Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn
O
cluster with and without water insertion in the S
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
state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn
Ca cluster. The optimized Mn
-Mn
distance determined by QM/MM was about 5.0 Å for the S
structure without an inserted hydroxide anion, but this is elongated by 0.2-0.3 Å after insertion. These computational results are discussed in relation to the possible mechanisms of O-O bond formation in water oxidation by the OEC of PSII.
Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn
4
O
5
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 Mn
4
Ca cluster. The optimized Mn
a(4)
-Mn
d(1)
distance determined by QM/MM was about 5.0 Å for the S
3
structure without an inserted hydroxide anion, but this is elongated by 0.2-0.3 Å after insertion. These computational results are discussed in relation to the possible mechanisms of O-O bond formation in water oxidation by the OEC of PSII.
Photosystem II (PSII) is a huge membrane-protein complex which catalyzes light-driven water-oxidationreaction at its catalytic center, the oxygen evolving complex (OEC). The crystal structure of PSII ...hasbeen determined at 1.9 Å resolution using synchrotron radiation which revealed that the OEC is aMn4CaO5 cluster. Some of the manganese atoms of the OEC are, however, rapidly reduced by X-rayirradiation which results in slight elongation of the distances between manganese cations. Furthermore,high-resolution 3D structural information is only limited to the dark-stable S1 state and the structures inthe other intermediate states are missing. X-ray free electron laser (XFEL) has the potential to addressthese unsolved problems, and unveil the water-splitting reaction mechanism of PSII. In this review, wewill introduce the analyses of the damage-free structure and an intermediate structure of PSII usingXFEL, demonstrating the potential to obtain high spatial resolution of biological samples by XFEL.
Oxygenic photosynthesis synthesizes sugars from water and carbon dioxide using light energy from the sun, thereby converts light energy into chemical energy and provides oxygen for aerobic life on ...the earth. The light-harvesting, electron transfer, and water-splitting reactions of photosynthesis are catalyzed by two large membrane-protein complexes photosystem II (PSII) and photosystem I (PSI). Through high-resolution crystal structural analysis by synchrotron X-rays as well as femtosecond X-ray free electron lasers, the mechanisms of these reactions have become understandable at the atomic level. Here we review the recent progresses in analyzing the structures of PSII and PSI as well as their functional implications.
Pyrococcus furiosus is a hyperthermophilic archaeal microorganism found near deep-sea thermal vents and its optimal growth temperature of 100 °C. Recently, a 38.8-kDa protein from
P. furiosus DSM ...3638 was isolated and characterized. Electron microscopy revealed that this protein aggregated as spheres of approximately 30 nm in diameter, which we designated
P. furiosus virus-like particles (PfVs). X-ray crystallographic analysis at 3.6-Å resolution revealed that each PfV consisted of 180 copies of the 38.8-kDa protein and retained
T
=
3 icosahedral symmetry, as is often the case in spherical viruses. The total molecular mass of each particle was approximately 7 MDa. An examination of capsid structures suggested strong evolutionary links among PfV, tailed double-stranded DNA bacteriophages, and herpes viruses. The similar three-dimensional structures of the various coat proteins indicate that these viral capsids might have originated and evolved from a common ancestor. The structure of PfV provides a previously undescribed example of viral relationships across the three domains of life (Eukarya, Bacteria, and Archaea).
Abstract The Chi and W strains of Melon necrotic spot virus (MNSV) are efficiently transmitted by isolates Y1 and NW1, respectively, of the fungal vector Olpidium bornovanus . Analysis of chimeric ...viruses constructed by switching the coat protein (CP) gene between the two strains unveiled the involvement of the CP in the attachment of MNSV to zoospores of a compatible isolate of O. bornovanus and in the fungal transmission of the virus. Furthermore, analysis of the chimeric virus based on the Chi strain with the protruding domain of the CP from strain W suggested the involvement of the domain in compatibility with zoospore. Comparison of the three-dimensional structures between the CP of the two MNSV strains showed that many of the differences in these amino acid residues are present on the surface of the virus particles, suggesting that these affects the recognition of fungal vectors by the virus.
Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of S
states (i = 0-4) at the Mn
CaO
cluster
, during which an extra oxygen (O6) is incorporated at the S
state to form ...a possible dioxygen
. 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). Y
, a tyrosine residue that connects the reaction centre P680 and the Mn
CaO
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 Ca
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.
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