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Cullin-RING E3 ubiquitin ligases (CRLs) spatiotemporally regulate the proteasomal degradation of numerous cellular proteins involved in cell cycle control, DNA replication, and maintenance of genome stability. Activation of CRLs is controlled via neddylation by NEDD8-activating, -conjugating, and -attaching enzymes to the C-terminus of scaffold cullins (CULs), whereas the COP9 signalosome (CSN) inactivates CRLs via deneddylation. Here, we show that the deneddylation rate of each CUL is differentially modulated. Dose- or time-dependent treatment with pevonedistat, a small molecule inhibitor of NEDD8-activating enzyme (NAE), rapidly inhibits neddylation in most CULs, including CUL1, CUL3, CUL4A/B, and CUL5, whereas the deneddylation of CUL2 is slowly increased. We revealed that the different deneddylation speeds of each CUL depend on its binding strength with CSN5, the catalytic core of the CSN complex. Immunoprecipitation analysis revealed that CUL2 has a lower binding affinity for CSN5 than other CULs. Consistently, released cells treated with CSN5 inhibitor showed that CUL2 was slowly converted to the deneddylated form compared to the rapid deneddylation of other CULs. These findings provide mechanistic insights into the different dynamics of CULs in neddylation-deneddylation conversion.

1-Deoxynojirumycin (1-DNJ) is a representative iminosugar with α-glucosidase inhibition (AGI) activity. In this study, the full genome sequencing of 1-DNJ-producing Bacillus velezensis K26 was performed. The genome consists of a circular chromosome (4,047,350 bps) with two types of putative virulence factors, five antibiotic resistance genes, and seven secondary metabolite biosynthetic gene clusters. Genomic analysis of a wide range of Bacillus species revealed that a 1-DNJ biosynthetic gene cluster was commonly present in four Bacillus species (B. velezensis, B. pseudomycoides, B. amyloliquefaciens, and B. atrophaeus). In vitro experiments revealed that the increased mRNA expression levels of the three 1-DNJ biosynthetic genes were closely related to increased AGI activity. Genomic comparison and alignment of multiple gene sequences indicated the conservation of the 1-DNJ biosynthetic gene cluster in each Bacillus species. This genomic analysis of Bacillus species having a 1-DNJ biosynthetic gene cluster could provide a basis for further research on 1-DNJ-producing bacteria.

Resistant starch (RS) is a complex prebiotic carbohydrate beneficial to the human gut. In the present study, four genes encoding for putative amylolytic enzymes, likely to be responsible for RS-degradation, were identified in the genome of Bifidobacterium adolescentis P2P3 by comparative genomic analysis. Our results showed that only three enzymes (RSD1, RSD2, and RSD3) exhibited non-gelatinized high amylose corn starch (HACS)-degrading activity in addition to typical α-amylase activity. These three RS-degrading enzymes (RSD) were composed of multiple domains, including signal peptide, catalytic domain, carbohydrate binding domains, and putative cell wall-anchoring domains. Typical catalytic domains were conserved by exhibiting seven typical conserved regions (I-VII) found mostly in α-amylases. Analysis of enzymatic activity revealed that RSD2 displayed stronger activity toward HACS-granules than RSD1 and RSD3. Comparative genomics in combination with enzymatic experiments confirmed that RSDs might be the key enzymes used by RS-degrading bifidobacteria to degrade RS in a particular ecological niche, such as the human gut.

Branch-chain elongated starches can be synthesized by amylosucrase (AS). In this study, potato starches with different branch-chain length were produced using the temperature-dependent elongation property of AS from Deinococcus geothermalis (DGAS). Decreasing the reaction temperature led to a significant rise in the length of the branch-chains, in addition to amylose content. As branch-chain length increased, B-type crystal structure increased significantly alongside it, and the thermal transitions were enhanced, suggesting that the crystalline structure was further stabilized. In addition, a decrease in solubility and swelling power was observed, whereas the gelatinization temperatures and peak viscosities increased accordingly. With respect to digestive properties, a remarkable rise in slowly digestible starch (0–19.8%) and resistant starch (38.2%–62.2%) contents was observed, along with an enhanced resistance to mammalian mucosal α-glucosidase. In conclusion, enzymatic modification by DGAS might be an innovative method to regulate the physicochemical and digestive properties of starches.

The inherent weakness of conventional panel speakers is the inevitable multi-modal vibration behavior, resulting in severe fluctuation in the radiated sound spectrum, which is detrimental to the sound quality. A panel speaker that is actively controlled by array actuators at the panel edges has been proposed as a solution to the problem, but the increased cost and complexity due to a large number of actuators remain a challenge. In this study, a panel speaker using a thin beam, called a strip speaker, that adopts only three actuators is proposed to alleviate the modal fluctuation problem. When the middle position of the beam is excited by the primary actuator, the propagated bending wave field there from is controlled by two actuators at either end of the beam that prevents reflection of the wave. To achieve this, the inverse problem is derived by using the transfer function between the actuators and the coefficients of the reflected waves, from which an appropriate gain of the two control actuators is obtained as the inverse solution. For validation, a thin beam with a size of 315 × 40 × 2 mm3 is tested by simulation and experiment. Peaky resonant responses are made to disappear by controlling the vibration field, and the input mobility of the primary actuator becomes like that of an infinite beam. The boundary of the beam, which is newly defined at the location of the control actuators, is converted into an anechoic termination. The effect of the beam material is also tested by comparing aluminum and acrylic beams. It is shown that the damping of the acrylic beam is favorable in resulting a flat response, but its effective frequency range is lowered from that of the aluminum beam. In the experiment, the control actuators near the ends of unknown boundary conditions are located at the position to minimize the total input power for control. The experimental results of the controlled vibration field and radiated sound spectrum agree well with the predicted characteristics. It is shown that the proposed strip speaker with the traveling wave control method can be used to produce excellent acoustic performance.

The inclusion of heptagonal, octagonal, or larger rings in an sp2-bonded carbon network introduces negative Gaussian curvature that can lead to a high network porosity. Here we investigated a particular negatively curved nonplanar sp2-carbon structure namely 688P schwarzite, with a view toward the possible use of negatively curved carbons as lithium ion battery anodes. Our first principles calculations show that the presence of pores in schwarzites can lead to three-dimensional Li ion diffusion paths with relatively small energy barriers. We calculated the binding energy of Li (which donates 1 electron to the schwarzite) in different positions in the schwarzite structure, and the open-circuit voltage (OCV) with respect to Li metal and found that this schwarzite has a positive OCV for a Li concentration as high as LiC4. The advantages of the particular schwarzite studied here for use as an anode are expected to be present in other sp2-bonded carbon networks that feature large polygonal rings.

Amylosucrase (AS), maltooligosyltrehalose synthase (MTS), and maltooligosyltrehalose trehalohydrolase (MTH) were used in combined cross-linked enzyme aggregates (combi-CLEAs) to achieve one-step bioconversion of sucrose to trehalose. Combi-CLEAs of three enzymes were successfully established with acetone and glutaraldehyde (GA) as a precipitant and a cross-linker, respectively. The optimum enzyme ratio was 8:0.5:0.5 (AS, 4 mg:MTS, 0.25 mg:MTH, 0.25 mg). To improve trehalose production, bovine serum albumin was co-aggregated with enzymes as a proteic feeder. The trehalose production yield of combi-CLEAs was about 8% in each cycle on the basis of substrate added up to 400 mM. Finally, the combi-CLEAs used in this experiment showed reusability of about five cycles without any activity loss.

For the liquid crystal display (LCD) black matrix (BM) with a low dielectric constant and high light absorption property, it is advantageous to employ dyes instead of carbon black or pigments. For this purpose, the dyes should have high solubility in industrial organic solvents. For improved solubility in industrial solvents, three metal-free phthalocyanines (PC), peripherally substituted with bulky groups, were synthesized and dye-based BMs were fabricated. The solubility as well as the spectral and thermal properties of the dyes were examined, and the optical, thermal and dielectric properties of a dye-based black matrix were tested. The greenish phthalocyanine dyes with high molar extinction coefficients and high thermal stability showed enhanced solubility in industrial solvents as a result of the greater steric hindrance among the dye molecules and higher affinity between the dye molecules and solvents. The dye-based BMs had low dielectric constants and exhibited superior optical properties and satisfactory thermal stability.

The crystal structures of a yellowish-red pigment, 1,4-diketo-3,6-diphenylpyrrolo(3,4-c)pyrrole (DPP), and its derivative with high proton affinity, 1,4-diketo-3,6-bis(4′-dipyridyl)-pyrrolo-[3,4-c]pyrrole(DPPP), were predicted using Polymorph Predictor in Materials Studio 4.4. The possible structures were generated using Monte Carlo method and they were minimized with COMPASS and Dreiding forcefields. Among the predicted structures with the space groups same as those of the experimental X-ray crystal structures, structures fitting best to the experimental structures were searched. The resulting structures are in good agreement with the experimental structures showing that Monte Carlo simulated annealing is an efficient method for predicting crystal structures of DPP derivatives.

As a core structure for a new functional dye which can be used as materials for electronic devices such as field-effect transistors or light-emitting diodes, indenofluorene and indenopyrazine have been studied. CIS/6-31G* level was applied to optimize the geometry of the first excited state used to calculate the emission spectrum. Their UV absorption and PL emission spectra were calculated by using time-dependent density functional theory (TDDFT) method at B3LYP/6-31G* level. The influence of THF solvent was considered using polarized continuum model TDDFT (PCM-TDDFT) method as well. PCM-TDDFT results are red-shifted by about 10 nm in comparison to the corresponding predicted absorption and emission maximum in vacuum. In PCM-TDDFT results, the absorption maxima of indenopyrazine were red-shifted by about 25 nm compared to those of indenofluorene. This spectral shift, induced by the nitrogen atoms in the pyrazine ring of indenopyrazine, are explained by the analysis of electronic structures of indenofluorene and indenopyrazine and the atomic contributions of the pyrazine nitrogen atoms to the frontier molecular orbital of indenopyrazine.

A promising class of blue–violet emitters based on a new functional core, the indenopyrazine group, has successfully been synthesized for the first time by substitution with bulky m-terphenyl side groups in the ortho, meta, or para positions. There are larger blue shifts in the UV–visible absorption and PL spectra of the synthesized ortho- and para-substituted derivatives than in those of the meta-substituted derivative. Molecular calculations verified that these differences are due to the variation in the π-conjugation length of the derivatives with the position at which the side group is attached to the indenopyrazine core. When the synthesized compounds were used as emitting layers in non-doped OLED devices, a related trend was observed in their optical properties. In particular, the OLED containing the para-substituted derivative was found to exhibit excellent characteristics, with maximum EL emission at 423 nm, a full width at half maximum of 42 nm, pure violet emission with CIE coordinates (0.173, 0.063), and an external quantum efficiency of 1.88%.

We performed molecular dynamics simulations at 77 K on the non-interpenetrating isoreticular (having the same underlying topology) metal-organic frameworks (IRMOFs) and the interpenetrating IRMOFs to investigate the adsorption behavior of hydrogen on the surface of MOFs, catenation effect on the density of adsorbed hydrogen, and dynamic behavior of adsorbed hydrogen molecules. We tested two classical force fields, universal force field (UFF) and DREIDING force field for the simulations and found out that the UFF describes the adsorption of hydrogen more reliably than DREIDING force field. The simulations showed the density values of adsorbed hydrogen in the small pores of the interpenetrating IRMOFs are higher than those in the larger pores of the non-interpenetrating IRMOFs, and the diffusion of the hydrogen molecules in the interpenetrating IRMOFs is highly restricted compared to the non-interpenetrating IRMOFs. From the simulation results, we concluded that the small pores created by the catenation might contribute the increase of the adsorption capacity of the interpenetrating IRMOFs.

Isoreticular metal organic frameworks (IRMOFs), which have the regular and uniform topology throughout the whole lattice structure, can be varied by using different aromatic organic linkers, and the resultant IRMOFs have different hydrogen adsorption capacity. In order to design new hydrogen storage materials with the larger capacity, we need to investigate the change of hydrogen adsorption according to the change of the aromatic linkers. We calculated the electronic structure of full framework of metal organic frameworks (MOFs) using density functional theory calculations, and analyzed the interactions of hydrogen molecules with the aromatic organic linkers, and zinc–oxo clusters. The comparison of binding energies and pairing energies showed that more hydrogen molecules could be adsorbed on the organic linker with a larger surface area, and this adsorption was stable. The simulation results also indicate that the steeper slope at the initial stage of adsorption in the MOFs can be related to the larger binding energy between metal cluster sites and hydrogen molecules.

We have investigated the relationship between the molecular structures of metal-organic frameworks (MOFs) and their hydrogen uptake capabilities. Quantitative structure–property analysis was used to find out MOF structural factors important for hydrogen adsorption. To determine the quantitative interaction strength between hydrogen molecules and MOFs, the iso-value surface area of electrostatic potential was developed as a new descriptor. Quantitative analysis of structurally similar MOFs showed that the functionalization of aromatic organic linkers could induce noticeable polarization effect on the framework surface. We also found that the topology of MOFs plays an important role in determining the amount of ultimate hydrogen uptake. Through this quantitative structure–uptake relationship analysis, structural descriptors for the prediction of MOF hydrogen sorption capacity have been identified.

Hydrogen adsorption mechanism into MOF-5, a porous metal-organic framework (MOF) has been studied by density functional theory calculation. The selected functionals for the prediction of interaction energies between hydrogen and potential adsorption sites of MOF-5 were utilized after the evaluation with the various functionals for interaction energy of H 2 ⋯C 6 H 6 model system. The adsorption energy of hydrogen molecule into MOF-5 was investigated with the consideration of the favorable adsorption sites and the orientations. We also calculated the second favorable adsorption sites by geometry optimization using every combination of two first adsorbed hydrogen molecules. Based on the calculation of the first and the second adsorption sites and energies, it has been suggested that the hydrogen adsorption into MOF-5 follows a cooperative mechanism in which the metal sites initiate the propagation of the hydrogen adsorption on the whole frameworks. In addition, the interaction mode between the simple benzene ring with hydrogen is significantly changed when the benzene ring has been incorporated into the framework of MOF-5.

Molecular dynamics simulations with an umbrella potential function in solution were carried out to obtain the potential of mean force for sodium-dimethyl phosphate (Na + -DMP − ) and sodium-methyl phosphate (Na + -MP 2− ). The Na + -DMP − showed two minima in pmf profile, a less stable minimum of ca. 3.5 A and a more stable minimum of ca. 5.0 A, resulting in direct and indirect contact between two ions. On the other hand, the Na + -MP 2− showed one prominent minimum in pmf profile, at approximately ca. 4.5 A. Water molecules around Na + -DMP − better formed a hydrogen-bonded network than around Na + -MP 2− , showing a stronger interaction between water and the Na + -MP 2− .

Using molecular dynamics simulations with the rigid TIP4P water model, we have analyzed the structural change of liquid water induced by an external electric field. The temperature was controlled with a Nose–Hoover thermostat. In this paper, we report the acquisition of liquid water with the enhanced structural regularity by applying an electric field. From the simulations under various strengths of the electric field, we can see that the threshold for the significant structural change is thought to be between 0.2 and 0.15 V/A. When the number of six-membered rings is increased by the external electric field, so that water is forced to have structural regularity, we calculate the diffusion coefficients and discover that water we make in the simulations is not solid but still liquid under the electric field.