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RIKEN Center for Biosystems Dynamics Research Laboratory for Dynamic Biomolecule Design

Team Leader: Ai Niitsu (Ph.D.)

Research Summary

Ai Niitsu

To understand functions of biomolecules, it is crucial to grasp their structural dynamics. The Laboratory for Dynamic Biomolecule Design aims to develop methods for designing biomolecules, such as membrane proteins and peptides, with controllable conformational dynamics through combination of protein design and molecular simulation techniques. Our primary objective is to uncover the mechanisms governing biomolecular functions through experimental characterization of the designed molecules. By incorporating a chemical perspective, we also aim to expand the application of our designed biomolecules as tools for perturbing cell dynamics, imaging cells and tissues, and sensing environment, useful to life science research.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Chemistry
  • Interdisciplinary Science & Engineering
  • Bio-related Chemistry
  • Biophysics-related


  • Protein Design
  • Synthetic Biology
  • Chemistry
  • Molecular Simulation
  • Biomembrane

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1. C. Tan, A. Niitsu, and Y. Sugita
    "Highly charged proteins and their repulsive interactions antagonize biomolecular condensation”
    J. Am. Chem. Soc. Au 3, 834 (2023)
  • 2. A. Niitsu and Y. Sugita
    "Towards de novo design of transmembrane alpha-helical assemblies using structural modelling and molecular dynamics simulation”
    Phys. Chem. Chem. Phys. 25, 3595 (2023)
  • 3. *A.J. Scott, A. Niitsu, H.T. Kratochvil, et al.
    "Constructing ion-channels from water-soluble alpha-helical barrels”
    Nat. Chem., 13, 643 (2021)
  • 4. A. Niitsu, S. Re, H. Oshima, M. Kamiya, and Y. Sugita
    "De novo prediction of binders and nonbinders for T4 Lysozyme by gREST simulations”
    J. Chem. Inf. Model. 59 (9), 3879 (2019)
  • 5. A. Niitsu, A. Egawa, K. Ikeda, K. Tachibana, and T. Fujiwara
    "Veratridine binding to a transmembrane helix of sodium channel Nav1.4 determined by solid-state NMR”
    Bioorg. Med. Chem. 26, 5644 (2018)
  • 6. *F. Thomas, A. Niitsu, A. Oregioni, G. Bartlett, and D.N. Woolfson
    "Conformational dynamics of asparagine at coiled-coil interfaces”
    Biochemistry 56, 6544 (2017)
  • 7. *A. Niitsu, J.W. Heal, K. Fauland, A.R. Thomson, and D.N. Woolfson
    "Membrane-spanning alpha-helical barrels as tractable protein-design targets”
    Phil. Trans. B 372, 20160213 (2017)
  • 8. *K.R. Mahendran, A. Niitsu, L. Kong, R.B. Session, A.R. Thomson, D.N. Woolfson, and H. Bayley
    "A monodisperse alpha-helical peptide barrel”
    Nat. Chem. 9, 411 (2017)

Related Links

Lab Members

Principal investigator

Ai Niitsu
Team Leader


Position Deadline
Seeking a Postdoctoral Researcher (Y24031) Open until filled

Contact Information

Room W209, West Building
1-7-22 Suehiro-cho, Tsurumi-ku
Yokohama, Kanagawa
230-0045, Japan
Email: ai.niitsu [at] riken.jp