Laboratory for Biomolecular Structure and Dynamics

In actual biological cellular environment, biomolecules such as proteins are generally surrounded by high concentrations of macromolecules, so-called ‘macromolecular crowding’ and these molecules are dynamically and co-operatively working. We will elucidate cellular events at atomic resolution by analyzing structural dynamics of biomolecules in the cellular environment mainly by using NMR spectroscopy. We will also develop and improve the technologies for sample preparations, stable-isotope labeling, NMR measurements, and data analyses. In collaboration with laboratories in Computational Biology Research Core. QBiC, we will contribute to the modeling of the cell from the viewpoint of structural dynamics of biomolecules.

Research Fields

Engineering / Chemistry / Biology & Biochemistry / Molecular Biology & Genetics / Immunology / Pharmacology & Toxicology / Plant & Animal Science / Microbiology / Computer Science

Research Subjects

• NMR analysis of structural dynamics of biomolecules in cellular environments
• Development of technologies for NMR measurements and data analyses
• Development of technologies for stable-isotope labeling of proteins by using the cell-free synthesis

Publications

1. Matsuda, T., Watanabe, S., and Kigawa, T.:
   "Cell-free synthesis system suitable for disulfide-containing proteins"
   Biochem. Biophys. Res. Commun. doi:10.1016/j.bbrc.2012.12.107 (2013).
2. Matsuda, T., Furumoto, S., Higuchi, K., Yokoyama, J., Zhang, M.R., Yanai, K., Iwata, R., and Kigawa, T.:
   "Rapid biochemical synthesis of (11)C-labeled single chain variable fragment antibody for immuno-PET by cell-free protein synthesis"
   Bioorg. Med. Chem. 20, 6579-82, (2012).
3. Akama, S., Yamamura, M., and Kigawa, T.:
   "A multiphysics model of in vitro transcription coupling enzymatic reaction and precipitation formation"
   Biophys. J. 102, 221-30, (2012).
4. Yokoyama, J., Matsuda, T., Koshiba, S., Tochio, N., and Kigawa, T.:
   "A practical method for cell-free protein synthesis to avoid stable isotope scrambling and dilution"
   Anal. Biochem. 411, 223-9, (2011).
5. Shin, J., Chakraborty, G., Bharatham, N., Kang, C., Tochio, N., Koshiba, S., Kigawa, T., Kim, W., Kim, K.T., and Yoon, H.S.:
   "NMR solution structure of human vaccinia-related kinase 1 (VRK1) reveals the C-terminal tail essential for its structural stability and autocatalytic activity"
   J. Biol. Chem. 286, 22131-8, (2011).
6. Arai, H., Watanabe, S., Kigawa, T., and Yamamura, M.:
   "A new modeling method in feature construction for the HSQC spectra screening problem"
   Bioinformatics 25, 948-53, (2009).
7. Aoki, M., Matsuda, T., Tomo, Y., Miyata, Y., Inoue, M., Kigawa, T., and Yokoyama, S.:
   "Automated system for high-throughput protein production using the dialysis cell-free method"
   Protein Expr. Purif. 68, 128-36, (2009).
8. Li, H., Koshiba, S., Hayashi, F., Tochio, N., Tomizawa, T., Kasai, T., Yabuki, T., Motoda, Y., Harada, T., Watanabe, S., Inoue, M., Hayashizaki, Y., Tanaka, A., Kigawa, T., and Yokoyama, S.:
   "Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode"
   J. Biol. Chem. 283, 27165-78, (2008).
9. Yabuki, T., Motoda, Y., Hanada, K., Nunokawa, E., Saito, M., Seki, E., Inoue, M., Kigawa, T., and Yokoyama, S.:
   "A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis"
   J. Struct. Funct. Genomics 8, 173-91, (2007).
10. Kobayashi, N., Iwahara, J., Koshiba, S., Tomizawa, T., Tochio, N., Guntert, P., Kigawa, T., and Yokoyama, S.:
    "KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies"
    J. Biomol. NMR 39, 31-52, (2007).