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Research Scientist Hiraku Oshima

EDUCATION

2004 B.S., Department of Physics, School of Science, Kyushu University
2006 M.S., Department of Physics, Graduate School of Science, Kyushu University
2009 Ph.D.(Science), Department of Physics, Graduate School of Science, Kyushu University

RESEARCH AND TEACHING EXPERIENCES

2009-2011 Researcher, Pioneering Research Unit for Next Generation, Kyoto University
2011-2013 Postdoctoral Fellow, Institute of Advanced Energy, Kyoto University
2013-2016 Research Fellow of the Japan Society for the Promotion of Science (PD), Institute of Advanced Energy, Kyoto University
2016-2018 Postdoctoral Researcher, RIKEN Quantitative Biology Center
2018-present Research Scientist, RIKEN Center for Biosystems Dynamics Research
2019 Part-time lecturer, Graduate School of System Informatics, Kobe University

AWARDS

2020 The 20th Annual Meeting of the Protein Science Society of Japan, Young Scientist Excellence Award

PROFESSIONAL AFFILIATIONS

The Physical Society of Japan, The Biophysical Society of Japan, The Protein Science Society of Japan, The Biophysical Society(US)

RESEARCH PROJECTS

  1. Application of the free-energy calculation for the ligand-receptor binding to drug discovery.
  2. Development of free-energy calculation methods

PUBLICATIONS

  1. 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)
  2. Free-energy Calculation of Protein–Ligand Binding Using Molecular Dynamics Simulation Software “GENESIS”.
    Hiraku Oshima, Suyong Re, Ai Niitsu, Yuji Sugita
    Simulation (Journal of Japan Society for Simulation Technology), 40, 22–28 (2021)(in Japanese)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. Population Shift Mechanism for Partial Agonism of AMPA Receptor.
    H. Oshima1, S. Re, M. Sakakura, H. Takahashi, Y. Sugita.
    Biophysical Journal, 116, 57-68 (2019).
  13. 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).
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18. 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).
  19. 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).
  20. 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).
  21. 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).
  22. 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).
  23. Effects of sugars on the thermal stability of a protein.
    H. Oshima and M. Kinoshita.
    J. Chem. Phys., 138, 245101 (2013).
  24. 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).
  25. Structural stability of proteins in aqueous and nonpolar environments.
    S. Yasuda, H. Oshima, and M. Kinoshita.
    J. Chem. Phys., 137, 135103 (2012).
  26. 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).
  27. Boundary Perturbation Analysis of Complex Networks.
    H. Oshima and T. Odagaki.
    J. Phys. Soc. Japan, 81, 124009 (2012).
  28. Finite Memory Walk and Its Application to Small-World Network.
    H. Oshima and T. Odagaki.
    J. Phys. Soc. Japan, 81, 074004 (2012).
  29. 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).
  30. 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).
  31. 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).
  32. 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).
  33. 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).
  34. 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).
  35. 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).
  36. Storage capacity and retrieval time of small-world neural networks.
    H. Oshima and T. Odagaki.
    Phys. Rev. E, 76, 036114 (2007).
  37. 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).