KINDAI UNIVERSITY


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SHIMAMOTO Shigeru

Profile

FacultyDepartment of Life Science / Graduate School of Science and Engineering Research
PositionLecturer
Degree
Commentator Guidehttps://www.kindai.ac.jp/meikan/906-shimamoto-shigeru.html
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Last Updated :2020/04/04

Education and Career

Academic & Professional Experience

  •   2015 04 ,  - 現在, Faculty of Science and Engineering, Department of Life Science, Kindai University
  •   2011 04 ,  - 2014 03 , Faculty of Science and Engineering, Department of Life Science, Kindai University

Research Activities

Research Areas

  • Life sciences, Structural biochemistry
  • Nanotechnology/Materials, Molecular biochemistry
  • Life sciences, Pharmaceuticals - analytical and physicochemistry

Research Interests

  • protein folding, ITC, NMR

Published Papers

  • N-terminal HCV core protein fragment decreases 20S proteasome activity in the presence of PA28γ., Zheng Y, Shimamoto S, Maruno T, Kobayashi Y, Matsuura Y, Kawahara K, Yoshida T, Ohkubo T, Biochemical and biophysical research communications, Biochemical and biophysical research communications, 509(2), 590 - 595, Feb. 2019 , Refereed
  • Thermodynamic and NMR analyses of NADPH binding to lipocalin-type prostaglandin D synthase., Qin S, Shimamoto S, Maruno T, Kobayashi Y, Kawahara K, Yoshida T, Ohkubo T, Biochemical and biophysical research communications, Biochemical and biophysical research communications, 468(1-2), 234 - 239, Dec. 2015 , Refereed
  • H-1, C-13, and N-15 resonance assignments of mouse lipocalin-type prostaglandin D synthase/substrate analog complex, Shigeru Shimamoto, Hiroko Maruo, Takuya Yoshida, Tadayasu Ohkubo, BIOMOLECULAR NMR ASSIGNMENTS, BIOMOLECULAR NMR ASSIGNMENTS, 8(1), 129 - 132, Apr. 2014 , Refereed
    Summary:Lipocalin-type Prostaglandin D synthase (L-PGDS) acts as the PGD(2)-synthesizing enzyme in the brain of various mammalian species. It belongs to the lipocalin superfamily and is the first member of this family to be recognized as an enzyme. Although the solution and crystal structure of L-PGDS has been determined to understand the molecular mechanism of catalytic reaction, the structural analysis of L-PGDS in complex with its substrate remains to be performed. Here, we present the nearly complete assignment of the backbone and side chain resonances of L-PGDS/substrate analog (U-46619) complex. This study lays the essential basis for further understanding the substrate recognition mechanism of L-PGDS.
  • Chemical methods for producing disulfide bonds in peptides and proteins to study folding regulation., Okumura M, Shimamoto S, Hidaka Y, Current protocols in protein science, Current protocols in protein science, 76, 28.7.1 - 13, Apr. 2014 , Refereed
  • Chemical methods and approaches to the regioselective formation of multiple disulfide bonds., Shimamoto S, Katayama H, Okumura M, Hidaka Y, Curr. Protoc. Protein Sci., Curr. Protoc. Protein Sci., 76, 28.8.1 - 28.8.28, Apr. 2014 , Refereed
  • Folding of Peptides and Proteins: Role of Disulfide Bonds, Recent Developments., Hidaka Y, Shimamoto S, BioMol. Concepts, BioMol. Concepts, 4(6), 597 - 604, Dec. 2013 , Refereed
  • Effects of positively charged redox molecules on disulfide-coupled protein folding., Okumura M, Shimamoto S, Nakanishi T, Yoshida Y, Konogami T, Maeda S, Hidaka Y, FEBS Lett., FEBS Lett., 586(21), 3926 - 3930, Nov. 2012 , Refereed
  • A chemical method for investigating disulfide-coupled peptide and protein folding., Okumura M, Shimamoto S, Hidaka Y, FEBS J., FEBS J., 279(13), 2283 - 2295, Jul. 2012 , Refereed
  • Drug delivery system for poorly water-soluble compounds using lipocalin-type prostaglandin D synthase., Fukuhara A, Nakajima H, Miyamoto Y, Inoue K, Kume S, Lee Y.H, Noda M, Uchiyama S, Shimamoto S, Nishimura S, Ohkubo T, Goto Y, Takeuchi T, Inui T, J. Control. Release, J. Control. Release, 159(1), 143 - 150, Apr. 2012 , Refereed
  • The middle region of an HP1-binding protein, HP1-BP74, associates with linker DNA at the entry/exit site of nucleosomal DNA., Hayashihara K, Uchiyama S, Shimamoto S, Kobayashi S, Tomschik M, Wakamatsu H, No D, Sugahara H, Hori N, Noda M, Ohkubo T, Zlatanova J, Matsunaga S, Fukui K, The Journal of biological chemistry, The Journal of biological chemistry, 285(9), 6498 - 6507, Feb. 2010 , Refereed
  • Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR., Miyamoto Y, Nishimura S, Inoue K, Shimamoto S, Yoshida T, Fukuhara A, Yamada M, Urade Y, Yagi N, Ohkubo T, Inui T, J. Struct. Biol., J. Struct. Biol., 169(2), 209 - 218, Feb. 2010 , Refereed
  • Biochemical, functional, and pharmacological characterization of AT-56, an orally active and selective inhibitor of lipocalin-type prostaglandin D synthase., Irikura D, Aritake, K, Nagata N, Maruyama T, Shimamoto S, Urade Y, J. Biol. Chem., J. Biol. Chem., 284(12), 7623 - 7630, Mar. 2009 , Refereed
  • NMR solution structure of lipocalin-type prostaglandin D synthase: evidence for partial overlapping of catalytic pocket and retinoic acid-binding pocket within the central cavity., Shimamoto S, Yoshida T, Inui T, Gohda K, Kobayashi Y, Fujimori K, Tsurumura T, Aritake K, Urade Y, Ohkubo T, The Journal of biological chemistry, The Journal of biological chemistry, 282(43), 31373 - 31379, Oct. 2007 , Refereed

Misc

  • ITC Analysis of Ligand Binding to Lipocalin-type Prostaglandin D Synthase, Shigeru Shimamoto, Netsu Sokutei, 44, 3, 108, 116,   2017 07 , Refereed, 招待有り
  • Ligand Recognition Mechanism of Lipocalin-type Prostaglandin D Synthase, SHIMAMOTO Shigeru, YOSHIDA Takuya, OHKUBO Tadayasu, YAKUGAKU ZASSHI, 131, 11, 1575, 1581,   2011 , Refereed, 招待有り, 10.1248/yakushi.131.1575, http://ci.nii.ac.jp/naid/130001491111
    Summary:Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is a multi functional protein acting as a PGD2 synthesizing enzyme, a transporter or scavenger of various lipophilic ligands, and an amyloid β chaperon in the brain. L-PGDS is a member of the lipocalin superfamily and has the ability to bind various lipophilic molecules such as prostanoid, retinoid, bile pigment, and amyloid β peptide. However, the molecular mechanism for a wide variety of ligand binding has not been well understood. In this study, we determined by NMR the structure of recombinant mouse L-PGDS and L-PGDS/PGH2 analog complex. L-PGDS has the typical lipocalin fold, consisting of an eight-stranded β-barrel and a long α-helix. The interior of the barrel formed a hydrophobic cavity opening to the upper end of the barrel, the size of which was larger than those of other lipocalins and the cavity contained two pockets. Kinetic studies and molecular docking studies based on the result of NMR titration experiments provide the direct evidence for two binding sites for PGH2 and retinoic acid in the large cavity of L-PGDS. Structural comparison of L-PGDS/U-46619 complex with apo-L-PGDS showed that the H2-helix, CD-loop, and EF-loop located at the upper end of the β-barrel change the conformation to cover the entry of the cavity upon U-46619 binding. These results indicated that the two binding sites in the large cavity and induced fit mechanism were responsible for the broad ligand specificity of L-PGDS.