メンバー構成員

研究員 尾嶋 拓

学歴

2004年 九州大学理学部物理学科 卒業
2006年 九州大学大学院理学府凝縮系科学修士課程 修了
2009年 九州大学大学院理学府凝縮系科学博士課程 修了 (博士(理学))

研究歴

2009年 京都大学次世代開拓研究ユニット 研究員
2011年 京都大学エネルギー理工学研究所 博士研究員
2013年 京都大学エネルギー理工学研究所 日本学術振興会特別研究員(PD)
2016年 理化学研究所生命システム研究センター 特別研究員
2016年 理化学研究所計算科学研究機構 特別研究員(兼務)
2018年-現在 理化学研究所生命機能科学研究センター 研究員
2018年-現在 理化学研究所計算科学研究センター 特別研究員(兼務)

教育歴

2019年-現在 神戸大学大学院システム情報学研究科 非常勤講師
2021年-現在 兵庫県立大学大学院情報科学研究科 理研クロスアポイントメント准教授(兼務)

受賞歴

2020年 第20回日本蛋白質科学会年会 若手奨励賞優秀賞

所属学会

日本物理学会、日本生物物理学会、日本蛋白質科学会、Biophysical Society

研究テーマ

  1. リガンド-レセプター結合自由エネルギー計算の創薬応用
  2. 自由エネルギー計算法の新規開発

出版物

  1. Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions.
    Daiki Matsubara, Kento Kasahara, Hisham M. Dokainish, Hiraku Oshima, and Yuji Sugita
    Molecules 27, 5726 (2022)
  2. Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions.
    H. Oshima and Y. Sugita
    J. Chem. Inf. Model. 62, 2846-2856 (2022)
  3. Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems.
    J. Jung, K. Kasahara, C. Kobayashi, H. Oshima, T. Mori, Y. Sugita
    J. Chem. Theory Comput. 17, 5312-5321 (2021)
  4. Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution.
    Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, and Yuji Sugita
    Nat. Comm., 12, 4099 (2021)
  5. 分子動力学ソフトウェアGENESISを用いたタンパク質―リガンド結合の自由エネルギー計算
    尾嶋 拓,李 秀栄,新津 藍,杉田 有治
    シミュレーション (日本シミュレーション学会), 40, 22–28 (2021)
  6. Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations.
    Weitong Ren, Hisham M Dokainish, Ai Shinobu, Hiraku Oshima, Yuji Sugita
    J. Phys. Chem. B, 125,2898-2909 (2021)
  7. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.
    S. Kim, H. Oshima, H. Zhang, N. R. Kern, S. Re, J. Lee, B. Roux, Y. Sugita, W. Jiang, W. Im
    J. Chem. Theory Comput., 16, 7207-7218 (2020)
  8. Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+FEP Method.
    H. Oshima, S. Re, Y. Sugita
    J. Chem. Inf. Model., 60, 5382-5394 (2020)
  9. Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis.
    D. Fujinami, H. Motomura, H. Oshima, Abdullah-Al Mahin, K. M. Elsayed, T. Zendo, Y. Sugita, K. Sonomoto, D. Kohda.
    J. Phys. Chem. Lett., 11, 1934-1939 (2020)
  10. Structural mechanisms underlying activity changes in an AMPA-type glutamate receptor induced by substitutions in its ligand-binding domain.
    M. Sakakura, Y. Ohkubo, H. Oshima, S. Re, M. Ito, Y. Sugita, and H. Takahashi.
    Structure, 27, 1698-1709 (2019)
  11. Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules.
    H. Oshima, S. Re, Y. Sugita.
    J. Chem. Theory Comput., 15, 5199-5208 (2019)
  12. Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape.
    S. Re, H. Oshima, K. Kasahara, M. Kamiya, and Y. Sugita
    Proc. Natl. Acad. Sci. USA, 116, 18404-18409 (2019)
  13. De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.
    A. Niitsu, S. Re, H. Oshima, M. Kamiya, Y. Sugita
    J. Chem. Inf. Model., 59, 3879-3888 (2019)
  14. Replica-Exchange Methods for Biomolecular Simulations.
    Y. Sugita, M. Kamiya, H. Oshima, S. Re
    In: Bonomi M., Camilloni C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022, Humana, New York, NY (2019)
  15. Population Shift Mechanism for Partial Agonism of AMPA Receptor.
    H. Oshima, S. Re, M. Sakakura, H. Takahashi, Y. Sugita.
    Biophysical Journal, 116, 57-68 (2019).
  16. Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed.
    T. Hayashi, H. Oshima, Y. Harano, and M. Kinoshita.
    J. Phys.: Condens. Matter, 28, 344003 (2016).
  17. Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects.
    H. Oshima, T. Hayashi, and M. Kinoshita.
    Biophys. J., 110, 2496-2506 (2016).
  18. A highly efficient hybrid method for calculating the hydration free energy of a protein.
    H. Oshima and M. Kinoshita.
    J. Comput. Chem., 37, 712-723 (2016).
  19. Mechanism of One-to-Many Molecular Recognition Accompanying Target-Dependent Structure Formation: For the Tumor Suppressor p53 Protein as an Example.
    T. Hayashi, H. Oshima, S. Yasuda, and M. Kinoshita.
    J. Phys. Chem. B, 119, 14120-14129 (2015).
  20. On the physics of thermal-stability changes upon mutations of a protein.
    S. Murakami, H. Oshima, T. Hayashi, and M. Kinoshita.
    J. Chem. Phys., 143, 125102 (2015).
  21. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water.
    H. Oshima and M. Kinoshita.
    J. Chem. Phys., 142, 145103 (2015).
  22. Statistical Thermodynamics for Functionally Rotating Mechanism of the Multidrug Efflux Transporter AcrB.
    H. Mishima, H. Oshima, S. Yasuda, and M. Kinoshita.
    J. Phys. Chem. B, 119, 3423-3433 (2015).
  23. Changes in hydrophobic and hydrophilic hydration properties caused by raising the pressure or by lowering the temperature.
    M. Kinoshita and H. Oshima.
    Chem. Phys. Lett., 610-611, 1-7 (2014).
  24. Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.
    T. Hayashi, H. Oshima, T. Mashima, T. Nagata, M. Katahira, and M. Kinoshita.
    Nucleic Acids Res., 42, 6861-6875 (2014).
  25. Entropic release of a big sphere from a cylindrical vessel.
    H. Mishima, H. Oshima, S. Yasuda, K.-I. Amano, and M. Kinoshita.
    Chem. Phys. Lett., 561-562, 159-165 (2013).
  26. Effects of sugars on the thermal stability of a protein.
    H. Oshima and M. Kinoshita.
    J. Chem. Phys., 138, 245101 (2013).
  27. On the physics of multidrug efflux through a biomolecular complex.
    H. Mishima, H. Oshima, S. Yasuda, K.-I. Amano, and M. Kinoshita.
    J. Chem. Phys., 139, 205102 (2013).
  28. Structural stability of proteins in aqueous and nonpolar environments.
    S. Yasuda, H. Oshima, and M. Kinoshita.
    J. Chem. Phys., 137, 135103 (2012).
  29. Characterization of Experimentally Determined Native-Structure Models of a Protein Using Energetic and Entropic Components of Free-Energy Function.
    H. Mishima, S. Yasuda, T. Yoshidome, H. Oshima, Y. Harano, M. Ikeguchi, and M. Kinoshita. J. Phys. Chem. B, 116, 7776-7786 (2012).
  30. Boundary Perturbation Analysis of Complex Networks.
    H. Oshima and T. Odagaki.
    J. Phys. Soc. Japan, 81, 124009 (2012).
  31. Finite Memory Walk and Its Application to Small-World Network.
    H. Oshima and T. Odagaki.
    J. Phys. Soc. Japan, 81, 074004 (2012).
  32. An efficient method for analyzing conformational properties of a polymer in solvent.
    K.-I. Amano, H. Oshima, and M. Kinoshita.
    Chem. Phys. Lett., 504, 7-12 (2011).
  33. Free-energy function for discriminating the native fold of a protein from misfolded decoys.
    S. Yasuda, T. Yoshidome, Y. Harano, R. Roth, H. Oshima, K. Oda, Y. Sugita, M.Ikeguchi, and M. Kinoshita.
    Proteins, 79, 2161-2171 (2011).
  34. Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes.
    H. Oshima, S. Yasuda, T. Yoshidome, M. Ikeguchi, and M. Kinoshita.
    Phys. Chem. Chem. Phys., 13, 16236-16246 (2011).
  35. Potential of mean force between a large solute and a biomolecular complex: A model analysis on protein flux through chaperonin system.
    K.-I. Amano, H. Oshima, and M. Kinoshita.
    J. Chem. Phys., 135, 185101 (2011).
  36. Effects of network structure on associative memory.
    H. Oshima and T. Odagaki.
    Modelling Perception with Artificial Neural Networks edited by C. R. Tosh and G. D. Ruxton, 134-148 (2010).
  37. Effects of side-chain packing on the formation of secondary structures in protein folding.
    S. Yasuda, T. Yoshidome, H. Oshima, R. Kodama, Y. Harano, and M. Kinoshita.
    J. Chem. Phys., 132, 065105 (2010).
  38. A theoretical analysis on characteristics of protein structures induced by cold denaturation.
    H. Oshima, T. Yoshidome, K.-I. Amano, and M. Kinoshita.
    J. Chem. Phys., 131, 205102 (2009).
  39. Storage capacity and retrieval time of small-world neural networks.
    H. Oshima and T. Odagaki.
    Phys. Rev. E, 76, 036114 (2007).
  40. Subway networks in cities.
    K. H. Chang, K. Kim, H. Oshima, and S.-M. Yoon.
    J. Korean Phys. Soc., 48 (SUPPL. 2), S143-S145 (2006).