Biomedical subjects

Kazunori Yanagi

Publications and source records attributed to Kazunori Yanagi.

6 recordsLinked to original sources

PubMed2005

Cloning, purification, crystallization and preliminary X-ray diffraction analysis of nitrile hydratase from the themophilic Bacillus smithii SC-J05-1.

Nitrile hydratase (NHase) converts nitriles to the corresponding amides and is recognized as having important industrial applications. Purification, cloning, crystallization and initial crystallographic studies of the NHase from Bacillus smithii SC-J05-1 (Bs NHase) were conducted to analyze the activity, specificity and thermal stability of this hydrolytic enzyme. Bs NHase was purified to homogeneity from microbial cells of B. smithii SC-J05-1 and the nucleotide sequences of both the alpha- and beta-subunits were determined. Purified Bs NHase was used for crystallization and several crystal forms were obtained by the vapour-diffusion method. Microseeding and the addition of magnesium ions were essential components to obtain crystals suitable for X-ray diffraction analysis.

Bacillus↗

PubMed2005

18O-labeling quantitative proteomics using an ion trap mass spectrometer.

We describe a method for simultaneous identification and quantitation of proteins within complex mixtures. The method consists of 18O-labeling, a simple stable isotope-coding that requires merely enzymatic digestion in 18O-water, in combination with a capillary-liquid chromatography electrospray ion-trap mass spectrometer. In a separate experiment using the same sample and a spike test, we demonstrate that the difference ration was calculated accurately using the 18O-labeling method even if the protein was part of a complex mixture. Our data also suggest that the accuracy of the quantitation can be improved by averaging the difference ratios of several peptides. In comparing our method with the isotope-coded affinity tag (ICAT) method, we show that the 18O-labeling method has the advantages of better recovery and fewer isotope effects. Therefore, the 18O-labeling method is a powerful tool for large-scale proteomics applications.

Animals↗

PubMed2003

Ubiquitination-mediated regulation of biosynthesis of the adhesion receptor SHPS-1 in response to endoplasmic reticulum stress.

Misfolding of proteins during endoplasmic reticulum (ER) stress results in the formation of cytotoxic aggregates. The ER-associated degradation pathway counteracts such aggregation through the elimination of misfolded proteins by the ubiquitin-proteasome system. We now show that SHP substrate-1 (SHPS-1), a transmembrane glycoprotein that regulates cytoskeletal reorganization and cell-cell communication, is a physiological substrate for the Skp1-Cullin1-NFB42-Rbx1 (SCF(NFB42)) E3 ubiquitin ligase, a proposed mediator of ER-associated degradation. SCF(NFB42) mediated the polyubiquitination of immature SHPS-1 and its degradation by the proteasome. Ectopic expression of NFB42 both suppressed the formation of aggresome-like structures and the phosphorylation of the translational regulator eIF2alpha induced by overproduction of SHPS-1 as well as increased the amount of mature SHPS-1 at the cell surface. An NFB42 mutant lacking the F box domain had no such effects. Our results suggest that SCF(NFB42) regulates SHPS-1 biosynthesis in response to ER stress.

Amino Acid Sequence↗

PubMed2003

Crystal structure of nitrile hydratase from a thermophilic Bacillus smithii.

The crystal structure of the nitrile hydratase (NHase) from Bacillus smithii SC-J05-1 was determined. Our analysis of the structure shows that some residues that seem to be responsible for substrate recognition are different from those of other NHases. In particular, the Phe52 in the beta subunit of NHase from B. smithii covers the metal center partially like a small lid and narrows the active site cleft. It is well known that the NHase from B. smithii especially prefers aliphatic nitriles for its substrate rather than aromatic ones, and we can now infer that the Phe52 residue may play a key role in the substrate specificity for this enzyme. This finding leads us to suggest that substitution of these residues may alter the substrate specificity of the enzyme.

Bacillus↗

PubMed2002

Synthesis and fungicidal activity of 1-(alpha-tert-butylcinnamoyl)imidazoles.

Several 1-(alpha-tert-butylcinnamoyl)imidazoles were prepared to examine their fungicidal activity. The (Z)-4-chlorocinnamoyl derivative was prepared from (anti)-2-tert-butyl-3-(4-chlorophenyl)-3-hydroxypropanoic acid by treating with 1,1'-carbonyldiimidazole and a subsequent beta-elimination reaction at an elevated temperature. The (Z)-isomer of the 4-chlorocinnamoyl derivative showed good fungicidal activity against Erysiphe graminis and Botrytis cinerea in pot tests, whereas the corresponding (E)-isomer derived from the (Z)-isomer through photoisomerization was much less active.

Ascomycota↗

PubMed1996

Synthesis of Novel Heteroquaterphenoquinones and Their Electrochemical, Structural, and Spectroscopic Characterization.

Novel heteroquaterphenoquinones, 5,5'-bis(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadien-1-ylidene)-5,5'-dihydro-2,2'-bithienyl (3) and its 2,2'-biselenienyl (4), 2,2'-bifuryl (5), and 2,2'-bi-N-methylpyrrolyl (6) analogues, were synthesized by a stepwise cross-coupling reaction or by a more convenient one-pot oxidative homocoupling reaction of heterocycle-substituted phenols. Despite a highly conjugation-extended system, the quinones 3-6 are very stable in the solid state and in solution in common organic solvents. These quinones undergo a reversible one-stage, two-electron reduction up to dianions and a two-stage, one-electron oxidation reaction up to dications. The E(1)(red) of these quinones increases with the increase in the aromaticity of the incorporated heterocycles. The E(1)(ox) of these quinones appears to be specified by the ionization potential of the incorporated heterocycles. Thus, the N-methylquinone 6 exhibiting the lowest E(1)(ox) value exhibits the smallest E(1)(sum) among the quinones 3-6. The quinone 5 was revealed to exist in an unusual O-cis conformation in the solid state by X-ray crystallography, whereas the quinone 3 exists in an S-trans conformation in the solid state. The cis and trans isomers are interconvertible in solution in 3-5, whereas only N-trans isomer was detected for 6 in (1)H NMR spectroscopy. The quinones 3-6 exhibit a very intense absorption maximum in the near-infrared region of 662-827 nm. Of these, the maximum absorption wave length of 6 shifts to a more bathochromic region by 149-165 nm than those of 3-5. The quinones 3-6 can be used as dyestuffs in various fields for laser-driven high-density optical storage media.

Journal Article↗