Engineering the promiscuous racemase activity of an arylmalonate decarboxylase

Variant G74C of arylmalonate decarboxylase (AMDase) from Bordatella bronchoseptica has a unique racemising activity towards profens. By protein engineering, variant G74C/V43A with a 20-fold shift towards promiscuous racemisation was obtained, based on a reduced activity in the decarboxylation reaction and a two-fold increase in the racemisation activity. The mutant showed an extended substrate range, with a 30-fold increase in the reaction rate towards ketoprofen. Molecular dynamics simulations and the substrate profile of the racemase indicate that the steric and polar effects of the substrate structure play a more dominant role on catalysis than mere kinetic α-proton acidity. The observation that the conversion of β,γ-unsaturated carboxylic acids does not lead to a rearrangement to form their α,β isomers indicates a concerted rather than a stepwise mechanism. Interestingly, a substrate bearing a nitro group instead of the carboxylic acid group on the α-carbon atom was also converted by the racemase.     

Label-free molecular beacon system based on DNAs containing abasic sites and fluorescent ligands that bind abasic sites

A new class of label-free molecular beacon (MB) system based on DNA strands that contain abasic (AP) sites (AP-DNA) and adopt stem-loop structures, in combination with fluorescent ligands that bind these AP sites, has been developed. Unlike a conventional MB, which requires covalent labeling of the MB with a fluorophore and a quencher, the developed system (APMB) does not require covalent attachment of signal transduction units. Detailed sensing functions of a series of APMB systems were examined with the aid of the fluorescent ligand named ATMND to provide insight into the design strategy for APMB systems. The effects of the stem length and the position of the AP site in the stem moiety on the fluorescence response of the APMB system were examined. Genotyping of a G/C SNP of PCR amplification products was successfully demonstrated with the APMB system and blue-fluorescent ATMND as a ligand. The APMB system was further extended to a system that utilized green-fluorescent lumiflavin.     

Nb2O5·nH2O as a heterogeneous catalyst with water-tolerant Lewis acid sites

Niobic acid, Nb(2)O(5)·nH(2)O, has been studied as a heterogeneous Lewis acid catalyst. NbO(4) tetrahedra, Lewis acid sites, on Nb(2)O(5)·nH(2)O surface immediately form NbO(4)-H(2)O adducts in the presence of water. However, a part of the adducts can still function as effective Lewis acid sites, catalyzing the allylation of benzaldehyde with tetraallyl tin and the conversion of glucose into 5-(hydroxymethyl)furfural in water.     

Shape- and size-controlled synthesis in hard templates: sophisticated chemical reduction for mesoporous monocrystalline platinum nanoparticles

Here we report a novel hard-templating strategy for the synthesis of mesoporous monocrystalline Pt nanoparticles (NPs) with uniform shapes and sizes. Mesoporous Pt NPs were successfully prepared through controlled chemical reduction using ascorbic acid by employing 3D bicontinuous mesoporous silica (KIT-6) and 2D mesoporous silica (SBA-15) as a hard template. The particle size could be controlled by changing the reduction time. Interestingly, the Pt replicas prepared from KIT-6 showed polyhedral morphology. The single crystallinity of the Pt fcc structure coherently extended over the whole particle.     

Investigation of thermal hazard during the hydrosilylation of 1,6-divinyl(perfluorohexane) with trichlorosilane

In this study, we examined the reaction hazard during the hydrosilylation reaction between trichlorosilane (TCS) and 1,6-divinyl(perfluorohexane) (FDV) in the presence of a butanol solution of chloroplatinic acid (Pt-Cat) as the catalyst. Assuming the three industrial risks of excessive addition of Pt-Cat, contamination by iron rust and mixing with cooling water, we observed the temperature and pressure change of TCS/FDV with an excessive amount of Pt-Cat, TCS/FDV/Pt-Cat with Fe₂O₃ and TCS/FDV/Pt-Cat with distilled water, using an accelerating rate calorimeter (ARC). The temperature and pressure greatly increased, especially in the sample with Fe₂O₃. For instance, in TCS/FDV/Pt-Cat with 1.5 wt.% Fe₂O₃, the heat release rate exceeded 624 K · min^?1 and the pressure rose above 25 MPa during the exothermic reaction.     

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions

Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins.     

Effects of temperature and anion species on CO2 permeability and CO2/N2 separation coefficient through ionic liquid membranes

The permeability of carbon dioxide (CO₂) through imidazolium-based ionic liquid membranes was measured by a sweep gas method. Six species of ionic liquids were studied in this work as follows: [emim][BF₄], [bmim][BF₄], [bmim][PF₆], [bmim][Tf₂N], [bmim][OTf], and [bmim][dca]. The ionic liquids were supported with a polyvinylidene fluoride porous membrane. The measurements were performed at T = (303.15 to 343.15) K. The partial pressure difference between feed and permeate sides was 0.121 MPa. The permeability of the CO₂ increases with temperature for the all ionic liquid species. Base on solution diffusion theory, it can be explained that the diffusion coefficient of CO₂ in an ionic liquid affects the temperature dependence more strongly than the solubility coefficient. The greatest permeability was obtained with the [bmim][Tf₂N] membrane. The membrane of [bmim][PF₆] presents the lowest permeability.The separation coefficient between CO₂ and N₂ through the ionic liquid membranes was also investigated at the volume fraction of CO₂ at feed side 0.10. The separation coefficient decreases with the increase of temperature for the all ionic liquid species. The membrane of [emim][BF₄] and [bmim][BF₄] gives the highest separation coefficient at constant temperature. The lowest separation coefficient was obtained from [bmim][Tf₂N] membrane which presents the highest permeability of CO₂.     

Development of quality assessment method for optically active food flavor chemicals

A quality assessment method for commercially available, optically active flavor compounds, namely, menthol, menthyl acetate, borneol, perillaldehyde, and 1,8-cineol, was developed. A gas chromatograph equipped with a flame ionization detector and a DB-5ms capillary column was used for the chemical purity test. A GC/MS with a beta-DEX cyclodextrin column was used for the optical purity test, by which the enantiomeric separation of each flavor compound was achieved. Enantiomeric excess was calculated as an expression of optical purity. Of the 25 standard samples subjected to the chemical purity test, six were found to have lower purity than the data provided by the manufacturers. When the same samples were subjected to the optical purity test, 11 were found to have lower purity than that indicated on the reagent labels. These results suggest that there is a need to conduct an optical purity test, in addition to a chemical purity test, for the quality assessment of flavor standards.     

Determination of proline enantiomers in honey and royal jelly by LC-UV

The chiral separation and quantification of D-proline and L-proline in honey and royal jelly were examined by LC with UV detection. Most of the endogenous compounds existing in honey, such as sugars, were removed by using SPE cartridges containing C18 and strong cation-exchange sorbent. Other components, such as primary amino acids, were also removed by two-step derivatization with o-phthalaldehyde (OPA) and 9-fluorenylmethyl chloroformate (FMOC-CI). The components that were derivatized with OPA were separated from proline with a C18 cartridge. Proline was then converted into an FMOC derivative that could be subsequently measured by LC-UV. Sufficient chiral separation of D-proline and L-proline was achieved with an LC chiral column made of a beta-cyclodextrin phase in the polar organic-phase mode. The average recoveries of D-proline and L-proline from honey and royal jelly were in the range of 81.3-98.6% (RSD of < 1.8%). When this method was applied to commercial honey and royal jelly samples, L-proline was detected at concentrations of 369-1930 microg/g, whereas D-proline was not detected.     

Rational development of caged-biotin protein-labeling agents and some applications in live cells

Biotin-(strept)avidin complex is widely used in biotechnology because of its extremely high binding constant, but there is no report describing spatiotemporally controlled formation of the complex in live cells. Here, based on X-ray crystal structure analysis and calorimetric data, we designed and synthesized photoreleasable biotins, which show greatly reduced affinity for (strept)avidin, but recover native affinity after UV irradiation. For application at the cell surface, we introduced an amine-reactive moiety into these "caged" biotin molecules. Specific fluorescence imaging of live cells that had been labeled with these agents and then UV-irradiated, was accomplished by addition of streptavidin conjugated with a fluorophore. We also demonstrated the applicability of these compounds for UV-irradiated-cell-specific drug delivery by using caged-biotin-labeled cells, a prodrug, and streptavidin conjugated with a prodrug-activating enzyme.