研究内容

サブ課題1:クライオ電子顕微鏡による蛋白質複合体の立体構造解析

Time-resolved XFEL crystallography and vibrational spectroscopy for capturing protein dynamics at work
1.Time-resolved XFEL crystallography and vibrational spectroscopy for capturing protein dynamics at work RIKEN SPring-8 Center, Imaging development Team
Senior Research Scientist: Minoru Kubo

We develop the time-resolved techniques of X-ray crystallography and vibrational spectroscopy, and study protein reaction dynamics at the atomic and electronic levels in real time.

Structural studies of the macromolecular complexes with chromatin
2.Structural studies of the macromolecular complexes with chromatin Laboratory of structural biology
Team leader: Hitoshi Kurumizaka

We reconstitute the macromolecular complexes with chromatin and determine their three dimensional structures by cryo-EM.

Development of the dynamic structural biology platform for membrane proteins
3.Development of the dynamic structural biology platform for membrane proteins Center for Life Science Technologies, Protein Functional and Structural Biology Team
Senior Scientist: Hideki Shigematsu

We develop the new method in cryoEM single particle analysis to visualize conformational ensembles of membrane proteins in function.

Macromolecular sample production and cryo-EM analyses for dynamic structural biology
4.Macromolecular sample production and cryo-EM analyses for dynamic structural biology RIKEN BDR Laboratory for Protein Functional and Structural Biology
Team leader: Mikako Shirouzu

We develop the methods for preparation of biomolecules reflecting their dynamic functional states and operate an integrated structural analysis pipeline including cryo-electron microscopy.

High-resolution single particle cryo-EM and crystallography of membrane protein complexes
5.High-resolution single particle cryo-EM and crystallography of membrane protein complexes Biostructural mechanism laboratory
Chief scientist: Koji Yonekura

We carry out single particle cryo-EM and crystallography of membrane protein complexes, and develop methodologies for higher-resolution cryo-EM and analyses of charge information and multi conformational states.

Cooperative conformational changes of microtubules and their functional implications
6.Cooperative conformational changes of microtubules and their functional implications Laboratory for Cell Polarity Regulation
Team leader: Yasushi Okada

Microtubule is a dynamic cytoskeleton and playing various essential roles in living cells. To investigate their regulation, we examine the dynamic conformational changes of tubulin subunits in microtubules by using various measurement technologies.

サブ課題2:核磁気共鳴分光法の高感度化技術の開発

Efficient Synthetic Route to Novel Pi-Conjugated Molecules and Development of their Function,
1.Efficient Synthetic Route to Novel Pi-Conjugated Molecules and Development of their Function, Hamura Lab in Kwansei Gakuin University
Team leader: Toshiyuki Hamura

The purpose of this research is development of an efficient synthetic route to various pi-conjugated systems based on the reaction integration using the reactive molecules, having potentially attractive reactivities. Three kinds of activations by heat, light, and transition metal catalyst enable the selective construction of complex structures by introducing diverse functionalities.

NMR analyses of functional dynamics of proteins / Triplet DNP application to membrane-related proteins.
2.NMR analyses of functional dynamics of proteins / Triplet DNP application to membrane-related proteins. Functional Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University
Team leader: Hideo Takahashi

We analyze functionally important but hidden dynamics of drug-target proteins by using NMR spectroscopy. We also tackle the triplet DNP application to membrane-related proteins.

Development of methods for facile preparation of pentacene-biomolecule conjugates
3.Development of methods for facile preparation of pentacene-biomolecule conjugates Graduate School of Engineering, The University of Tokyo
Team leader: Shinsuke Sando

We have taken a challenge to develop a facile method to conjugate key molecule “Pentacene” with various biomolecules

Development of the method for sensitivity-enhanced NMR spectroscopy by Triplet-DNP
4.Development of the method for sensitivity-enhanced NMR spectroscopy by Triplet-DNP Laboratory for Biomolecular Structure and Dynamics
Team leader: Takanori Kigawa

We will develop the new method for observing molecular interaction using sensitivity-enhanced NMR spectroscopy by Triplet-DNP.

Hyperpolarization of biomolecules in solution
5.Hyperpolarization of biomolecules in solution Uesaka Spin-isospin Laboratory
Team leader: Tomohiro Uesaka

We will develop a method to hyper-polarize biomolecules using laser and microwave for sensitivity-enhanced NMR spectroscopy.

サブ課題3:実験データ駆動型分子シミュレーション法の開発

Development of new modeling algorithms combining cryo-EM data and simulation
1.Development of new modeling algorithms combining cryo-EM data and simulation R-CCS Computational Structural Biology Research Unit
Team leader: Florence Tama

We develop new algorithms to construct 3D models and obtain dynamical information from Cryo-EM experimental data of biological molecules

Development of fragment-based methods for cryo-EM structure modeling and refinement
2.Development of fragment-based methods for cryo-EM structure modeling and refinement Structural Bioinformatics Team
Team leader: Kam Zhang

We develop fragment-based modeling of structures for cryo-EM map fitting and the refinement of cryo-EM structures using fragment-assembly.

Understanding Sequence-Dependent Nucleosome Stability
3.Understanding Sequence-Dependent Nucleosome Stability Molecular Modeling and Simulation,
National Institutes for Quantum and Radiological Science and Technology (QST)
Team leader: Hidetoshi Kono

We try to characterize and address sequence-dependent nucleosome stability using all atom simulations, bioinformatics and FRET experiments. In particular, we focus on +1 nucleosomes and elucidate the functional role in gene regulation.

Coarse grained molecular dynamics simulations for dynamic structural biology of chromatin and transcription regulation
4.Coarse grained molecular dynamics simulations for dynamic structural biology of chromatin and transcription regulation Kyoto University
Shoji Takada

We develop coarse-grained models for protein-DNA complexes and apply them to pursue dynamic aspects of nucleosome structures and their correlation with transcription activity.

Development of the fast cryo-EM flexible fitting software for large biomolecular systems
5.Development of the fast cryo-EM flexible fitting software for large biomolecular systems Theoretical molecular science laboratory
Team leader: Yuji Sugita

We develop the new parallelization algorithm and multi-scale algorithm for the fast and reliable cryo-EM flexible fitting simulations of large biomolecular systems.

Multiscale molecular dynamics simulations in combination with structural biology experiments
6.Multiscale molecular dynamics simulations in combination with structural biology experiments Yokohama City University
Team leader: Mitsunori Ikeguchi

We perform multiscale molecular dynamics simulations in combination with structural biology experiments such as small-angle x-ray scattering (SAXS) and NMR.

Development of the special-purpose computer for molecular dynamics simulations
7.Multiscale molecular dynamics simulations in combination with structural biology experiments Laboratory for computational molecular design
Team leader: Makoto Taiji

We develop the new special-purpose computer MDGRAPE-4A for all atom simulations of biomolecules and perform unbiased microseconds simulations of target proteins.