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

• Project/Area Number: 15K18515
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biophysics
• Research Institution: Kyoto 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: ¥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.

Research Products

• [Int'l Joint Research] ラウエランジュバン研究所(フランス)
• [Int'l Joint Research] ANSTO(オーストラリア)
• [Journal Article] New insight into the dynamical system of αB-crystallin oligomers (2016)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF4 (2016)
  • 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
  • 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 scattering (2016)
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering (2015)
  • 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
  • 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 scatterings (2015)
  • 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
  • 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 range (2015)
  • 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
  • Peer Reviewed
• [Presentation] Inter-dynamics of protein as studied by small-angle neutron scattering (2017)
  • Author(s): Rintaro Inoue
  • Organizer: Neutron Biology for Next Generation
  • Place of Presentation: J-PARC
  • Year and Date: 2017-03-22
  • Int'l Joint Research / Invited
• [Presentation] Dynamic Quaternary Structure of Alpha-Crystallin (2016)
  • 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
  • Int'l Joint Research / Invited
• [Remarks] 研究室ホームページ
  • URL: http://www.rri.kyoto-u.ac.jp/PSlab/