Research Summary

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

• 1.Matsuura, T., Tanimura, N., Hosoda, K., Yomo, T. & Shimizu, Y.:
  "Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling."
  Proc. Natl. Acad. Sci. U. S. A. 114, E1336-E1344 (2017).
• 2.Narumi, R., Shimizu, Y., Ukai-Tadenuma, M., Ode, K. L., Kanda, G. N., Shinohara, Y., et al.:
  "Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins."
  Proc. Natl. Acad. Sci. U. S. A. 113, E3461-E3467 (2016).
• 3.Tanaka, Y. & Shimizu, Y.:
  "Integration of a Reconstituted Cell-free Protein-synthesis System on a Glass Microchip"
  Anal. Sci. 31, 67-71 (2015).
• 4.Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., et al.:
  "Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis"
  Cell 157, 726-739 (2014)
• 5.Shimizu, Y.:
  "Biochemical aspects of bacterial strategies for handling the incomplete translation processes"
  Front. Microbiol. 5 (2014).
• 6.Shimizu, Y.:
  "ArfA Recruits RF2 into Stalled Ribosomes"
  J. Mol. Biol. 423, 624-631 (2012)
• 7.Kihira, K. Shimizu, Y., Shomura, Y., Shibata, N., Kitamura, M., Nakagawa, A, et al.:
  "Crystal structure analysis of the translation factor RF3 (release factor 3)"
  FEBS Lett. 586, 3705-3709 (2012).
• 8.*Shimizu, Y. & Ueda, T.:
  "SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans- translation initiation"
  J. Biol. Chem. 281, 15987-15996 (2006)
• 9.*Shimizu, Y., Kanamori, T. & Ueda, T.:
  "Protein synthesis by pure translation systems"
  Methods 36, 299-304 (2005)
• 10.*Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., et al.:
  "Cell-free translation reconstituted with purified components"
  Nat. Biotechnol. 19, 751-755 (2001)

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