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

Development of new analysis of protein dynamics as studied by MD-NSE

Research Project

Project/Area Number 15K18515
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionKyoto University

Principal Investigator

Inoue Rintaro  京都大学, 原子炉実験所, 准教授 (80563840)

Project Period (FY) 2015-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Keywords中性子散乱 / 蛋白質 / ダイナミクス / スピンエコー法 / MDシミュレーション / MD-simulation / NSE
Outline of Final Research Achievements

It is known that protein domain motion is highly relevant to its intrinsic function, however the experimental method and analysis has not been well-established. In order to overcome such a situation, we tried to establish the method that can describe protein domain motion properly through the combination of neutron spin echo (NSE) and MD simulation, "MD-NSE". By comparing the Q dependence of diffusion coefficient (D(Q)) derived from NSE to that calculated from the trajectory of MD simulation, experimentally observed D(Q) was described by the combination of rotational diffusion and domain motion, nicely. In addition, it was revealed that domain motion from MD simulation mainly corresponded to the opening and closing of two domains from careful analysis on MD simulation results. Finally, we succeeded to describe the protein domain dynamics by newly developed MD-NSE method.

Report

(3 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • Research Products

    (12 results)

All 2017 2016 2015 Other

All Int'l Joint Research (2 results) Journal Article (7 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 7 results,  Open Access: 4 results,  Acknowledgement Compliant: 3 results) Presentation (2 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results) Remarks (1 results)

  • [Int'l Joint Research] ラウエランジュバン研究所(フランス)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] ANSTO(オーストラリア)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] New insight into the dynamical system of αB-crystallin oligomers2016

    • Author(s)
      R. Inoue, T. Takata, N. Fujii, K. Ishii, S. Uchiyama, N. Sato, Y. Oba, K. Wood, K. Kato, N. Fujii, and M. Sugiyama
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 29208-29208

    • DOI

      10.1038/srep29208

    • NAID

      120006323745

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF42016

    • Author(s)
      E. Hibino, R. Inoue, M. Sugiyama, J. Kuwahara, K. Matsuzaki, and M. Hoshino
    • Journal Title

      Protein Science

      Volume: 25 Issue: 11 Pages: 2006-2017

    • DOI

      10.1002/pro.3013

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structural characterization of the circadian clock protein complex composed of KaiB and KaiC by inverse contrast matching small-angle neutron scattering2016

    • Author(s)
      M. Sugiyama, H. Yagi, K. Ishii, L. Porcar, A. Martel, K. Oyama, M. Noda, Y. Yunoki, R. Murakami, R. Inoue, N. Sato, Y. Oba, K. Terauchi, S. Uchiyama, K. Kato
    • Journal Title

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 35567-35567

    • DOI

      10.1038/srep35567

    • NAID

      120006223630

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Studies on dynamics of polybutadiene reinforced with an unsaturated carboxylate by muon spin relaxation (μSR)2016

    • Author(s)
      R. Mashita, H. Kishimoto, R. Inoue A. Koda, R. Kadono and T. Kanaya
    • Journal Title

      Polymer

      Volume: 105 Pages: 510-515

    • DOI

      10.1016/j.polymer.2016.07.050

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering2015

    • Author(s)
      61.E. Chatani, R. Inoue, H. Imamura, M. Sugiyama, M. Kato, M. Yamamoto, K. Nishida and T. Kanaya
    • Journal Title

      Scientific Report

      Volume: 5 Issue: 1 Pages: 15485-15498

    • DOI

      10.1038/srep15485

    • NAID

      120005672389

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Solution structure of variant H2A.Z.1 nucleosome investigated by small-angle X-ray and neutron scatterings2015

    • Author(s)
      M. Sugiyama, N. Horikoshi, Y. Suzuki, H. Taguchi, T. Kujirai, R. Inoue, Y. Oba, N. Sato, A. Martel, L. Porcar, and H. Kurumizaka
    • Journal Title

      Biochemistry and Biophysics Reports

      Volume: 4 Pages: 28-32

    • DOI

      10.1016/j.bbrep.2015.08.019

    • NAID

      120005893550

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A small-angle X-ray scattering study of gliadins in distilled water over a wide concentration range2015

    • Author(s)
      N. Sato, A. Matsumiya, Y. Higashino, S. Funaki, Y. Kitao, Y. Oba, R. Inoue, F. Arisaka, M. Sugiyama, and R. Urade, Molecular assembly of wheat gliadins into nanostructures
    • Journal Title

      Journal of Agricultural and Food Chemistry

      Volume: 63 Issue: 39 Pages: 8715-8721

    • DOI

      10.1021/acs.jafc.5b02902

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Presentation] Inter-dynamics of protein as studied by small-angle neutron scattering2017

    • Author(s)
      Rintaro Inoue
    • Organizer
      Neutron Biology for Next Generation
    • Place of Presentation
      J-PARC
    • Year and Date
      2017-03-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamic Quaternary Structure of Alpha-Crystallin2016

    • Author(s)
      R. Inoue, T. takumi, N. Fujii, K. Ishii, S. Uchiyama, N. Sato, Y. Oba, K. Wood, K. Kato, N. Fujii, M. Sugiyama
    • Organizer
      The 7th Japan-Taiwan Joint Meeting on Neutron and X-ray Scattering
    • Place of Presentation
      京都大学原子炉実験所
    • Year and Date
      2016-03-11
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Remarks] 研究室ホームページ

    • URL

      http://www.rri.kyoto-u.ac.jp/PSlab/

    • Related Report
      2016 Annual Research Report

URL: 

Published: 2015-04-16   Modified: 2018-03-22  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi