Mapping the emergence of molecular vibrations mediating bond formation.

Fundamental studies of chemical reactions often consider the molecular dynamics along a reaction coordinate using a calculated or suggested potential energy surface1-5. But fully mapping such dynamics experimentally, by following all nuclear motions in a time-resolved manner-that is, the motions of wavepackets-is challenging and has not yet been realized even for the simple stereotypical bimolecular reaction6-8: A-B + C â†’ A + B-C. Here we track the trajectories of these vibrational wavepackets during photoinduced bond formation of the gold trimer complex [Au(CN)2-]3 in an aqueous monomer solution, using femtosecond X-ray liquidography9-12 with X-ray free-electron lasers13,14. In the complex, which forms when three monomers A, B and C cluster together through non-covalent interactions15,16, the distance between A and B is shorter than that between B and C. Tracking the wavepacket in three-dimensional nuclear coordinates reveals that within the first 60 femtoseconds after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 femtoseconds to give a linear and covalently bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we map and unambiguously assign to specific normal modes using only the experimental data. In principle, more intense X-rays could visualize the motion not only of highly scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door to the direct tracking of the atomic motions involved in many chemical reactions.

Antidiabetic Effect of Urolithin A in Cultured L6 Myotubes and Type 2 Diabetic Model KK-Ay/Ta Mice with Glucose Intolerance.

Diabetes is caused by abnormal glucose metabolism, and muscle, the largest tissue in the human body, is largely involved. Urolithin A (UroA) is a major intestinal and microbial metabolite of ellagic acid and ellagitannins and is found in fruits such as strawberry and pomegranate. In this present study, we investigated the antidiabetic effects of UroA in L6 myotubes and in KK-Ay/Ta, a mouse model of type 2 diabetes (T2D). UroA treatment elevated the glucose uptake (GU) of L6 myotubes in the absence of insulin. This elevation in GU by UroA treatment was partially inhibited by the concurrent addition of LY294002, an inhibitor of phosphatidylinositol 3-kinase (PI3K) which activates Akt (PKB: protein kinase B) or Compound C, an inhibitor of 5'-adenosine monophosphate-activated protein kinase (AMPK). Moreover, UroA was found to activate both pathways of Akt and AMPK, and then to promote translocation of glucose transporter 4 (GLUT4) from the cytosol to the plasma membrane in L6 myotubes. Based on these in vitro findings, an intraperitoneal glucose tolerance test (IPGTT) was performed after the oral administration of UroA for 3 weeks to KK-Ay/Ta mice with glucose intolerance. UroA was demonstrated to alleviate glucose intolerance. These results suggest that UroA is a biofactor with antihyperglycemic effects in the T2D state.

Mechanism of H+ dissociation-induced O-O bond formation via intramolecular coupling of vicinal hydroxo ligands on low-valent Ru(III) centers.

The understanding of O-O bond formation is of great importance for revealing the mechanism of water oxidation in photosynthesis and for developing efficient catalysts for water oxidation in artificial photosynthesis. The chemical oxidation of the RuII2(OH)(OH2) core with the vicinal OH and OH2 ligands was spectroscopically and theoretically investigated to provide a mechanistic insight into the O-O bond formation in the core. We demonstrate O-O bond formation at the low-valent RuIII2(OH) core with the vicinal OH ligands to form the RuII2(µ-OOH) core with a µ-OOH bridge. The O-O bond formation is induced by deprotonation of one of the OH ligands of RuIII2(OH)2 via intramolecular coupling of the OH and deprotonated O- ligands, conjugated with two-electron transfer from two RuIII centers to their ligands. The intersystem crossing between singlet and triple states of RuII2(µ-OOH) is easily switched by exchange of H+ between the µ-OOH bridge and the auxiliary backbone ligand.

Operando time-resolved soft x-ray absorption spectroscopy for photoexcitation processes of metal complexes in solutions.

Operando time-resolved soft x-ray absorption spectroscopy (TR-SXAS) is an effective method to reveal the photochemical processes of metal complexes in solutions. In this study, we have developed the TR-SXAS measurement system for observing various photochemical reactions in solutions by the combination of laser pump pulses with soft x-ray probe pulses from the synchrotron radiation. For the evaluation of the developed TR-SXAS system, we have measured nitrogen K-edge x-ray absorption spectroscopy (XAS) spectra of aqueous iron phenanthroline solutions during a photoinduced spin transition process. The decay process of the high spin state to the low spin state in the iron complex has been obtained from the ligand side by N K-edge XAS, and the time constant is close to that obtained from the central metal side by time-resolved Fe K-edge XAS in the previous studies.

Time-resolved resonant soft X-ray scattering combined with MHz synchrotron X-ray and laser pulses at the Photon Factory.

A picosecond pump-probe resonant soft X-ray scattering measurement system has been developed at the Photon Factory storage ring for highly efficient data collection. A high-repetition-rate high-power compact laser system has been installed to improve efficiency via flexible data acquisition to a sub-MHz frequency in time-resolved experiments. Data are acquired by gating the signal of a channel electron multiplier with a pulse-counting mode capable of discriminating single-bunch soft X-ray pulses in the dark gap of the hybrid operation mode in the storage ring. The photoinduced dynamics of magnetic order for multiferroic manganite SmMn2O5 are clearly demonstrated by the detection of transient changes in the resonant soft X-ray scattering intensity around the Mn LIII- and O K-edges.

Trial Analysis of the Relationship between Taste and Biological Information Obtained While Eating Strawberries for Sensory Evaluation.

This paper presents a trial analysis of the relationship between taste and biological information obtained while eating strawberries (for a sensory evaluation). This study used the visual analog scale (VAS); we collected questionnaires used in previous studies and human brain activity obtained while eating strawberries. In our analysis, we assumed that brain activity is highly correlated with taste. Then, the relationships between brain activity and other data, such as VAS and questionnaires, could be analyzed through a canonical correlation analysis, which is a multivariate analysis. Through an analysis of brain activity, the potential relationship with "taste" (that is not revealed by the initial simple correlation analysis) can be discovered. This is the main contribution of this study. In the experiments, we discovered the potential relationship between cultural factors (in the questionnaires) and taste. We also found a strong relationship between taste and individual information. In particular, the analysis of cross-loading between brain activity and individual information suggests that acidity and the sugar-to-acid ratio are related to taste.

Diarylethene-Powered Light-Induced Folding of Supramolecular Polymers.

Helical folding of randomly coiled linear polymers is an essential organization process not only for biological polypeptides but also for synthetic functional polymers. Realization of this dynamic process in supramolecular polymers (SPs) is, however, a formidable challenge because of their inherent lability of main chains upon changing an external environment that can drive the folding process (e.g., solvent, concentration, and temperature). We herein report a photoinduced reversible folding/unfolding of rosette-based SPs driven by photoisomerization of a diarylethene (DAE). Temperature-controlled supramolecular polymerization of a barbiturate-functionalized DAE (open isomer) in nonpolar solvent results in the formation of intrinsically curved, but randomly coiled, SPs due to the presence of defects. Irradiation of the randomly coiled SPs with UV light causes efficient ring-closure reaction of the DAE moieties, which induces helical folding of the randomly coiled structures into helicoidal ones, as evidenced by atomic force microscopy and small-angle X-ray scattering. The helical folding is driven by internal structure ordering of the SP fiber that repairs the defects and interloop interaction occurring only for the resulting helicoidal structure. In contrast, direct supramolecular polymerization of the ring-closed DAE monomers by temperature control affords linearly extended ribbon-like SPs lacking intrinsic curvature that are thermodynamically less stable compared to the helicoidal SPs. The finding represents an important concept applicable to other SP systems; that is, postpolymerization (photo)reaction of preorganized kinetic structures can lead to more thermodynamically stable structures that are inaccessible directly through temperature-controlled protocols.

Antidiabetic Effect of Taxifolin in Cultured L6 Myotubes and Type 2 Diabetic Model KK-Ay/Ta Mice with Hyperglycemia and Hyperuricemia.

Muscle is the largest tissue in our body and plays an important role in glucose homeostasis and hence diabetes. In the present study, we examined the effects of taxifolin (TXF) on glucose metabolism in cultured L6 muscle cells (myotubes) and in type 2 diabetic (T2D) model KK-Ay/Ta mice. TXF dose-dependently increased glucose uptake (GU) in L6 myotubes under the condition of insulin absence. This increase in GU was partially, but significantly canceled by TXF treatment in combination with either LY294002, an inhibitor of phosphatidylinositol 3-kinase (PI3K), which phosphorylates protein kinase B (Akt) or Compound C, an inhibitor of 5'-adenosine monophosphate-activated protein kinase (AMPK). Furthermore, TXF was demonstrated to activate (=phosphorylate) both Akt and AMPK, and promote glucose transporter 4 (GLUT4) translocation to the plasma membrane from cytosol of L6 myotubes via both PI3K/Akt and AMPK signaling pathways. Based on these in vitro findings, we conducted an in vivo experiment in KK-Ay/Ta mice with hyperglycemia and hyperuricemia. Fasting plasma glucose, insulin, uric acid levels and an index of insulin resistance (HOMA-IR) increased significantly in the T2D model mice compared with normal ones. Such rises in the T2D state were significantly suppressed by oral administration of TXF for four weeks. These results suggest that TXF is a potent antihyperglycemic and antihyperuricemic phytochemical in the T2D state.

Diffracted X-ray blinking measurements of interleukin 15 receptors in the inner/outer membrane of living NK cells.

Interleukin 15 receptor (IL-15R) is a transmembrane signalling protein consisting of 3 subsets: α, ß (IL-15Rß), and γ (γc). IL-2 and IL-15 share the signalling domains IL-15Rß and γc, although they bind to intrinsic α-subsets and non-signalling domains. Additionally, IL-2 and IL-15 play different roles; therefore, there have been many observations of the dynamic behaviours of IL-15R, which are linked to physiological functions. For more practical discrimination between IL-2 and IL-15, a study was designed and carried out in which α-subsets were removed and a cytoplasmic inhibitor was applied to create a simplified environment in which secondary signalling molecules were reduced. We also applied a new measurement method, diffracted X-ray blinking (DXB), to achieve higher accuracy (<0.01 Å). The dynamics of IL-2 binding (confined motion, max range = 0.71 Å) and IL-15 binding (normal motion) in live natural killer cells were different. We also confirmed. that DXB was a suitable method to quantitatively evaluate the transmembrane protein dynamics of inner/outer live cell membranes by labeling the extracellular domain since the measurements were dependent on the cytosolic environment.

Prolyl-hydroxyproline, a collagen-derived dipeptide, enhances hippocampal cell proliferation, which leads to antidepressant-like effects in mice.

Depression has been a mental health issue worldwide. We previously reported that ginger-degraded collagen hydrolysate (GDCH) suppressed depression-like behavior in mice. Furthermore, prolyl-hydroxyproline (PO) and hydroxyprolyl-glycine (OG) were detected in the circulating blood after the oral administration of GDCH. In the present study, PO, but not OG, was detected in the cerebrospinal fluid of rats after the oral administration of GDCH, suggesting that PO is transported from blood to the brain. We then investigated the effects of PO and OG on the depression-like behavior of mice. The oral administration of PO significantly decreased depression-like behavior in the forced swim test. OG had no antidepressant-like effect. In addition, proline and hydroxyproline, components of PO, also had no antidepressant-like effect after their oral administration. PO significantly increased the gene expression of brain-derived neurotrophic factor and nerve growth factor in the hippocampus, and promoted the proliferation of neural progenitor cells in vivo and in vitro. PO also increased the dopamine concentration in the prefrontal cortex. Thus, PO-dependent regulation of neurotrophic function and neurotransmitter may be the mechanism for antidepressant-like behavior. Together, these results demonstrate that PO is an antidepressant bioactive peptide accompanying the proliferation of hippocampal neural progenitor cells.

Determining Excited-State Structures and Photophysical Properties in Phenylphosphine Rhenium(I) Diimine Biscarbonyl Complexes Using Time-Resolved Infrared and X-ray Absorption Spectroscopies.

We have explored the structural factors on the photophysical properties in two rhenium(I) diimine complexes in acetonitrile solution, cis,trans-[Re(dmb)(CO)2(PPh2Et)2]+ (Et(2,2)) and cis,trans-[Re(dmb)(CO)2(PPh3)2]+ ((3,3)) (dmb = 4,4'-dimethyl-2,2'-bipyridine, Ph = phenyl, Et = ethyl) using the combination method of time-resolved infrared spectroscopy, time-resolved extended X-ray absorption fine structure, and quantum chemical calculations. The difference between these complexes is the number of phenyl groups in the phosphine ligand, and this only indirectly affects the central Re(I). Despite this minor difference, the complexes exhibit large differences in emission wavelength and excited-state lifetime. Upon photoexcitation, the bond length of Re-P and angle of P-Re-P are significantly changed in both complexes, while the phenyl groups are largely rotated by ∼20° only in (3,3). In contrast, there is little change in charge distribution on the phenyl groups when Re to dmb charge transfer occurs upon photoexcitation. We concluded that the instability from steric effects of phenyl groups and diimine leads to a smaller Stokes shift of the lowest excited triplet state (T1) in (3,3). The large structural change between the ground and excited states causes the longer lifetime of T1 in (3,3).

Direct observation of bond formation in solution with femtosecond X-ray scattering.

The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2(-)]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of ∼500 femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-ångström spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.

Structural Dynamics of C2F4I2 in Cyclohexane Studied via Time-Resolved X-ray Liquidography.

The halogen elimination of 1,2-diiodoethane (C2H4I2) and 1,2-diiodotetrafluoroethane (C2F4I2) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute-solvent interactions in solution-phase reactions. While the kinetics and reaction pathways of the halogen elimination reaction of C2H4I2 were reported to vary substantially depending on the solvent, the solvent effects on the photodissociation of C2F4I2 remain to be explored, as its reaction dynamics have only been studied in methanol. Here, to investigate the solvent dependence, we conducted a time-resolved X-ray liquidography (TRXL) experiment on C2F4I2 in cyclohexane. The data revealed that (ⅰ) the solvent dependence of the photoreaction of C2F4I2 is not as strong as that observed for C2H4I2, and (ⅱ) the nongeminate recombination leading to the formation of I2 is slower in cyclohexane than in methanol. We also show that the molecular structures of the relevant species determined from the structural analysis of TRXL data provide an excellent benchmark for DFT calculations, especially for investigating the relevance of exchange-correlation functionals used for the structural optimization of haloalkanes. This study demonstrates that TRXL is a powerful technique to study solvent dependence in the solution phase.

X-ray-based living-cell motion analysis of individual serotonin receptors.

G protein-coupled receptors (GPCRs) are seven-transmembrane proteins, which transmit extracellular signals inside cells via activating G proteins. GPCRs are involved in a wide variety of physiological functions, such as signal sensing, immune system processes, and neurotransmission. Although the structures and functions of GPCRs have been well studied, little has been known about their real-time dynamics on live cells. In this study, we used Diffracted X-ray Tracking (DXT) and Diffracted X-ray Blinking (DXB) techniques for analysis. These methods are very precise single-molecular analytical techniques that elucidate protein dynamics by analyzing the diffraction spots from the gold nanocrystals labeled on the protein surface. DXT tracks diffraction spot movements, whereas DXB analyzes continuation of signals by calculating the autocorrelation function of each pixel from the recorded data. Serotonin receptor subtype 2A (5-HT2A receptors) were transiently expressed on HEK 293 cells, and the gold nanocrystals were attached to the N-terminally introduced FLAG-tag via anti-FLAG antibodies. Fast- and mid-range motions were recorded by DXT with 100µs and 1.25 ms/frame rate, respectively. Slow-range motion was obtained using the DXB method with 100 ms/frame rate. An agonist interestingly suppressed the fluctuations of 5-HT2A receptors at the microsecond-ranged fast measurement. On the contrary, the motion was enhanced by the agonist in the hundred-millisecond-ranged slow time scale. These dual-natured data may suggest that we succeeded in extracting different modes of receptor's motion on live cells; microsecond ranged fluctuation on the cell membrane, and millisecond-ranged dynamic movement comprising interactions with intracellular signaling molecules.

Development of shock-dynamics study with synchrotron-based time-resolved X-ray diffraction using an Nd:glass laser system.

The combination of high-power laser and synchrotron X-ray pulses allows us to observe material responses under shock compression and release states at the crystal structure on a nanosecond time scale. A higher-power Nd:glass laser system for laser shock experiments was installed as a shock driving source at the NW14A beamline of PF-AR, KEK, Japan. It had a maximum pulse energy of 16 J, a pulse duration of 12 ns and a flat-top intensity profile on the target position. The shock-induced deformation dynamics of polycrystalline aluminium was investigated using synchrotron-based time-resolved X-ray diffraction (XRD) under laser-induced shock. The shock pressure reached up to about 17 GPa with a strain rate of at least 4.6 × 107 s-1 and remained there for nanoseconds. The plastic deformation caused by the shock-wave loading led to crystallite fragmentation. The preferred orientation of the polycrystalline aluminium remained essentially unchanged during the shock compression and release processes in this strain rate. The newly established time-resolved XRD experimental system can provide useful information for understanding the complex dynamic compression and release behaviors.

Photoinduced anisotropic distortion as the electron trapping site of tungsten trioxide by ultrafast W L1-edge X-ray absorption spectroscopy with full potential multiple scattering calculations.

Understanding the excited state of photocatalysts is significant to improve their activity for water splitting reaction. X-ray absorption fine structure (XAFS) spectroscopy in X-ray free electron lasers (XFEL) is a powerful method to address dynamic changes in electronic states and structures of photocatalysts in the excited state in ultrafast short time scales. The ultrafast atomic-scale local structural change in photoexcited WO3 was observed by W L1 edge XAFS spectroscopy using an XFEL. An anisotropic local distortion around the W atom could reproduce well the spectral features at a delay time of 100 ps after photoexcitation based on full potential multiple scattering calculations. The distortion involved the movement of W to shrink the shortest W-O bonds and elongate the longest one. The movement of the W atom could be explained by the filling of the dxy and dzx orbitals, which were originally located at the bottom of the conduction band with photoexcited electrons.

Antihyperuricemic Effect of Urolithin A in Cultured Hepatocytes and Model Mice.

Hyperuricemia is defined as a disease with high uric acid (UA) levels in the blood and a strong risk factor for gout. Urolithin A (UroA) is a main microbial metabolite derived from ellagic acid (EA), which occurs in strawberries and pomegranates. In this study, we evaluated antihyperuricemic effect of UroA in both cultured hepatocytes and hyperuricemic model mice. In cultured hepatocytes, UroA significantly and dose-dependently reduced UA production. In model mice with purine bodies-induced hyperuricemia, oral administration of UroA significantly inhibited the increase in plasma UA levels and hepatic xanthine oxidase (XO) activity. In addition, DNA microarray results exhibited that UroA, as well as allopurinol, a strong XO inhibitor, induced downregulation of the expression of genes associated with hepatic purine metabolism. Thus, hypouricemic effect of UroA could be, at least partly, attributed to inhibition of purine metabolism and UA production by suppressing XO activity in the liver. These results indicate UroA possesses a potent antihyperuricemic effect and it could be a potential candidate for a molecule capable of preventing and improving hyperuricemia and gout.

Topological Impact on the Kinetic Stability of Supramolecular Polymers.

Kinetically formed metastable molecular assemblies have attracted increasing interest especially in the field of supramolecular polymers. In most cases, metastable assemblies are ensemblies of aggregates based on the same supramolecular motif but with different lengths or sizes, and therefore their kinetic stabilities are experimentally indistinguishable. Herein, we demonstrate a topological effect on kinetic stabilities in a complex mixture of metastable supramolecular polymers. Our azobenzene-incorporated monomer upon heating in nonpolar solvent at ambient temperature kinetically forms complex mixtures of supramolecular polymers with cyclized and open-ended randomly coiled topologies. Upon further heating, we obtained thermodynamically stable twisted fibrils organizing into crystalline fibers. Through the direct visualization of the complex supramolecular polymer mixtures by atomic force microscopy, we demonstrate that the cyclized supramolecular polymer has superior kinetic stability compared to the open-ended species toward the thermal transformation into twisted fibrils. Since the superior kinetic stability of the cyclized species can be attributed to the absence of aggregate termini, we could convert them fully into the thermodynamic species through photoinduced opening of the cyclized structures.

Apobec2 deficiency causes mitochondrial defects and mitophagy in skeletal muscle.

Apobec2 is a member of the activation-induced deaminase/apolipoprotein B mRNA editing enzyme catalytic polypeptide cytidine deaminase family expressed in differentiated skeletal and cardiac muscle. We previously reported that Apobec2 deficiency in mice leads to a shift in muscle fiber type, myopathy, and diminished muscle mass. However, the mechanisms of myopathy caused by Apobec2 deficiency and its physiologic functions are unclear. Here we show that, although Apobec2 localizes to the sarcomeric Z-lines in mouse tissue and cultured myotubes, the sarcomeric structure is not affected in Apobec2-deficient muscle. In contrast, electron microscopy reveals enlarged mitochondria and mitochondria engulfed by autophagic vacuoles, suggesting that Apobec2 deficiency causes mitochondrial defects leading to increased mitophagy in skeletal muscle. Indeed, Apobec2 deficiency results in increased reactive oxygen species generation and depolarized mitochondria, leading to mitophagy as a defensive response. Furthermore, the exercise capacity of Apobec2-/- mice is impaired, implying Apobec2 deficiency results in ongoing muscle dysfunction. The presence of rimmed vacuoles in myofibers from 10-mo-old mice suggests that the chronic muscle damage impairs normal autophagy. We conclude that Apobec2 deficiency causes mitochondrial defects that increase muscle mitophagy, leading to myopathy and atrophy. Our findings demonstrate that Apobec2 is required for mitochondrial homeostasis to maintain normal skeletal muscle function.-Sato, Y., Ohtsubo, H., Nihei, N., Kaneko, T., Sato, Y., Adachi, S.-I., Kondo, S., Nakamura, M., Mizunoya, W., Iida, H., Tatsumi, R., Rada, C., Yoshizawa, F. Apobec2 deficiency causes mitochondrial defects and mitophagy in skeletal muscle.