Keisuke Saito

Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, Q(A) and Q(B), working in series. Q(A) is a one-electron carrier, whereas Q(B) undergoes sequential reduction and protonation to form Q(B)H(2). Q(B)H(2) exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical a

In photosystem II (PSII), the Mn4CaO5 cluster catalyses the water splitting reaction. The crystal structure of PSII shows the presence of a hydrogen-bonded water molecule directly linked to O4. Here we show the detailed properties of the H-bonds associated with the Mn4CaO5 cluster using a quantum mechanical/molecular mechanical approach. When O4 is taken as a μ-hydroxo bridge acting as a hydrogen-bond donor to water539 (W539), the S0 redox state best describes the unusually short O4-OW539 distan

The crystal structure of photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed a remarkably short H-bond between redox-active tyrosine Y(Z) and D1-His190 (2.46 Å 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 [Y(Z)O···H···N(ε)-His-N(δ)H···O═Asn] state, but not in the

Identifying the p<i>K</i>_a values of aspartic acid (Asp) and glutamic acid (Glu) in active sites is essential for understanding enzyme reaction mechanisms. In this study, we investigated the correlation between the C═O stretching vibrational frequency (ν_C═O) of protonated carboxylic acids and the p<i>K</i>_a values using density functional theory calculations. In unsaturated carboxylic acids (e.g., benzoic acid analogues), ν_C═O decreases as the p<i>K</i

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 Mn(4)CaO(5) cluster. Using the PSII crystal structure analyzed at 1.9 Å resolution, the redox potentials of P(D1)/P(D2) for one-electron oxidation (E(m)) were calculated by considering all PSII subunits and the protonation patte

High-resolution X-ray diffraction reciprocal space mapping (HRXRD-RSM) was applied for the structural characterization of epitaxial BiFeO3 thin film grown on SrRuO3-coated (001) SrTiO3 single crystal substrate with a variety of film thicknesses ranging from 15 to 500 nm. Distinguishing monoclinic structure from rhombohedral or tetragonal structures was accomplished with a set of HRXRD-RSMs measured for several hkl diffraction conditions. The BiFeO3 thin films showed both monoclinic and tetragona

This paper investigates the performance and design of successive interference cancellation (SIC) receiver for downlink non-orthogonal multiple access (NOMA) combined with 2-by-2 open-loop single-user (SU)-MIMO. Compared to NOMA with 1-by-2 SIMO (Single Input Multiple Output), for NOMA with 2-by-2 SU-MIMO we have to deal with both inter-user and interstream interference at the receiver of each user. Therefore, we introduce different weight generation schemes for both before SIC and after SIC acco

Using quantum mechanics/molecular mechanics calculations and the 1.9-Å crystal structure of Photosystem II [Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Nature 473(7345):55-60], we investigated the H-bonding environment of the redox-active tyrosine D (TyrD) and obtained insights that help explain its slow redox kinetics and the stability of TyrD(•). The water molecule distal to TyrD, located ~4 Å away from the phenolic O of TyrD, corresponds to the presence of the tyrosyl radical state. The wa

Remanent polarizations (Pr) of 200-nm-thick epitaxial Pb(Zr0.35,Ti0.65)O3 (PZT) thin films deposited on (001), (110), and (111) SrTiO3 (STO) substrates coated with SrRuO3 (SRO) were compared to the domain configurations that were precisely and quantitatively characterized by high-resolution x-ray diffraction reciprocal space mapping (HRXRD-RSM). (001)/(100), (101)/(110), and (111) oriented domains were obtained for films grown on (001), (110), and (111) STO substrates coated with SRO, respective

In the Sr–Bi–Ta–Nb–O system, three crystallographic phases are known to exist: the SrBi 2 (Ta 1- x Nb x )O 9 (SBTN) perovskite, fluorite and pyrochlore phases. It is considered that the fluorite phase is a low-temperature phase of SBT, which tends to grow in excess bismuth compositions, and the pyrochlore phase tends to grow in bismuth-deficient compositions. In conventional X-ray diffraction (XRD) characterization, the SBTN phase shows strong (115) diffraction around 29 [2θ deg]. Unfortunately,

Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK(a) calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (i) In the QM/MM optimized geometry, we reproduced

Recent studies have suggested an association between certain members of the Fusobacterium genus, especially F. nucleatum, and the progression of advanced colorectal carcinoma (CRC). We assessed such an association of the gut microbiota in Japanese patients with colorectal adenoma (CRA) or intramucosal CRC using colonoscopy aspirates. We analyzed samples from 81 Japanese patients, including 47 CRA and 24 intramucosal CRC patients, and 10 healthy subjects. Metagenomic analysis of the V3-V4 region