Waka Uchida

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.

Photochromism of a Diarylethene Having an Azulene Ring

Diarylethene derivatives incorporating an azulene ring at the ethene moiety were synthesized. One derivative having thiazole rings showed the expected coloration reaction by excitation at 313 nm (to a higher singlet state) but not when excited at 635 nm (S(0) to S(1) excitation). The system demonstrates that the cyclization reaction can be controlled by selective excitation at different wavelengths of the absorption spectrum. On the other hand, another derivative having thiophene rings did not show any photochromism. The results clearly show the importance of the coplanarity of the system for the photoisomerization.

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.

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.

A study of QM/Langevin-MD simulation for oxygen-evolving center of photosystem II

We have performed three QM/Langevin-MD simulations for oxygen-evolving complex (OEC) and surrounding residues, which are different configurations of the oxidation numbers on Mn atoms in the Mn4O5Ca cluster. By analyzing these trajectories, we have observed sensitivity of the change to the configuration of Mn oxidation state on O atoms of carboxyl on three amino acids, Glu354, Ala344, and Glu333. The distances from Mn to O atoms in residues contacting with the Mn4O5Ca cluster were analyzed for the three trajectories. We found the good correlation of the distances among the simulations. However, the distances with Glu354, Ala344, and Glu333 have not shown the correlation. These residues can be sensitive index of the changes of Mn oxidation numbers.

Theoretical study on OH{sup −} site and electronic spin state of oxygen-evolving complex in photosystem II at the dark S{sub 1} state

Possible protonation and electronic-spin states of oxygen-evolving complex (OEC) in photosystem II have been investigated by using QM(DFT-UB3LYP)/MM(Amber) calculation, in order to elucidate which OEC state satisfies the known experimental results at the dark stable state (S1), i.e. OEC involves Mn4(III2,IV4)-cluster and a S=0 state as the lowest energy electronic-spin state at S1. The configuration of Mn oxidation numbers and the lowest energy spin state within the Mn4-cluster depend on the protonation state of one oxo-anion bridging three Mn ions. When all water-ligands and oxo-bridges form H2O and O2−, respectively, the resulting OEC model involved Mn4(III2,IV2)-cluster and one S=0 state as the lowest energy spin state. To rationalize the O2−-bridge model at S1 state, a new H+-release scheme during the H2O-splitting reaction is proposed.