Akiko Shimizu‐Ibuka

ORCID: 0000-0002-5310-9216
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Research Areas
  • Antibiotic Resistance in Bacteria
  • Biochemical Analysis and Sensing Techniques
  • Olfactory and Sensory Function Studies
  • Enzyme Structure and Function
  • Enzyme Production and Characterization
  • Advanced Chemical Sensor Technologies
  • Antibiotics Pharmacokinetics and Efficacy
  • Food Chemistry and Fat Analysis
  • Bacterial biofilms and quorum sensing
  • Microbial Natural Products and Biosynthesis
  • Amino Acid Enzymes and Metabolism
  • Phytase and its Applications
  • Vibrio bacteria research studies
  • Glycosylation and Glycoproteins Research
  • RNA and protein synthesis mechanisms
  • Bacterial Genetics and Biotechnology
  • Neurobiology and Insect Physiology Research
  • Antimicrobial Resistance in Staphylococcus
  • Carbohydrate Chemistry and Synthesis
  • Tuberculosis Research and Epidemiology
  • Microbial Metabolites in Food Biotechnology
  • Ocular Infections and Treatments
  • Protein Structure and Dynamics
  • Adipose Tissue and Metabolism
  • Phytoestrogen effects and research

Niigata University of Pharmacy and Medical and Life Sciences
2015-2024

Kanagawa University
2023-2024

University Medical Center
2024

Niigata University
2024

Ehime University Hospital
2024

Yamagata University
2012-2016

The University of Tokyo
1995-2015

Tokyo University of Agriculture
2006-2012

University of Shizuoka
1999-2008

Nippon Shinyaku (Japan)
2008

Bacterial resistance to β-lactam antibiotics is a serious problem limiting current clinical therapy. The most common form of the production β-lactamases that inactivate antibiotics. Toho-1 an extended-spectrum β-lactamase has acquired efficient activity not only penicillins but also cephalosporins including expanded-spectrum were developed be stable in former β-lactamases. We present acyl-intermediate structures complex with cefotaxime (expanded-spectrum cephalosporin), cephalothin...

10.1074/jbc.m207884200 article EN cc-by Journal of Biological Chemistry 2002-11-01

Miraculin (MCL) is a homodimeric protein isolated from the red berries of Richadella dulcifica. MCL, although flat in taste at neutral pH, has taste-modifying activity to convert sour stimuli sweetness. Once MCL held on tongue, strong sweetness sensed over 1 h each time we solution. Nevertheless, no molecular mechanism underlying been clarified. In this study, succeeded quantitatively evaluating acid-induced using cell-based assay system and found that activated hT1R2-hT1R3 pH-dependently as...

10.1073/pnas.1016644108 article EN Proceedings of the National Academy of Sciences 2011-09-26

ABSTRACT Neoculin (NCL), a protein with sweetness approximately 500-fold that of sugar, can be utilized as nonglycemic sweetener. It also has taste-modifying activity to convert sourness sweetness. NCL is heterodimer composed an N -glycosylated acidic subunit (NAS) and basic (NBS), which are conjugated by disulfide bonds. For the production recombinant (rNCL) Aspergillus oryzae , α-amylase KEX2 cleavage site, -K-R-, was fused upstream each NAS NBS resulting fusion proteins were...

10.1128/aem.72.5.3716-3723.2006 article EN Applied and Environmental Microbiology 2006-05-01

The crystallographic structure of the class A β-lactamase Toho-1, an extended-spectrum with potent activity against expanded-spectrum cephems, has been determined at 1.65 Å resolution. result reveals that Lys73 side chain can adopt two alternative conformations. predominant conformation is different from observed in E166A mutant, indicating removal Glu166 changes and thus interaction between Glu166. would play important role proton relay, switching its one to other depending on...

10.1021/bi0342822 article EN Biochemistry 2003-08-21

The pyruvate kinase (PK) from a moderate thermophile, Geobacillus stearothermophilus, is an allosteric enzyme activated by AMP and ribose 5-phosphate but not fructose 1, 6-bisphosphate (FBP), which common activator of PKs. It has extra C-terminal sequence (ECTS), contains highly conserved phosphoenolpyruvate (PEP) binding motif, its function structure remain unclear. To elucidate the structural characteristics effector-binding site ECTS, crystal C9S/C268S mutant was determined at 2.4 Å...

10.1093/jb/mvn069 article EN The Journal of Biochemistry 2008-05-15

We identified epicatechin-(4 β→6)-epicatechin-(2 β→O→7, 4 β→8)-catechin (EEC) in the skin of peanut (Arachis hypogaea L.). EEC (a trimer) showed more potent cholesterol micelle-degrading activity than procyanidin A1 dimer) did vitro. The hypercholesterolemia suppressing effect a polyphenol on rats fed high-cholesterol diet our preceding experiments might thus have been due primarily to micelle degrading intestine.

10.1271/bbb.121023 article EN Bioscience Biotechnology and Biochemistry 2013-06-06

ABSTRACT The heterologous production in Escherichia coli , the purification, and kinetic characterization of four plasmid-encoded class C β-lactamases (ACT-1, MIR-1, CMY-2, CMY-1) were performed. Except for their instability, these enzymes are very similar to known chromosomally encoded AmpC β-lactamases. Their parameters did not show major differences from those obtained corresponding chromosomal enzymes. However, K m values CMY-2 cefuroxime, cefotaxime, oxacillin significantly decreased...

10.1128/aac.49.10.4240-4246.2005 article EN Antimicrobial Agents and Chemotherapy 2005-09-27

Neoculin (NCL) is a sweet protein that also has taste-modifying activity to convert sourness sweetness. However, it been unclear how NCL induces this unique sensation. Here we quantitatively evaluated the pH-dependent acid-induced sweetness of using cell-based assay system. The human taste receptor, hT1R2-hT1R3, was functionally expressed in HEK293T cells together with G alpha protein. When applied under different pH conditions, activated hT1R2-hT1R3 manner as condition changed from 8 5....

10.1096/fj.07-100289 article EN The FASEB Journal 2008-02-08

Peanut skin contains large amounts of polyphenols having antiallergic effects. We found that a peanut-skin extract (PSE) inhibits the degranulation induced by antigen stimulation rat basophilic leukemia (RBL-2H3) cells. A low-molecular-weight fraction from PSE, PSEL, also had inhibitory activity against allergic degranulation. main polyphenol in PSEL was purified gel chromatography and fractionated YMC-gel ODS-AQ 120S50 column. Electrospray ionization mass spectrometry (ESI-MS) analysis gave...

10.1271/bbb.110085 article EN Bioscience Biotechnology and Biochemistry 2011-09-07

Among more than 20 yeast strains isolated from the traditional starter "murcha" in Nepal, we characterized a that might be involved saccharification. This strain, identified as Pichia burtonii, produced an extracellular amylolytic enzyme when cultured presence of starch medium. Since no amylase secreted by P. burtonii has yet been reported, purified and determined its N-terminal amino acid sequence. Together with results hydrolyzing activity assay toward various substrates, it was found to...

10.1271/bbb.60430 article EN Bioscience Biotechnology and Biochemistry 2006-12-23

Neoculin, a sweet protein occurring in Curculigo latifolia, is unique that it also has taste-modifying activity capable of converting sourness to sweetness. Calcium imaging analysis with HEK cells expressing the human taste receptor, hT1R2/T1R3 demonstrated intracellular calcium concentration increased following addition 20 μM neoculin. The use lactisole, blocker hT1R3, inhibited increase almost completely. In sensory tests, when acetate buffers different pH values were placed on tongue...

10.1097/01.wnr.0000230513.01339.3b article EN Neuroreport 2006-08-01

Peanut skin (PS) is characterized by almost exclusively consisting of polyphenols and fiber. We fractionated PS into a water-soluble fraction (WSF) water-insoluble (WIF), further WSF soluble dietary fiber (DF) fiber-free, (DFF-WSF). Male Sprague-Dawley rats were fed on high-cholesterol diets supplemented with its fractions. PS, WSF, DFF-WSF decreased the serum lipid cholesterol levels increased those in feces. This effect was probably due to that inhibited intestinal absorption.

10.1271/bbb.80539 article EN Bioscience Biotechnology and Biochemistry 2009-01-23

Neoculin occurring in the tropical fruit of Curculigo latifolia is currently only protein that possesses both a sweet taste and taste-modifying activity converting sourness into sweetness. Structurally, this heterodimer consisting neoculin acidic subunit (NAS) basic (NBS). Recently, we found variant which all five histidine residues are replaced with alanine elicits intense sweetness at neutral pH but has no activity. To identify critical residue(s) responsible for activity, produced series...

10.1371/journal.pone.0019448 article EN cc-by PLoS ONE 2011-04-29

TVA I, an α-amylase from Thermoactinomyces vulgaris R-47, is a versatile enzyme which hydrolyzes the α-(1→4)-glucosidic linkages of pullulan to produce panose, known as neopullulanase activity, and α-(1→6)-glucosidic certain oligosaccharides. We modified Ala-357, Gln-359, Tyr-360 residues located in region II, one four regions conserved family enzymes, deleted 11 consecutive amino acid after C-terminus II I sequence by means site-directed mutagenesis. The action pattern mutated for was...

10.1093/oxfordjournals.jbchem.a021933 article EN The Journal of Biochemistry 1998-02-01

Feeding a high-cholesterol diet with water-soluble peanut skin polyphenol fraction to rats reduced their plasma cholesterol level, an increase in fecal excretion. The hypocholesterolemic effect was greater the lower-molecular-weight rather than higher-molecular-weight fraction. This possibly due some oligomeric polyphenols which solubility of dietary intestinal bile acid-emulsified micelles.

10.1271/bbb.110866 article EN Bioscience Biotechnology and Biochemistry 2012-04-09

We have previously found that fatty acids can mask the bitterness of certain nitrogenous substances through direct molecular interactions. Using isothermal titration calorimetry, we investigated interactions between sodium oleate and 22 bitter substances. The hydrochloride salts quinine, promethazine, propranolol interacted strongly with containing 12 or more carbon atoms. 1H NMR spectra these substances, obtained in presence dimethyl sulfoxide, revealed formation hydrogen bonds nitrogen...

10.1021/acs.jafc.5b03193 article EN publisher-specific-oa Journal of Agricultural and Food Chemistry 2015-09-12

An α-amylase secreted by Pichia burtonii 15-1 isolated from a traditional starter murcha of Nepal, named (PBA), was studied. The gene cloned and its nucleotide sequence determined. PBA deduced to consist 494 amino acid residues. It shared certain degrees identity with other homologous proteins: 60% Schwanniomyces occidentalis α-amylase, 58% Saccharomycopsis sp. 47% Taka-amylase A Aspergillus oryzae. three-dimensional structural model generated using the known structure as template suggested...

10.1271/bbb.70407 article EN Bioscience Biotechnology and Biochemistry 2007-12-23
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