PRESTO Researcher Ai Niitsu


2007 B.S., Department of Chemistry, School of Science, University of Tokyo
2009 M.S., Department of Chemistry, School of Science, University of Tokyo
2012 Ph.D. (Science), Department of Chemistry, School of Science, University of Tokyo


2008 Visiting Researcher, the Scripps Research Institute, USA
2009-2012 Research Fellowship for Young Scientists from Japan Society for the Promotion of Science
2012-2016 Research Accociate, University of Bristol, UK
2016-2017 Postdoctoral Reseacher, RIKEN, Quantitative Biology Center
2017-2021 Special Postdoctoral Researcher, Theoretical Molecular Science Laboratory
2021-present JSPS Research Fellow (RPD), Theoretical Molecular Science Laboratory


2015 Gordon Research Conference (membrane protein folding, MA, USA) Outstanding Poster Award
2017 Protein Science Society of Japan, Young Scientist Excellence Award
2017 Biophysical Society of Japan, Early Career Award


Protein Science Society of Japan, Biophysical Society of Japan, The Chemical Society of Japan


Molecular dynamics simulation of folding pathways of transmembrane self-assembling peptides and its application for designing novel peptide assemblies


Peer-reviewed journal articles

  1. Constructing ion-channels from water-soluble alpha-helical barrels.
    A.J. Scott*, A. Niitsu*, H.T. Kratochvil, E.J.M. Lang, J.T. Sengel, W.M. Dawson, K.R. Mahendran, M. Mravic, A.R. Thomson, L.R. Brady, L. Liu, A.J. Mulholland, H. Bayley, W.F. DeGrado, M.I. Wallace, and D.N. Woolfson *contributed equally
    Nat. Chem., in press
  2. De novo prediction of binders and non-binders for T4 Lysozyme by gREST simulations.
    A. Niitsu*, S. Re*, H. Oshima, M. Kamiya and Y. Sugita *contributed equally
    J. Chem. Inf. Model., 59, 3879-3888 (2019)
  3. Veratridine binding to a transmembrane helix of sodium channel Nav1.4 determined by solid-state NMR
    A. Niitsu, A. Egawa, K. Ikeda, K. Tachibana, T. Fujiwara
    Bioorg. Med. Chem., 26, 5644-5653 (2018)
  4. Conformational dynamics of asparagine at coiled-coil interfaces
    F. Thomas*, A. Niitsu*, A. Oregioni*, G. Bartlett*, and D.N. Woolfson *contributed equally
    Biochemistry, 56, 6544-6554 (2017)
  5. A monodisperse transmembrane α-helical peptide barrel
    K.R. Mahendran*, A. Niitsu*, L. Kong, R.B. Session, A. R. Thomson, D.N. Woolfson, and H. Bayley *contributed equally
    Nat. Chem., 9, 411–419 (2017)
  6. Ophiobolin O and 6-epi-ophiobolin O, two new cytotoxic sesterterpenes from the marine derived fungus Aspergillus sp
    D. Zhang, S. Fukuzawa, M. Satake, X. Li, T. Kuranaga, A. Niitsu, K. Yoshizawa, and K. Tachibana
    Nat. Prod. Commun., 7, 1411-1414 (2012)
  7. Solution NMR analysis of the binding mechanism of DIVS6 model peptides of voltage-gated sodium channels and the lipid soluble alkaloid veratridine
    A. Niitsu, T. Yamagaki, M. Harada, and K. Tachibana
    Bioorg. Med. Chem., 20, 2796-2802 (2012)
  8. Two new indole alkaloids, 2-(3,3-dimethylprop-1-ene)-costaclavine and 2-(3,3-dimethylprop-1-ene)-epicostaclavine, from the marine-derived fungus Aspergillus fumigatus
    D. Zhang, M. Satake, S. Fukuzawa, K. Sugahara, A. Niitsu, T. Shirai, and K. Tachibana
    J. Nat. Med., 66, 222-226 (2012)
  9. Conformations of 3-carboxylic esters essential for neurotoxicity in veratrum alkaloids are loosely restricted and fluctuate
    A. Niitsu, M. Harada, T. Yamagaki and K. Tachibana
    Bioorg. Med. Chem., 16, 3025–3031 (2008)

Review and protocol articles

  1. Designing Novel Peptide Pores from a Barrel-Shaped Protein Scaffold
    A. Niitsu
    Seibutsu Butsuri, 58, 211-213 (2018)
  2. Characterization of protein/peptide pores in a planar lipid bilayer by single channel current recording
    A. Niitsu
    PSSJ Archives, 10, e086 (2017)
  3. Membrane-spanning α-helical barrels as tractable protein-design targets
    A. Niitsu, J.W. Heal, K. Fauland, A.R. Thomson, D.N. Woolfson
    Phil. Trans. R. Soc. B, 372, 20160213 (2017)
  4. De novo protein design: how do we expand into the universe of possible protein structures?
    D.N. Woolfson, G.J. Bartlett, A.J. Burton, J.W. Heal, A. Niitsu, A.R. Thomson, and C.W. Wood
    Curr. Opin. Struct. Biol., 33, 16–26 (2015)