Laboratory for Cellular Structural Biology

Research Summary

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.

Structural dynamics of biomolecules in cellular environments

Stable-isotope encoding (SiCode)

Bioelectricity generation technology

Research Theme

• 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

Main Publications List

• 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 (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 (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