• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to project page

2005 Fiscal Year Final Research Report Summary

Studies on the principle of protein architecture by the simplification of amino acid sequence

Research Project

Project/Area Number 16370074
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionNARA INSTITUTE OF SCIENCE AND TECHNOLOGY

Principal Investigator

KATAOKA Mikio  NARA INSTITUTE OF SCIENCE AND TECHNOLOGY, GRADUATE SCHOOL OF MATERIALS SCIENCE, PROFESSOR, 物質創成科学研究科, 教授 (30150254)

Co-Investigator(Kenkyū-buntansha) IMAMOTO Yasushi  NARA INSTITUTE OF SCIENCE AND TECHNOLOGY, GRADUATE SCHOOL OF MATERIALS SCIENCE, ASSOCIATE PROFESSOR, 物質創成科学研究科, 助教授 (80263200)
YAMAZAKI Yoichi  NARA INSTITUTE OF SCIENCE AND TECHNOLOGY, GRADUATE SCHOOL OF MATERIALS SCIENCE, INSTRUCTOR, 物質創成科学研究科, 助手 (40332770)
KAMIKUBO Hironari  NARA INSTITUTE OF SCIENCE AND TECHNOLOGY, GRADUATE SCHOOL OF MATERIALS SCIENCE, INSTRUCTOR, 物質創成科学研究科, 助手 (20311128)
Project Period (FY) 2004 – 2005
Keywordsphotoactive yellow protein / simplification of sequence / circular dichroism / structure-function relationship / amyloid / chromoprotein / PAS family / β scaffold
Research Abstract

In order to understand the information encoded in an amino-acid sequence, we have created variants of photoactive yellow protein (PYP) with simplified amino-acid sequences. We simplified the amino-acid sequence of PYP using a simple set of rules to reduce overlapping structural information. The simplified PYP protein (sPYP0), which was composed of only nine species of amino acids (Ser,Val,Asp,Lys,Phe,Met,Gly,Pro, and Cys), showed a completely different structure than the native conformation. Even after the evolutionarily conserved residues were restored in the simplified protein (sPYPI), the PYP variant did not properly fold. Additional restorations of the substituted hydrophobic (sPYPII) or hydrophilic residues (sPYPIII) did not lead to a variant that formed the native structure. sPYPIII only shows the tendency of helical formation by TFE. Partial simplification was successfully performed by creating chimeric proteins composed of combinations of wild-type PYP and sPYPIII. Hybrid mutants containing a wild-type β scaffold adopted native-like structures. In contrast, the hybrid mutants that contained the simplified β scaffold demonstrated a tendency to adopt non-native conformations, suggesting that there is a wealth of information about the formation of the structure in the β scaffold. 5 hydrophobic residues in the β scaffold were identified to be responsible for the structure formation. It is also demonstrated that sPYPII takes amyloid-like fibril structure.

  • Research Products

    (8 results)

All 2006 2004

All Journal Article (8 results)

  • [Journal Article] pH-Dependent equilibrium between lone-lived near-UV intermediates of photoactive yellow protein2006

    • Author(s)
      Nobutake Shimizu
    • Journal Title

      Journal of Biological Chemistry 281(7)

      Pages: 4318-4325

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pK_a Regulation in Photoactive Yellow Protein2006

    • Author(s)
      Nobutaka Shimizu
    • Journal Title

      Biochemistry 45(11)

      Pages: 3542-3547

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] pH-Dependent equilibrium between long-lived near-UV intermediates of photoactive yellow protein.2006

    • Author(s)
      N.Shimizu, Y.Imamoto, M.Harigai, H.Kamikubo, Y.Yamazaki, M.Kataoka
    • Journal Title

      J.Biol.Chem. 281

      Pages: 4318-4325

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pK_a Regulation in Photoactive Yellow Protein.2006

    • Author(s)
      N.Shimizu, H.Kamikubo, Y.Yamazaki, Y.Imamoto, M.Kataoka
    • Journal Title

      Biochemistry 45(11)

      Pages: 3542-3547

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Raman Spectroscopy Reveals the Origin of an Intermediate Wavelength Form in Photoactive Yellow Protein2004

    • Author(s)
      S.F.El-Mashtoly
    • Journal Title

      biochemistry 43

      Pages: 2279-2287

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Direct ovservation of the pH-dependent equilibrium between L-like and M intermediates of photoactive yellow protein2004

    • Author(s)
      Yasushi Imamoto
    • Journal Title

      FEBS Letters 577

      Pages: 75-80

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Raman Spectroscopy Reveals the Origin of an Intermediate Wavelength Form in Photoactive Yellow Protein.2004

    • Author(s)
      S.F.El-Mashtoly, M.Unno, M.Kumauchi, N.Hamada, K.Fujiwara, J.Sasaki, Y.Imamoto, M.Kataoka, F.Tokunaga, S.Yamauchi
    • Journal Title

      Biochemistry 43

      Pages: 2279-2287

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Direct observation of the pH-dependent equilibrium between L-like and M intermediates of photoactive yellow protein2004

    • Author(s)
      Y.Imamoto, M.Harigai, M.Kataoka
    • Journal Title

      FEBS Lett. 577

      Pages: 75-80

    • Description
      「研究成果報告書概要(欧文)」より

URL: 

Published: 2007-12-13  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi