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Research

Research

BDR researchers coming from diverse research fields are working together to achieve higher goals.

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BDR hosts annual symposium and regular seminars inviting international scientists in life science.

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Careers & Study

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About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team Leader, Takanori Kigawa

Team Leader
Takanori Kigawa D. Sci.

Laboratory for Cellular Structural Biology

Location Yokohama

E-mailkigawa[at]riken.jp

Please replace [at] with @.

Understanding biological phenomena based on the structure and dynamics of biomolecules in cellular environments

In actual biological cellular environments, biomolecules such as proteins are working dynamically and co-operatively, generally surrounded by high concentrations of macromolecules, so-called “macromolecular crowding” and also “confined” by/in the plasma membrane and/or cellular organelles. In recent years, it has become important to directly investigate the structure and the dynamics of biomolecules in cellular environments because protein behaviors in cells are, at least in some cases, different from those in a dilute, homogeneous solution. We will elucidate cellular events at atomic resolution by analyzing structural dynamics of biomolecules in the cellular environment mainly by using NMR spectroscopy integrated with information science technologies. We will also develop and improve the technologies for sample preparation, stable-isotope labeling, NMR measurements, and data analyses in order to address the issues of low sensitivity and resolution from which NMR measurement of biomolecules in cellular environments usually suffers. In addition, based on our findings, we will develop new technologies by taking advantage of biological functions, for example, the development of technologies for bioelectricity generation based on the mechanisms of energy generation in the living cells.

Project

  • NMR analysis of biomolecular structural dynamics in cellular environments
  • Development of NMR-related technologies with information sciences
  • Development of technologies for stable-isotope labeling of proteins using cell-free synthesis
  • Development of technology for bioelectricity generation by taking advantage of biological functions

Selected Publications

Shitanda I, Morigayama Y, Iwashita R, et al.
Paper-based lactate biofuel cell array with high power output.
Journal of Power Sources 489, 229533 (2021) doi: 10.1016/j.jpowsour.2021.229533

Ito K, Murayama Y, Kurokawa Y, et al.
Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51.
Nature Communications 11, 2950 (2020) doi: 10.1038/s41467-020-16750-3

Higuchi K, Yabuki T, Ito M, Kigawa T.
Cold shock proteins improve E. coli cell-free synthesis in terms of soluble yields of aggregation-prone proteins.
Biotechnology and Bioengineering 117(6), 1628-1639 (2020) doi: 10.1002/bit.27326

Kasai T, Ono S, Koshiba S, et al.
Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra.
Journal of Biomolecular NMR 74, 125-137 (2020) doi: 10.1007/s10858-019-00295-9

Inomata K, Kamoshida H, Ikari M, et al.
Impact of cellular health conditions on the protein folding state in mammalian cells.
Chemical Communications (Cambridge) 53(81), 11245-11248 (2017) doi: 10.1039/c7cc06004a

Kigawa T.
Advances in stable isotope assisted labeling strategies with information science.
Archives of Biochemistry and Biophysics 628, 17-23 (2017) doi: 10.1016/j.abb.2017.06.014

Kasai T, Nagata K, Okada M, Kigawa T.
NMR spectral analysis using prior knowledge.
Journal of Physics: Conference Series 699(1), 012003 (2016) doi: 10.1088/1742-6596/699/1/012003

Okamura H, Nishimura H, Nagata T, et al.
Accurate and molecular-size-tolerant NMR quantitation of diverse components in solution.
Scientific Reports 6, 21742 (2016) doi: 10.1038/srep21742

Shigeno-Nakazawa Y, Kasai T, Ki S, et al.
A pre-metazoan origin of the CRK gene family and co-opted signaling network.
Scientific Reports 6, 34349 (2016) doi: 10.1038/srep34349

Kasai T, Koshiba S, Yokoyama J, Kigawa T.
Stable isotope labeling strategy based on coding theory.
Journal of Biomolecular NMR 63(2), 213-221 (2015) doi: 10.1007/s10858-015-9978-8

Harada R, Tochio N, Kigawa T, et al.
Reduced native state stability in crowded cellular environment due to protein-protein interactions.
Journal of the American Chemical Society 135(9), 3696-3701 (2013) doi: 10.1021/ja3126992

Matsuda T, Furumoto S, Higuchi K, et al.
Rapid biochemical synthesis of C-11-labeled single chain variable fragment antibody for immuno-PET by cell-free protein synthesis.
Bioorganic & Medicinal Chemistry 20(22), 6579-6582 (2012) doi: 10.1016/j.bmc.2012.09.038

Akama S, Yamamura M, Kigawa T.
A Multiphysics Model of In Vitro Transcription Coupling Enzymatic Reaction and Precipitation Formation.
Biophysical Journal 102(2), 221-230 (2012) doi: 10.1016/j.bpj.2011.12.014

Yokoyama J, Matsuda T, Koshiba S, et al.
A practical method for cell-free protein synthesis to avoid stable isotope scrambling and dilution.
Analytical Biochemistry 411(2), 223-229 (2011) doi: 10.1016/j.ab.2011.01.017

Members

Takanori Kigawa

Team Leader

Tsutomu Mikawa

Senior Research Scientist

Takuma Kasai

Research Scientist

Naoya Tochio

Research Scientist

Hiromasa Yagi

Research Scientist

Masaomi Ikari

Technical Scientist

Satoko Yasuda

Technical Staff I

Tomoto Ura

Student Trainee

Nanako Sakakibara

Student Trainee

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