Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins of Bacillus subtilis membrane based on a proteomic approach

We analyzed ABC transporter solute-binding proteins (SBPs) of the Bacillus subtilis membrane using a proteomic approach. We prepared a washed cell membrane fraction that was insoluble in 134 mM nondetergent sulfobetaine and then extracted proteins using mixtures of detergents in a stepwise manner. The membrane proteins were resolved by three two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) or two one-dimensional (1-D) PAGE procedures, electroblotted, and digested in the presence of 5% or 80% acetonitrile. Thereafter, matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS) identified 637 proteins corresponding to 15.9% of the total cellular proteins. We predicted that among these, 256 were membrane proteins, 101 were lipoproteins or secretory proteins and 280 were soluble proteins containing peripheral proteins that function in both the cytoplasm and the cell membrane such as SecA and FtsY. Among the 637 proteins, we identified 30 SBPs among 38 importers predicted by a bioinformatic search of the genome. We confirmed expression of the genes for the 30 SBPs using DNA microarray analysis. We compared the 2-D gel separation profiles of submembrane fractions solubilized by 1% n-dodecyl-beta-D-maltoside from cells cultured on Luria Bertani (LB), S7, and S7 medium without glutamate as well as DNA microarray data on LB and S7. The results suggested that YcdH, YtmK and YurO are binding proteins for Mn(++), glutamate and glucose, respectively, and that YqiX and YxeM are binding proteins for amino acids (tryptophan in S7 medium).     

Synthesis of pyrimidine derivatives by the reaction of ketene dithioacetals with amides

Reactions of methyl 2-cyano-3,3-bis(methylthio)acrylate ( 1a ) with carboxamides 2a-g in the presence of sodium hydride in a mixture of benzene and N,N-dimethylacetamide took place displacement with the methylthio group to give the corresponding methyl 3-N-acylamino-2-cyano-3-(methylthio)acrylates 3a-g which were readily converted to the corresponding pyrimidine derivatives at reflux in methanol in good yields. Reactions of 2-cyano-3,3-bis(methylthio)acrylonitrile ( 1b ) with the carboxamides 2a-f gave directly pyrimidine-5-carbonitrile derivatives 7a-f . Ketene dithioacetals 1a,b smoothly reacted with thioamide 2g or urea 2h,i to give the expected pyrimidine derivatives 9,10a,b . Polyfunctionalized pyrimidines, thus obtained, were also used for the synthesis of fused pyrimidine derivatives.     

Dissipative structures formed in the course of drying the colloidal crystals of silica spheres on a cover glass

Macroscopic and microscopic dissipative structural patterns formed in the course of drying the deionized aqueous colloidal crystal suspensions of silica spheres (diameter: 103 nm) on a cover glass have been observed. Spoke-like and ring-like patterns are formed in the macroscopic scale; the former is the crack in the sphere film and the latter is the hill accumulated with spheres formed around the outside edge. The neighbored inter-spoke angle, thickness of the film, and other morphological parameters have been discussed as a function of sphere concentration, concentration of sodium chloride, and the inclined angle of the cover glass. Fractal patterns of the mud cracks are observed in the microscopic scale. Capillary forces between spheres at the air-liquid surface and the relative rates between the water flow at the drying front and the convection flow of spheres are important for the pattern formation. Electronic Publication     

Structural colors in nature: the role of regularity and irregularity in the structure.

Coloring in nature mostly comes from the inherent colors of materials, but it sometimes has a purely physical origin, such as diffraction or interference of light. The latter, called structural color or iridescence, has long been a problem of scientific interest. Recently, structural colors have attracted great interest because their applications have been rapidly progressing in many fields related to vision, such as the paint, automobile, cosmetics, and textile industries. As the research progresses, however, it has become clear that these colors are due to the presence of surprisingly minute microstructures, which are hardly attainable even by ultramodern nanotechnology. Fundamentally, most of the structural colors originate from basic optical processes represented by thin-film interference, multilayer interference, a diffraction grating effect, photonic crystals, light scattering, and so on. However, to enhance the perception of the eyes, natural creatures have produced various designs, in the course of evolution, to fulfill simultaneously high reflectivity in a specific wavelength range and the generation of diffusive light in a wide angular range. At a glance, these two characteristics seem to contradict each other in the usual optical sense, but these seemingly conflicting requirements are realized by combining appropriate amounts of regularity and irregularity of the structure. In this Review, we first explain the fundamental optical properties underlying the structural colors, and then survey these mysteries of nature from the viewpoint of regularity and irregularity of the structure. Finally, we propose a general principle of structural colors based on structural hierarchy and show their up-to-date applications.     

Convergent synthesis of the ABCDE ring fragment of ciguatoxins

Synthesis of the ABCDE ring fragment of ciguatoxins has been achieved in a highly stereocontrolled and convergent manner via the B-alkyl Suzuki-Miyaura coupling-based approach.     

Long-range magnetic ordering of quasi-one-dimensional S=1/2 Heisenberg antiferromagnet Sr2Cu(PO4)2

Magnetic properties of quasi-one-dimensional S=1/2 Heisenberg antiferromagnet Sr₂Cu(PO₄)₂ were investigated by temperature and field dependence of AC susceptibility down to 0.03 K. A sharp peak was observed at on the temperature dependence of AC susceptibility indicating long-range magnetic ordering. Taking into account the exchange constant, (Hamiltonian =J∑S_iS_i+1), the ratio k_BT_N/J is 0.06%. Sr₂Cu(PO₄)₂ is, therefore, one of the best one-dimensional Heisenberg antiferromagnet known so far.     

Collective dynamics of sub- and supercritical methanol by inelastic X-ray scattering

Inelastic X-ray scattering experiments have been performed on methanol as a function of density from ambient to the supercritical state. Positive dispersion of the sound velocity, as compared to the hydrodynamic values, is 50% in the ambient condition and decreases to zero at 0.50 g cm⁻³ over the momentum transfer Q = 1–10 nm⁻¹ with lowering density; however, it increases again with a further decrease in density down to 0.20 g cm⁻³in the supercritical state only in the Q-range above 5 nm⁻¹. These results have been interpreted as the formation of small oligomers in the low-density supercritical methanol.     

Diastereoselective imino-aldol condensation of chiral 3-(p-Tolylsulfinyl)-2-furaldimine and ester enolates

(Ss)-3-(p-Tolylsufinyl)-2-furaldimine was synthesized, and condensation of the chiral furaldimine with lithium ester enolates has been examined. The product distribution of the reaction is dependent upon reaction conditions and on the kind of the substituent placed on the esters. Disubstituted ester enolate resulted in the exclusive formation of (4R)-beta-lactam, while unsubstituted, tert-butyl ester enolate preferentially gave (3R)-beta-amino ester. With the monosubstituted ester enolates, the condensation afforded (4R)-beta-lactams and/or (3R)-beta-amino esters as major products. This method has been applied to an efficient route to chiral furyl beta-lactams.     

Reversed-phase liquid chromatographic retention and membrane activity relationships of local anesthetics

The chromatographic retention and membrane activity relationships of local anesthetics were studied to address the possible mechanisms for structure specificity and inflammation-associated decrease of their effects. Five representative drugs (3 mM for each) were reacted with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine liposomes in 25 mM potassium phosphate buffer (pH 5.9-7.9, containing 100 mM NaCl and 0.1 mM EDTA) for 10 min at 37 degrees C and the membrane fluidity changes were analyzed by measuring fluorescence polarization with 1,6-diphenyl-1,3,5-hexatriene. Their capacity factors were determined on octadecyl-, octyl- and phenyl-bonded silica columns with a mobile phase consisting of 25 mM potassium phosphate buffer (pH 5.9-7.9, containing 100 mM NaCl and 0.1 mM EDTA)-methanol (30:70, v/v) at a flow rate of 1.0 ml/min and at a column temperature of 37 degrees C and diode-array detection. Mepivacaine, prilocaine, lidocaine, ropivacaine and bupivacaine fluidized membranes in increasing order of intensity, which agreed with their clinical potency. The relative degree of membrane fluidization correlated with that of retention on an octadecyl stationary phase more significantly than the other phases. Both membrane-fluidizing effects and capacity factors decreased by lowering the reaction and mobile phase pH, being consistent with the hypothesis that anesthetic potency is reduced in inflammation because of tissue acidity. Reversed-phase liquid chromatography appears to be useful for estimating the structure-specific and pH-dependent membrane-fluidizing effects of local anesthetics.     

How constant are Ritchie's "constant selectivity relationships"? A general reactivity scale for n-, pi-, and sigma-nucleophiles

The kinetics of 82 reactions of benzhydrylium ions (Ar(2)CH(+)) with n-nucleophiles has been determined at 20 degrees C. Evaluation by the equation log k = s(N + E) delivered the reactivity parameters N and s for 15 n-nucleophiles (water, hydroxide, amines, etc.). All nucleophiles except water (s = 0.89) and (-)SCH(2)CO(2)(-) (s = 0.43) have closely similar slope parameters (0.52 < s < 0.71), indicating that the reactions of most n-nucleophiles approximately follow Ritchie's constant selectivity relationship (s = constant). The different slope parameter for water is recognized as the main reason for the deviations from the Ritchie relationship reported in 1986. Correlation analysis of the rate constants for the reactions of benzhydrylium ions with the n-nucleophiles (except H(2)O) on the basis of Ritchie's equation log k = N(+) + log k(0) yields a statistically validated set of N(+) parameters for Ritchie-type nucleophiles and log k(0) parameters for benzhydrylium ions. The N and s parameters of the n-nucleophiles derived from their reactions with benzhydrylium ions were combined with literature data for the reactions of these nucleophiles with other carbocations to yield electrophilicity parameters E for tritylium, tropylium, and xanthylium ions. While the E parameters for tropylium and xanthylium ions appear to be generally applicable, it is demonstrated that the E parameters of tritylium ions can be used to predict reactivities toward n-nucleophiles as well as hydride transfer rate constants but not rates for the reactions of tritylium ions with pi-nucleophiles. It is now possible to merge the large data sets determined by Ritchie and others with our kinetic data and present a nucleophilicity scale comprising n- (e.g., amines), pi- (e.g., alkenes and arenes), and sigma-nucleophiles (e.g., hydrides).