Biomedical subjects

Nobuo Tanaka

Publications and source records attributed to Nobuo Tanaka.

At least 37 records · Page 2Linked to original sources

PubMed2006

Enhanced sequence coverage in tryptic fragment analysis by two-dimensional HPLC/MS using a monolithic silica capillary column.

The HPLC/MS system, in which a monolithic silica capillary column is directly connected to an electronspray-ionization mass spectrometer, showed superior performance at high mobile phase linear velocity. A two-dimensional (2D) HPLC/MS system was established, using an ion-exchange particle-packed capillary column at the first dimension and a monolithic silica capillary column at the second dimension. In an analysis of tryptic fragments from bovine serum albumin, an 81% sequence coverage, obtained by the 2D-HPLC/MS system, increased by 23% as compared to a 1D-HPLC/MS system. This 2D-HPLC/MS system using a monolithic silica capillary column should be useful for enhancing sequence coverage of tryptic fragments in proteomics.

Amino Acid Sequence↗

PubMed2006

Properties of monolithic silica columns for HPLC.

Monolithic silica columns and their use in high peak-capacity HPLC separations are reviewed. Monolithic silica columns can potentially provide higher overall performance than particle-packed columns based on the variable external porosity and variable through-pore size/skeleton size ratios. The high permeability of monolithic silica columns resulting from the high porosity is shown to be advantageous to generate large numbers of theoretical plates with long capillary columns. High permeability together with the high stability of the network structures of silica allows their use in high-speed separations required for a second-dimension column in two dimensional HPLC. Disadvantages of monolithic silica columns are also described.

Benzene Derivatives↗

PubMed2005

Faster axial band dispersion in a monolithic silica column than in a particle-packed column.

The contribution of molecular diffusion to peak broadening was studied in a reversed-phase HPLC system, consisting of a monolithic silica C18 column and methanol-water mobile phase. Study on the band broadening effect of holding a solute in a column or elution at very low linear velocity of mobile phase allowed facile determination of the contribution of the molecular diffusion term. Less obstruction against molecular diffusion, or the faster axial band dispersion in a monolithic silica column than in a particle-packed column, was found both in mobile phase and in stationary phase.

Benzene Derivatives↗

PubMed2005

Crystallization and preliminary crystallographic analysis of endo-1,3-beta-glucanase from alkaliphilic Nocardiopsis sp. strain F96.

Endo-1,3-beta-glucanase, an enzyme that hydrolyzes the 1,3-beta-glycosyl linkages of beta-glucan, belongs to the family 16 glycosyl hydrolases, which are widely distributed among bacteria, fungi and higher plants. Crystals of a family 16 endo-1,3-beta-glucanase from the alkaliphilic Nocardiopsis sp. strain F96 were obtained by the hanging-drop vapour-diffusion method. The crystals belonged to space group P2(1), with unit-cell parameters a = 34.59, b = 71.84, c = 39.67 A, beta = 90.21 degrees, and contained one molecule per asymmetric unit. The Matthews coefficient (VM) and solvent content were 1.8 A3 Da(-1) and 31.8%, respectively. Diffraction data were collected to a resolution of 1.3 A and gave a data set with an overall Rmerge of 6.4% and a completeness of 99.3%.

Actinomycetales↗

PubMed2005

Two-dimensional reversed-phase liquid chromatography using two monolithic silica C18 columns and different mobile phase modifiers in the two dimensions.

Comprehensive two-dimensional (2D) HPLC in the reversed-phase liquid chromatography (RPLC) mode using C18 silica monolith columns at first dimension (1st-D) (10 cm x 4.6mm I.D.) and second dimension (2nd-D) (5 cm x 4.6mm I.D.) was carried out successfully. A mixture of water and tetrahydrofuran (THF) was used as a mobile phase in the 1st-D separation, and a mixture of water and methanol (CH3OH) in the 2nd-D separation. Sample fractions from 1st-D column were directly loaded into an injection loop of the 2nd-D HPLC equipped with two injector valves for one column. The fractionation time at the 1st-D that was equal to the separation time at the 2nd-D was 45 or 60s. Total peak capacity up to 900 was obtained in about 60 min for the isocratic mode separation of aromatic compounds in this system. Gradient elution mode applied to both 1st-D and 2nd-D separations resulted in shorter separation time and better separation efficiencies than the isocratic mode. It was demonstrated that 2D-HPLC systems employing popular C18 stationary phases with different organic modifiers in mobile phases for each dimension could produce large peak capacity. The different selectivities were provided by the difference in polar interactions between a solute and the organic modifier existing in the stationary phase.

Chromatography, High Pressure Liquid↗

PubMed2005

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.

Bacterial Proteins↗

PubMed2005

A simple method for minimizing non-linear image contrast in spherical aberration-corrected HRTEM.

A simple and practical method for minimizing non-linear image contrast in spherical aberration-corrected (C(S)-corrected) high-resolution transmission electron microscopy is presented. The effectiveness of the method is considered from the viewpoints of theoretical formulations and image simulations including second-order imaging effects. The method is one of the advantages of C(S)-correction and applied to high-resolution images down to 0.1 nm. The dynamical diffraction effect is carefully evaluated, which shows that the phase deviation of diffracted waves from pi/2 violates the present method in thicker crystals over approximately 10 nm.

Journal Article↗

PubMed2005

Preparation of a novel molecularly imprinted polymer using a water-soluble crosslinking agent.

A molecularly imprinted polymer was prepared using a water-soluble crosslinking agent. An ionic complex was utilized as the assembly for the template molecule and the functional monomer, and water as porogenic solvent during preparation of the imprinted polymer. The results of chromatographic evaluations for the prepared polymer suggested that the polymer had much lower hydrophobicity compared with usual octadecyl group bonded silica or the usual molecular imprinted polymer prepared from ethyleneglycol dimethacrylate, and the selective recognition ability for template molecule in the completely aqueous condition.

Journal Article↗

PubMed2005

Precipitation diagram and optimization of crystallization conditions at low ionic strength for deglycosylated dye-decolorizing peroxidase from a basidiomycete.

The growth of suitably sized protein crystals is essential for protein structure determination by X-ray crystallography. In general, crystals are grown using a trial-and-error method. However, these methods have been modified with the advent of microlitre dispensing-robot technology and of protocols that rapidly screen for crystal nucleation conditions. The use of one such automatic dispenser for mixing protein drops (1.3-2.0 microl in volume) of known concentration and pH with precipitating solutions (ejecting 2.0 microl droplets) containing salt is described here. The results of the experiments are relevant to a crystallization approach based on a two-step procedure: screening for the crystal nucleation step employing robotics followed by optimization of the crystallization conditions using incomplete factorial experimental design. Large crystals have successfully been obtained using quantities as small as 3.52 mg protein.

Basidiomycota↗

PubMed2005

Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics.

A recombinant 2-deoxy-scyllo-inosose synthase from Bacillus circulans has been crystallized at 277 K using PEG 4000 as precipitant. The diffraction pattern of the crystal extends to 2.30 A resolution at 100 K using synchrotron radiation at the Photon Factory. The crystals are monoclinic and belong to space group P2(1), with unit-cell parameters a = 80.5, b = 70.4, c = 83.0 A, beta = 117.8 degrees. The presence of two molecules per asymmetric unit gives a crystal volume per protein weight (VM) of 2.89 A3 Da(-1) and a solvent constant of 57.4% by volume.

Aminoglycosides↗

PubMed2005

First experiments of selected area nano-diffraction from semiconductor interfaces using a spherical aberration corrected TEM.

Selected area diffraction (SAD) from localized areas that are approximately 20 nm in diameter has been demonstrated for the first time using a spherical-aberration-corrected transmission electron microscope (Cs-corrected TEM). We have succeeded in obtaining sharp diffraction patterns from well-defined areas on both sides of the interface between a Ti-Si-Ge alloy and Si0.54Ge0.46. The errors in the area selection by an SAD aperture are reduced to <2 nm by the Cs-correction. The applications of this technique in studies of nanometer-sized materials are discussed.

Letter↗

PubMed2005

Novel surface modified molecularly imprinted polymer focused on the removal of interference in environmental water samples for chromatographic determination.

Uniformly sized molecularly imprinted polymers (MIPs) for bisphenol A (BPA) with surface modification and immobilized intervals of functional monomers afforded by utilizing 4,4'-methylenebisphenol as a pseudo component have been prepared. MIPs for BPA were prepared using 4-vinyl pyridine immobilized in the most effective interval and ethylene glycol dimethacrylate as a functional monomer and cross-linking agent, respectively. Prepared MIPs showed significant selectivity for BPA retention and removal performance for interference in actual samples as the HPLC stationary phase compared to those of ordinary MIPs. These MIPs were employed as pretreatment media of column switching HPLC and the HPLC system provided a detection limit of 0.36 ppt when electrochemical detection was used. Actual samples, including Suwannee River natural organic matter (NOM), were applied and BPA was detected in the NOM even if widely used UV detection was employed.

Chromatography, High Pressure Liquid↗

PubMed2005

Silica monolithic membrane as separation medium. Summable property of different membranes for high-performance liquid chromatographic separation.

We studied an applicability of a silica monolithic membrane as separation medium for high-performance liquid chromatography (HPLC). We prepared porous monolithic silica membranes having a three-dimensional network structure to cut and shape into a membrane separation medium. We evaluated chromatographic properties of a variety of solutes using a column containing the membranes with HPLC to elucidate summable property of the membrane separation media. In addition, we made brief study on separation of HbA1c in whole blood with the stacked" membranes having different surface characteristics in one column, which is a membrane column. We confirmed that the membrane column was able to separate HbA1c from other matrix in whole blood to some extent, and it also had an excellent ability for hydrophobic and ion exchange adsorption.

Chromatography, High Pressure Liquid↗

PubMed2005

LC/MS determination of bisphenol A in river water using a surface-modified molecularly-imprinted polymer as an on-line pretreatment device.

A new analytical method for the determination of bisphenol A (BPA) by LC/MS was developed and applied to environmental water samples. Quantitative MS detection of BPA was carried out in the negative mode. In order to preconcentrate the target compound yet prevent serious contamination of the water samples from the experimental environment, we employed column switching HPLC coupled with a pretreatment column of surface-modified molecularly-imprinted polymers. The recovery of BPA from a spiked environmental water sample was 102% and the repeatability of actual determinations of water samples containing 20 ng/L of BPA was 5.4% RSD. By modifying the surfaces of the molecularly-imprinted polymer particles packed in the pretreatment column, interference from the water samples was effectively removed, resulting in a significant increase in sensitivity and more reliable results. This method was successfully applied to the trace determination of BPA in environmental water samples using LC/MS.

Benzhydryl Compounds↗

PubMed2005

Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity.

A novel method has been developed to improve protein-crystal perfection during crystallization in a high magnetic field and structural studies have been undertaken. The three-dimensional structure of orthorhombic hen egg-white (HEW) lysozyme crystals grown in a homogeneous and static magnetic field of 10 T has been determined and refined to a resolution of 1.13 angstroms and an R factor of 17.0%. The 10 T crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.54 (3), b = 73.86 (6), c = 30.50 (2) angstroms and one molecule per asymmetric unit. A comparison of the structures of the 0 T and 10 T crystals has been carried out. The magnitude of the structural changes, with a root-mean-square deviation value of 0.75 angstroms for the positions of all protein atoms, is similar to that observed when an identical protein structure is resolved in two different crystalline lattices. The structures remain similar, with the exception of a few residues e.g. Arg68, Arg73, Arg128 and Gln121. The shifts of the arginine residues result in very significant structural fluctuations, which can have large effects on a protein's crystallization properties. The high magnetic field contributed to an improvement in diffraction intensity by (i) the displacement of the charged side chains of Arg68 and Arg73 in the flexible loop and of Arg128 at the C-terminus and (ii) the removal of the alternate conformations of the charged side chains of Arg21, Lys97 or Arg114. The improvement in crystal perfection might arise from the magnetic effect on molecular orientation without structural change and differences in molecular interactions. X-ray diffraction and molecular-modelling studies of lysozyme crystals grown in a 10 T field have indicated that the field contributes to the stability of the dihedral angle. The average difference in conformational energy has a value of -578 kJ mol(-1) per charged residue in favour of the crystal grown in the magnetic field. For most protein atoms, the average B factor in the 10 T crystal shows an improvement of 1.8 angstroms(2) over that for the 0 T control; subsequently, the difference in diffraction intensity between the 10 T and 0 T crystals corresponds to an increase of 22.6% at the resolution limit. The mosaicity of the 10 T crystal was better than that of the 0 T crystal. More highly isotropic values of 0.0065, 0.0049 and 0.0048 degrees were recorded along the a, b and c axes, respectively. Anisotropic mosaicity analysis indicated that crystal growth is most perfect in the direction that corresponds to the favoured growth direction of the crystal, and that the crystal grown in the magnetic field had domains that were three times the volume of those of the control crystal. Overall, the magnetic field has improved the quality of these crystals and the diffracted intensity has increased significantly with the magnetic field, leading to a higher resolution.

Animals↗

PubMed2005

Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis.

Growth-limiting stresses in bacteria induce the general stress response to protect the cells against future stresses. Energy stress caused by starvation conditions in Bacillus subtilis is transmitted to the sigma(B) transcription factor by stress-response regulators. RsbP, a positive regulator, is a phosphatase containing a PAS (Per-ARNT-Sim) domain and requires catalytic function of a putative alpha/beta hydrolase, RsbQ, to be activated. These two proteins have been found to interact with each other. We determined the crystal structures of RsbQ in native and inhibitor-bound forms to investigate why RsbP requires RsbQ. These structures confirm that RsbQ belongs to the alpha/beta hydrolase superfamily. Since the catalytic triad is buried inside the molecule due to the closed conformation, the active site is constructed as a hydrophobic cavity that is nearly isolated from the solvent. This suggests that RsbQ has specificity for a hydrophobic small compound rather than a macromolecule such as RsbP. Moreover, structural comparison with other alpha/beta hydrolases demonstrates that a unique loop region of RsbQ is a likely candidate for the interaction site with RsbP, and the interaction might be responsible for product release by operating the hydrophobic gate equipped between the cavity and the solvent. Our results support the possibility that RsbQ provides a cofactor molecule for the mature functionality of RsbP.

Bacillus subtilis↗

PubMed2005

Two-dimensional separation system of coupling capillary liquid chromatography to capillary electrophoresis for analysis of Escherichia coli metabolites.

A two-dimensional (2-D) separation system of coupling chromatography to electrophoresis was developed for profiling Escherichia coli metabolites. Capillary liquid chromatography (LC) with a monolithic silica-octadecyl silica column (500 x 0.2 mm ID) was used as the first dimension, from which the effluent fractions were further analyzed by capillary electrophoresis (CE) acting as the second dimension. Field-enhanced stacking was selectively employed as a concentration strategy to interface the two dimensions, which proved to be beneficial for the detection of metabolites. An artificial sample containing 118 standards, some of which lack chromophores or have weak UV absorbance, was used to optimize the 2-D separation system. Under the optimum conditions, 63 components in the artificial sample having absorbance at 254 nm could be well resolved and detected. The utility of the system was demonstrated by comprehensive analysis of E. coli metabolites. Comparing with the previous 2-D separation system we published in Anal. Chem. 2004, 76, 1419-1428, using a longer monolithic column in the first dimension improved the separation efficiency and offered the possibility of increasing the injection volume without compromising the separation efficiency. In the second dimension, field-enhanced stacking was used to improve the concentration sensitivity of the metabolites, and more metabolites in E. coli cell extract were detected and identified using the developed 2-D separation system. In addition, preliminary investigation for future CE-mass spectrometry coupling was also made in the study by using volatile buffers in the capillary LC and CE techniques.

Amino Acids↗

PubMed2005

A new simply and effective fractionation method for cylindrospermopsin analyses.

A new simply and effective fractionation method for cylindrospermopsin (CYN) analyses was developed. The extract from cells of Cylindrospermopsis raciborskii was resuspended with 0.1 M carbonate buffer at pH 10.5, and pass through the double-cartridges column which was consisted of a styrene polymer cartridge and an anion exchange cartridge. CYN and deoxy-CYN were adsorbed with the anion exchange cartridge. After separation of the anion exchange cartridge, adsorbed compounds were eluted from the cartridge with 50% methanol containing 1% formic acid solution. CYN and deoxy-CYN were selectively condensed in the eluted solution. When CYN was analyzed by LC-photodiode array or LC/MS, only two peaks of CYN and deoxy-CYN were detected quantitatively. The results suggest that the fractionation method is a useful method for CYN analyses and must be utilized for CYN purification.

Alkaloids↗