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Research Theme

Time-resolved analyses of protein dynamics at atomic and electronic levels by novel IR spectroscopic and XFEL diffraction techniques

Minoru Kubo
Researchers
Name
Minoru Kubo
Position, Research site
Senior Research Scientist, RIKEN SPring-8 Center, RIKEN Harima Institute,
This project aims to establish new techniques for studying protein reactions at both atomic and electronic levels, in real time. XFEL is used for time-resolved X-ray structural analysis to observe atomic motions during reactions, whereas a novel time-resolved IR spectroscopic method using a femtosecond IR laser gives information on electronic structures (i.e., chemical reactivity) of functional sites. The new techniques will be applied to elucidate the reaction mechanism of cytochrome c oxidase, a key enzyme of cell respiration, as a model of highly-efficient energy conversion systems.

Structural elucidation of the intracellular transport machinery

Takahide Kon
Researchers
Name
Takahide Kon
Position, Research site
Professor, Department of Biological Sciences, Graduate School of Science, and Faculty of Science, Osaka University
Eukaryotic cells are equipped with an efficient intracellular transport system that is critical for diverse biological activities. The goal of this research is to understand the molecular mechanism underlying transport to the center of the cells. To elucidate how the dynein motor, that is the heart of the transport system, generates force, we will obtain the crystal structures of dynein trapped in intermediate states before and after the force generation. To further elucidate the structural basis of the transport mechanism, we will obtain the structures of supramolecular complexes constituting the transport machinery.

Next-generation structural biology of Sec protein translocation machinery

Tsukazaki Tomoya
Researchers
Name
Tomoya Tsukazaki
Position, Research site
Associate Professor, Graduate School of Biological Sciences, Department of Systems Biology, Nara Institute of SCIENCE and TECHNOLOGY
Protein translocation across the membrane via Sec translocon is one of the essential machinery in cells, coupled with dynamic interaction and structural changes. However the details of the molecular mechanism remains unclear. In this project, we perform structural biological analysis, including a new technique, for visualizing the protein translocation. Our result will lead to understanding of not only the protein transport across the membrane but also the transport mechanism of various materials including drugs.

Investigation of dynamics of actin filament network by electron microscopy

Akihiro Narita
Researchers
Name
Akihiro Narita
Position, Research site
Associate Professor, Nagoya University 'Structural Biology Research Center', Graduate School of Science, Nagoya University
Actin filament plays various roles in the cell, including cell motility, cell adhesion and cell division through its dynamics. I will investigate a wide range of the actin filament dynamics and their regulation by electron microscopy, electron tomography for the cell and single paritcle analysis for purified and reconstituted filamentous complexes.

Elucidation of spatiotemporal dynamics and regulation of P2X receptors

Motoyuki Hattori
Researchers
Name
Motoyuki Hattori
Position, Research site
Professor, School of Life Sciences, Fudan University
ATP is widely utilized as the vital energy currency of life. It is also an essential extracellular signaling molecule to activate ATP receptors. P2X receptors are ionotropic ATP receptors and are potential therapeutic targets, due to the physiological importance. The aim of this research is to understand the dynamics and regulation of P2X receptors through the structural and functional analyses. The outcome of the research would lead to the development of new therapeutic agents.

Advanced electron cryomicroscopy studies on muscle contraction regulation

Takashi Fujii
Researchers
Name
Takashi Fujii
Position, Research site
RIKEN QUANTITATIVE BIOLOGY CENTER
Developing a novel electron cryomicroscopy method, we will reveal the high resolution structure of thin-filament which plays important role in the muscle regulation.We visualize how calcium ion binding with troponin causes a drastic structural change of thin filament and control the interaction between actin and myosin.This study will provide a useful knowledge to develop new medicines for muscle-related disease such as cardiac myopathy.

Structure-based Design of Chemical Probes for Fuctional Regulation and Localization Imaging of Proteins

Yuichiro Hori
Researchers
Name
Yuichiro Hori
Position, Research site
Associate Professor, Osaka University Graduate School of Engineering
Proteins in living cells transduce various sinals to many other proteins upon receiving external stimuli, and the signal transduction pathways generally form complex networks. In this research, we resolve the networks one by one and elucidate the mechanism of the signal transduction by utilizing a protein labeling technique and chemical probes. In addition, we develop a method for simultaneous imaging of protein function and localization in living cells and aim to contribute toward identifying signal transduction disorders in disease and exploring drug targets.

Three-dimensional mapping of conformational changes and functions of single-molecule membrane proteins under the microscope

Tomoko Masaike
Researchers
Name
Tomoko Masaike
Position, Research site
Lecturer, Department of Applied Biological Science, Tokyo University of Science
The aim of the present project is to transform "still images" of membrane-embedded proteins into "motion pictures". The dynamic relationship between functions and conformational changes of domains will be revealed under the optical microscope. Single fluorescent molecules are linked to membrane proteins or substrates, and changes in their orientation are probed three-dimensionally in real time. The first target of this study is Ca2+-ATPase, whose still images, crystal structures, have been determined in multiple intermediate states.

Molecular architecture and transition/regulation mechanism of the DNA replication fork complex

Kouta Mayanagi
Researchers
Name
Kouta Mayanagi
Position, Research site
Assistant Professor, Kyushu University Medical Institute of Bioregulation
Numerous protein factors are involved in DNA replication, which is crucial for the transmission of genetic information. In general, these factors form a huge complex, and accomplish each function through precise regulation. This project aims to investigate the molecular architecture and reaction mechanism of the replication fork complex, using a hybrid method approach, which includes single particle analysis, EM tomography, crystallography, mutational analysis, and computational macromolecule modeling.

Elucidation of molecular mechanism of the nano-molecular rotary membrane motor by correlative structural analyses

Takeshi Murata
Researchers
Name
Takeshi Murata
Position, Research site
Professor, Chiba University Graduate School of Science
V-ATPase is a nano-molecular membrane protein which functions as an ion pump through the rotational catalysis using ATP hydrolysis energy, and is involved in a number of human diseases such as osteoporosis and cancer. In this research, I would like to elucidate the molecular mechanism of the rotary motor by correlative structural analyses such as X-ray crystallography, molecular simulation, mass spectrometry, and single-molecule observation of the rotation, which shall help us understand better the molecular basis of cell physiology and related diseases, and which will be useful for designing future drugs targeting V-ATPase.

Structural analysis of the entire molecular machinery that enables transcription through nucleosome-containing regions of chromatin

Kazuhiro Yamada
Researchers
Name
Kazuhiro Yamada
Position, Research site
JST/PRESTO Researcher(Max-Planck-Institute for Medical Research, Heidelberg)
In eukaryotes, nuclesome structures on double stranded DNA are physical barriers for mRNA elongation by RNA polymerase (Pol-II), which by itself is unable to disassemble nucleosomes. To enable mRNA transcription to traverse through a nucleosome region, Pol-II needs to cooperate with other factors of the PAF1c-hub complex, including chromatin remodeling factors (Chd1) and histone chaperones (FACT). By solving the X-ray crystal structure of the entire transcriptional machinery including Pol-II, PAFc, Chd1 and FACT, I aim to reveal the interactions and cooperative activities of the components in this massive biological machine.