Masahiro Ueda

Fluctuation and signal integration dynamics in hierarchical molecular system of living cells

Research Director

Masahiro Ueda

Outline

In eukaryotic chemotaxis, the intracellular self-organization of Ras and phosphatidylinositol lipids signaling system provides a mechanism to generate celularl polarity from the molecular noise. In this research project, we will quantitatively analyze the stochastic properties of the molecular components of the system by using single-molecule and super-resolution microscopy, and based on the measurement results, we will develop cellular simulations with single-molecule granularity to computationally reproduce the spatiotemporal dynamics of the signaling functions. In this way, we will elucidate the mechanism of the “fluctuation from micro to macro” or “organized randomness” of hierarchical molecular system in which the molecular noise is utilized to generate flexible environmental adaptation of living cells.

Haruo Kasai

Mechanisms of the synaptic mechanical coupling in brain spine synapses

Research Director

Haruo Kasai

Collaborator

Yoshiyuki Kubota	Associate Professor National Institute of Physiological Sciences National Institutes of Natural Sciences
Yusuke Hirabayashi	Associate Professor Graduate School of Engineering The University of Tokyo

Outline

We investigate the origin of the mechanical coupling of brain spine synapses using optical microscopes (STED, confocal, 2-phtone) and electronmicroscopes (TEM and FIB-SEM). We will pay attention to the presynatpic synaptic vesicle clusters and to supra-molecular structure of SNARE proteins. In addition, we develop application for genetically encoded Au particle methods (AuNP) to elucidate the status of SNAREs in the vesicles and chemical manipulation of the pushing effects.

Koichi Kato

Glycosylation control based on the elucidation of Golgi dynamics

Research Director

Koichi Kato

Collaborator

Daisuke Koga	Associate Professor Department of Microscopic Anatomy and Cell Biology Asahikawa Medical University
Takuro Tojima	Senior Research Scientist Center for Advanced Photonics RIKEN
Totai Mitsuyama	Research Team Leader Artificial Intelligence Research Center National Institute of Advanced Industrial Science and Technology (AIST)

Outline

The control of protein glycosylation is an important issue in the development of biopharmaceuticals. This study focuses on the Golgi apparatus as a stage for glycosylation and elucidates the spatio-temporal dynamics of its microstructure and the transport pathway of glycoproteins. By exploring the molecular mechanisms underlying the localization of glycosyltransferases and the selective transport of cargo molecules in the complexly compartmentalized Golgi, we aim to decipher the program of the secretory pathway and to control protein glycosylation by its modification.

Toshiyuki Shimizu

Lysosomal spatiotemporal dynamics controlling Toll like receptor responses

Research Director

Toshiyuki Shimizu

Collaborator

Tomohiko Taguchi	Professor Graduate School of Life Sciences Tohoku University
Kensuke Miyake	Professor Institute of Medical Science The University of Tokyo

Outline

Nucleic acid sensing TLRs reside in the endosomal compartment and induce innate immune responses as pathogenic sensors. Recently, we found that these TLRs in macrophages sense lysosomal metabolite accumulation and activate stress responses such as macrophage proliferation. We here study mechanisms behind a decision by TLRs to activate innate immune responses or stress responses. We focus on: the structural studies of TLR complexes initiating immune responses or stress responses; and the relationship between these TLR complexes and spatiotemporal dynamics of lysosomes.

Noritaka Nishida

Elucidation of the structure, dynamics and function of intracellular proteins by in-cell NMR measurements

Research Director

Noritaka Nishida

Collaborator

Teppei Ikeya

Associate Professor Graduate School of Science Tokyo Metropolitan Univerity

Outline

In this research project, we will develop (1) the methods for analyzing dynamic conformational equilibrium and ensemble structures of intracellular proteins, (2) the methods for extracting contribution of intracellular regulatory factors by in-cell NMR measurements using knockout cells, and (3) the techniques for subcellular localization of target proteins and their highly sensitive detection. We will apply these developed methods to higher-order structures such as LLPSs that are formed locally in cells, and quantitatively clarify the relationship between the dynamic structure and the functional role.

Tatsuo Fukagawa

Structural dynamics on the kinetochore

Research Director

Tatsuo Fukagawa

Collaborator

Masato T. Kanemaki	Professor National Institute of Genetics Research Organization of Information and Systems
Toru Hirota	Division Head Cancer Institute Japanese Foundation for Cancer Research

Outline

The kinetochore, which contains more than 100 proteins, is an essential structure for accurate chromosome segregation. Whereas various studies on the kinetochore are progressed, there remain many unsolved questions such as how the kinetochore structure is regulated in cells or how accurate chromosome segregation is performed through the kinetochore. In this project, using cryo-EM, high-resolution imaging, and genetic approach combined with cell biological methods, we will try to clarify how the structural changes of the kinetochore are related to the chromosome segregation process in cells.