Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations.

At room temperature and neutral pH, the oxygen-evolving center (OEC) of photosystem II (PSII) catalyzes water oxidation. During this process, oxygen is released from the OEC, while substrate waters are delivered to the OEC and protons are passed from the OEC to the lumen through water channels known as the narrow or the O4 channel, broad or the Cl1 channel, and large or the O1 channel. Protein residues lining the surfaces of these channels play a critical role in stabilizing the hydrogen-bonding networks that assist in the process.

Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors.

The oxygen-evolving complex (OEC) of Photosystem II catalyzes the water-splitting reaction using solar energy. Thus, understanding the reaction mechanism will inspire the design of biomimetic artificial catalysts that convert solar energy to chemical energy. Conceptual Density Functional Theory (CDFT) focuses on understanding the reactivity of molecules and the atomic contribution to the overall nucleophilicity and electrophilicity of the molecule using quantum descriptors.

Electronic structure and energetics of a heterodimeric BChl '/Chl ' special pair generated by exposure of to dioxygen.

Heliobacteria are anoxygenic phototrophs that have a Type I homodimeric reaction center containing bacteriochlorophyll (BChl ). Previous experimental studies have shown that in the presence of light and dioxygen, BChl is converted into 8-OH-chlorophyll (hereafter Chl ), with an accompanying loss of light-driven charge separation. These studies suggest that the reaction center only loses the ability to transfer electrons once both BChl ' molecules of the P special pair have been converted to Chl '.

Comparison of proton transfer paths to the Q and Q sites of the Rb. sphaeroides photosynthetic reaction centers.

The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the Q site cycles between quinone, Q, and anionic semiquinone, Q, being reduced once and never binding protons. In the Q site, ubiquinone is reduced twice by Q, binds two protons and is released into the membrane as the quinol, QH.

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient.

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy.

Proton exit pathways surrounding the oxygen evolving complex of photosystem II.

Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a MnCaO inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen.

Identifying the proton loading site cluster in the ba cytochrome c oxidase that loads and traps protons.

Cytochrome c Oxidase (CcO) is the terminal electron acceptor in aerobic respiratory chain, reducing O to water. The released free energy is stored by pumping protons through the protein, maintaining the transmembrane electrochemical gradient. Protons are held transiently in a proton loading site (PLS) that binds and releases protons driven by the electron transfer reaction cycle.

Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I.

Complex I, NADH-ubiquinone oxidoreductase, is the first enzyme in the mitochondrial and bacterial aerobic respiratory chain. It pumps four protons through four transiently open pathways from the high pH, negative, N-side of the membrane to the positive, P-side driven by the exergonic transfer of electrons from NADH to a quinone. Three protons transfer through subunits descended from antiporters, while the fourth, E-channel is unique.

Thermodynamics of the S-to-S state transition of the oxygen-evolving complex of photosystem II.

The room temperature pump-probe X-ray free electron laser (XFEL) measurements used for serial femtosecond crystallography provide remarkable information about the structures of the catalytic (S-state) intermediates of the oxygen-evolution reaction of photosystem II. However, mixed populations of these intermediates and moderate resolution limit the interpretation of the data from current experiments. The S XFEL structures show extra density near the OEC that may correspond to a water/hydroxide molecule.

Photosystem II oxygen-evolving complex photoassembly displays an inverse H/D solvent isotope effect under chloride-limiting conditions.

Photosystem II (PSII) performs the solar-driven oxidation of water used to fuel oxygenic photosynthesis. The active site of water oxidation is the oxygen-evolving complex (OEC), a MnCaO cluster. PSII requires degradation of key subunits and reassembly of the OEC as frequently as every 20 to 40 min.

Relative stability of the S isomers of the oxygen evolving complex of photosystem II.

The oxidation of water to O is catalyzed by the Oxygen Evolving Complex (OEC), a MnCaO complex in Photosystem II (PSII). The OEC is sequentially oxidized from state S to S. The S state, (Mn)(Mn), coexists in two redox isomers: S, where Mn4 is Mn and S, where Mn1 is Mn.

A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.

As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host-guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye-Hückel treatment of salt effects were in good agreement with experimental measurements.