Team Director
Ai Niitsu
Ph.D.
Laboratory for Dynamic Biomolecule Design
[Affiliation has changed to RIKEN Center for Integrated Medical Sciences (IMS) as of April 2025]
LocationYokohama / West Research Building
E-mailai.niitsu@riken.jp
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.
Selected Publications
Tan C, Niitsu A, Sugita Y.
Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation.
Journal of American Chemical Society Au
3(3), 834-848 (2023)
doi: 10.1021/jacsau.2c00646
Niitsu A, Sugita Y.
Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation.
Physical Chemistry Chemical Physics
25(5), 3595-3606 (2023)
doi: 10.1039/d2cp03972a
Scott AJ, Niitsu A, Kratochvil HT, et al.
Constructing ion channels from water-soluble α-helical barrels.
Nature Chemistry
13(7), 643-650 (2021)
doi: 10.1038/s41557-021-00688-0
Niitsu A, Re S, Oshima H, et al.
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.
Journal of Chemical Information and Modeling
59(9), 3879-3888 (2019)
doi: 10.1021/acs.jcim.9b00416
Niitsu A, Egawa A, Ikeda K, et al.
Veratridine binding to a transmembrane helix of sodium channel Nav1.4 determined by solid-state NMR.
Bioorganic & Medicinal Chemistry
26(21), 5644-5653 (2018)
doi: 10.1016/j.bmc.2018.10.012
Thomas F, Niitsu A, Oregioni A, et al.
Conformational Dynamics of Asparagine at Coiled-Coil Interfaces.
Biochemistry
56(50), 6544-6554 (2017)
doi: 10.1021/acs.biochem.7b00848
Niitsu A, Heal JW, Fauland K, et al.
Membrane-spanning α-helical barrels as tractable protein-design targets.
Philosophical Transactions of the Royal Society B
372(1726), 20160213 (2017)
doi: 10.1098/rstb.2016.0213
Mahendran KR, Niitsu A, Kong L, et al.
A monodisperse transmembrane α-helical peptide barrel.
Nature Chemistry
9(5), 411-419 (2017)
doi: 10.1038/nchem.2647
