Koji Ogata

All-Atom Molecular Dynamics Simulation of Photosystem II Embedded in Thylakoid Membrane

The molecular dynamics simulation is reported. The latest data on photosystem II structure, a thylakoid membrane model with the same lipid class distribution and fatty acid composition as the native thylakoid membrane, are used. The results indicate that the transfer of water, oxygen and protons has different pathways. The root mean square (rms)-fluctuation analysis of trajectory revealed that the residues surrounding the oxygen-evolving center (OEC) show small fluctuations and that most of the water molecules there show large fluctuation and are on proposed pathways for water and oxygen transfer. The water molecules near the OEC having small fluctuation could be involved in proton transfer. We assume that each kind of pathway characterized in this study plays a role in photosynthesis.

Unrestricted Hartree-Fock based on the fragment molecular orbital method: Energy and its analytic gradient

A consideration of the surrounding environment is necessary for a meaningful analysis of the reaction activity in large molecular systems. We propose an approach to perform unrestricted Hartree-Fock (UHF) calculations within the framework of the fragment molecular orbital (FMO) method (FMO-UHF) to study large systems with unpaired electrons. Prior to an energy analysis one has to optimize geometry, which requires an accurate analytic energy gradient. We derive the FMO-UHF energy and its analytic gradient and implement them into GAMESS. The performance of FMO-UHF is evaluated for a solvated organic molecule and a solvated metal complex, as well as for the active part of a protein, in terms of energy, gradient, and geometry optimization.

Photochromism of 1,2-bis(2-thienyl)perfluorocyclopentene derivatives: substituent effect on the reactive carbon atoms.

In this work, we prepared a new 1,2-bis(3-cyanothiophen-2-yl)perfluorocyclopentene with electro-withdrawing cyano groups at both reactive carbon atoms. Furthermore, we studied the substituent effects of the reactive carbon atoms on the photochromic properties of 1,2-bis(3-R-substituted thiophen-2-yl)perfluorocyclopentene derivatives by comparing the absorption wavelengths and quantum yields of the derivatives having R = cyano, methyl, and methoxy groups. The absorption bands of the closed-ring isomers generated by UV irradiation shifted to longer wavelengths with an increase in the electron-donating characteristic of the substituents. The closed-ring isomer having cyano groups at both reactive carbon atoms has an absorption band at 427 nm (λ(max)), whereas those of methyl and methoxy derivatives have bands at 432 and 481 nm, respectively. The derivative with cyano groups shows the largest cycloreversion quantum yield (0.45), and this yield decreased with an increase in the substituents donating characteristic. Theoretical calculation explains that the excited state of the closed-ring isomer with cyano groups has the highest energy, because there is no barrier to ring-opening on the excited potential surface.

Theoretical Study on the Role of Ca2+ at the S2 State in Photosystem II

In photosynthesis, calcium is crucial for oxygen evolution. In the absence of Ca(2+), the Kok cycle has been proven to stop at S2 with Yz•. To explore the reason, photosystem II (PSII) S2 models (in total 32452 atoms) with different metal ions (Ca(2+), Sr(2+), and K(+)) or without Ca(2+) involved in the oxygen evolution complex (OEC) have been theoretically studied based on the previous dynamic study of PSII. It is found that the portion of the Mn1 d-orbital decreases in the highest occupied molecular orbitals for Ca(2+)-depleted PSII. This feature is unfavorable for the electron transfer from the OEC to the Yz•. Furthermore, the proton donor-acceptor distance was found elongated by the alternation of the binding water in the absence of Ca(2+). The isolated vibrational modes of the key water molecules along the path and their high frequency of the OH stretching modes also suggested the difficulty of the proton transfer from the OEC toward the proton exit channel. This work provides one mechanistic explanation for the inactivity of Ca(2+)-depleted PSII.

Improvement of Parameters of the AMBER Potential Force Field for Phospholipids for Description of Thermal Phase Transitions

In this study, we improved parameters of the AMBER potential force field for phospholipids in order to describe the thermal phase transition using molecular dynamic (MD) simulations. To estimate the errors of the main phase transition temperature (Tm), first, MD simulations using the GAFFlipid and Gaff parameters were performed for six phospholipid bilayers, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), with increasing temperature. The Tm values were characterized according to the structural parameter, area per lipid, and gauche ratio in alkyl chains. The Tm values of the six lipids showed ∼50 K differences from the experimentally measured values. To reduce these errors, the well-depth values in the Lennard-Jones potential of the alkyl chains were modified to fit the Tm values of the simulation to the experimental values in a single DPPC bilayer. After the fitting procedure, the Tm values of the six lipids improved, and the errors of Tm improved from ∼50 to ∼15 K. We show that the simulation applying the improved parameters provides more accurate results than the original parameters. These modified parameters were also found to be useful for performing MD simulation of transmembrane proteins with membrane models.

Understanding thermal phases in atomic detail by all-atom molecular-dynamics simulation of a phospholipid bilayer.

All-atom molecular dynamics (MD) simulations were used to investigate the thermal phase behavior of two hydrated phospholipids, namely, DPPC and DPPE, at the atomic level. The trajectories in the MD simulations clearly identified the structures of DPPC in the crystalline (Lc), gel (Lβ), ripple (Pβ), and liquid-crystalline (Lα) phases and those of DPPE in the Lc and Lα phases. The physicochemical and structural properties of these phases agree well with the experimental results. Moreover, the structural transformations between phases were observed. In the Lβ phase, forces are directed in opposite directions in the upper and lower layers of the bilayer. These forces, which are due to the thermal motion of each monolayer, strongly influence the series of phase transitions from Lβ to Pβ. The MD simulations in this work can provide an understanding of the dynamics of the lipid bilayer in each thermal phase and suggest the mechanism that generates the Pβ phase.

Structural Changes in the S3 State of the Oxygen Evolving Complex in Photosystem II

The S3 state of the Mn4 CaO5 -cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S2 to S3 transition that becomes a substrate water, we examined if the water insertion is essential for the S3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S3 stage. The novel S3 state structure consisting of only short 2.7–2.8 Å Mn—Mn distances was discussed.

Diastereomeric resolution directed towards chirality determination focussing on gas-phase energetics of coordinated sodium dissociation.

Defining chiral centres is addressed by introducing a pair of chiral auxiliary groups. Ions of diastereomeric pairs of molecules could be distinguished utilising energy-resolved mass spectrometry, and the applicability of the method to a series of compounds carrying amine, carboxylic acid, alcohol, and all the amino acids was verified. The method was further strengthened by distinguishing diastereomeric ions that did not undergo fragmentation. Mass spectrometric evaluation of the dissociation process of adducted sodium cations from the diastereomeric precursors agreed with the theoretical calculations, indicating the potential usefulness of the method for the determination of absolute configurations.

Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method

Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.

Structural changes in the S 3 state of the oxygen evolving complex in photosystem II

The S3 state of the Mn4 CaO5 -cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S2 to S3 transition that becomes a substrate water, we examined if the water insertion is essential for the S3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S3 stage. The novel S3 state structure consisting of only short 2.7–2.8 Å Mn—Mn distances was discussed.