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
2018年 理化学研究所生命機能科学研究センター 研究員

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

出版物

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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).
  7. 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).
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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).
  13. 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).
  14. 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).
  15. 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).
  16. 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).
  17. Effects of sugars on the thermal stability of a protein.
    H. Oshima and M. Kinoshita.
    J. Chem. Phys., 138, 245101 (2013).
  18. 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).
  19. Structural stability of proteins in aqueous and nonpolar environments.
    S. Yasuda, H. Oshima, and M. Kinoshita.
    J. Chem. Phys., 137, 135103 (2012).
  20. 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).
  21. Boundary Perturbation Analysis of Complex Networks.
    H. Oshima and T. Odagaki.
    J. Phys. Soc. Japan, 81, 124009 (2012).
  22. Finite Memory Walk and Its Application to Small-World Network.
    H. Oshima and T. Odagaki.
    J. Phys. Soc. Japan, 81, 074004 (2012).
  23. 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).
  24. 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).
  25. 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).
  26. 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).
  27. 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).
  28. 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).
  29. 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).
  30. Storage capacity and retrieval time of small-world neural networks.
    H. Oshima and T. Odagaki.
    Phys. Rev. E, 76, 036114 (2007).
  31. 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).