Hiroshi Ishikita

In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two

The crystal structure of photosystem II (PSII) at 3.0-A resolution suggests that titratable residues on the lumenal side of D1/D2 and PsbO form a polar channel, which might serve as a proton exit pathway associated with water oxidation on the Mn-cluster. With full account of protein environment, we calculated the pK(a) of these residues by solving the linearized Poisson-Boltzmann equation. Along the prospective proton channel, the calculated pK(a) of titratable residues (namely via D1-Asp61, D1-

At the heart of photosynthetic reaction centers (RCs) are pairs of chlorophyll a (Chla), P700 in photosystem I (PSI) and P680 in photosystem II (PSII) of cyanobacteria, algae, or plants, and a pair of bacteriochlorophyll a (BChla), P870 in purple bacterial RCs (PbRCs). These pairs differ greatly in their redox potentials for one-electron oxidation, E(m). For P680, E(m) is 1,100-1,200 mV, but for P700 and P870, E(m) is only 500 mV. Calculations with the linearized Poisson-Boltzmann equation repro

The redox potentials of the two electron transfer (ET) active quinones in the central part of photosystem I (PSI) were determined by evaluating the electrostatic energies from the solution of the Poisson-Boltzmann equation based on the crystal structure. The calculated redox potentials are -531 mV for A1A and -686 mV for A1B. From these results we conclude the following. (i) Both branches are active with a much faster ET in the B-branch than in the A-branch. (ii) The measured lifetime of 200-290

In O(2)-evolving complex Photosystem II (PSII), an unimpeded transfer of electrons from the primary quinone (Q(A)) to the secondary quinone (Q(B)) is essential for the efficiency of photosynthesis. Recent PSII crystal structures revealed the protein environment of the Q(A/B) binding sites. We calculated the plastoquinone (Q(A/B)) redox potentials (E(m)) for one-electron reduction with a full account of the PSII protein environment. We found two different H-bond patterns involving Q(A) and D2-Thr

Water oxidation generating atmospheric oxygen occurs in photosystem II (PSII), a large protein-pigment complex located in the thylakoid membrane. The recent crystal structures at 3.2 and 3.5 A resolutions provide novel details on amino acid side chains, especially in the D1/D2 subunits. We calculated the redox potentials for one-electron oxidation of the chlorophyll a (Chla) molecules in PSII, considering the protein environment in atomic detail. The calculated redox potentials for the dimer Chl

The mechanism for tyrosyl radical generation in the [Re(P-Y)(phen)(CO)3]PF6 complex is investigated with a multistate continuum theory for proton-coupled electron transfer (PCET) reactions. Both water and the phosphate buffer are considered as potential proton acceptors. The calculations indicate that the model in which the proton acceptor is the phosphate buffer species HPO(4)2- can successfully reproduce the experimentally observed pH dependence of the overall rate and H/D kinetic isotope effe

We report redox potentials (<i>E</i>_m) for one-electron reduction for all chlorophylls in the two electron-transfer branches of water-oxidizing enzyme photosystem II (PSII), photosystem I (PSI), and purple bacterial photosynthetic reaction centers (PbRC). In PSI, <i>E</i>_m values for the accessory chlorophylls were similar in both electron-transfer branches. In PbRC, the corresponding <i>E</i>_m value was 170 mV less negative in the active L-branch (B_L)

In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the

The absolute values of the one-electron redox potentials of the two quinones (Q(A) and Q(B)) in bacterial photosynthetic reaction centers from Rhodobacter sphaeroides were calculated by evaluating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation at pH 7.0. The redox potential for Q(A) was calculated to be between -173 and -160 mV, which is close to the lowest measured values that are assumed to refer to nonequilibrated protonation patterns in the redox st

Ser-L223 is close to ubiquinone (Q(B)) in the B-branch of the bacterial photosynthetic reaction center (bRC) from Rhodobacter (Rb) sphaeroides. Therefore, the presence of a hydrogen bond (H bond) between the two was naturally proposed from the crystal structure. The hydrogen bonding pattern of Q(B) from the light-exposed structure was studied by generating hydrogen atom coordinates based on the CHARMM force field. In the Q(B) neutral charge state (Q(B)(0)), no H bond was found between the oxygen

In photosystem II (PSII), water oxidation occurs in the Mn₄CaO₅ cluster with the release of electrons via the redox-active tyrosine (TyrZ) to the reaction-center chlorophylls (P_D1/P_D2). Using a quantum mechanical/molecular mechanical approach, we report the redox potentials (<i>E</i>_m) of these cofactors in the PSII protein environment. The <i>E</i>_m values suggest that the Mn₄CaO₅ cluster, TyrZ, and P<sub>D1

The crystal structure of the ammonia transport (Amt) protein AmtB at 1.4 Angstrom resolution revealed four ammonia/ammonium (NH(3)/NH(4)(+)) binding sites along the approximately 20 Angstrom narrow pore. It is an open question whether the bound NH(3)/NH(4)(+) are neutral (NH(3)) or cationic (NH(4)(+)). On the basis of the AmtB crystal structure, we calculated the pK(a) of these four NH(3)/NH(4)(+) by solving the Poisson-Boltzmann equation. Except for one NH(3)/NH(4)(+) binding site (Am1) at the