Porphyrin derivatives including hemes and chlorophylls are indispensable for all organisms because they are involved in respiration, photosynthesis, and various enzymatic reactions. However, because excess free heme is toxic for organisms, heme metabolism is important to reduce oxidative stress produced by excess heme. Heme and bilin metabolism are also crucial for photosynthetic organisms because the metabolites, bilin pigments, are utilized for photosynthesis and photoreception. In this review, our structural study of enzymes involved in heme and bilin metabolisms is summarized. Especially, molecular interaction between heme oxygenase and NADPH-cytochrome P450 reductase and the reaction mechanism of ferredoxin-dependent bilin reductases are discussed.

The genetic information encoded in DNA is transcribed into mRNA and then translated into protein. DNA, RNA, and proteins are modified by various enzymes and change their functions by the modifications. Phosphorylation or methylation are well-known modifications. Modifications to mRNA are called post-transcriptional modifications, and those to proteins are called post-translational modifications. Enzymatic modifications are essential to maintain the normal function of the cells and must be strictly controlled. Their failure causes serious diseases. Establishing the structural base to understand the catalytic mechanism of modification enzymes or functional changes of proteins induced by modifications is very important, not only for basic research but also for drug discovery. In this article, I would like to introduce my recent studies relating to the post-translational and post-transcriptional modifications.

The planarity of the peptide bond plays a crucial role in protein stability and structural formation. However, recent high-resolution structural studies have revealed considerable deviations from ideal peptide bond planarity. In this study, we present a high-resolution neutron structure（1.2 Å resolution）of the oxidized form of high-potential iron-sulfur protein（HiPIP）to investigate peptide bond geometry, including amide protons, with explicit visualization of hydrogen atoms. Our neutron structure clearly showed deviations in the nuclear positions of amide protons from the peptide plane, particularly shifting toward hydrogen bond acceptors. This proton displacement strongly correlates with pyramidalization of the nitrogen atom, which significantly influences the planarity of the H–N–C=O plane. Moreover, the orientation of the amide proton in Cys75 is different between the reduced and oxidized states because of the electron storage capacity of the iron-sulfur cluster. These results show the importance of local conformation in regulating peptide bond geometry. This study demonstrates the unique advantages of high-resolution neutron crystallography in elucidating fine structural details and understanding protein function.

The versatility of diamond anvil cells（DACs） makes them essential for fields such as geoscience, condensed matter physics and materials synthesis. At BL10XU, SPring-8, we have developed a user-friendly measurement platform to facilitate advanced experiments for all users. While DACs have been widely used for static high-pressure studies, recent advancements have driven a growing demand for dynamic and non-equilibrium high-pressure experiments. To meet this need, we developed a submillisecond X-ray diffraction（XRD） system for in-situ measurements of small high-pressure samples using DACs. By synchronizing a high-speed 2D X-ray detector, laser heating and temperature measurement system and gas-pressure control system, we achieved precise control over rapid heating（up to 5000 K）, fast cooling and dynamic compression/decompression processes. This system enables real-time observation of structural changes under extreme conditions, such as those simulating meteorite impacts. I will present details of this system and experimental results under complex dynamic conditions.

The effects of temperature and alkali metal ions on the structure and crystallization process of amorphous magnesium carbonate（AMC） were investigated using synchrotron X-ray total scattering and X-ray absorption fine structure（XAFS） spectroscopy. The pair distribution function（PDF） analysis revealed that no substantial structural differences were observed between AMCs synthesized at 20℃, 60℃, and 80℃. The presence of Na or K ions in the solution promotes the formation of nesquehonite, but the presence of Rb or Cs ions inhibits the long-range ordering of atoms and suppresses crystallization. These findings indicate that alkali metal ions play an important role in controlling the crystallization of AMC.

We have carried out molecular-dynamics simulations of SiO₂ melt and glass at 60 GPa in a system of about 30,000 atoms, with robust machine-learning interatomic potentials based on ab initio calculations. The large-scale simulations not only reproduced the ab initio calculations, but were also found to significantly improve the precision of the intermediate-range structure and reproduce the emergence of a nanometer-scale heterogeneous intermediate state during the pressure-induced phase transformation. Interatomic potentials determined using machine learning easily destabilize simulations of highly covalent melts under high pressure in an extended system with over one order of magnitude more atoms than those in the initial calculations used for data generation. The combination of potential averaging and active learning can efficiently suppress computational instability.

In situ high-pressure sound velocity measurements of CaAl₂O₄ glass demonstrated irreversible discontinuities in the sound velocities at ~8–10 GPa. In situ high-pressure synchrotron x-ray diffraction measurements showed an intermediate-range structure change attributed to a rearrangement of calcium ions over this narrow pressure region. Atomistic models obtained from molecular dynamics simulations revealed that this structure change originates from a transition from a bimodal Ca-O void radius distribution including voids larger than ~2.4 Å to a unimodal distribution without the large voids.

Understanding the structural response of silicate glasses and melts to pressure and composition is crucial for discussing deep magmatism, which plays a central role in geochemical processes throughout Earth’s evolution. To investigate these responses, high pressure X-ray and neutron diffraction experiments were conducted on two samples：one is a basaltic glass, and the other is a Na₆Si₈O₁₉ melt. In the basaltic glass, compression up to 9 GPa results in an increase in the mean O-O coordination number（CN_OO）, while the mean O-O distance（r_OO）remains nearly constant. The onset of the increase in CN_OO around 2 GPa is interpreted because of elastic softening of the fourfold-coordinated silicate network. Above ～9 GPa, the CN_OO reaches a plateau, and r_OO begins to decrease. This shift is interpreted as a transition in the compression mechanism from the bending of tetrahedral networks to densification through increased oxygen packing. For the hydrous Na₆Si₈O₁₉ melts, in-situ neutron experiments revealed that the D-O distance increases with pressure, attributed to the formation of -O-D-O- bridging species. This pressure-induced formation indicates a more rigid incorporation of hydrogen into the melt structure. In addition to the shrinkage of modifier domains, this structural change governs the compression behavior of the hydrous silicate melt. In contrast, the compression of the dry Na₆Si₈O₁₉ melt is primarily controlled by the bending of Si-O-Si angles.