of native PSII.

DOI： 10.1038/s41477-021-00961-7

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Photosynthetic organisms finely tune their photosynthetic machinery including pigment compositions and antenna systems to adapt to various light environments. However, it is poorly understood how the photosynthetic machinery in the green flagellate Euglena gracilis is modified under high-light conditions. In this study, we examined high-light modification of excitation-energy-relaxation processes in Euglena cells. Oxygen-evolving activity in the cells incubated at 300 µmol photons m-2 s-1 (HL cells) cannot be detected, reflecting severe photodamage to photosystem II (PSII) in vivo. Pigment compositions in the HL cells showed relative increases in 9'-cis-neoxanthin, diadinoxanthin, and chlorophyll b compared with the cells incubated at 30 µmol photons m-2 s-1 (LL cells). Absolute fluorescence spectra at 77 K exhibit smaller intensities of the PSII and photosystem I (PSI) fluorescence in the HL cells than in the LL cells. Absolute fluorescence decay-associated spectra at 77 K of the HL cells indicate suppression of excitation-energy transfer from light-harvesting complexes (LHCs) to both PSI and PSII with the time constant of 40 ps. Rapid energy quenching in LHCs and PSII in the HL cells is distinctly observed by averaged Chl-fluorescence lifetimes. These findings suggest that Euglena modifies excitation-energy-relaxation processes in addition to pigment compositions to deal with excess energy. These results provide insights into the photoprotection strategies of this alga under high-light conditions.

DOI： 10.1007/s11120-021-00849-9

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Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c6 ) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A0 , A1 , and three Fe4 S4 clusters, FX , FA , and FB . Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A0 is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light.

DOI： 10.1111/jipb.13113

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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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Photosystem I (PSI) is one of the two photosystems in photosynthesis, and performs a series of electron transfer reactions leading to the reduction of ferredoxin. In higher plants, PSI is surrounded by four light-harvesting complex I (LHCI) subunits, which harvest and transfer energy efficiently to the PSI core. The crystal structure of PSI-LHCI supercomplex has been analyzed up to 2.6 Å resolution, providing much information on the arrangement of proteins and cofactors in this complicated supercomplex. Here we have optimized crystallization conditions, and analyzed the crystal structure of PSI-LHCI at 2.4 Å resolution. Our structure showed some shift of the LHCI, especially the Lhca4 subunit, away from the PSI core, suggesting the indirect connection and inefficiency of energy transfer from this Lhca subunit to the PSI core. We identified five new lipids in the structure, most of them are located in the gap region between the Lhca subunits and the PSI core. These lipid molecules may play important roles in binding of the Lhca subunits to the core, as well as in the assembly of the supercomplex. The present results thus provide novel information for the elucidation of the mechanisms for the light-energy harvesting, transfer and assembly of this supercomplex. This article is protected by copyright. All rights reserved.

DOI： 10.1111/jipb.13095

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

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 angstrom 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. Kato, Miyazaki, Hamaguchi et al. report the structure of Photosystem II in solution at 1.95 angstrom resolution by single-particle cryo-electron microscopy. They find that reducing the electron beam dosage decreases the electron beam damage while keeping the resolution of the cryo-EM structure, providing insights into the best practice for the determination of cryo-EM structures.

DOI： 10.1038/s42003-021-01919-3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Bryopsis corticulans is a marine green macroalga adapted to the intertidal environment. It possesses siphonaxanthin-binding light-harvesting complexes of photosystem II (LHCII) with spectroscopic properties markedly different from the LHCII in plants. By applying a phenomenological fitting procedure to the two-dimensional electronic spectra of the LHCII from B. corticulans measured at 77 K, we can extract information about the excitonic states and energy-transfer processes. The fitting method results in well-converged parameters, including excitonic energy levels with their respective transition dipole moments, spectral widths, energy-transfer rates, and coupling properties. The 2D spectra simulated from the fitted parameters concur very well with the experimental data, showing the robustness of the fitting method. An excitonic energy-transfer scheme can be constructed from the fitting parameters. It shows the rapid energy transfer from chlorophylls (Chls) b to a at subpicosecond time scales and a long-lived state in the Chl b region at around 659 nm. Three weakly connected terminal states are resolved at 671, 675, and 677 nm. The lowest state is higher in energy than that in plant LHCII, which is probably because of the fewer number of Chls a in a B. corticulans LHCII monomer. Modeling based on existing Hamiltonians for the plant LHCII structure with two Chls a switched to Chls b suggests several possible Chl a-b replacements in comparison with those of plant LHCII. The adaptive changes result in a slower energy equilibration in the complex, revealed by the longer relaxation times of several exciton states compared to those of plant LHCII. The strength of our phenomenological fitting method for obtaining excitonic energy levels and energy-transfer network is put to the test in systems such as B. corticulans LHCII, where prior knowledge on exact assignment and spatial locations of pigments are lacking.

DOI： 10.1021/acs.jpcb.0c10634

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

Photosystem I (PSI) and II (PSII) balance their light energy distribution absorbed by their light-harvesting complexes (LHCs) through state transition to maintain the maximum photosynthetic performance and to avoid photodamage. In state 2, a part of LHCII moves to PSI, forming a PSI-LHCI-LHCII supercomplex. The green alga Chlamydomonas reinhardtii exhibits state transition to a far larger extent than higher plants. Here we report the cryo-electron microscopy structure of a PSI-LHCI-LHCII supercomplex in state 2 from C. reinhardtii at 3.42 angstrom resolution. The result reveals that the PSI-LHCI-LHCII of C. reinhardtii binds two LHCII trimers in addition to ten LHCI subunits. The PSI core subunits PsaO and PsaH, which were missed or not well-resolved in previous Cr-PSI-LHCI structures, are observed. The present results reveal the organization and assembly of PSI core subunits, LHCI and LHCII, pigment arrangement, and possible pathways of energy transfer from peripheral antennae to the PSI core. Photosystems (PS) I and II undergo state transitions to optimize photosynthesis and photoprotection. Here the authors report a cryo-electron microscopy structure of the state 2 PSI-LHCI-LHCII supercomplex from C. reinhardtii revealing subunit organization and possible pathways of energy transfer.

DOI： 10.1038/s41467-021-21362-6

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular oxygen. Psb27 is a small thylakoid lumen-localized protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex. The exact location and binding fashion of Psb27 in the intermediate PSII remain elusive. Here, we report the structure of a dimeric Psb27-PSII complex purified from a psbV deletion mutant (Delta PsbV) of the cyanobacterium Thermosynechococcus vulcanus, solved by cryo-electron microscopy. Our structure showed that Psb27 is associated with CP43 at the luminal side, with specific interactions formed between Helix 2 and Helix 3 of Psb27 and a loop region between Helix 3 and Helix 4 of CP43 (loop C) as well as the large, lumen-exposed and hydrophilic E-loop of CP43. The binding of Psb27 imposes some conflicts with the N-terminal region of PsbO and also induces some conformational changes in CP43, CP47, and D2. This makes PsbO unable to bind in the Psb27-PSII. Conformational changes also occurred in D1, PsbE, PsbF, and PsbZ; this, together with the conformational changes occurred in CP43, CP47, and D2, may prevent the binding of PsbU and induce dissociation of PsbJ. This structural information provides important insights into the regulation mechanism of Psb27 in the biogenesis and repair of PSII.

DOI： 10.1073/pnas.2018053118

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

Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of green plants, moss is at an evolutionarily intermediate position from aquatic photosynthetic organisms to land plants, being the first photosynthetic organisms that landed. Here, we report the structure of the PSI-LHCI supercomplex from the moss Physcomitrella patens (Pp) at 3.23 angstrom resolution solved by cryo-electron microscopy. Our structure revealed that four Lhca subunits are associated with the PSI core in an order of Lhca1-Lhca5-Lhca2-Lhca3. This number is much decreased from 8 to 10, the number of subunits in most green algal PSI-LHCI, but the same as those of land plants. Although Pp PSI-LHCI has a similar structure as PSI-LHCI of land plants, it has Lhca5, instead of Lhca4, in the second position of Lhca, and several differences were found in the arrangement of chlorophylls among green algal, moss, and land plant PSI-LHCI. One chlorophyll, PsaF-Chl 305, which is found in the moss PSI-LHCI, is located at the gap region between the two middle Lhca subunits and the PSI core, and therefore may make the excitation energy transfer from LHCI to the core more efficient than that of land plants. On the other hand, energy-transfer paths at the two side Lhca subunits are relatively conserved. These results provide a structural basis for unravelling the mechanisms of light-energy harvesting and transfer in the moss PSI-LHCI, as well as important clues on the changes of PSI-LHCI after landing.

DOI： 10.1038/s41421-021-00242-9

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Photosynthetic organisms regulate pigment composition and molecular oligomerization of light-harvesting complexes in response to solar light intensities, in order to improve light-harvesting efficiency. Here we report excitation-energy dynamics and relaxation of fucoxanthin chlorophyll alpha/c-binding protein (FCP) complexes isolated from a diatom Phaeodactylum tricornutum grown under high-light (HL) illumination. Two types of FCP complexes were prepared from this diatom under the HL condition, whereas one FCP complex was isolated from the cells grown under a low-light (LL) condition. The subunit composition and oligomeric states of FCP complexes under the HL condition are different from those under the LL condition. Absorption and fluorescence spectra at 77 K of the FCP complexes also vary between the two conditions, indicating modifications of the pigment composition and arrangement upon the HL illumination. Time-resolved fluorescence curves at 77 K of the FCP complexes under the HL condition showed shorter lifetime components compared with the LL condition. Fluorescence decay-associated spectra at 77 K showed distinct excitation-energy-quenching components and alterations of energy-transfer pathways in the FCP complexes under the HL condition. These findings provide insights into molecular and functional mechanisms of the dynamic regulation of FCPs in this diatom under excess-light conditions.

DOI： 10.1016/j.bbabio.2020.148350

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Photosystem II (PSII) uses solar energy to oxidize water and delivers electrons for life on Earth. The photochemical reaction center of PSII is known to possess two stationary states. In the open state (PSIIO), the absorption of a single photon triggers electron-transfer steps, which convert PSII into the charge-separated closed state (PSIIC). Here, by using steady-state and time-resolved spectroscopic techniques on Spinacia oleracea and Thermosynechococcus vulcanus preparations, we show that additional illumination gradually transforms PSIIC into a light-adapted charge-separated state (PSIIL). The PSIIC-to-PSIIL transition, observed at all temperatures between 80 and 308 K, is responsible for a large part of the variable chlorophyll-a fluorescence (Fv) and is associated with subtle, dark-reversible reorganizations in the core complexes, protein conformational changes at non-cryogenic temperatures and marked variations in the rates of photochemical and photophysical reactions. The build-up of PSIIL requires a series of light-induced events generating rapidly recombining primary radical pairs, spaced by sufficient waiting times between these events - pointing to the roles of local electric-field transients and dielectric relaxation processes. We show that the maximum fluorescence level, Fm, is associated with PSIIL rather than with PSIIC, and thus the Fv/Fm parameter cannot be equated with the quantum efficiency of PSII photochemistry. Our findings resolve the controversies and explain the peculiar features of chlorophyll-a fluorescence kinetics, a tool to monitor the functional activity and the structural-functional plasticity of PSII in different wild-type and mutant organisms and under stress conditions.

DOI： 10.1093/plcell/koab008

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

Photosynthetic oxidation of water to dioxygen is catalyzed by the Mn4CaO5 cluster in the protein-cofactor complex photosystem II. The light-driven catalytic cycle consists of four observable intermediates (S-0, S-1, S-2, and S-3) and one transient S-4 state. Recently, using X-ray free-electron laser crystallography, two experimental groups independently observed incorporation of one additional oxygen into the cluster during the S-2 to S-3 transition, which is likely to represent a substrate. The present study implicates two competing reaction routes encountered during the structural rearrangement of the catalyst induced by the water binding and immediately preceding the formation of final stable forms in the S-3 state. This mutually exclusive competition involves concerted versus stepwise conformational changes between two isomers, called open and closed cubane structures, which have different consequences on the immediate product in the S-3 state. The concerted pathway involves a one-step conversion between two isomeric hydroxo forms without changes to the metal oxidation and total spin (S-total = 3) states. Alternatively, in the stepwise process, the bound waters are oxidized and transformed into an oxyl-oxo form in a higher spin (S-total = 6) state. Here, density functional calculations are used to characterize all relevant intermediates and transition structures and demonstrate that the stepwise pathway to the substrate activation is substantially favored over the concerted one, as evidenced by comparison of the activation barriers (11.1 and 20.9 kcal mol(-1), respectively). Only after formation of the oxyl-oxo precursor can the hydroxo species be generated; this occurs with a slow kinetics and an activation barrier of 17.8 kcal mol(-1). The overall thermodynamic driving force is likely to be controlled by the movements of two glutamate ligands, D1-Glu189 and CP43-Glu354, in the active site and ranges from very weak (+0.4 kcal mol(-1)) to very strong (-23.5 kcal mol(-1)).

DOI： 10.1016/j.jphotochem.2020.112905

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Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions, and surround photosystem I (PSI) trimer with a ring formation. A cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, it is unknown how the IsiAs are associated with PSI. Here we report on molecular organizations and function of the IsiAs in this cyanobacterium. A deletion mutant of the isiA1 gene was constructed, and the four types of thylakoids were prepared from the wild-type (WT) and Delta isiA1 cells under iron-replete (+Fe) and iron-deficient (-Fe) conditions. Immunoblotting analysis exhibits a clear expression of the IsiA1 in the WT-Fe. The PSI-IsiA1 supercomplex is found in the WT-Fe, and excitation-energy transfer from IsiA1 to PSI is verified by time-resolved fluorescence analyses. Instead of the IsiA1, both IsiA2 and IsiA3 are bound to PSI monomer in the Delta isiA1-Fe. These findings provide insights into multiple-expression system of the IsiA family in this cyanobacterium.

DOI： 10.1016/j.bbabio.2020.148327

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Photosynthetic organisms have diversified light-harvesting complexes (LHCs) to collect solar energy efficiently, leading to an acquisition of their ecological niches. Herein we report on biochemical and spectroscopic characterizations of fucoxanthin chlorophyll a/c-binding protein (FCP) complexes isolated from a marine pinguiophyte Glossomastix chrysoplasta. The pinguiophyte FCP showed one subunit band in SDS-PAGE and one protein-complex band with a molecular weight at around 66 kDa in clear-native PAGE. By HPLC analysis, the FCP possesses chlorophylls a and c, fucoxanthin, and violaxanthin. To clarify excitation-energy-relaxation processes in the FCP, we measured time-resolved fluorescence spectra at 77 K of the FCP adapted to pH 5.0, 6.5, and 8.0. Fluorescence curves measured at pH 5.0 and 8.0 showed shorter lifetime components compared with those at pH 6.5. The rapid decay components at pH 5.0 and 8.0 are unveiled by fluorescence decay-associated (FDA) spectra; fluorescence decays occur in the 270 and 160-ps FDA spectra only at pH 5.0 and 8.0, respectively. In addition, energy-transfer pathways with time constants of tens of picoseconds are altered under the basic pH condition but not the acidic pH condition. These findings provide novel insights into pH-dependent energy-transfer and energy-quenching machinery in not only FCP family but also photosynthetic LHCs.

DOI： 10.1016/j.bbabio.2020.148306

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

In vascular plants, bryophytes and algae, the photosynthetic light reaction takes place in the thylakoid membrane where two transmembrane supercomplexes PSII and PSI work together with cytochrome b6f and ATP synthase to harvest the light energy and produce ATP and NADPH. Vascular plant PSI is a 600-kDa protein-pigment supercomplex, the core complex of which is partly surrounded by peripheral light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core to be used for charge separation. PSI is unique mainly in absorption of longer-wavelengths than PSII, fast excitation energy transfer including uphill energy transfer, and an extremely high quantum efficiency. From the early 1980s, a lot of effort has been dedicated to structural and functional studies of PSI-LHCI, leading to the current understanding of how more than 200 cofactors are kept at the correct distance and geometry to facilitate fast energy transfer in this supercomplex at an atomic level. In this review, we review the history of studies on vascular plant PSI-LHCI, summarise the present research progress on its structure, and present some new and further questions to be answered in future studies.

DOI： 10.1071/fp21077

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

A marine pennate diatom Phaeodactylum tricornutum (Pt) and a marine centric diatom Chaetoceros gracilis (Cg) possess unique light-harvesting complexes, fucoxanthin chlorophyll a/c-binding proteins (FCPs). FCPs have dual functions: light harvesting in the blue to green regions and quenching of excess energy. So far, excitation dynamics including FCPs have been studied by altering continuous light conditions. In the present study, we examined responses of the diatom cells to fluctuating light (FL) conditions. Excitation dynamics in the cells incubated under the FL conditions were analyzed by time-resolved fluorescence measurements followed by global analysis. As responses common to the Pt and Cg cells, quenching behaviors were observed in photosystem (PS) II with time constants of hundreds of picoseconds. The PSII -> PSI energy transfer was modified only in the Pt cells, whereas quenching in FCPs was suggested only in the Cg cells, indicating different strategy for the dissipation of excess energy under the FL conditions.

DOI： 10.1007/s11120-020-00720-3

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PsbO-D158 is a highly conserved residue of the PsbO protein in photosystem II (PSII), and participates in one of the hydrogen-bonding networks connecting the manganese cluster with the lumenal surface. In order to examine the role of PsbO-D158, we mutated it to E, N or K in Thermosynechococcus vulcanus and characterized photosynthetic properties of the mutants obtained. The growth rates of these three mutants were similar to that of the wild type, whereas the oxygen-evolving activity of the three mutant cells decreased to 60-64% of the wild type. Fluorescence kinetics showed that the mutations did not affect the electron transfer from Q(A) to Q(B), but slightly affected the donor side of PSII. Moreover, all of the three mutant cells were more sensitive to high light and became slower to recover from photoinhibition. In the isolated thylakoid membranes from the three mutants, the PsbU subunit was lost and the oxygen-evolving activity was reduced to a lower level compared to that in the respective cells. PSII complexes isolated from these mutants showed no oxygen-evolving activity, which was found to be due to large or complete loss of PsbO, PsbV and PsbU during the process of purification. Moreover, PSII cores purified from the three mutants contained Psb27, an assembly co-factor of PSII. These results suggest that PsbO-D158 is required for the proper binding of the three extrinsic proteins to PSII and plays an important role in maintaining the optimal oxygen-evolving activity, and its mutation caused incomplete assembly of the PSII complex.

DOI： 10.1007/s11120-020-00715-0

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PsbV (cytochrome c(550)) is one of the three extrinsic proteins of photosystem II (PSII) and functions to maintain the stability and activity of the Mn4CaO5 cluster, the catalytic center for water oxidation. PsbV-Y137 is the C-terminal residue of PsbV and is located at the exit of a hydrogen-bond network mediated by the D1-Y161-H190 residue pair. In order to examine the function of PsbV-Y137, four mutants, PsbV-Y137A, PsbV-Y137F, PsbV-Y137G, and PsbV-Y137W, were generated with Thermosynechococcus vulcanus (T. vulcanus). These mutants showed growth rates similar to that of the wild-type strain (WT); however, their oxygen-evolving activities were different. At pH 6.5, the oxygen evolution rates of Y137F and Y137W were almost identical to that of WT, whereas the oxygen evolution rates of the Y137A, Y137G mutants were 64% and 61% of WT, respectively. However, the oxygen evolution in the latter two mutants decreased less at higher pHs, suggesting that higher pHs facilitated oxygen evolution probably by facilitating proton egress in these two mutants. Furthermore, thylakoid membranes isolated from the PsbV-Y137A, PsbV-Y137G mutants exhibited much lower levels of oxygen-evolving activity than that of WT, which was found to be caused by the release of PsbV. In addition, PSII complexes purified from the PsbV-Y137A and PsbV-Y137G mutants lost all of the three extrinsic proteins but instead bind Psb27, an assembly cofactor of PSII. These results demonstrate that the PsbV-Tyr137 residue is required for the stable binding of PsbV to PSII, and the hydrogen-bond network mediated by D1-Y161-H190 is likely to function in proton egress during water oxidation.

DOI： 10.1007/s11120-020-00753-8

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Photosynthetic organisms use different means to regulate their photosynthetic activity in respond to different light conditions under which they grow. In this study, we analyzed changes in the photosystem I (PSI) light-harvesting complex I (LHCI) supercomplex from a red algaCyanidioschyzon merolae, upon growing under three different light intensities, low light (LL), medium light (ML), and high light (HL). The results showed that the red algal PSI-LHCI is separated into two bands on blue-native PAGE, which are designated PSI-LHCI-A and PSI-LHCI-B, respectively, from cells grown under LL and ML. The former has a higher molecular weight and binds more Lhcr subunits than the latter. They are considered to correspond to the two types of PSI-LHCI identified by cryo-electron microscopic analysis recently, namely, the former with five Lhcrs and the latter with three Lhcrs. The amount of PSI-LHCI-A is higher in the LL-grown cells than that in the ML-grown cells. In the HL-grown cells, PSI-LHCI-A completely disappeared and only PSI-LHCI-B was observed. Furthermore, PSI core complexes without Lhcr attached also appeared in the HL cells. Fluorescence decay kinetics measurement showed that Lhcrs are functionally connected with the PSI core in both PSI-LHCI-A and PSI-LHCI-B obtained from LL and ML cells; however, Lhcrs in the PSI-LHCI-B fraction from the HL cells are not coupled with the PSI core. These results indicate that the red algal PSI not only regulates its antenna size but also adjusts the functional connection of Lhcrs with the PSI core in response to different light intensities.

DOI： 10.1007/s11120-020-00778-z

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

Fucoxanthin-chlorophyll (Chl)a/c-binding proteins (FCPs) are light-harvesting pigment-protein complexes found in diatoms and brown algae. Due to the characteristic pigments, such as fucoxanthin and Chlc, FCPs can capture light energy in blue-to green regions. A pennate diatomPhaeodactylum tricornutumsynthesizes a red-shifted form of FCP under weak or red light, extending a light-absorption ability to longer wavelengths. In the present study, we examined changes in light-harvesting and energy-transfer processes ofP. tricornutumcells grown under white- and single-colored light-emitting diodes (LEDs). The red-shifted FCP appears in the cells grown under the green, yellow, and red LEDs, and exhibited a fluorescence peak around 714 nm. Additional energy-transfer pathways are established in the red-shifted FCP; two forms (F713 and F718) of low-energy Chlawork as energy traps at 77 K. Averaged fluorescence lifetimes are prolonged in the cells grown under the yellow and red LEDs, whereas they are shortened in the blue-LED-grown cells. Based on these results, we discussed the light-adaptation machinery ofP. tricornutumcells involved in the red-shifted FCP.

DOI： 10.1007/s11120-020-00714-1

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Diatoms are a major group of microalgae in marine and freshwater environments. To utilize the light energy in blue to green region, diatoms possess unique antenna pigment-protein complexes, fucoxanthin chlorophyll a/c-binding proteins (FCPs). Depending on light qualities and quantities, diatoms form FCPs with different energies: normal-type and red-shifted FCPs. In the present study, we examined changes in light-harvesting and energy-transfer processes of a diatom Chaetoceros gracilis cells grown using white- and single-colored light-emitting diodes (LEDs), by means of time-resolved fluorescence spectroscopy. The blue LED, which is harvested by FCPs, modified energy transfer involving CP47, and suppressed energy transfer to PSI. Under the red-LED conditions, which is absorbed by both FCPs and PSs, energy transfer to PSI was enhanced, and the red-shifted FCP appeared. The red-shifted FCP was also recognized under the green- and yellow-LEDs, suggesting that lack of the shorter-wavelength light induces the red-shifted FCP. Functions of the red-shifted FCPs are discussed.

DOI： 10.1007/s11120-020-00713-2

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CO2 concentration and temperature for growth of photosynthetic organisms are two important factors to ensure better photosynthetic performance. In this study, we investigated the effects of CO2 concentration and temperature on the photosynthetic performance in a marine centric diatom Chaetoceros gracilis. Cells were grown under four different conditions, namely, at 25 degrees C with air bubbling, at 25 degrees C with a supplementation of 3% CO2, at 30 degrees C with air bubbling, and at 30 degrees C with the CO2 supplementation. It was found that the growth rate of cells at 30 degrees C with the CO2 supplementation is faster than those at other three conditions. The pigment compositions of cells grown under the different conditions are altered, and fluorescence spectra measured at 77 K also showed different peak positions. A novel fucoxanthin chlorophyll a/c-binding protein complex is observed in the cells grown at 30 degrees C with the CO2 supplementation but not in the other three types of cells. Since oxygen-evolving activities of the four types of cells are almost unchanged, it is suggested that the CO2 supplementation and growth temperature are involved in the regulation of photosynthetic light-harvesting apparatus in C. gracilis at different degrees. Based on these observations, we discuss the favorable growth conditions for C. gracilis.

DOI： 10.1007/s11120-020-00729-8

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

The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from Chlorobaculum tepidum. The GsbRC binds considerably fewer (bacterio) chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.

DOI： 10.1126/science.abb6350

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

DOI： 10.1021/acs.jpcb.0c09575

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Publisher：Cold Spring Harbor Laboratory  

Abstract

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 because of the low efficiencies of the S-state transitions in the crystals. 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, which was reduced by reducing the electron dose. 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： 10.1101/2020.10.18.344648

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The high-spin S-2 state was investigated with photosystem II (PSII) from spinach, Thermosynechococcus vulcanus, and Cyanidioschyzon merolae. In extrinsic protein-depleted PSII, high-spin electron paramagnetic resonance (EPR) signals were not detected in either species, whereas all species showed g similar to 5 signals in the presence of a high concentration of Ca2+ instead of the multiline signal. In the intact and PsbP/Qdepleted PSII from spinach, the g = 4.1 EPR signal was detected. These results show that formation of the high-spin S-2 state of the manganese cluster is regulated by the extrinsic proteins through a charge located near the Mn4 atom in the Mn4CaO5 cluster but is independent of the intrinsic proteins. The shift to the g similar to 5 state is caused by tilting of the z-axis in the Mn4 coordinates through hydrogen bonds or external divalent cations. The structural modification may allow insertion of an oxygen atom during the S-2-to-S-3 transition.

DOI： 10.1021/acs.jpclett.0c02411

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

Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of fucoxanthin-chlorophyll a/c proteins (FCPIs). We report the structure of PSI-FCPI from a diatom Chaetoceros gracilis at 2.38 angstrom resolution by single-particle cryo-electron microscopy. PSI-FCPI is a monomeric supercomplex consisting of 12 core and 24 antenna subunits (FCPIs), and 326 chlorophylls a, 34 chlorophylls c, 102 fucoxanthins, 35 diadinoxanthins, 18 beta -carotenes and some electron transfer cofactors. Two subunits designated PsaR and PsaS were found in the core, whereas several subunits were lost. The large number of pigments constitute a unique and huge network ensuring efficient energy harvesting, transfer and dissipation. These results provide a firm structural basis for unraveling the mechanisms of light-energy harvesting, transfer and quenching in the diatom PSI-FCPI, and also important clues to evolutionary changes of PSI-LHCI. Diatoms are marine algae with an important role in global photosynthetic carbon fixation. Here, the authors present the 2.38 angstrom cryo-EM structure of photosystem I (PSI) in complex with its 24 fucoxanthin chlorophyll a/c-binding (FCPI) antenna proteins from the diatom Chaetoceros gracilis, which provides mechanistic insights into light-energy harvesting, transfer and quenching of the PSI-FCPI supercomplex.

DOI： 10.1038/s41467-020-18867-x

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

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

Light-harvesting complex II (LHCII) from the marine green macroalga Bryopsis corticulans is spectroscopically characterized to understand the structural and functional changes resulting from adaptation to intertidal environment. LHCII is homologous to its counterpart in land plants but has a different carotenoid and chlorophyll (Chl) composition. This is reflected in the steady-state absorption, fluorescence, linear dichroism, circular dichroism and anisotropic circular dichroism spectra. Time-resolved fluorescence and two-dimensional electronic spectroscopy were used to investigate the consequences of this adaptive change in the pigment composition on the excited-state dynamics. The complex contains additional Chl b spectral forms - absorbing at around 650 nm and 658 nm - and lacks the red-most Chl a forms compared with higher-plant LHCII. Similar to plant LHCII, energy transfer between Chls occurs on timescales from under hundred fs (mainly from Chl b to Chl a) to several picoseconds (mainly between Chl a pools). However, the presence of long-lived, weakly coupled Chl b and Chl a states leads to slower exciton equilibration in LHCII from B. corticulans. The finding demonstrates a trade-off between the enhanced absorption of blue-green light and the excitation migration time. However, the adaptive change does not result in a significant drop in the overall photochemical efficiency of Photosystem II. These results show that LHCII is a robust adaptable system whose spectral properties can be tuned to the environment for optimal light harvesting.

DOI： 10.1016/j.bbabio.2020.148191

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

pH influences excitation-energy-relaxation processes in photosynthetic light-harvesting complexes. Here, we report the excitation-energy dynamics by pH changes in fucoxanthin chlorophyll a/c-binding proteins (FCPs) isolated from a diatom Phaeodactylum tricornutum, probed by time-resolved fluorescence spectroscopy at 77 K. The fluorescence curve measured at pH 5.0 showed a shorter lifetime component than that measured at pH 6.5 and 8.0. The rapid decay component at pH 5.0 is supported by fluorescence decay-associated (FDA) spectra, where strong fluorescence decays relative to fluorescence rises appear in the pH-5.0 FDA spectrum with 70 ps. These results indicate that the diatom FCPs switch their function from light-harvesting to energy-quenching via arrangements of the energy-transfer pathways under acidic pHs. Based on the crystal structure of the diatom FCPs, we propose a model for the energy-quenching machinery through structural changes of the pigment environments, thus providing insights into the pH-dependent light-harvesting strategy in the diatom FCPs.

DOI： 10.1021/acs.jpcb.0c04231

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The light-harvesting complexes II (LHCIIs) of spinach and Bryopsis corticulans as a green alga are similar in structure, but differ in carotenoid (Car) and chlorophyll (Chl) compositions. Carbonyl Cars siphonein (Spn) and siphonaxanthin (Spx) bind to B. corticulans LHCII likely in the sites as a pair of lutein (Lut) molecules bind to spinach LHCII in the central domain. To understand the light-harvesting and photoprotective properties of the algal LHCII, we compared its excitation dynamics and relaxation to those of spinach LHCII been well documented. It was found that B. corticulans LHCII exhibited a substantially longer chlorophyll (Chl) fluorescence lifetime (4.9 ns vs 4.1 ns) and a 60% increase of the fluorescence quantum yield. Photoexcitation populated (3)Car* equally between Spn and Spx in B. corticulans LHCII, whereas predominantly at Lut620 in spinach LHCII. These results prove the functional differences of the LHCIIs with different Car pairs and Chl a/b ratios: B. corticulans LHCII shows the enhanced blue-green light absorption, the alleviated quenching of 1 Chl*, and the dual sites of quenching (3)Chl*, which may facilitate its light-harvesting and photoprotection functions. Moreover, for both types of LHCIIs, the triplet excitation profiles revealed the involvement of extra (3)Car* formation mechanisms besides the conventional Chl-to-Car triplet transfer, which are discussed in relation to the ultrafast processes of (1)Chl* quenching. Our experimental findings will be helpful in deepening the understanding of the light harvesting and photoprotection functions of B. corticulans living in the intertidal zone with dramatically changing light condition.

DOI： 10.1016/j.bbabio.2020.148186

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In photosynthesis, light energy is captured by pigments bound to light-harvesting antenna proteins (LHC) that then transfer the energy to the photosystem (PS) cores to initiate photochemical reactions. The LHC proteins surround the PS cores to form PS-LHC supercomplexes. In order to adapt to a wide range of light environments, photosynthetic organisms have developed a large variety of pigments and antenna proteins to utilize the light energy efficiently under different environments. Diatoms are a group of important eukaryotic algae and possess fucoxanthin (Fx) chlorophyll a/c proteins (FCP) as antenna which have exceptional capabilities of harvesting blue-green light under water and dissipate excess energy under strong light conditions. We have solved the structure of a PSII-FCPII supercomplex from a centric diatom Chaetoceros gracilis by cryo-electron microscopy, and also the structure of an isolated FCP dimer from a pennate diatom Phaeodactylum tricornutum by X-ray crystallography at a high resolution. These results revealed the oligomerization states of FCPs distinctly different from those of LHCII found in the green lineage organisms, the detailed binding patterns of Chl c and Fxs, a huge pigment network, and extensive protein-protein, pigment-protein, and pigment-pigment interactions within the PSII-FCPII supercomplex. These results therefore provide a solid structural basis for examining the detailed mechanisms of the highly efficient energy transfer and quenching processes in diatoms.

DOI： 10.1111/febs.15183

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Cyanobacteria, green algae, and higher plants provide the major part of molecular O-2 of Earth atmosphere via water oxidation of oxygenic photosynthesis. The water-oxidizing complex is a manganese-calcium oxide-based cluster embedded in Photosystem II that oxidizes water with high turnover frequency. The atomic structure and analysis of the Mn-Ca cluster are important in understanding the mechanism of water oxidation and for the design of efficient artificial water-oxidizing catalysts. With this short review, we aim to introduce the basic features of the biological water oxidation to the new-comers in the field. Taking into account the recent structural studies, including a high-resolution, radiation-damage-free structure of the water-oxidizing complex, and structures of intermediate S-states revealed by femtosecond X-ray free electron lasers, we discuss the structure and functions of the biologically active site and its implications for the development of inorganic catalysts for solar fuels production. (C) 2020 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.ccr.2020.213183

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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-angstrom 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. Akita et al. present the latest approach to solve IsiA-PSI supercomplex molecular structure with increased resolution using cryo-EM and time-resolved fluorescence studies. With 2.7 angstrom resolution, they reveal molecular interactions between PSI and IsiA subunits and that IsiA functions as an energy donor in the supercomplex.

DOI： 10.1038/s42003-020-0949-6

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Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-angstrom resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs. One of the major photosynthetic light-harvesting complexes (LHCs) are fucoxanthin chlorophyll a/c-binding proteins (FCPs), which are present in diatoms, a major group of algae. Here, the authors present the cryo-EM structure of the photosystem I-FCP (PSI-FCPI) supercomplex isolated from the marine centric diatom Chaetoceros gracilis that contains 16 FCPI subunits surrounding the PSI core and discuss possible excitation energy transfer pathways.

DOI： 10.1038/s41467-020-16324-3

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In eukaryotic cells, organelle biogenesis is pivotal for cellular function and cell survival. Chloroplasts are unique organelles with a complex internal membrane network. The mechanisms of the migration of imported nuclear-encoded chloroplast proteins across the crowded stroma to thylakoid membranes are less understood. Here, we identified two Arabidopsis ankyrin-repeat proteins, STT1 and STT2, that specifically mediate sorting of chloroplast twin arginine translocation (cpTat) pathway proteins to thylakoid membranes. STT1 and STT2 form a unique hetero-dimer through interaction of their C-terminal ankyrin domains. Binding of cpTat substrate by N-terminal intrinsically disordered regions of STT complex induces liquid-liquid phase separation. The multivalent nature of STT oligomer is critical for phase separation. STT-Hcf106 interactions reverse phase separation and facilitate cargo targeting and translocation across thylakoid membranes. Thus, the formation of phase-separated droplets emerges as a novel mechanism of intra-chloroplast cargo sorting. Our findings highlight a conserved mechanism of phase separation in regulating organelle biogenesis.

DOI： 10.1016/j.cell.2020.02.045

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Excitation energy-transfer processes in pigment-protein complexes in photosynthetic organisms are often changed under different pH conditions. However, it is unclear how the pH changes affect excitation energy relaxations in photosystem I (PSI) cores. In this study, we examined the pH sensitivity of energy dynamics in the PSI tetramer, dimer, and monomer isolated from a cyanobacterium, Anabaena sp. PCC 7120, by means of time-resolved fluorescence spectroscopy. Each PSI was adapted to pH 5.0, 6.5, and 8.0. Fluorescence decay-associated (FDA) spectra of the pH 8.0 PSI dimer and monomer showed positive and negative peaks within 5 ps, whereas the FDA spectra of the PSI tetramer did not show such a 5 ps fluorescence component. Mean lifetimes of the fluorescence at pH 6.5 are shorter in the PSI tetramer than in the PSI dimer and monomer, indicating an accelerated energy quenching in the tetramer. The effects of the acidic and basic pHs on the energy-transfer processes differ significantly among the three types of PSIs, suggesting different pH-sensing sites around pigment molecules in the three PSIs. Based on these results, together with our recent structural finding of the PSI tetramer, we discuss functional implications for the pH-sensing regulation of the excitation energy transfer in the PSI tetramer.

DOI： 10.1021/acs.jpcb.0c01136

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Excitation-energy transfer in photosystem I (PSI) is changed by a cation formation of a special pair chlorophyll P700 in the PSI core; however, it remains unclear how light-harvesting pigment-protein complexes are involved in the P700-related energy-transfer mechanisms. Here, we report effects of the redox changes of P700 on excitation-energy dynamics in diatom PSI-fucoxanthin chlorophyll a/c-binding protein (PSI-FCPI) and PSI core complexes by means of time-resolved fluorescence (TRF) spectroscopy. For the TRF measurements, the PSI-FCPI and PSI were adapted under P700 neutral and cation conditions using chemical reagents. Upon the P700(+) formation, fluorescence decay-associated (FDA) spectra constructed from the TRF spectra exhibit a larger fluorescence decay amplitude relative to a fluorescence rise magnitude within 100 ps in each of the PSI-FCPI and PSI. The decay components are shifted to lower wavelengths in each of the P700-cation PSI-FCPI and PSI than in the P700-neutral PSIs. The rapid fluorescence decays upon the P700(+) formation are clearly verified by mean lifetimes reconstructed from the FDA spectra. Because the P700-cation PSI does not cause charge-separation reactions, the relatively strong decay components and rapid fluorescence decays observed are likely attributed to excitation-energy quenching. These observations suggest that chlorophylls in PSI and around/within FCPI are involved in the energy-quenching events by the redox changes of P700.

DOI： 10.1021/acs.jpcb.0c00715

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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, damagefree 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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Microcrystals of photosystem II (PSII) have recently been used to investigate the intermediate structures of the water oxidizing complex during water oxidation by serial femtosecond crystallography using X-ray free electron lasers. To clarify the water oxidation mechanism, it is crucial to know whether the reaction proceeds properly in the microcrystals. In this work, we monitored the water oxidation reaction in a single PSII microcrystal using Fourier transform infrared (FTIR) microspectroscopy with the transmission method. Flash-induced micro-FTIR difference spectra of S-state transitions in a PSII microcrystal showed features virtually identical to the corresponding spectra previously obtained using the attenuated total reflection method for multiple microcrystals, representing the reactions near the crystal surface, as well as the spectra in solution. This observation indicates that the reaction processes of water oxidation proceed with relatively high efficiencies retaining native intermediate structures in the entire inside of a PSII microcrystal.

DOI： 10.1021/acs.jpcb.9b10154

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Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.

DOI： 10.1038/s41467-019-13898-5

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In recent years, there has been considerable interest in incorporating naturally occurring components of the photosynthetic apparatus into man-made solar cells, because of the high quantum efficiency of photosynthetic reaction centers. One hurdle to overcome regarding the use of native membranes in these devices is their limited lifespans. In this study, we used stabilizers to increase the long-term viability of biomolecules in vitro, thereby alleviating this challenge. In this regard, it is known that osmolytes, such as glycine betaine (GB) and sucrose, preserve photosynthetic activity in isolated photosystems. Upon investigation of the thermal protection properties of GB and sucrose in thylakoid-based dye-sensitized solar cells, we report that the addition of GB and sucrose to the thylakoid photosensitizer maintains nonzero photocurrent in the thylakoid-based solar cell upon heating to 50 degrees C. At 50 degrees C, the GB-containing cell displayed about a fourfold increase in photocurrent than the control cell, in which the photocurrent was decreased to nearly zero. The addition of 0.5M and 1M sucrose has respectively caused nearly 40% and 70% increases in photoinduced electron transfer activity over the control at 35 degrees C. Similarly, though to a lesser extent, 1M GB caused an approximate 40% increase in electron transfer activity as well. Moving forward, this approach will be extended to alternative membrane protein isolation strategies, allowing for an accurate comparison with traditional detergent-isolated complexes, with the ultimate goal of developing a cost-effective and sustainable solar cell.

DOI： 10.1002/er.4866

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Photosynthetic [2Fe-2S] plant-type ferredoxins have a central role in electron transfer between the photosynthetic chain and various metabolic pathways. Several genes are coding for [2Fe-2S] ferredoxins in cyanobacteria, with four in the thermophilic cyanobacterium Thermosynechococcus elongatus. The structure and functional properties of the major ferredoxin Fd1 are well known but data on the other ferredoxins are scarce. We report the structural and functional properties of a novel minor type ferredoxin, Fd2 of T. elongatus, homologous to Fed4 from Synechocystis sp. PCC 6803. Remarkably, the midpoint potential of Fd2, Em = -440 mV, is lower than that of Fd1, Em = -372 mV. However, while Fd2 can efficiently react with photosystem I or nitrite reductase, time-resolved spectroscopy shows that Fd2 has a very low capacity to reduce ferredoxin-NADP(+) oxidoreductase (FNR). These unique Fd2 properties are discussed in relation with its structure, solved at 1.38 angstrom resolution. The Fd2 structure significantly differs from other known ferredoxins structures in loop 2, N-terminal region, hydrogen bonding networks and surface charge distributions. UV-Vis, EPR, and Mid- and Far-IR data also show that the electronic properties of the [2Fe2S] cluster of Fd2 and its interaction with the protein differ from those of Fd1 both in the oxidized and reduced states. The structural analysis allows to propose that valine in the motif Cys(53)ValAsnCys(56) of Fd2 and the specific orientation of Phe72, explain the electron transfer properties of Fd2. Strikingly, the nature of these residues correlates with different phylogenetic groups of cyanobacterial Fds. With its low redox potential and its discrimination against FNR, Fd2 exhibits a unique capacity to direct efficiently photosynthetic electrons to metabolic pathways not dependent on FNR.

DOI： 10.1016/j.bbabio.2019.148084

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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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Photosystem II (PSII) in the thylakoid membranes of plants, algae, and cyanobacteria catalyzes light-induced oxidation of water by which light energy is converted to chemical energy and molecular oxygen is produced. In higher plants and most eukaryotic algae, the PSII core is surrounded by variable numbers of light-harvesting antenna complex II (LHCII), forming a PSII-LHCII supercomplex. In order to harvest energy efficiently at low-light-intensity conditions under water, a complete PSII-LHCII supercomplex (C2S2M2N2) of the green alga Chlamydomonas reinhardtii (Cr) contains more antenna subunits and pigments than the dominant PSII-LHCII supercomplex (C2S2M2) of plants. The detailed structure and energy transfer pathway of the Cr-PSII-LHCII remain unknown. Here we report a cryoelectron microscopy structure of a complete, C2S2M2N2-type PSIILHCII supercomplex from C. reinhardtii at 3.37-A resolution. The results show that the Cr-C2S2M2N2 supercomplex is organized as a dimer, with 3 LHCII trimers, 1 CP26, and 1 CP29 peripheral antenna subunits surrounding each PSII core. The N-LHCII trimer partially occupies the position of CP24, which is present in the higher-plant PSII-LHCII but absent in the green alga. The M trimer is rotated relative to the corresponding M trimer in plant PSII-LHCII. In addition, some unique features were found in the green algal PSII core. The arrangement of a huge number of pigments allowed us to deduce possible energy transfer pathways from the peripheral antennae to the PSII core.

DOI： 10.1073/pnas.1912462116

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Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 A resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.

DOI： 10.1038/s41467-019-12942-8

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Fucoxanthin chlorophyll a/c-binding proteins (FCPs) are unique light harvesters for some photosynthetic organisms. There were several reports for the alterations of FCPs in response to light conditions. Here, we present the spectral profiles and excitation dynamics of novel FCP complexes isolated from the diatom Chaetoceros gracilis. Under a red-light condition, C. gracilis cells expressed three types of FCP complexes, two of which are very similar to FCP complexes found in the white-light grown cells, and one of which is the novel FCP complex. The combination of steady-state absorption and fluorescence spectra and time-resolved fluorescence spectra revealed that, compared to other types of FCP complexes, the novel FCP complexes exhibited red-shifted absorption and fluorescence spectra and fast decay of excitation. This finding will provide new insights into not only the light-harvesting strategies of diatoms but also the diversity of light adaptation machinery for photosynthetic organisms.

DOI： 10.1021/acs.jpclett.9b02093

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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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Controlling excitation energy flow is a fundamental ability of photosynthetic organisms to keep a better performance of photosynthesis. Among the organisms, diatoms have unique light-harvesting complexes, fucoxanthin chlorophyll (Chl) a/c-binding proteins. We have recently investigated light-adaptation mechanisms of a marine centric diatom, Chaetoceros gracilis, by spectroscopic techniques. However, it remains unclear how pennate diatoms regulate excitation energy under different growth light conditions. Here, we studied light-adaptation mechanisms in a marine pennate diatom Phaeodactylum tricornutum grown at 30 mu mol photons m(-2) s(-1) and further incubated for 24 h either in the dark, or at 30 or 300 mu mol photons m(-2) s(-1) light intensity, by time-resolved fluorescence (TRF) spectroscopy. The high-light incubated cells showed no detectable oxygen-evolving activity of photosystem II, indicating the occurrence of a severe photodamage. The photodamaged cells showed alterations of steady-state absorption and fluorescence spectra and TRF spectra compared with the dark and low-light adapted cells. In particular, excitation-energy quenching is significantly accelerated in the photodamaged cells as shown by mean lifetime analysis of the Chl fluorescence. These spectral changes by the high-light treatment may result from arrangements of pigment-protein complexes to maintain the photosynthetic performance under excess light illumination. These growth-light dependent spectral properties in P. tricornutum are largely different from those in C. gracilis, thus providing insights into the different light-adaptation mechanisms between the pennate and centric diatoms.

DOI： 10.1007/s11120-019-00639-4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PHYSICAL SOC JAPAN  

The photosynthetic water oxidation reaction in photosystem II (PSII) causes the ejection of four protons (H+) and electrons from the substrate water bound to the Mn4CaO5 cluster, denoting the catalytic center of the system. Two Cl+ ions, Cl1 and Cl2 sites, were found in the vicinity of the Mn4CaO5 moiety. Herein, a novel H+ transfer mechanism (amide H+ exchange-driven scheme) was identified to operate in the Cl2 pathway based on the hybrid ab initio quantum mechanics (QM) molecular dynamics (MD) simulations of PSII. The analysis revealed that H+ can be displaced across the peptide bond of the D1-His337 and D1-Asn338 backbones, interrupting the hydrogen bond network spanning to the lumenal side in the crystal structure. The estimated energy barrier was consistent with the previous kinetic data. This is the first report to address unidirectional H+ transfer through a peptide bond based on the theoretical analysis involving the environmental protein structure.

DOI： 10.7566/JPSJ.88.084802

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Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo-electron microscopy structure of the photosystem II ( PSII)-fucoxanthin ( Fx) chlorophyll ( Chl) a/c binding protein ( FCPII) supercomplex from the centric diatom Chaetoceros gracilis. The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms.

DOI： 10.1126/science.aax4406

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Phthalocyanines are a promising class of ligands for manganese because of their high binding affinity. This effect is suggested to be an important factor because phthalocyanines tightly bind manganese and stabilize it under moderate conditions. The strong donor power of phthalocyanine is also suggested as a critical factor to stabilize high-valent manganese phthalocyanine. Herein, a manganese(ii) phthalocyanine, which is stable under moderate conditions, was investigated under harsh electrochemical water oxidation. By scanning electron microscopy, transmission electron microscopy, energy dispersive spectrometry, X-ray diffraction, extended X-ray absorption fine structure analysis, X-ray absorption near edge structure analysis, chronoamperometry, magnetic measurements, Fourier-transform infrared spectroscopy, and electrochemical methods, it is shown that manganese phthalocyanine, a known molecular complex showing good stability under moderate conditions, could not withstand water oxidation catalysis and ultimately is altered to form catalytic oxide particles. Such nanosized Mn oxides are the true catalyst for water oxidation. Besides, we try to go a step forward to find an answer as to how Mn oxides form on the surface of the electrode.

DOI： 10.1039/c9dt01790a

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Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red-and green-lineage oxyphototrophs during evolution.

DOI： 10.1038/s41477-019-0477-x

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Excitation energy-transfer processes in photosynthetic light-harvesting complexes are strongly affected by the surrounding environments of pigments. Here we report on the effects of pH changes on excitation energy dynamics in both diatom photosystem I-fucoxanthin chlorophyll a/c-binding protein (PSI-FCPI) and PSI core complexes by means of fluorescence spectroscopies. The steady-state fluorescence spectra of the PSI-FCPI showed similar features among three samples at pH 5.0, 6.5, and 8.0. However, fluorescence decay-associated spectra of the pH 5.0- and 8.0-adapted PSI-FCPI within 100 ps exhibit peak shifts to longer and shorter wavelengths, respectively, than the peaks in the pH 6.5 spectra. Because such spectral changes hardly occur in the PSI complexes, the peak shifts at pH 5.0 and 8.0 in the PSI-FCPI can be ascribed to alterations of pigment pigment and/or pigment protein interactions around/within FCPI caused by the pH changes. These findings provide novel physical insights into the pH-sensing light-harvesting strategy in diatom PSI-FCPI.

DOI： 10.1021/acs.jpclett.9b01314

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Plastoquinones (PQs) act as electron and proton mediators in photosystem II (PSII) for solar-to-chemical energy conversion. It is known that the redox potential of PQ varies in a wide range spanning hundreds of millivolts; however, its structural origin is not known yet. Here, by developing a pump-probe ultraviolet resonance Raman technique, we measured the vibrational structures of PQs including Q(A) and Q(B) in cyanobacterial PSII directly The conversion of Q(A) to Q(A)(center dot-) in the Mn-depleted PSII is verified by direct observation of the distinct Q(A)(center dot-) vibrational bands. A frequency upshift of the ring C=O/C=C stretch band at 1565 cm(-1) for Q(A)(center dot-) was observed, which suggests a pi-pi interaction between the quinone ring and Trp253. In contrast, proton-coupled reduction of Q(A) to Q(A)H upon light-driven electron transfer is demonstrated in PSII without Q(B) bound. The H-bond between Q(A) and His214 is likely the proton origin of this proton-coupled electron transfer.

DOI： 10.1021/acs.jpclett.9b00959

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Diatoms are dominant phytoplankton in aquatic environments and have unique light-harvesting apparatus, fucoxanthin chlorophyll a/c-binding protein (FCP). Diatom photosystem I (PSI) interacts with specific FCPs (FCPI); however, it remains unclear how PSI cores receive excitation energy from FCPI. To analyze the energy transfer dynamics, it is necessary to isolate both PSI cores and PSI-FCPI complexes. In this study, we prepared three PSI complexes, which are PSI-FCPI membrane fragments, detergent-solubilized PSI-FCPI supercomplexes and PSI core-like complexes, from the marine centric diatom, Chaetoceros gracilis, and examined their biochemical properties. Both the PSI-FCPI membrane fragments and supercomplexes showed similar subunit compositions including FCPI, whereas the PSI complexes were devoid of most FCPI subunits. The purity and homogeneity of the two detergent-solubilized PSI preparations were verified by clear-native PAGE and electron microscopy. The difference of pigment contents among the three PSI samples was shown by absorption spectra at 77K. The intensity in the whole spectrum of PSI-FCPI membranes was much higher than those of the other two complexes, while the spectral shape of PSI complexes was similar to that of cyanobacterial PSI core complexes. 77-K fluorescence spectra of the three PSI preparations exhibited different spectral shapes, especially peak positions and band widths. Based on these observations, we discuss the merits of three PSI preparations for evaluating excitation energy dynamics in diatom PSI-FCPI complexes.

DOI： 10.1007/s11120-018-0576-y

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

Recent chlorophyll-a fluorescence yield measurements, using single-turnover saturating flashes (STSFs), have revealed the involvement of a rate-limiting step in the reactions following the charge separation induced by the first flash. As also shown here, in diuron-inhibited PSII core complexes isolated from Thermosynechococcus vulcanus the fluorescence maximum could only be reached by a train of STSFs. In order to elucidate the origin of the fluorescence yield increments in STSF series, we performed transient absorption measurements at 819nm, reflecting the photooxidation and re-reduction kinetics of the primary electron donor P680. Upon single flash excitation of the dark-adapted sample, the decay kinetics could be described with lifetimes of 17ns (approximate to 50%) and 167ns (approximate to 30%), and a longer-lived component (approximate to 20%). This kinetics are attributed to re-reduction of P680(center dot+) by the donor side of PSII. In contrast, upon second-flash (with t between 5s and 100ms) or repetitive excitation, the 819nm absorption changes decayed with lifetimes of about 2ns (approximate to 60%) and 10ns (approximate to 30%), attributed to recombination of the primary radical pair P680(center dot+)Pheo(center dot-), and a small longer-lived component (approximate to 10%). These data confirm that only the first STSF is capable of generating stable charge separation-leading to the reduction of Q(A); and thus, the fluorescence yield increments elicited by the consecutive flashes must have a different physical origin. Our double-flash experiments indicate that the rate-limiting steps, detected by chlorophyll-a fluorescence, are not correlated with the turnover of P680.

DOI： 10.1111/ppl.12945

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Photocatalytic Z-scheme water splitting is considered as a promising approach to produce solar hydrogen. However, the forward hydrogen production reaction is often impeded by backward reactions. In the present study, in a photosystem II-integrated hybrid Z-scheme water splitting system, the backward hydrogen oxidation reaction was significantly suppressed by loading a PtCrOx cocatalyst on a ZrO2/TaON photocatalyst. Due to the weak chemisorption and activation of molecular hydrogen on PtCrOx, where Pt is stabilized in the oxidized forms, POII and Pt-IV, hydrogen oxidation is inhibited. However, it is remarkably well-catalyzed by the metallic Pt cocatalyst, thereby rapidly consuming the produced hydrogen. This work describes an approach to inhibit the backward reaction in the photosystem II-integrated hybrid Z-scheme water splitting system using Fe(CN)(6)(3-)/Fe(CN)(6)(4-) redox couple as an electron shuttle. (C) 2019, Dalian Institute of Chemical Physics, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

DOI： 10.1016/S1872-2067(19)63311-5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Photosynthetic water oxidation is catalyzed by a Mn4CaO5-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo-oxo, oxyl-oxo, peroxo, and superoxo species) in the S(3 )state. Our extensive study reveals several factors that affect the spin ground state: (1) (formal) Mn oxidation state; (2) metal-ligand covalency; (3) coordination geometry; and (4) structural change of the Mn cluster induced by alternations in Mn...Mn distances. Some combination of these effects could selectively stabilize/destabilize some spin states. We found that the high spin state (S-total= 6) of the oxyl-oxo species can be causative for catalytic function, which manifests through mixing of the metal-ligand character in magnetic orbitals at relatively short 05...06 distances (<2.0 angstrom) and long Mn-A center dot center dot center dot O5 distances (>2.0 angstrom). These results will serve as a basis to conceptually identify and rationalize the physicochemical synergisms that can be evoked by the unique "distorted chair" topology of the cluster through cooperative Jahn-Teller effects on multimetallic centers.

DOI： 10.1021/acs.jctc.8b01055

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Water splitting to produce molecular hydrogen is an essential method to store sustainable energies. One of the bottlenecks for water splitting is the availability of an efficient and stable water-oxidizing catalyst. Herein, metallic cobalt foil, after the treatment under high potential (10-60.0 V), was used for water oxidation. The cobalt/ cobalt oxide surface was characterized by various spectroscopic, microscopy, X-ray diffraction, and electrochemical methods. Diffuse reflectance infrared Fourier transform spectroscopy showed peaks for Co oxide at 489 and 595 cm(-1) attributed to the stretching of Co-O and bending of O-Co-O bonds in the CoO6 octahedra. Small aggregated particles (ca. 50-100 nm) with a spherical morphology were detected by scanning electron microscopy, and high-resolution transmission electron microscopy from the mechanically separated particles indicated spacings of 2.5-2.6 angstrom corresponding to the interplanar spacings of the (011) plane for Co3O4. Selected area (electron) diffraction showed concentric rings centered on a bright central spot, indicating a polycrystalline material. Each ring is related to planes of different orientation and different interplanar spacing, attributed to metallic cobalt and cobalt oxides. X-ray diffraction resulted in patterns corresponding to Co3O4 and CoO(OH), and X-ray photoelectron spectroscopy could confirm the formation of metallic cobalt, Co(II) and Co(III) oxides on the surface of the electrode. These results suggest that the oxide on the surface of foil could be a mixture of different phases of Co oxide containing Co3O4 and CoO(OH). Under overpotentials of 460 and 780 mV, current densities of 0.144 and 0.5 A/cm(2) were observed at pH-14 without dropping of IR. To the best of our knowledge, the three-dimensional electrode obtained here is among the most efficient cobalt-based water-oxidizing electrodes under alkaline conditions reported so far and may be applied in large scale water-splitting systems.

DOI： 10.1021/acssuschemeng.8b06269

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Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) are unique light-harvesting antennas in diatoms. Recent time-resolved fluorescence analysis of photosystem I with FCP associated (PSI-FCPI) has mainly shown excitation energy transfer among Chls a from FCPI to PSI in tens of picoseconds. However, it remains unclear how each pigment, especially carotenoids and Chl c, in the FCPI is functionally related to the energy transfer in a femtosecond time range. Here, we reveal ultrafast excitation energy transfer mechanism in the PSI-FCPI preparations isolated from a diatom, Chaetoceros gracilis, by means of femtosecond time-resolved fluorescence spectroscopy with an upconversion system. Compared with the fluorescence lifetime components of PSI core-like complexes, the energy transfer of Chl c -> Chl a in the FCPI was observed within hundreds of femtoseconds, and the energy in the FCPI was transferred to PSI in similar to 2 ps. The comparative fluorescence analyses provide physical insights into the energy transfer machinery within FCPI and from FCPI to PSI.

DOI： 10.1021/acs.jpcb.8b12086

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The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c, and one of two low-potential cytochrome c(552) (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c(552) (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.

DOI： 10.1007/s11120-018-0507-y

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Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an extremely large light-harvesting complex I (LHCI) captures and transfers energy to the PSI core. Here, we report the structure of PSI-LHCI from a green alga Bryopsis corticulans at 3.49 angstrom resolution, obtained by single-particle cryo-electron microscopy, which revealed 13 core subunits including subunits characteristic of both prokaryotes and eukaryotes, and 10 light-harvesting complex a (Lhca) antennas that form a double semi-ring and an additional Lhca dimer, including a novel four-transmembrane-helix Lhca. In total, 244 chlorophylls were identified, some of which were located at key positions for the fast energy transfer. These results provide a firm structural basis for unravelling the mechanisms of light-energy harvesting, transfer and quenching in the green algal PSI-LHCI, and important clues as to how PSI-LHCI has changed during evolution.

DOI： 10.1038/s41477-019-0379-y

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X-ray crystallographic analysis (1.9-angstrom resolution) of the cyanobacterial photosystem II (PSII) dimer showed the presence of five phosphatidylglycerol (PG) molecules per reaction center. One of the PG molecules, PG772, is located in the vicinity of the Q(B)-binding site. To investigate the role of PG772 in PSII, we performed site-directed mutagenesis in the cytochrome (Cyt) b(559) subunit of Synechocystis sp. PCC 6803 to change two amino acids, Thr-5 and Ser-11, which interact with PG772. The photosynthetic activity of intact cells was slightly lower in all mutants than that of cells in the control strain; however, the oxygen-evolving PSII activity was decreased markedly in cells of mutants, as measured using artificial quinones (such as p-benzoquinone). Furthermore, electron transport from Q(A) to Q(B) was inhibited in mutants incubated with quinones, particularly under high-intensity light conditions. Lipid analysis of purified PSII showed approximately one PG molecule per reaction center, presumably PG772, was lost in the PSII dimer from the T5A and S11A mutants compared with that in the PSII dimer from the control strain. In addition, protein analysis of monomer and dimer showed decreased levels of PsbV and PsbU extrinsic proteins in the PSII monomer purified from T5A and S11A mutants. These results suggest that site-directed mutagenesis of Thr-5 and Ser-11, which presumably causes the loss of PG772, induces quinone-dependent inhibition of PSII activity under high-intensity light conditions and destabilizes the binding of extrinsic proteins to PSII.

DOI： 10.1007/s11120-018-0555-3

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

Diatoms are abundant photosynthetic organisms in aquatic environments and contribute 40% of its primary productivity. An important factor that contributes to the success of diatoms is their fucoxanthin chlorophyll a/c-binding proteins (FCPs), which have exceptional light-harvesting and photoprotection capabilities. Here, we report the crystal structure of an FCP from the marine diatom Phaeodactylum tricornutum, which reveals the binding of seven chlorophylls (Chls) a, two Chls c, seven fucoxanthins (Fxs), and probably one diadinoxanthin within the protein scaffold. Efficient energy transfer pathways can be found between Chl a and c, and each Fx is surrounded by Chls, enabling the energy transfer and quenching via Fx highly efficient. The structure provides a basis for elucidating the mechanisms of blue-green light harvesting, energy transfer, and dissipation in diatoms.

DOI： 10.1126/science.aav0365

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Photosynthetic organisms handle solar energy precisely to achieve efficient photochemical reactions. Because there are a wide variety of light-harvesting antennas in oxyphototrophs, the excitation energy transfer mechanisms are thought to differ significantly. In this study, we compared excitation energy dynamics between photosystem I (PSI) cores and a complex between PSI and fucoxanthin chlorophyll (Chl) a/c-binding protein I (PSI FCPI) isolated from a diatom, Chaetoceros gracilis, by means of picosecond time-resolved fluorescence analyses. Time-resolved spectra measured at 77 K clearly show that low-energy Chls in the FCPI transfer not only most of the excitation energy to the reaction center Chls in the PSI cores but also the remaining energy to carotenoids for quenching. Under room-temperature conditions, the energy in the low-energy Chls is rapidly equilibrated on Chls in the PSI cores by uphill energy transfer within a few tens of picoseconds. These findings provide solid evidence that the low-energy Chls in the FCPI contribute to the photochemical reactions in PSI.

DOI： 10.1021/acs.jpcb.8b09253

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Hydrogen production by water splitting is a promising method to store energy. Water-oxidation reaction is a bottleneck in water-splitting systems. Herein, a mononuclear nickel(II) phosphine complex with 1,2-bis(dicyclohexylphosphino)ethane ligand, was synthesized and characterized by X-ray crystallography method. The water-oxidizing catalyst under the electrochemical condition was studied. The role of Ni compound for the water-oxidation reaction on the surface of fluorine-doped tin oxide as one of the true catalysts was investigated by the electrochemical methods and Scanning Electron Microscopy coupled with Energy Dispersive X-ray (SEM/EDX) Spectroscopy. The big ligand around the Ni ion causes a very small size of Ni-based particles on the surface of the electrode, which are the active catalysts for the water-oxidation reaction. Such small nanosized Ni-based compounds are transparent and have no effect on the transparency of the obtained fluorine-doped tin oxide. Thus, it is a promising method to synthesize a transparent fluorine-doped tin oxide with water-oxidizing activity. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.ijhydene.2018.10.146

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

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 (Q(B)) exchange at the acceptor site. We further solved the crystal structure of the PSII dimer from the SQDG deletion mutant at 2.1 angstrom 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 Q(B) provides a possible explanation for the Q(B) 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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Maintenance of energy balance under changeable light conditions is an essential function of photosynthetic organisms to achieve efficient photochemical reactions. Among the photosynthetic organisms, diatoms possess light-harvesting fucoxanthin chlorophyll (Chl) a/c-binding protein (FCP) as peripheral antennas. However, how diatoms regulate excitation-energy distribution between FCP and the two photosystem cores during light adaptation is poorly understood. In this study, we examined spectroscopic properties of a marine diatom Chaetoceros gracilis adapted in the dark and at photosynthetic photon flux density at 30 and 300 mu mol photons m(-2)s(-1). Absorption spectra at 77 K showed significant changes in the Soret region, and 77-K steady-state fluorescence spectra showed significant differences in the spectral shape and relative fluorescence intensity originating from both PSII and PSI, among the cells grown under different light conditions. These results suggest alterations of pigment composition and their interactions under the different light conditions. These alterations affected the excitation-energy dynamics monitored by picosecond time-resolved fluorescence analyses at 77 K significantly. The contributions of Chls having lower energy levels than the reaction center Chls in the two photosystems to the energy dynamics were clearly identified in the three cells but with presumably different roles. These findings provide insights into the regulatory mechanism of excitation-energy balance in diatoms under various light conditions.

DOI： 10.1016/j.bbabio.2018.04.003

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Main conclusion The macroalga Bryopsis corticulans relies on a sustained protective NPQ and a peculiar body architecture to efficiently adapt to the extreme light changes of intertidal shores.During low tides, intertidal algae experience prolonged high light stress. Efficient dissipation of excess light energy, measured as non-photochemical quenching (NPQ) of chlorophyll fluorescence, is therefore required to avoid photodamage. Light-harvesting regulation was studied in the intertidal macroalga Bryopsis corticulans, during high light and air exposure. Photosynthetic capacity and NPQ kinetics were assessed in different filament layers of the algal tufts and in intact chloroplasts to unravel the nature of NPQ in this siphonous green alga. We found that the morphology and pigment composition of the B. corticulans body provides functional segregation between surface sunlit filaments (protective state) and those that are underneath and undergo severe light attenuation (light-harvesting state). In the surface filaments, very high and sustained NPQ gradually formed. NPQ induction was triggered by the formation of transthylakoid proton gradient and independent of the xanthophyll cycle. PsbS and LHCSR proteins seem not to be active in the NPQ mechanism activated by this alga. Our results show that B. corticulans endures excess light energy pressure through a sustained protective NPQ, not related to photodamage, as revealed by the unusually quick restoration of photosystem II (PSII) function in the dark. This might suggest either the occurrence of transient PSII photoinactivation or a fast rate of PSII repair cycle.

DOI： 10.1007/s00425-018-2854-5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Photosynthetic water oxidation is performed in photosystem II (PSII) through a light-driven cycle of intermediates called S states (S-0-S-4) 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 S-2 -> S-3 and S-3 -> S-0 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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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 angstrom. 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-ionbinding 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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga Cyanidioschyzon merolae in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls a and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls a and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.

DOI： 10.1073/pnas.1722482115

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Vyacheslav Vasilevich (V.V.) Klimov (or Slava, as most of us called him) was born on January 12, 1945 and passed away on May 9, 2017. He began his scientific career at the Bach Institute of Biochemistry of the USSR Academy of Sciences (Akademy Nauk (AN) SSSR), Moscow, Russia, and then, he was associated with the Institute of Photosynthesis, Pushchino, Moscow Region, for about 50 years. He worked in the field of biochemistry and biophysics of photosynthesis. He is known for his studies on the molecular organization of photosystem II (PSII). He was an eminent scientist in the field of photobiology, a well-respected professor, and, above all, an outstanding researcher. Further, he was one of the founding members of the Institute of Photosynthesis in Pushchino, Russia. To most, Slava Klimov was a great human being. He was one of the pioneers of research on the understanding of the mechanism of light energy conversion and of water oxidation in photosynthesis. Slava had many collaborations all over the world, and he is (and will be) very much missed by the scientific community and friends in Russia as well as around the World. We present here a brief biography and some comments on his research in photosynthesis. We remember him as a friendly and enthusiastic person who had an unflagging curiosity and energy to conduct outstanding research in many aspects of photosynthesis, especially that related to PSII.

DOI： 10.1007/s11120-017-0440-5

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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.) volcanos 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 S-2 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 (4)A -> E-2 spin-flips within the d(3) 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. S-3 exhibits a more intense (-) MCD peak at 764 nm and has a stronger MCD saturation characteristic. This S-3 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 S-2 EPR spectra of T. volcanos and not Mn(Ill)-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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Photosystem II (PSII) catalyses the photoinduced oxygen evolution and, by producing reducing equivalents drives, in concert with PSI, the conversion of carbon dioxide to sugars. Our knowledge about the architecture of the reaction centre (RC) complex and the mechanisms of charge separation and stabilisation is well advanced. However, our understanding of the processes associated with the functioning of RC is incomplete: the photochemical activity of PSII is routinely monitored by chlorophyll-a fluorescence induction but the presently available data are not free of controversy. In this work, we examined the nature of gradual fluorescence rise of PSII elicited by trains of singleturnover saturating flashes (STSFs) in the presence of a PSII inhibitor, permitting only one stable charge separation. We show that a substantial part of the fluorescence rise originates from lightinduced processes that occur after the stabilisation of charge separation, induced by the first STSF; the temperature-dependent relaxation characteristics suggest the involvement of conformational changes in the additional rise. In experiments using double flashes with variable waiting times (Delta tau) between them, we found that no rise could be induced with zero or short Delta tau, the value of which depended on the temperature -revealing a previously unknown rate-limiting step in PSII.

DOI： 10.1038/s41598-018-21195-2

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Language：English   Publishing type：Part of collection (book)   Publisher：Academic Press Inc.  

Photosystem II (PSII) is a membrane protein complex which functions to catalyze light-induced water oxidation in oxygenic photosynthesis. Through the water-splitting reaction of PSII, light energy is converted into biologically useful chemical energy, and molecular oxygen is formed which transformed the atmosphere into an aerobic one and sustained aerobic life on the Earth. The PSII core complex from cyanobacteria consists of 17 transmembrane subunits and 3 extrinsic subunits with a total molecular mass of approximately 350 kDa per monomer, and PSII exists predominately in a dimeric form in vivo. This chapter describes the purification procedures leading to highly pure, homogenous, and highly active PSII core dimers from a thermophilic cyanobacterium, Thermosynechococcus vulcanus (T. vulcanus), that are used for successful crystallization and diffraction at atomic resolution. The purity and homogeneity of the PSII dimers thus obtained are characterized by absorption spectra, low-temperature fluorescence spectra, SDS-PAGE, clear native PAGE, blue native PAGE, gel filtration chromatography, and oxygen-evolving activity measurements. Finally, high-quality crystals obtained from the purified PSII dimers are shown.

DOI： 10.1016/bs.mie.2018.10.002

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

Among different strategies, water splitting toward hydrogen production is a promising process to store energy from intermittent sources. However, the anodic water oxidation is a bottleneck for water splitting. In this paper, we report an aluminum/cobalt/iron/nickel alloy as a precatalyst for the electrochemical water oxidation. The alloy electrode contains different metal ions including cobalt, iron, and nickel which all are efficient for water oxidation is tested. We characterized this electrode using scanning electron microscopy, transmission electron microscopy, diffuse reflectance infrared Fourier transform spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy and electrochemical methods. After stabilization, the electrode shows an onset overpotential of 200.0 mV and affords a current density of 3.5 mA cm(-2) at an overpotential of 600.0 mV in KOH solution at pH 13. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.ijhydene.2017.12.025

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

The native core light-harvesting complex (LH1) from the thermophilic purple phototrophic bacterium Thermochromatium tepidum requires Ca2+ for its thermal stability and characteristic absorption maximum at 915 nm. To explore the role of specific amino acid residues of the LH1 polypeptides in Ca-binding behavior, we constructed a genetic system for heterologously expressing the Tch. tepidum LH1 complex in an engineered Rhodobacter sphaeroides mutant strain. This system contained a chimeric pufBALM gene cluster (pufBA from Tch. tepidum and pufLM from Rba. sphaeroides) and was subsequently deployed for introducing site-directed mutations on the LH1 polypeptides. All mutant strains were capable of phototrophic (anoxic/light) growth. The heterologously expressed Tch. tepidum wild-type LH1 complex was isolated in a reaction center (RC)-associated form and displayed the characteristic absorption properties of this thermophilic phototroph. Spheroidene (the major carotenoid in Rba. sphaeroides) was incorporated into the Tch. tepidum LH1 complex in place of its native spirilloxanthins with one carotenoid molecule present per alpha beta-subunit. The hybrid LH1-RC complexes expressed in Rba. sphaeroides were characterized using absorption, fluorescence excitation, and resonance Raman spectroscopy. Site-specific mutagenesis combined with spectroscopic measurements revealed that alpha-D49, beta-L46, and a deletion at position 43 of the alpha-polypeptide play critical roles in Ca binding in the Tch. tepidum LH1 complex; in contrast, alpha-N50 does not participate in Ca2+ coordination. These findings build on recent structural data obtained from a high-resolution crystallographic structure of the membrane integrated Tch. tepidum LH1-RC complex and have unambiguously identified the location of Ca2+ within this key antenna complex.

DOI： 10.1073/pnas.1703584114

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

We recently revealed that positively charged amino acids of Psb31, an extrinsic subunit found in diatom photosystem II (PSII), are involved in electrostatic interactions with PSII intrinsic subunits. However, the molecular interactions of Psb31 with PSII remain unclear. Here, we report the functional contribution of Lys residues in the binding of Psb31 to PSII using site-directed mutants of Psb31. Each of the K33A, K39A, K54A, K56A, K57A, and K69A mutants exhibits decreased binding affinities to PSII concomitantly with decreases in the O-2 evolution activity. Conversely, each of the K24A, K76A, K80A, and K117A mutants functionally binds to PSII in a manner similar to wild-type Psb31. These results provide evidence that some Lys residues of Psb31 are responsible for electrostatic interactions with PSII.

DOI： 10.1002/1873-3468.12830

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

Photosystem I (PSI)-light-harvesting complex I (LHCI) super-complex and its sub-complexes PSI core and LHCI, were purified from a unicellular red alga Cyanidioschyzon merolae and characterized. PSI-LHCI of C. merolae existed as a monomer with a molecular mass of 580 kDa. Mass spectrometry analysis identified 11 subunits (PsaA, B, C, D, E, F, I, J, K, L, O) in the core complex and three LHCI subunits, CMQ142C, CMN234C, and CMN235C in LHCI, indicating that at least three Lhcr subunits associate with the red algal PSI core. PsaG was not found in the red algae PSI-LHCI, and we suggest that the position corresponding to Lhca1 in higher plant PSI-LHCI is empty in the red algal PSI-LHCI. The PSI-LHCI complex was separated into two bands on native PAGE, suggesting that two different complexes may be present with slightly different protein compositions probably with respective to the numbers of Lhcr subunits. Based on the results obtained, a structural model was proposed for the red algal PSI-LHCI. Furthermore, pigment analysis revealed that the C. merolae PSI-LHCI contained a large amount of zeaxanthin, which is mainly associated with the LHCI complex whereas little zeaxanthin was found in the PSI core. This indicates a unique feature of the carotenoid composition of the Lhcr proteins and may suggest an important role of Zea in the light-harvesting and photoprotection of the red algal PSI-LHCI complex.

DOI： 10.1007/s11120-017-0384-9

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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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DOI： 10.1039/c7fd90016c

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DOI： 10.1039/c7fd90017a

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

We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.

DOI： 10.1039/c7cp01673e

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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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DOI： 10.1038/540536a

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Positively charged lysines are crucial to maintaining the native structures of proteins and protein complexes by forming hydrogen bonds and electrostatic interactions with their proximal amino acid residues. However, it is still a challenge to develop an efficient method for probing the active proximal microenvironments of lysines without changing their biochemical/physical properties. Herein, we developed an active covalent labeling strategy combined with mass spectrometry to systematically probe the lysine proximal microenvironments within membrane protein complexes (similar to 700 kDa) with high throughput. Our labeling strategy has the advantages of high labeling efficiency and stability, preservation of the active charge states, as well as biological activity of the labeled proteins. In total, 121 lysines with different labeling levels were obtained for the photosystem II complexes from cyanobacteria, red algae, and spinach and provided important insights for understanding the conserved and nonconserved local structures of PSII complexes among evolutionarily divergent species that perform photosynthesis.

DOI： 10.1021/acs.analchem.6b02502

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

Integrating natural and artificial photosynthetic platforms is an important approach to developing solar-driven hybrid systems with exceptional function over the individual components. A natural-artificial photosynthetic hybrid platform is formed by wiring photosystem II (PSII) and a platinum-decorated silicon photoelectrochemical (PEC) cell in a tandem manner based on a photocatalytic-PEC Z-scheme design. Although the individual components cannot achieve overall water splitting, the hybrid platform demonstrated the capability of unassisted solar-driven overall water splitting. Moreover, H-2 and O-2 evolution can be separated in this system, which is ascribed to the functionality afforded by the unconventional Z-scheme design. Furthermore, the tandem configuration and the spatial separation between PSII and artificial components provide more opportunities to develop efficient natural-artificial hybrid photosynthesis systems.

DOI： 10.1002/anie.201604091

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The development of artificial photosynthesis has focused on the efficient coupling of reaction at photoanode and cathode, wherein the production of hydrogen (or energy carriers) is coupled to the electrons derived from water splitting reactions. The natural photosystem II (PSII) complex splits water efficiently using light energy. The PSII complex is a large pigment protein complex (20 nm in diameter) containing a manganese cluster. A new photoanodic device was constructed incorporating stable PSII purified from a cyanobacterium Thermosynechococcus vulcanus through immobilization within 20 or 50 nm nanopores contained in porous glass plates (PGPs). PSII in the nanopores retained its native structure and high photoinduced water splitting activity. The photocatalytic rate (turnover frequency) of PSII in PGP was enhanced 11-fold compared to that in solution, yielding a rate of 50-300 mol e(-) /(mol PSII.s) with 2,6-dichloroindophenol (DCIP) as an electron acceptor. The PGP system realized high local concentrations of PSII and DCIP to enhance the collisional reactions in nanotubes with low disturbance of light penetration. The system allows direct visualization/determination of the reaction inside the nanotubes, which contributes to optimize the local reaction condition. The PSII/PGP device will substantively contribute to the construction of artificial photosynthesis using water as the ultimate electron source.

DOI： 10.1021/acs.langmuir.6b02106

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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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Language：Chinese   Publishing type：Research paper (scientific journal)   Publisher：Chinese Academy of Sciences  

Photosynthesis uses light energy from the sun to convert CO2 and water into carbohydrates and oxygen, thus sustaining all aerobic life forms on Earth. Energy conversion in photosynthesis is carried out by two large membrane-protein complexes: photosystemI(PSI) and photosystemII(PSII). In higher plants, the PSIcore is surrounded by a belt of 4 light-harvestingIsubunits (LHCIor Lhca), forming a PSI-LHCIsupercomplex. The PSI-LHCIsupercomplex is an extremely efficient solar energy converter with a quantum efficiency close to 100%. In order to reveal the mechanism of energy harvesting and transfer within this large pigment-protein complex, it is essential to solve its crystal structure. The structure of the PSI-LHCIsupercomplex has been analyzed at a resolution up to 3.3 Å previously. However, this resolution was not enough to elucidate the detailed mechanism of light-harvesting and energy transfer in this complex. Recently we succeeded in analyzing the structure of the PSI-LHCIsupercomplex from pea at 2.8 Å resolution (1). Our studies showed that the PSI-LHCIsupercomplex contains 16 different subunits (including 12 core subunits PsaA-L and 4 LHCIsubunits Lhca1-4) and 205 cofactors (143 chlorophylls a, 12 chlorophylls b, 26 β-carotenes, 5 luteins, 4 violaxanthin, 10 lipids), with a total molecular mass of 600 kD. Our results identified chlorophyll a, chlorophyll b, and some carotenoids in the 4 LHCIsubunits for the first time, and revealed the differences in the structures of the 4 LHCI subunits, their interactions, and the interactions between them and the PSIcore subunits. Comparison among the available six structures of the Lhc family members (Lhca1 to Lhca4, LHCIIand CP29) revealed that, although all these Lhc proteins have a highly conserved second protein structure, notable differences were found in the two loop regions AC and BC as well as the N-terminal region. Most pigments are arranged at the same position except some distinct differences among different Lhc subunits in the position of several Chls bound at the interface between adjacent Lhca complexes, and between Lhca and PSIcore complex. Based on the structure resolved, 4 plausible energy transfer pathways (1Bs, 1Fl, 2Js, 3As/l) from LHCIto the PSIcore complex were deduced. Red forms of Chls were found to be involved in energy transfer from each Lhca to PSIcore. Our structure revealed that each Lhca binds a red chlorophyll dimer of Chl a3-Chl a9, which contribute to red-shifted spectra of Lhca complexes and have a pronounced effect on the energy transfer and trapping in the whole PSI-LHCIcomplex. All the four red dimers locate at the interface between LHCIand PSIcore complex, which looks like four bridges connecting Lhca with the core. The Chl-Chl interactions between each Lhca and the core complex suggested that excitation energy from the LHCIbelt to the PSIcore would mainly flow via Lhca1 and Lhca3. In this review, we discuss the detailed structure of the PSI-LHCIsupercomplex and the possible energy transfer mechanism within it. Taken together, this structure provides a solid structural basis for our understanding on energy transfer and photoprotection mechanisms within PSI-LHCIsupercomplex, and thus will be a big step forward toward understanding the mechanisms of photosynthesis.

DOI： 10.1360/N972016-00217

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Language：English   Publishing type：Part of collection (book)   Publisher：Wiley-VCH Verlag  

Hydrogen gas (H 2) is considered to be one of the most important gases on earth
it can be used as an important alternative source of renewable energy. Although the amount of this gas in the Earth's atmosphere is far less compared to other gases, H 2 can be produced in different ways either by physical, chemical, or biological reactions, or obtained from fossil fuels. It can be produced biologically by lower or higher organisms, and this can contribute as an alternative source of H 2 for future generations. For biological H 2 production, bacteria, cyanobacteria, algae, and higher plants are the major organisms that can produce pure H 2 for sustainable usage. In this chapter, we briefly review different methods of production of H 2 and focus on modern studies devoted to photosynthetic production of H 2 by algae and microorganisms.

DOI： 10.1002/9783527674268.ch20

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Water oxidation is the bottleneck for hydrogen production by water-splitting systems using sunlight or other sustainable energies. Herein we report nano-sized Mn-Ca oxide in an engineered polypeptide (Glu-Glu-Glu-Glu-Glu-Glu-Glu-His-Val-Val-Val-Val-Val-Val-Val-Val) as a structural model for biological water-oxidizing site in plants, algae, and cyanobacteria. The compound was synthesized by a simple procedure and characterized by transmission electron microscopy, atomic absorption spectroscopy, scanning electron microscopy, energy-dispersive spectroscopy, X-ray diffraction spectrometry, UV-Visible spectroscopy, dynamic light scattering, and some electrochemical methods. Using hydrogen to store sustainable energies is a promising strategy in near future and such nano-sized Mn-Ca oxide/polypeptide is a promising strategy in water-splitting systems to provide cheap electrons from water toward hydrogen production. Copyright (C) 2016, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.ijhydene.2016.01.131

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

Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 resolution, which revealed the structure and interaction sites of PsbQ, a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

DOI： 10.1074/jbc.M115.711689

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All cyanobacteria, algae, and plants use a similar water-oxidizing catalyst for water oxidation. This catalyst is housed in Photosystem II, a membrane-protein complex that functions as a light-driven water oxidase in oxygenic photosynthesis. Water oxidation is also an important reaction in artificial photosynthesis because it has the potential to provide cheap electrons from water for hydrogen production or for the reduction of carbon dioxide on an industrial scale. The water-oxidizing complex of Photosystem II is a Mn-Ca cluster that oxidizes water with a low overpotential and high turnover frequency number of up to 25-90 molecules of O-2 released per second. In this Review, we discuss the atomic structure of the Mn-Ca cluster of the Photosystem II water-oxidizing complex from the viewpoint that the underlying mechanism can be informative when designing artificial water-oxidizing catalysts. This is followed by consideration of functional Mn-based model complexes for water oxidation and the issue of Mn complexes decomposing to Mn oxide. We then provide a detailed assessment of the chemistry of Mn oxides by considering how their bulk and nanoscale properties contribute to their effectiveness as water-oxidizing catalysts.

DOI： 10.1021/acs.chemrev.5b00340

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DOI： 10.1038/530168a

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We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S-3 state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol(1) that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn4CaO5 cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which MnO and OO bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed.

DOI： 10.1021/acs.inorgchem.5b02471

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Manganese oxide structure with lanthanum(III) or cerium(III) ions between the layers was synthesized by a simple method. The ratio of Mn to Ce or La in samples was 0.00, 0.04, 0.08, 0.16, 0.32, 0.5, 0.82, or 1.62. The compounds were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction studies, and atomic absorption spectroscopy. The compounds show efficient catalytic activity of water oxidation in the presence of cerium(IV) ammonium nitrate with a turnover frequency of 1.6 mmol O-2/mol Mn.s. In contrast to the water-oxidizing complex in Photosystem II, calcium(II) has no specific role to enhance the water-oxidizing activity of the layered manganese oxides and other cations can be replaced without any significant decrease in water-oxidizing activities of these layered Mn oxides. Based on this and previously reported results from oxygen evolution in the presence of H (2) (18) O, we discuss the mechanism and the important factors influencing the water-oxidizing activities of the manganese oxides.

DOI： 10.1007/s11120-015-0098-9

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DOI： 10.1007/s11120-015-0116-y

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Recent X-ray crystallographic analysis of photosystem (PS) II at 1.9- resolution identified 20 lipid molecules in the complex, five of which are phosphatidylglycerol (PG). In this study, we mutagenized amino acid residues S232 and N234 of D1, which interact with two of the PG molecules (PG664 and PG694), by site-directed mutagenesis in Synechocystis sp. PCC 6803 to investigate the role of the interaction in PSII. The serine and asparagine residues at positions 232 and 234 from the N-terminus were mutagenized to alanine and aspartic acid, respectively, and a mutant carrying both amino acid substitutions was also produced. Although the obtained mutants, S232A, N234D, and S232AN234D, exhibited normal growth, they showed decreased photosynthetic activities and slower electron transport from Q(A) to Q(B) than the control strain. Thermoluminescence analysis suggested that this slower electron transfer in the mutants was caused by more negative redox potential of Q(B), but not in those of Q(A) and S-2. In addition, the levels of extrinsic proteins, PsbV and PsbU, were decreased in PSII monomer purified from the S232AN234D mutant, while that of Psb28 was increased. In the S232AN234D mutant, the content of PG in PSII was slightly decreased, whereas that of monogalactosyldiacylglycerol was increased compared with the control strain. These results suggest that the interactions of S232 and N234 with PG664 and PG694 are important to maintain the function of Q(B) and to stabilize the binding of extrinsic proteins to PSII.

DOI： 10.1007/s11120-015-0150-9

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DOI： 10.1007/s11120-015-0191-0

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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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We have studied the early phase of the S-2 -> S-3 transition in the oxygen-evolving complex (OEC) of photosystem II using the hybrid density functional theory with a quantum mechanical model composed of 338-341 atoms. Special attention is given to the vital role of water molecules in the vicinity of the Mn4CaO5 core. Our results demonstrate how important the dynamic behavior of surrounding water molecules is in mediating critical chemical transformations such as binding and deprotonation of substrates and hydration of the catalytic site and identify a strong coupling of water-chain relocation near the redox-active tyrosine residue Tyr161 (Tyr(Z)) with oxidation of the Mn4CaO5 cluster by Tyr(Z)center dot(+). The oxidation reaction is further promoted when the catalytic site is more solvated by water. These results indicate the importance of surrounding water molecules in biological catalysts as they ultimately lead to effective catalytic function and/or favorable electron-transfer dynamics.

DOI： 10.1021/acs.jpcb.5b05740

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

Photosynthesis is one of the most important processes on our planet, providing food and oxygen for the majority of living organisms on Earth. Over the past 30 years scientists have made great strides in understanding the central photosynthetic process of oxygenic photosynthesis, whereby water is used to provide the hydrogen and reducing equivalents vital to CO2 reduction and sugar formation. A recent crystal structure at 1.9-1.95 angstrom has made possible an unparalleled map of the structure of photosystem II (PSII) and particularly the manganese-calcium (Mn-Ca) cluster, which is responsible for splitting water. Here we review how knowledge of the water-splitting site provides important criteria for the design of artificial Mn-based water-oxidizing catalysts, allowing the development of clean and sustainable solar energy technologies.

DOI： 10.1016/j.tplants.2015.06.005

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Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography ({IUCr})  

DOI： 10.1107/s2053273315099751

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Language：English   Publisher：ELSEVIER  

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

Photosynthetic splitting of water into oxygen by plants, algae, and cyanobacteria is catalyzed by the oxygen-evolving center (OEC). Synthetic mimics of the OEC, which is composed of an asymmetric manganese-calcium-oxygen cluster bound to protein groups, may promote insight into the structural and chemical determinants of biological water oxidation and lead to development of superior catalysts for artificial photosynthesis. We synthesized a Mn4Ca-cluster similar to the native OEC in both the metal-oxygen core and the binding protein groups. Like the native OEC, the synthetic cluster can undergo four redox transitions and shows two magnetic resonance signals assignable to redox and structural isomerism. Comparison with previously synthesized Mn3CaO4-cubane clusters suggests that the fourth Mn ion determines redox potentials and magnetic properties of the native OEC.

DOI： 10.1126/science.aaa6550

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Language：English   Publisher：AMER CHEMICAL SOC  

Current energy resources largely rely on fossil fuels that are expected to be depleted in 50-200 years. On a global scale, the intensive use of this energy source has resulted in highly detrimental effects to the environment. Hydrogen production by water splitting, with sunlight as the main energy source, is a promising way to augment the production of renewable energy; however, the development of an efficient and stable water-oxidizing catalyst remains a key task before a technological breakthrough based on water splitting can be realized. A main issue hampering the development of commercially viable, non-precious-metal-based catalysts is their susceptibility to degradation. To efficiently address this major drawback, self-healing catalysts that can repair their structure without human intervention will be necessary. In this review, we focus on water oxidation by natural and artificial Mn-, Co-, and Ni-based catalysts and then discuss the self-healing properties that contribute to sustaining their catalytic activity.

DOI： 10.1021/cs5015157

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

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

Hexokinase 1 from Arabidopsis thaliana (AtHXK1) plays a dual role in glycolysis and sugar sensing for vital metabolic and physiological processes. The uncoupling of glucose signalling from glucose metabolism was demonstrated by the analysis of two mutants (AtHXK1(G104D) and AtHXK1(S177A)) that are catalytically inactive but still functional in signalling. In this study, substrate-binding experiments indicate that the two catalytically inactive mutants have a high affinity for glucose, and an ordered substrate-binding mechanism has been observed for wild-type AtHXK1. The structure of AtHXK1 was determined both in its inactive unliganded form and in its active glucose-bound form at resolutions of 1.8 and 2.0 angstrom, respectively. These structures reveal a domain rearrangement of AtHXK1 upon glucose binding. The 2.1 angstrom resolution structure of AtHXK1(S177A) in the glucose-bound form shows similar glucose-binding interactions as the wild type. A glucose-sensing network has been proposed based on these structures. Taken together, the results provide a structural explanation for the dual functions of AtHXK1.

DOI： 10.1107/S1399004714026091

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

"Back to Nature" is a promising way to solve the problems that we face today, such as air pollution and shortage of energy supply based on conventional fossil fuels. A Mn cluster inside photosystem II catalyzes light-induced water-splitting leading to the generation of protons, electrons and oxygen in photosynthetic organisms, and has been considered as a good model for the synthesis of new artificial water-oxidizing catalysts. Herein, we surveyed the structural and functional details of this cluster and its surrounding environment. Then, we review the mechanistic findings concerning the cluster and compare this biological catalyst with nano-sized Mn oxides, which are among the best artificial Mn-based water-oxidizing catalysts. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2014.11.006

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

Visible/UV absorption in PS II core complexes is dominated by the chl-a absorptions, which extend to similar 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 Chl(D1) and Chl(D2). 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 similar to 770 nm and similar to 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 b(559) or cyt C-550. The distinctive characteristics of the MCD signals seen at 770 nm allow us to assign absorption in this region to a d(z)(2) -> d(x2) (-) (y2) transition of Mn(III) in the Ca-Mn4O5 cluster of the oxygen evolving centre. Current measurements were performed in the S-1 state. Detailed analyses of this spectral region, especially in higher S states, promise to provide a new window on models of water oxidation. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2014.11.003

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

A novel super-complex of photosystem I (PSI)-light-harvesting complex I (LHCI) was isolated from a siphonaceous marine green alga, Bryopsis corticulans. The super-complex contained 9-10 Lhca antennas as external LHCI bound to the core complex. The super-complex was further disintegrated into PSI core and LHCI sub-complexes, and analysis of the pigment compositions by high-performance liquid chromatography revealed unique characteristics of the B. corticulans PSI in that one PSI core contained around 14 a-carotenes and 1-2 e-carotenes. This is in sharp contrast to the PSI core from higher plants and most cyanobacteria where only beta-carotenes were present, and is the first report for an alpha-carotenetype PSI core complex among photosynthetic eukaryotes, suggesting a structural flexibility of the PSI core. Lhca antennas from B. corticulans contained seven kinds of carotenoids (siphonaxanthin, all-trans neoxanthin, 9'-cis neoxanthin, violaxanthin, siphonein, e-carotene, and acarotene) and showed a high carotenoid: chlorophyll ratio of around 7.5: 13. PSI-LHCI super-complex and PSI core showed fluorescence emission peaks at 716 and 718 nm at 77 K, respectively; whereas two Lhca oligomers had fluorescence peaks at 681 and 684 nm, respectively. By comparison with spinach PSI preparations, it was found that B. corticulans PSI had less red chlorophylls, most of them are present in the core complex but not in the outer light-harvesting systems. These characteristics may contribute to the fine tuning of the energy transfer network, and to acclimate to the ever-changing light conditions under which the unique green alga inhabits.

DOI： 10.1007/s11120-014-0039-z

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Language：English   Publishing type：Part of collection (book)   Publisher：ANNUAL REVIEWS  

Oxygenic photosynthesis forms the basis of aerobic life on earth by converting light energy into biologically useful chemical energy and by splitting water to generate molecular oxygen. The water-splitting and oxygen-evolving reaction is catalyzed by photosystem II (PSII), a huge, multisubunit membrane-protein complex located in the thylakoid membranes of organisms ranging from cyanobacteria to higher plants. The structure of PSII has been analyzed at 1.9-angstrom resolution by X-ray crystallography, revealing a clear picture of the Mn4CaO5 cluster, the catalytic center for water oxidation. This article provides an overview of the overall structure of PSII followed by detailed descriptions of the specific structure of the Mn4CaO5 cluster and its surrounding protein environment. Based on the geometric organization of the Mn4CaO5 cluster revealed by the crystallographic analysis, in combination with the results of a vast number of experimental studies involving spectroscopic and other techniques as well as various theoretical studies, the article also discusses possible mechanisms for water splitting that are currently under consideration.

DOI： 10.1146/annurev-arplant-050312-120129

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

A hybrid photoanode integrating the cyanobacterial photosystem II (PSII) with a hematite film for water oxidation is constructed. Direct electron transfer from PSII to the excited Ti/Fe2O3 electrode occurs under light irradiation, resulting in a significant improvement of the photocurrent.

DOI： 10.1039/c5cc06900a

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

Photosystem II (PSII) has attracted a lot of attention for use in the construction of artificial photosynthetic materials due to its high activity of oxidation of water molecules. However, the robustness of PSII needs to be improved for in vitro application. In this study, we incorporated PSII (Thermosynechococcus vulcanus) into various phospholipid membranes to examine the activity and durability of oxygen evolution. PSII was incorporated into anionic 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (PSII-DOPG), zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphocholine (PSII-DOPC), and cationic 1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (PSII-EDOPC). Structural integrity of PSII was examined by absorption and fluorescence spectroscopy. Compared with PSII dissolved in a micellar solution of n-dodecyl-beta-d-maltoside (PSII-micelle), durability of PSII-DOPC and PSII-DOPG were enhanced by 1.3- and 1.5-fold, respectively. The activity and durability of PSII-EDOPC was significantly low. Lipid-dependent activity and durability were discussed in terms of kinetic parameters of V (max) and K (m), and inhibition of the electron acceptor, phenyl-p-benzoquinone.

DOI： 10.1007/s11164-014-1829-9

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

The water-oxidizing complex (WOC), also known as the oxygen-evolving complex (OEC), of photosystem II in oxygenic photosynthetic organisms efficiently catalyzes water oxidation. It is, therefore, responsible for the presence of oxygen in the Earth's atmosphere. The WOC is a manganese-calcium (Mn4CaO5(H2O)(4)) cluster housed in a protein complex. In this review, we focus on water exchange chemistry of metal hydrates and discuss the mechanisms and factors affecting this chemical process. Further, water exchange rates for both the biological cofactor and synthetic manganese water splitting are discussed. The importance of fully unveiling the water exchange mechanism to understand the chemistry of water oxidation is also emphasized here. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2014.03.008

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Language：English   Publisher：ELSEVIER SCIENCE BV  

DOI： 10.1016/j.bbabio.2014.07.002

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Language：English   Publisher：SPRINGER  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER  

The purpose of this review is to present recent advances in the structural and functional studies of water-oxidizing center of Photosystem II and its surrounding protein matrix in order to synthesize artificial catalysts for production of clean and efficient hydrogen fuel. (C) 2014 Elsevier Masson SAS. All rights reserved.

DOI： 10.1016/j.plaphy.2014.01.020

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

DOI： 10.1093/pcp/pcu085

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

We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-angstrom radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

DOI： 10.1038/NMETH.2962

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We investigated theoretically the catalytic mechanism of electrochemical water oxidation in aqueous solution by a dinuclear ruthenium complex containing redox-active quinone ligands, [Ru-2(X)(Y)(3,6-tBu(2)Q)(2)(btpyan)](m+) [X, Y = H2O, OH, O, O-2; 3,6-tBu(2)Q = 3,6-di-tert-butyl-1,2-benzoquinone; btpyan = 1,8-bis(2,2':6',2"-terpyrid-4'-yl)anthracene] (m = 2, 3, 4) (1). The reaction involves a series of electron and proton transfers to achieve redox leveling, with intervening chemical transformations in a mesh scheme, and the entire molecular structure and motion of the catalyst 1 work together to drive the catalytic cycle for water oxidation. Two substrate water molecules can bind to 1 with simultaneous loss of one or two proton(s), which allows pH-dependent variability in the proportion of substrate-bound structures and following pathways for oxidative activation of the aqua/hydroxo ligands at low thermodynamic and kinetic costs. The resulting bis-oxo intermediates then undergo endothermic O-O radical coupling between two Ru(III)-O-center dot units in an anti-coplanar conformation leading to bridged mu-peroxo or mu-superoxo intermediates. The mu-superoxo species can liberate oxygen with the necessity for the preceding binding of a water molecule, which is possible only after four-electron oxidation is completed. The magnitude of catalytic current would be limited by the inherent sluggishness of the hinge-like bending motion of the bridged mu-superoxo complex that opens up the compact, hydrophobic active site of the catalyst and thereby allows water entry under dynamic conditions. On the basis of a newly proposed mechanism, we rationalize the experimentally observed behavior of electrode kinetics with respect to potential and discuss what causes a high overpotential for water oxidation by 1.

DOI： 10.1021/ic402340d

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

Routinely prepared PS II core samples are often contaminated by a significant (similar to 1-5%) fraction of PSI, as well as related proteins. This contamination is of little importance in many experiments, but masks the optical behaviour of the deep red state in PS II, which absorbs in the same spectral range (700-730 nm) as PS I (Hughes et al. 2006). When contamination levels are less than similar to 1%, it becomes difficult to quantify the PS I related components by gelbased, chromatographic, circular dichroism or EPR techniques. We have developed a fluorescence-based technique, taking advantage of the distinctively different low-temperature emission characteristics of PS II and PS I when excited near 700 nm. The approach has the advantage of providing the relative concentration of the two photosystems in a single spectral measurement. A sensitivity limit of 0.01% PS I (or better) can be achieved. The procedure is applied to PS II core preparations from spinach and Thermosynechococcus volcanos. Measurements made of T. vulcanus PS II preparations prepared by re-dissolving crystallised material indicate a low but measurable PS I related content. The analysis provides strong evidence for a previously unreported fluorescence of PS II cores peaking near 780 nm. The excitation dependence of this emission as well as its appearance in both low PS I cyanobacterial and plant based PS II core preparations suggests its association with the deep red state of PS II. (C) 2013 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2013.09.008

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

The hydration of the oxygen-evolving complex (OEC) was characterized in the dark stable S-1 state of photosystem II using water R-1(omega) NMR dispersion (NMRD) profiles. The R-1(omega) NMRD profiles were recorded over a frequency range from 0.01 MHz to 40 MHz for both intact and Mn-depleted photosystem II core complexes from Thermosynechococcus vulcanus (T. vulcanus). The intact-minus-(Mn)-depleted difference NMRD profiles show a characteristic dispersion from approximately 0.03 MHz to 1 MHz, which is interpreted on the basis of the Solomon-Bloembergen-Morgan (SBM) and the slow motion theories as being due to a paramagnetic enhanced relaxation (PRE) of water protons. Both theories are qualitatively consistent with the S-T = 1, g = 4.9 paramagnetic state previously described for the S-1 state of the OEC; however, an alternative explanation involving the loss of a separate class of long-lived internal waters due to the Mn-depletion procedure can presently not be ruled out. Using a point-dipole approximation the PRE-NMRD effect can be described as being caused by 1-2 water molecules that are located about 10 angstrom away from the spin center of the Mn4CaO5 cluster in the OEC. The application of the SBM theory to the dispersion observed for PSII in the S-1 state is questionable, because the parameters extracted do not fulfil the presupposed perturbation criterion. In contrast, the slow motion theory gives a consistent picture indicating that the water molecules are in fast chemical exchange with the bulk (tau(w) < 1 mu s). The modulation of the zero-field splitting (ZFS) interaction suggests a (restricted) reorientation/ structural equilibrium of the Mn4CaO5 cluster with a characteristic time constant of tau(ZFS) = 0.6-0.9 mu s.

DOI： 10.1039/c3cp55232b

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DOI： 10.1039/c4cp90053g

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

The mechanism of solar water oxidation by photosystem II (PSII) is of fundamental interest and it is the object of extensive studies both in the past and present. The solar water oxidation reaction of PSII occurs in the oxygen-evolving complex (OEC). The OEC consists of a tetranuclear manganese calcium-oxo (Mn4Ca-oxo) cluster that is surrounded by amino acid residues and inorganic cofactors. The role of the Ca2+ ion in the water oxidation reaction is one of the most interesting questions that is yet to be answered. In this study, we probe the structural and functional differences induced by metal ion substitution in the Mn4Ca-oxo cluster by substituting the Ca2+ ion in the OEC by a Sr2+ ion. We apply two-dimensional (2D) hyperfine sublevel correlation (HYSCORE) spectroscopy to detect weak magnetic interactions between the paramagnetic Mn4Sr-oxo cluster and the surrounding protons in the S-2 state of the OEC of Sr2+-substituted PSII. We identify three groups of protons that are magnetically interacting with the Mn4Sr-oxo cluster. Using the recently reported 1.9 angstrom resolution X-ray structure of the OEC in the S-1 state [Umena et al.] and the high-resolution 2D HYSCORE spectroscopy studies of the S-2 state of the OEC of Ca2+-containing PSII [Milikisiyants et al., Energy Environ. Sci., 2012, 5, 7747], we discuss the assignments of the three groups of protons that are magnetically coupled to the Mn4Sr-oxo cluster. Since hyperfine interactions are highly sensitive to small perturbations in the electronic and geometric structure of paramagnetic centers, a comparison of the 2D HYSCORE spectra of Sr2+-substituted and Ca2+-containing PSII allows us to draw important conclusions with respect to the structure of the substrate water molecules in the OEC and the role of the Ca2+ ion in the water oxidation reaction. In addition, for the first time, we determine the experimental value of the spin projection factor for the Mn(III) ion of the Mn4Ca-oxo cluster as rho(1) = +/- 1.7 from the assignment of the hyperfine interaction of the paramagnetic cluster with the protons of the D1-His332 residue of PSII.

DOI： 10.1039/c4cp03082f

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

DOI： 10.2142/biophys.54.S237_6

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

DOI： 10.2142/biophys.54.S237_5

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Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The electron density map of the 3D crystal of Photosystem II from Thermosynechococcus vulcanus with a 1.9 angstrom resolution (PDB: 3ARC) exhibits, in the two monomers in the asymmetric unit cell, an, until now, unidentified and uninterpreted strong difference in electron density centered at a distance of around 1.5 angstrom from the nitrogen N delta of the imidazole ring of D2-His336. By MALDI-TOF/MS upon tryptic digestion, it is shown that similar to 20-30% of the fragments containing the D2-His336 residue of Photosystem II from both Thermosynechococcus vulcanus and Thermosynechococcus elongatus bear an extra mass of +16 Da. Such an extra mass likely corresponds to an unprecedented post-translational or chemical hydroxyl modification of histidine.

DOI： 10.1021/bi401213m

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

In this report, gold or silver deposited on layered manganese oxide has been synthesized by a simple method and characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction spectrometry, atomic absorption spectroscopy, and energy-dispersive X-ray mapping. The gold deposited on layered manganese oxide showed efficient catalytic activity toward water oxidation in the presence of cerium(IV) ammonium nitrate. The properties associated with this compound suggest it is a functional model for the water-oxidizing complex in photosystem II.

DOI： 10.1007/s11120-013-9899-x

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

Carotenoids with conjugated carbonyl groups possess special photophysical properties which have been studied in some water-soluble light-harvesting proteins (Polivka and Sundstrom, Chem Rev 104:2021-2071, 2004). However, siphonaxanthin-type light-harvesting complexes of photosystem II (LHCII) in siphonous green alga have received fewer studies. In the present study, we determined sequences of genes for several Bryopsis corticulans Lhcbm proteins, which showed that they belong to the group of major LHCII and diverged early from green algae and higher plants. Analysis of pigment composition indicated that this siphonaxanthin-type LHCII contained in total 3 siphonaxanthin and siphonein but no lutein and violaxanthin. In addition, 2 chlorophylls a in higher plant LHCII were replaced by chlorophyll b. These changes led to an increased absorption in green and blue-green light region compared with higher plant LHCII. The binding sites for chlorophylls, siphonaxanthin, and siphonein were suggested based on the structural comparison with that of higher plant LHCII. All of the ligands for the chlorophylls were completely conserved, suggesting that the two chlorophylls b were replaced by chlorophyll a without changing their binding sites in higher plant LHCII. Comparisons of the absorption spectra of isolated siphonaxanthin and siphonein in different organic solutions and the effect of heat treatment suggested that these pigments existed in a low hydrophobic protein environment, leading to an enhancement of light harvesting in the green light region. This low hydrophobic protein environment was maintained by the presence of more serine and threonine residues in B. corticulans LHCII. Finally, esterization of siphonein may also contribute to the enhanced harvesting of green light.

DOI： 10.1007/s11120-013-9808-3

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

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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DOI： 10.1007/s11120-013-9913-3

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We designed novel peptide gemini surfactants (PG-surfactants), DKDKC12K and DKDKC12D, which can solubilize Photosystem I (PSI) of Thermosynecoccus elongatus and Photosystem II (PRI) of Thermosynecoccus vulcanus in an aqueous buffer solution. To assess the detailed effects of PC-surfactants on the original supramolecular membrane protein complexes and functions of PSI and PSII, we applied the surfactant exchange method to the isolated PSI and PSII. Spectroscopic properties, light-induced electron transfer activity, and dynamic light scattering measurements showed that PSI and PSII could be solubilized not only with retention of the original supramolecular protein complexes and functions but also without forming aggregates. Furthermore, measurement of the lifetime of light-induced charge-separation state in PSI revealed that both surfactants, especially DKDKC12D, displayed slight improvement against thermal denaturation below 60 degrees C compared with that using beta-DDM. This degree of improvement in thermal resistance still seems low, implying that the peptide moieties did not interact directly with membrane protein surfaces. By conjugating an electron mediator such as methyl viologen (MV2+) to DKDKC12K (denoted MV-DKDKC12K), we obtained derivatives that can trap the generated reductive electrons from the light-irradiated PSI. After immobilization onto an indium tin oxide electrode, a cathodic photocurrent from the electrode to the PSI/MV-DKDKC12K conjugate was observed in response to the interval of light irradiation. These findings indicate that the PG-surfactants DKDKC12K and DKDKC12D provide not only a new class of solubilization surfactants but also insights into designing other derivatives that confer new functions on PSI and PSII.

DOI： 10.1021/la402167v

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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.

DOI： 10.1021/bi400770d

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The experimentally obtained time-resolved fluorescence spectra of photosystem H (PS II) core complexes, purified from a thermophilic cyanobacterium Thermosynechococcus vulcanus, at 5-180 K are compared with simulations. Dynamic localization effects of excitons are treated implicitly by introducing exciton domains of strongly coupled pigments. Exciton relaxations within a domain and exciton transfers between domains are treated on the basis of Redfield theory and generalized Forster theory, respectively. The excitonic couplings between the pigments are calculated by a quantum chemical/electrostatic method (Poisson-TrEsp). Starting with previously published values, a refined set of site energies of the pigments is obtained through optimization cycles of the fits of stationary optical spectra of PS II. Satisfactorily agreement between the experimental and simulated spectra is obtained for the absorption spectrum including its temperature dependence and the linear dichroism spectrum of PS II core complexes (PS II-CC). Furthermore, the refined site energies well reproduce the temperature dependence of the time-resolved fluorescence spectrum of PS II-CC, which is characterized by the emergence of a 695 nm fluorescence peak upon cooling down to 77 K and the decrease of its relative intensity upon further cooling below 77 K. The blue shift of the fluorescence band upon cooling below 77 K is explained by the existence of two red-shifted chlorophyll pools emitting at around 685 and 695 nm. The former pool is assigned to Chl45 or Chl43 in CP43 (Chl numbering according to the nomenclature of Loll et al. Nature 2005, 438, 1040) while the latter is assigned to Chl29 in CP47. The 695 nm emitting chlorophyll is suggested to attract excitations from the peripheral light-harvesting complexes and might also be involved in photoprotection.

DOI： 10.1021/ja312586p

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

Photosynthetic water splitting is catalyzed by a Mn4CaO5 cluster in photosystem II, whose structure was recently determined at a resolution of 1.9 angstrom [Umena, Y. et al. 2011, Nature, 473:55-60]. To determine the electronic structure of the Mn4CaO5 cluster, pulsed electron-electron double resonance (PELDOR) measurements were performed for the tyrosine residue Y-D(center dot) and S-2 state signals with non-oriented and oriented photosystem II (PS H) samples. Based on these measurements, the spin density distributions were calculated by comparing with the experimental results. The best fitting parameters were obtained with a model in which Mn1 has a large positive projection, Mn3 has a small positive projection, and Mn2 and Mn4 have negative projections (the numbering of Mni (i=1-4) is based on the crystal structure at a 1.9 angstrom resolution), which yielded spin projections of 1.97, -120, 1.19 and -0.96 for Mn1-4 ions. The results show that the Mn1 ion, which is coordinated by H332, 0342 and E189, has a valence of Mn(III) in the S-2 state. The sign of the exchange interactions J(13) is positive, and the other signs are negative. 2(C) 013 Els,evier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2012.12.011

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Oxygen-evolving complex of photosystem II ( PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca2+ in this cluster and the possible location of water substrates in this process, we crystallized Sr2+-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 angstrom, and compared it with the 1.9 angstrom structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the Mn4CaO5-cluster relative to that of Ca2+, resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca2+, W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr2+-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 angstrom structure of native PSII, was found in the Sr-PSII structure.

DOI： 10.1073/pnas.1219922110

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Language：English   Publishing type：Part of collection (book)   Publisher：CRC Press  

Cyanobacteria, or blue-green algae as they were called, are a group of bacteria that obtain their energy through oxygenic photosynthesis (for a perspective, see [1]
for evolution, see [2]).Cyanobacteria converted the early reducing atmosphere into an oxidizing one and changed the composition of life forms on Earth. The consensus is that chloroplasts in plants and eukaryotic algae have evolved from cyanobacterial ancestors via endosymbiosis [3]. In this chapter, we will discuss the structure and function of the water-oxidizing complex (WOC) in cyanobacteria [4,5].

DOI： 10.1201/b13853

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：AMER INST PHYSICS  

Photosynthetic water-splitting takes place in photosystem II (PSII), a membrane protein complex consisting of 20 subunits with an overall molecular mass of 350 kDa. The light-induced water-splitting reaction catalyzed by PSII not only converts light energy into biologically useful chemical energy, but also provides us with oxygen indispensible for sustaining oxygenic life on the earth. We have solved the structure of PSII at a 1.9 angstrom resolution, from which, the detailed structure of the Mn4CaO5-cluster, the catalytic center for water-splitting, became clear. Based on the structure of PSII at the atomic resolution, possible mechanism of light-induced water-splitting was discussed.

DOI： 10.1063/1.4848085

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

DOI： 10.2142/biophys.53.S82_4

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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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The distances between YD and active carotenoid have been determined in cyanobacterium (synecochoccus vulcanus) and spinach PSII by pulsed electron double resonance (PELDOR). The observed spectra were analyzed taking into spin distribution of over 30 carbon atoms in the carotenoid molecule. The result of simulations based on the recent crystal structure fitted well with the spectra. The observed spectra for spinach PSII was different, showing the crystal structure of spinach PSII is slightly different from that of cyanobacteria. The ELDOR spectra of YD-YZ radical pair were observed in a cyanobacterium. The result showed the different distance from Spinach PSII.

DOI： 10.1007/978-3-642-32034-7_13

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

Most of the chlorophyll (Chl) cofactors in photosystem II (PSII) from Acaryochloris marina are Chld, although a few Chla molecules are also present. To evaluate the possibility that Chla may participate in the P-D1/P-D2 Chl pair in PSII from A marina, the P-D1(.+)/P-D2(.+) charge ratio was investigated using the PSII crystal structure analyzed at 1.9-angstrom resolution, while considering all possibilities for the Chld-containing P-D1/P-D2 pair, i.e., Chld/Chld, Chla/Chld, and Chld/Chla pairs. Chld/Chld and Chla/Chld pairs resulted in a large P-D1(.+) population relative to P-D2(.+) as identified in Chla/Chla homodimer pairs in PSII from other species. e.g. Thermosynechococcus elongatus PSII. However, the Chld/Chla pair possessed a P-D1(.+)/P-D2(.+) ratio of approximately 50/50, which is in contrast to previous spectroscopic studies on A. marina PSII. The present results strongly exclude the possibility that the Chld/Chla pair serves as P-D1/P-D2 in A marina PSII. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2011.12.003

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In photosynthesis, cyanobacteria, algae and plants fix carbon dioxide (CO2) into carbohydrates; this is necessary to support life on Earth. Over 50 years ago, Otto Heinrich Warburg discovered a unique stimulatory role of CO2 in the Hill reaction (i.e., O-2 evolution accompanied by reduction of an artificial electron acceptor), which, obviously, does not include any carbon fixation pathway; Warburg used this discovery to support his idea that O-2 in photosynthesis originates in CO2. During the 1960s, a large number of researchers attempted to decipher this unique phenomenon, with limited success. In the 1970s, Alan Stemler, in Govindjee's lab, perfected methods to get highly reproducible results, and observed, among other things, that the turnover of Photosystem II (PSII) was stimulated by bicarbonate ions (hydrogen carbonate): the effect would, be on the donor or the acceptor, or both sides of PSII. In 1975, Thomas Wydrzynski, also in Govindjee's lab, discovered that there was a definite bicarbonate effect on the electron acceptor (the plastoquinone) side of PSII. The most recent 1.9 angstrom crystal structure of PSII, unequivocally shows HCO3- bound to the non-heme iron that sits in-between the bound primary quinone electron acceptor, Q(A), and the secondary quinone electron acceptor Q(B). In this review, we focus on the historical development of our understanding of this unique bicarbonate effect on the electron acceptor side of PSII, and its mechanism as obtained by biochemical, biophysical and molecular biological approaches in many laboratories around the World. We suggest an atomic level model in which HCO3-/CO32- plays a key role in the protonation of the reduced Q(B). In addition, we make comments on the role of bicarbonate on the donor side of PSII, as has been extensively studied in the labs of Alan Stemler (USA) and Vyacheslav Klimov (Russia). We end this review by discussing the uniqueness of bicarbonate's role in oxygenic photosynthesis and its role in the evolutionary development of O-2-evolving PSII. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. (C) 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2012.04.003

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The water-splitting protein, photosystem II, catalyzes the light-driven oxidation of water to dioxygen. The solar water oxidation reaction takes place at the catalytic center, referred to as the oxygen-evolving complex, of photosystem II. During the catalytic cycle, the oxygen-evolving complex cycles through five distinct intermediate states, S-0-S-4. In this study, we trap the oxygen-evolving complex in the S-2 intermediate state by low temperature illumination of photosystem II isolated from three different species, Thermosynechococcus vulcanus, the PsbB variant of Synechocystis PCC 6803 and spinach. We apply two-dimensional hyperfine sublevel correlation spectroscopy to detect weak magnetic interactions between the paramagnetic tetra-nuclear manganese cluster of the S-2 state of the OEC and the surrounding protons. We identify five groups of protons that are interacting with the tetra-nuclear manganese cluster. From the values of hyperfine interactions and using the recently reported 1.9 angstrom resolution X-ray structure of the OEC in the S-1 state [Umena et al., Nature, 2011, 473, 55], we discuss the assignments of the five groups of protons and draw important conclusions on the structure of the oxygen-evolving complex in the S-2 state. In addition, we conclude that the structure of OEC is nearly identical in photosystem II from Thermosynechococcus vulcanus, the PsbB variant of Synechocystis PCC 6803 and spinach.

DOI： 10.1039/c2ee21210b

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Influence of the axial ligand of P-D1 chlorophyll (D1-His-198) on the E-m of monomer chlorophylls P-D1 and P-D2, and the P-D1(center dot+)/P-D2(center dot+) charge ratio was investigated by theoretical calculations using the PSII crystal structure of Thermosynechococcus vulcanus analyzed at 1.9-angstrom resolution. It was found that the Em(P-D1)/E-m(P-D2) values and P-D1(center dot+)/P-D2(center dot+) ratio remained unchanged upon D1-H198Q mutation. However, Em(PD1) was increased in the D1-H198A mutant, resulting in a more even distribution of the positive charge over P-D1/P-D2. Introduction of a water molecule as an axial ligand resulted in equal E-m values and P-D1(center dot+)/P-D2(center dot+) ratios between the mutant and wild-type, thus confirming the presence of the water ligand in the mutant.

DOI： 10.1016/j.bpj.2012.04.016

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The crystal structure of Photosystem II (PSII) analyzed at a resolution of 1.9 angstrom revealed deformations of chlorin rings in the chlorophylls for the first time. We investigated the degrees of chlorin ring deformation and factors that contributed to them in the PSII crystal structure, using a normal-coordinate structural decomposition procedure. The out-of-plane distortion of the Pm chlorin ring can be described predominantly by a large "doming mode" arising from the axial ligand, D1-His198, as well as the chlorophyll side chains and PSII protein environment. In contrast, the deformation of P-D2 was caused by a "saddling mode" arising from the D2-Trp191 ring and the doming mode arising from D2-His197. Large ruffling modes, which were reported to lower the redox potential in heme proteins, were observed in P-D1 and Chl(D1), but not in P-D2 and ChlD(2). Furthermore, as P-D1 possessed the largest doming mode among the reaction center chlorophylls, the corresponding bacteriochlorophyll P-L possessed the largest doming mode in bacterial photosynthetic reaction centers. However, the majority of the redox potential shift in the protein environment was determined by the electrostatic environment. The difference in the chlorin ring deformation appears to directly refer to the difference in "the local steric protein environment" rather than the redox potential value in PSII.

DOI： 10.1021/bi300428s

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

DOI： 10.2142/biophys.52.S63_1

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DOI： 10.2142/biophys.52.S62_4

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DOI： 10.1039/c2dt31420g

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The crystal structure of photosystem IT (PSII) analyzed at a resolution of 1.9 A revealed a remarkably short H-bond between redox-active tyrosine Y-z and D1-His190 (2.46 angstrom donor-acceptor distance). Using large-scale quantum mechanical/molecular mechanical (QM/MM) calculations with the explicit PSII protein environment, we were able to reproduce this remarkably short H-bond in the original geometry of the crystal structure in the neutral [YzO center dot center dot center dot H center dot center dot center dot N-e-His-N delta H center dot center dot center dot O=Asn] state, but not in the oxidized states, indicating that the neutral state was the one observed in the crystal structure. In addition to the appropriate redox/protonation state of Y-z and D1-His190, we found that the presence of a cluster of water molecules played a key role in shortening the distance between Y-z and D1-His190. The orientations of the water molecules in the cluster were energetically stabilized by the highly polarized PSII protein environment, where the Ca ion of the oxygen-evolving complex (OEC) and the OEC ligand D1-Glu189 were also involved.

DOI： 10.1021/bi201366j

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The reaction center chlorophylls a (Chla) of photosystem II (PSII) are composed of six Chla molecules including the special pair Chla P-D1/P-D2 harbored by the D1/D2 heterodimer. They serve as the ultimate electron abstractors for water oxidation in the oxygen-evolving Mn4CaO5 cluster. Using the PSII crystal structure analyzed at 1.9 angstrom resolution, the redox potentials of P-D1/center dot P-D2 for one-electron oxidation (E-m) were calculated by considering all PSII subunits and the protonation pattern of all titratable residues. The Em(Chla) values were calculated to be 1015-1132 mV for P-D1 and 1141-1201 mV for P-D2, depending on the protonation state of the Mn4CaO5 cluster. The results showed that Em(P-D1) was lower than E-m(P-D2) P-D2 favoring localization of the charge of the cationic state more on P-D1. The P-D1(center dot+)/P-D2(center dot+) charge ratio determined by the large-scale QM/MM calculations with the explicit PS II protein environment yielded a P-D1(center dot+)/P-D2(center dot+) ratio of similar to 80/similar to 20, which was found to be due to the asymmetry in electrostatic characters of several conserved D1/D2 residue pairs that cause the E-m(P-D1)/E-m(P-D2) difference, e.g., Dl -Asn181/D2-Argl 80, D1-Asn298/D2-Arg294, D1-Asp61/D2-His61, D1-Glu189/D2-Phe188, and D1-Asp170/D2-Phe169. The larger P-D1(center dot+) population than P-D2(center dot+) appears to be an inevitable fate of the intact PSII that possesses water oxidation activity.

DOI： 10.1021/ja203947k

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The catalytic center for photosynthetic water-splitting consists of 4 Mn atoms and 1 Ca atom and is located near the lumenal surface of photosystem II. So far the structure of the Mn4Ca-cluster has been studied by a variety of techniques including X-ray spectroscopy and diffraction, and various structural models have been proposed. However, its exact structure is still unknown due to the limited resolution of crystal structures of PSII achieved so far, as well as possible radiation damages that might have occurred. Very recently, we have succeeded in solving the structure of photosystem II at 1.9 angstrom. which yielded a detailed picture of the Mn4CaO5-cluster for the first time. In the high resolution structure, the Mn4CaO5-cluster is arranged in a distorted chair form, with a cubane-like structure formed by 3 Mn and 1 Ca, 4 oxygen atoms as the distorted base of the chair, and 1 Mn and 1 oxygen atom outside of the cubane as the back of the chair. In addition, four water molecules were associated with the cluster, among which, two are associated with the terminal Mn atom and two are associated with the Ca atom. Some of these water molecules may therefore serve as the substrates for water-splitting. The high resolution structure of the catalytic center provided a solid basis for elucidation of the mechanism of photosynthetic water splitting. We review here the structural features of the Mn4CaO5-cluster analyzed at 1.9 angstrom resolution, and compare them with the structures reported previously. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.jphotobiol.2011.03.017

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We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S-1 Mn-4(IV,III,IV,III) state, where Ca2+ is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 1.9 angstrom resolution. The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals. Our results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting.

DOI： 10.1021/bi200681q

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Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 angstrom resolution. We find that chloride depletion induces formation of a salt bridge between D2-K317 and D1-D61 that could suppress the transfer of protons to the lumen.

DOI： 10.1021/bi200685w

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

Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 angstrom. These resolutions have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting. Here we report the crystal structure of photosystem II at a resolution of 1.9 angstrom. From our electron density map, we located all of the metal atoms of the Mn4CaO5 cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn4CaO5 cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water molecules in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. The determination of the high-resolution structure of photosystem II will allow us to analyse and understand its functions in great detail.

DOI： 10.1038/nature09913

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

UB3LYP calculations were first performed to elucidate electronic and spin structures of the CaMn4O5 cluster in the oxygen-evolving-complex of the PSII system refined to the 1.9 angstrom X-ray resolution by Kamiya, Shen, and their collaborators. Eight different UB3LYP solutions with axial spin structures were constructed to obtain the energy levels of the cluster on the basis of their X-ray structure. The energy diagrams were analyzed in terms of the Heisenberg model that involves six effective-exchange integrals between manganese ions. Several characteristic features of the electronic states of the cluster are revealed from these theoretical investigations based on the UB3LYP calculations. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2011.02.030

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The oxidation of a redox-active tyrosine residue Y-Z in photosystem II (PSII) is coupled with proton transfer to a hydrogen-bonded D1-His190 residue. Because of the apparent proximity of Y-Z to: the water-oxidizing complex and its redox activity, it is believed that Y-Z plays a significant role in water oxidation in PSII. We investigated the g-anisotropy of the tyrosine radical Y-Z(center dot) to provide insight into the mechanism of Y-Z(center dot) proton-coupled electron transfer in Nth-depleted PSII. The anisotropy was highly resolved by electron paramagnetic resonance spectroscopy at the W-band (94.9 GHz) using PSII single crystals. The g(x)-component along the phenolic C-O bond of Y-Z(center dot) was calculated by density functional theory (DFT). It was concluded from the highly resolved g-anisotropy that Y-Z loses a phenol proton to D1-His190 upon tyrosine oxidation, and D1-His190 redonates the same proton back to Y-Z(center dot) upon reduction.

DOI： 10.1021/ja2000566

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

PsbM and PsbI are two low molecular weight subunits of photosystem II (PSII), with PsbM being located in the center, and PsbI in the periphery, of the PSII dimer. In order to study the functions of these two subunits from a structural point of view, we crystallized and analyzed the crystal structure of PSII dimers from two mutants lacking either PsbM or PsbI. Our results confirmed the location of these two subunits in the current crystal structure, as well as their absence in the respective mutants. The relative contents of PSII dimers were found to be decreased in both mutants, with a concomitant increase in the amount of PSII monomers, suggesting a destabilization of PSII dimers in both of the mutants. On the other hand, the accumulation level of the overall PSII complexes in the two mutants was similar to that in the wild-type strain. Treatment of purified PSII dimers with lauryldimethylamine N-oxide at an elevated temperature preferentially disintegrated the dimers from the PsbM deletion mutant into monomers and CP43-less monomers, whereas no significant degradation of the dimers was observed from the PsbI deletion mutant. These results indicate that although both PsbM and PsbI are required for the efficient formation and stability of PSII dimers in vivo, they have different roles, namely, PsbM is required directly for the formation of dimers and its absence led to the instability of the dimers accumulated. On the other hand, PsbI is required in the assembly process of PSII dimers in vivo: once the dimers are formed. PsbI was no longer required for its stability. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2010.12.013

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

An oxygen-evolving photosynthetic reaction center complex (PSII) was adsorbed into nanopores in SBA, a mesoporous silica compound. We purified the dimer of PSII complex from a thermophilic cyanobacterium, Thermosynechococcus vulcanus, which grows optimally at 57 degrees C. The thermally stable PSII dimeric complex has a diameter of 20 nm and a molecular mass of 756 kDa and binds more than 60 chlorophylls. The SBA particles, with average internal pore diameters of 15 nm (SBA(15)) and 23 nm (SBA(23)), adsorbed 4.7 and 15 mg of PSII/g SBA, respectively. Measurement with a confocal laser-scanning microscope indicated the adsorption of PSII to the surface and the inner space of the SBA(23) particles, indicating the adsorption of PSII into the 23 nm silica nanopores. PSII did not bind to the inner pores of SBA(15). PSII bound to SBA(23) showed the high and stable activity of a photosynthetic oxygen-evolving reaction, indicating the light-driven electron transport from water to the quinone molecules added in the outer medium. The PSII-SBA conjugate can be a new material for photosensors and artificial photosynthetic systems.

DOI： 10.1021/la1032916

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

We describe methods to isolate highly active oxygen-evolving photosystem II (PSII) membranes and core complexes from higher plants, and to purify subunits of the oxygen-evolving complex (OEC). The membrane samples used as the material for various in vitro studies of PSII are prepared by solubilizing thylakoid membranes with the nonionic detergent Triton X-100, and the core complexes are prepared by further solubilization of the PSII membranes with n-dodecyl-β-D-maltoside (β-DDM). The OEC subunit proteins are dissociated from the PSII-enriched membranes by alkaline or salt treatment, and are then purified by ion-exchange chromatography using an automated high performance liquid chromatography system.

DOI： 10.1007/978-1-60761-925-3_1

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This chapter describes the purification and crystallization of oxygen-evolving photosystem II core dimer complex from a thermophilic cyanobacterium Thermosynechococcus vulcanus. Procedures used for purification of photosystem II from the cyanobacterium involves cultivation of cells, isolation of thylakoid membranes, purification of crude and pure photosystem II core complexes by detergent solubilization, followed by differential centrifugation and column chromatography. The purified core dimer particles were successfully used for crystallization, and the methods and conditions used for crystallization are presented. These purification and crystallization procedures can be applied for another thermophilic cyanobacterium T. elongatus.

DOI： 10.1007/978-1-60761-925-3_5

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

DOI： 10.2142/biophys.51.S95_2

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

DOI： 10.2142/biophys.51.S10_1

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

Oxygen-evolving photosystem II (PSII) isolated from a marine centric diatom, Chaetoceros gracilis, contains a novel extrinsic protein (Psb31) in addition to four red algal type extrinsic proteins of PsbO, PsbQ', PsbV, and PsbU. In this study, the five extrinsic proteins were purified from alkaline Tris extracts of the diatom PSII by anion and cation exchange chromatographic columns at different pH values. Reconstitution experiments in various combinations with the purified extrinsic proteins showed that PsbO, PsbQ', and Psb31 rebound directly to PSII in the absence of other extrinsic proteins, indicating that these extrinsic proteins have their own binding sites in PSII intrinsic proteins. On the other hand, PsbV and PsbU scarcely rebound to PSII alone, and their effective bindings required the presence of all of the other extrinsic proteins. Interestingly, PSII reconstituted with Psb31 alone considerably restored the oxygen evolving activity in the absence of PsbO, indicating that Psb31 serves as a substitute in part for PsbO in supporting oxygen evolution. A significant difference found between PSIIs reconstituted with Psb31 and with PsbO is that the oxygen evolving activity of the former is scarcely stimulated by Cl- and Ca2+ ions but that of the latter is largely stimulated by these ions, although rebinding of PsbV and PsbU activated oxygen evolution in the absence of Cl- and Ca2+ ions in both the former and latter PSIIs. Based on these results, we proposed a model for the association of the five extrinsic proteins with intrinsic proteins in diatom PSII and compared it with those in PSIIs from the other organisms.

DOI： 10.1074/jbc.M110.146092

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

The close association of the extrinsic PsbO, PsbP and PsbQ proteins with PSII core subunits in oxygen-evolving PSII complexes from a green alga, Chlamydomonas reinhardtii, was examined by cross-linking experiments with a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). The green algal PSII complexes treated with EDC were washed with alkaline Tris to remove the non-cross-linked extrinsic proteins, and then applied to Blue-Native-PAGE to prepare PSII core complexes. The extrinsic proteins cross-linked with PSII core complexes were detected by immunoblotting analysis using antibodies against extrinsic proteins and PSII core subunits. The results showed that the PsbO, PsbP and PsbQ proteins directly associated with CP47, the subunit of cytochrome b559 and a small subunit in PSII core complexes, respectively, through electrostatic interactions. In addition, a cross-linked product between the PsbP and PsbQ proteins was found in alkaline Tris extracts of EDC-treated PSII complexes, and its cross-linked site was examined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS) after digestions with trypsin and endoproteinase Asp-N. The results demonstrated that the positively charged amino group of K176 on the PsbP protein electrostatically interacts with the negatively charged carboxyl group of D28 on the PsbQ protein. These binding properties of the extrinsic proteins in the green algal PSII were compared with those in higher plant PSII.

DOI： 10.1093/pcp/pcq042

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Ycf12 (Psb30) and PsbZ are two low molecular weight subunits of photosystem II (PSII), with one and two trans-membrane helices, respectively. In order to study the functions of these two subunits from a structural point of view, we constructed deletion mutants lacking either Ycf12 or PsbZ from Thermosynechococcus elongatus, and purified, crystallized and analyzed the structure of PSII dimer from the two mutants. Our results showed that Ycf12 is located in the periphery of PSII, close to PsbK, PsbZ and PsbJ, and corresponded to the unassigned helix XI reported previously, in agreement with the recent structure at 2.9 angstrom resolution (A. Guskov, J. Kern. A. Gabdulkhakov, M. Broser, A. Zouni, W. Saenger, Cyanobacterial photosystem II at 2.9 angstrom resolution: role of quinones, lipids, channels and chloride, Nat Struct. Mol. Biol. 16 (2009) 334-342). On the other hand, crystals of PsbZ-deleted PSII showed a remarkably different unit cell constants from those of wild-type PSII, indicating a role of PsbZ in the interactions between PSII dimers within the crystal. This is the first example for a different arrangement of PSII dimers within the cyanobacterial PSII crystals. PSII dimers had a lower oxygen-evolving activity from both mutants than that from the wild type. In consistent with this, the relative content of PSII in the thylakoid membranes was lower in the two mutants than that in the wild type. These results suggested that deletion of both subunits affected the PSII activity, thereby destabilized PSII, leading to a decrease in the PSII content in vivo. While PsbZ was present in PSII purified from the Ycf12-deletion mutant, Ycf12 was present in crude PSII but absent in the finally purified PSII from the PsbZ-deletion mutant, indicating a preferential, stabilizing role of PsbZ for the binding of Ycf12 to PSII. These results were discussed in terms of the PSII crystal structure currently available. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2009.11.001

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Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S0108767310097291

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Language：English   Publisher：Springer  

DOI： 10.1007/978-90-481-3795-4_20

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

The chloride ion, Cl-, is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn4Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl- with a bromide ion (Br-) or an iodide ion (I-) in PSII and analyzed the crystal structures of PSII with Br- and I- substitutions. Substitution of Cl- with Br- did not inhibit oxygen evolution, whereas substitution of Cl- with I- completely inhibited oxygen evolution, indicating the efficient replacement of Cl- by I-. PSII with Br- and I- substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn4Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn4Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl- anions are required to maintain the coordination structure of the Mn4Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.

DOI： 10.1073/pnas.0812797106

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Tyrosine Z (Tyr(Z)) oxidation observed at liquid helium temperatures provides new insights into the structure and function of Tyr(Z) in active Photosystem II (PSII). However, it has not been reported in PSII core complex from higher plants. Here, we report Tyr(Z) oxidation in the S(1) and S(2) states in PSII core complex from spinach for the first time. Moreover, we identified a 500 G-wide symmetric EPR signal (peak position g = 2.18, trough position g = 1.85) together with the g = 2.03 signal induced by visible light at 10 K in the S(1) state in the PSII core complex. These two signals decay with a similar rate in the dark and both disappear in the presence of 6% methanol. We tentatively assign this new feature to the hyperfine structure of the S(1)Tyr(Z)(*) EPR signal. Furthermore, EPR signals of the S(2) state of the Mn-cluster, the oxidation of the non-heme iron, and the S(1)Tyr(Z)(*) in PSII core complexes and PSII-enriched membranes from spinach are compared, which clearly indicate that both the donor and acceptor sides of the reaction center are undisturbed after the removal of LHCII. These results suggest that the new spinach PSII core complex is suitable for the electron transfer study of PSII at cryogenic temperatures.

DOI： 10.1007/s11120-009-9410-x

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

Crystal structure of photosystem II (PSII) has been reported from prokaryotic cyanobacteria but not from any eukaryotes. In the present study, we improved the purification procedure of PSII dimers from an acidophilic, thermophilic red alga Cyanidium caldarium, and crystallized them in two forms tinder different crystallization conditions. One had a space group of P222(1) with unit cell constants of a = 146.8 angstrom, b = 176.9 angstrom, and c = 353.7 angstrom. and the other one had a space group of P2(1)2(1)2(1) with unit cell constants of a = 209.2 angstrom, b = 237.5 angstrom, and c = 299.8 angstrom. The unit cell constants of both crystals and the space group of the first-type crystals are different from those of cyanobacterial crystals, which may reflect the structural differences between the red algal and cyanobacterial PSII, as the former contains a fourth extrinsic protein of 20 kDa. X-ray diffraction data were collected and processed to a 3.8 angstrom resolution with the first type crystal. For the second type crystal, a post-crystallization treatment of dehydration was employed to improve the resolution, resulting in a diffraction data of 3.5 angstrom resolution. Analysis of this type of crystal revealed that there are 2 PSII dimers in each asymmetric unit, giving rise to 16 PSII monomers in each unit cell, which contrasts to 4 dimers per unit cell in cyanobacterial crystals. The molecular packing of PSII within the unit cell was constructed with the molecular replacement method and compared with that of the cyanobacterial crystals. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2008.11.004

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

DOI： 10.2142/biophys.49.S142_2

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

DOI： 10.2142/biophys.49.S60_6

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

Lipids are important components of transmembrane protein complexes. In order to study the roles of lipids in photosystem II (PSII), we treated the PSII core dimer complex from a thermophilic cyanobacterium Thermosynechococcus vulcanus with phospholipase A(2) (PLA(2)) and lipase, and examined their effects on PSII structure and function. PLA(2)-treatment decreased the content of phospholipid, phosphatidylglycerol (PG) by 59%, leading to a decrease of oxygen evolution by 40%. On the other hand, although treatment with lipase specifically decreased the content of monogalactosyldiacylglycerol (MGDG) by 52%, it decreased oxygen evolution only by 16%. This indicates that PG plays a more important role in PSII than MGDG. Both PLA(2)- and lipase-treatments induced neither the dissociation of PSII dimer, nor any loss of polypeptides. The degradation of PG resulted in a damage to the Q(B)-binding site as demonstrated from photoreduction activity of 2,6-dichlorophenolindophenol and chlorophyll fluorescence yields in the absence or presence of 3-(3,4-dichlorophenyl)1,1-dimethylurea, and the dependencies of oxygen evolution on various electron acceptors before and after PLA(2)- or lipase-treatments. However, there were approximately three and five molecules of PG and MGDG per PSII reaction center left in the PSII dimeric complex after the PLA(2)- and lipase-treatments. These lipids are therefore bound to the interior of the protein matrix and resistant to the lipase treatments. The resistance of these lipids against PLA(2)- and lipase-treatments may be a specific feature of PSII from the thermophilic cyanobacterium, suggesting a possible correlation between binding of lipids and thermostability of PSII.

DOI： 10.1007/s11120-008-9335-9

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Language：English   Publisher：SPRINGER  

This minireview presents a summary of information available on the variety and binding properties of extrinsic proteins that form the oxygen-evolving complex of photosystem II (PSII) of cyanobacteria, red alga, diatom, green alga, euglena, and higher plants. In addition, the structure and function of extrinsic PsbO, PsbV, and PsbU proteins are summarized based on the crystal structure of thermophilic cyanobacterial PSII together with biochemical and genetic studies from various organisms.

DOI： 10.1007/s11120-008-9343-9

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Language：English   Publishing type：Part of collection (book)   Publisher：Wiley-VCH Verlag GmbH &amp; Co. KGaA  

DOI： 10.1002/9783527623464.ch4

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