RIKEN Center for Biosystems Dynamics Research Laboratory for Dynamic Biomolecule Design

Team Leader: Ai Niitsu (Ph.D.)

Japanese Page

Research Summary

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

Keywords

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)

Lab Members

Principal investigator

Ai Niitsu: Team Leader

Contact Information

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