RIKEN Center for Integrative Medical Sciences Laboratory for Intracellular Structural Dynamics

Team Director: Noritaka Nishida (Ph.D.)

Japanese Page

Research Summary

The dynamic nature of proteins is essential for their functions, and the formation of higher-order assemblies such as LLPS plays key roles in the spatiotemporal regulation of cellular processes and disease mechanisms. Because these phenomena depend on cellular environments that cannot be fully captured in vitro, direct observation under physiological conditions is crucial. Our team integrates NMR spectroscopy with cryo-EM and computational approaches to characterize protein dynamics and functional mechanisms at atomic resolution within cells. This integrated strategy will deepen our understanding of fundamental biological processes and support the development of new therapeutic approaches.

Main Research Fields

Medicine, Dentistry & Pharmacy

Related Research Fields

Biological Sciences
Structural biochemistry-related
Biophysics-related
Pharmaceutical chemistry and drug development sciences-related

Keywords

Structural Biology
Nuclear Magnetic Resonance
Protein dynamics
In-cell NMR
Structure based drug development

Selected Publications

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

1. *Nishida N*, Zhao Q, Shimada I*
"Bioreactor in-cell NMR: A powerful tool for observing intracellular biological events."
Curr Opin Struct Biol. 93:103086 (2025)
2. *Zhao Q, Shimada I*, Nishida N*
"Real-Time Monitoring of RAS Activity Using In Vitro and In-Cell NMR Spectroscopy"
Methods Mol Biol. 2797:237-252 (2024)
3. *Watanabe K, Zhao Q, Iwatsuki R, Fukui R, Ren W, Sugita Y*, Nishida N*
"Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR Analysis"
J Am Chem Soc. 146(14):9790-9800 (2024)
4. *Zhao Q, Haga R, Tamura S, Shimada I, Nishida N*
"Real-time monitoring of the reaction of KRAS G12C mutant specific covalent inhibitor by in vitro and in-cell NMR spectroscopy"
Sci Rep 13, 19253 (2023)
5. *Nishide G, Lim K, Tamura M, Kobayashi A, Zhao Q, Hazawa M, Ando T, Nishida N*, Wong RW*
"Nanoscopic Elucidation of Spontaneous Self-Assembly of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Open Reading Frame 6 (ORF6) Protein"
J Phys Chem Lett. 14(38):8385-8396 (2023)
6. *Zhao Q, Fujimiya R, Kubo S, Marshall CB, Ikura M, Shimada I*, Nishida N*
"Real-time In-cell NMR Reveals the Intracellular Modulation of GTP-bound Levels of RAS"
Cell Rep. 32, 108074 (2020)
7. *Nishida N, Komori Y, Takarada O, Kubo S, Tamura S, Shimada I*, Kikkawa M*
"Structural basis for two-way communication between dynein and microtubules."
Nat Commun. 11, 1038 (2020)
8. *Nishida N, Ito Y*, Shimada I*
"in situ structural biology by in-cell NMR"
Biochim Biophys Acta Gen Subj. 1864(2):129421 (2020)
9. *Mochizuki A, Saso A, Zhao Q, Kubo S, Nishida N*, *Shimada I*
"Balanced Regulation of Redox Status of Intracellular Thioredoxin Revealed by in-Cell NMR."
J Am Chem Soc. 140:3784-3790 (2018)
10. *Huang S, Umemoto R, Tamura Y, Kofuku Y, Uyeda TQ, Nishida N, Shimada I*
"Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin"
Sci Rep. 6, 33690, (2016)

Lab Members

Principal investigator

Noritaka Nishida: Team Director

Contact Information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa,
230-0045, Japan
Email: ims-web@riken.jp