Senior research scientist Takaharu Mori


2008 Ph.D. (Science) Nagoya University, Japan
2005 M.A. (Chemistry) Tokyo University of Science, Japan
2003 B.S. (Chemistry) Tokyo University of Science, Japan

Research and Teaching experiences

2019- Senior research scientist, RIKEN Theoretical Molecular Science Laboratory, Japan
2013-2019 Research scientist, RIKEN Theoretical Molecular Science Laboratory, Japan
2013 Visiting Research Associate, Michigan State University, U.S.A
2012-2013 Special Postdoctoral Researcher, RIKEN Quantitative Biology Center, Japan
2011-2012 Postdoctoral Researcher, RIKEN Quantitative Biology Center, Japan
2008-2011 Contract Researcher, RIKEN Advanced Science Institute, Japan


2018 Protein Science Society of Japan, Young Scientist Excellence Award

Professional affiliations

The Biophysical Society of Japan, Biophysical Society (U.S.A), Protein Science Society of Japan, The Membrane Society of Japan, The molecular Simulation Society of Japan

Research projects

  1. Development of a new simulation technique (cryo-EM fitting etc.)
  2. Development of a new molecular dynamics simulation program
  3. Molecular dynamics simulations of membrane proteins


Peer Review Articles

  1. Molecular dynamics simulation with a large time step for accurate thermodynamic and kinetic properties of biological systems.
    J. Jung, K. Kasahara, C. Kobayashi, H. Oshima, T. Mori, and Y. Sugita
    J. Chem. Theory Comput., 17, 5312–5321 (2021)
  2. Efficient flexible fitting refinement with automatic error fixing for de novo structure modeling from cryo-EM density maps.
    T. Mori, G. Terashi, D. Matsuoka, D. Kihara, and Y. Sugita
    J. Chem. Inf. Model., 61, 3516–3528 (2021)
  3. Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein.
    T. Mori, J. Jung, C. Kobayashi, H. M. Dokainish, S. Re, and Y. Sugita
    Biophys. J., 120, 1060-1071 (2021)
  4. Multi-scale flexible fitting of proteins to cryo-EM density maps at medium resolution.
    M, Kulik, T. Mori, and Y. Sugita
    BFront. Mol. Biosci., 8, 631854 (2021)
  5. Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion.
    K. Matoba, T. Kotani, A. Tsutsumi, T. Tsuji, T. Mori, D. Noshiro, Y. Sugita, N. Nomura, S. Iwata, Y. Ohsumi, T. Fujimoto, H. Nakatogawa, M. Kikkawa, and N. N. Noda
    Nat. Struct. Mol. Biol., 27, 1185-1193 (2020).
  6. Implicit micelle model for membrane proteins using super-ellipsoid approximation.
    T. Mori and Y. Sugita
    J. Chem. Theory Comput., 16, 711-724 (2020).
  7. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.
    T. Mori, M. Kulik, O. Miyashita, J. Jung, F. Tama, Y. Sugita
    Structure, 27, 161-174 (2019).
  8. Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides.
    M. Kulik, T. Mori, Y. Sugita, J. Trylska
    Nucleic Acids Research, 46, 9960-9970 (2018).
  9. Dynamics of nitric oxide controlled by protein complex in bacterial system.
    E. Terasaka, K. Yamada, P.-H. Wang, K. Hosokawa, R. Yamagiwa, K. Matsumoto, S. Ishii, T. Mori, K. Yagi, H. Sawai, H. Arai, H. Sugimoto, Y. Sugita, Y. Shiro, and T. Tosha.
    Proc. Natl. Acad. Sci., U.S.A., 114, 9888-9893 (2017).
  10. GENESIS 1.1: a hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.
    C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita.
    J. Comput. Chem., 38, 2193-2206 (2017).
  11. Discrimination of native-like states of membrane proteins with implicit membrane-based scoring functions.
    B. Dutagaci, K. Wittayanarakul, T. Mori, M. Feig.
    J. Chem. Theory Comput., 13, 3049-3059 (2017).
  12. Tunnel formation inferred from the I-form structures of the proton-driven protein secretion motor SecDF.
    A. Furukawa, K. Yoshikaie, T. Mori, H. Mori, Y. V. Morimoto, Y. Sugano, S. Iwaki, T. Minamino, Y. Sugita, Y. Tanaka, and T. Tsukazaki.
    Cell Rep., 19, 895-901 (2017).
  13. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.
    O. Miyashita, C. Kobayashi, T. Mori, Y. Sugita, and F. Tama. J. Comput. Chem., 38, 1447-1461 (2017).
  14. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.
    I. Yu, T. Mori, T. Ando, R. Harada, J. Jung, Y. Sugita, and M. Feig.
    eLife, 5, e19274 (2016).
  15. Dimensionality of collective variables for describing conformational changes of a multi-domain protein.
    Y. Matsunaga, Y. Komuro, C. Kobayashi, J. Jung, T. Mori, and Y. Sugita.
    J. Phys. Chem. Lett., 7, 1446-1451 (2016).
  16. Crystal structures of SecYEG in lipidic cubic phase elucidate a precise resting and a peptide-bound state.
    Y. Tanaka, Y. Sugano, M. Takemoto, T. Mori, A. Furukawa, T. Kusakizako, K. Kumazaki, A. Kashima, R. Ishitani, Y. Sugita, O. Nureki, and T. Tsukazaki.
    Cell Reports, 13, 1561-1568 (2015).
  17. Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.
    M. Feig, R. Harada, T. Mori, I. Yu, K. Takahashi and Y. Sugita.
    J. Mol. Graph. Model., 58, 1-9 (2015).
  18. GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.
    J. Jung*, T. Mori*, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita.
    (*Equally contributed)
    WIREs Comput. Mol. Sci., 5, 310-323 (2015).
  19. Structural basis of Sec-independent membrane protein insertion by YidC.
    K. Kumazaki, S. Chiba, M. Takemoto, A. Furukawa, K. Nishiyama, Y. Sugano, T. Mori, N. Dohmae, K. Hirata, Y. Nakada-Nakura, A. D. Maturana, Y. Tanaka, H. Mori, Y. Sugita, F. Arisaka, K. Ito, R. Ishitani, T. Tsukazaki, and O. Nureki.
    Nature, 509, 516-520 (2014).
  20. Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations.
    J. Jung, T. Mori, and Y. Sugita.
    J. Comput. Chem., 35, 1064-1072 (2014).
  21. Surface-tension replica-exchange moleclar dynamics method for enhanced sampling of biological membrane systems.
    T. Mori, J. Jung, and Y. Sugita.
    J. Chem. Theory Comput., 9, 5629-5640 (2013).
  22. Efficient lookup table using a linear function of inverse distance squared.
    J. Jung, T. Mori, and Y. Sugita.
    J. Comput. Chem., 34, 2412-2420 (2013).
  23. Energetics of the presequence-binding poses in mitochondrial protein import through Tom20.
    Y. Komuro, N. Miyashita, T. Mori, E. Muneyuki, T. Saitoh, D. Kohda, and Y. Sugita.
    J. Phys. Chem. B, 117, 2864–2871 (2013).
  24. Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods.
    T. Mori, F. Ogushi, and Y. Sugita.
    J. Comput. Chem., 33, 286-293 (2012).
  25. Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data.
    M. Morita, A. V. S. K. Krishna Mohan, S. Ahmad, T. Mori, Y. Sugita, and K. Mizuguchi.
    BMC Biophysics, 4, 21 (2011).
  26. Dynamic structure of the polytheonamide B channel studied by normal mode analysis.
    T. Mori, H. Kokubo, S. Oiki, and Y. Okamoto.
    Mol. Simul., 37, 975-985 (2011).
  27. Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.
    S. Ahmad, Y. H. Singh, Y. Paudel, T. Mori, Y. Sugita, and K. Mizuguchi.
    BMC Bioinformatics, 11, 533 (2010).
  28. Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon.
    T. Mori, R. Ishitani, T. Tsukazaki, O. Nureki, and Y. Sugita.
    Biochemistry, 49, 945-950 (2010).
  29. Folding simulations of gramicidin A into the β-helix conformations: Simulated annealing molecular dynamics study.
    T. Mori and Y. Okamoto.
    J. Chem. Phys., 131, 165103 (2009).
  30. Conformational transition of Sec machinery inferred from bacterial SecYE structures.
    T. Tsukazaki, H. Mori, S. Fukai, R. Ishitani, T. Mori, N. Dohmae, A. Perederina, Y. Sugita, D. G. Vassylyev, K. Ito, and O. Nureki.
    Nature, 455, 988-992 (2008).
  31. Estimation of dye configuration from conventional chiroptical spectra of porphyrin Integrates: Combination of exciton theory with Monte Carlo molecular structural simulation.
    T. Yamamura, T. Mori, Y. Tsuda, T. Taguchi, and N. Josha.
    J. Phys. Chem. A, 111, 2128-2138 (2007).

Review Articles

  1. Weight average approaches for predicting dynamical properties of biomolecules.
    K. Yagi, S. Re, T. Mori, and Y. Sugita
    Curr. Opin. Struct. Biol., 72, 88-94 (2022).
  2. Overview of the “1SBA: integrative approaches towards understanding of gene expression” session at the 57th BSJ meeting.
    T. Mori and S. Sekine.
    Biophys. Rev., 12, 253-254 (2020).
  3. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.
    T. Mori, N. Miyashita, W. Im, M. Feig, and Y. Sugita.
    BBA-Biomembranes, 1858, 1635-1651 (2016).