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Biophysical Chemistry (Yuki SUDO)

Biophysical Chemistry (Yuki SUDO)

Biophysical Chemistry Yuki SUDO, PhD

 

Major Areas of Research

  1. Discovering novel photoactive proteins from the nature
  2. Investigating molecular properties of the proteins with biophysical techniques
  3. Applying the photoactive proteins for controlling the biological function

Current Research Interests

Light is one of the most important stimuli that provide huge energy and critical information to biological systems and therefore many organisms utilize light as an energy source and a signal. In the cells, photoactive proteins are responsible for a variety of biological functions such as photosynthesis, signal transduction, ion transportation and transcriptional regulation. Retinal (or Retinylidene) proteins contain vitamine-A aldehyde retinal as a chromophore within seven transmembrane a-helices and they are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. We are mainly working on the microbial retinal proteins. One of the major functions of them is to serve as light-driven ion pump across the cellular membrane, and such an ion gradient is utilized by adenosine triphosphate (ATP) synthase, indicating that organisms having light-driven pumps can produce ATP under light illumination. In addition to the simplest energy production system by the light, retinal proteins also function as a receptor for signal transduction. Although ~75% of amino acid residues differ among retinal proteins, their crystal structures show close similarities in architecture, helix positions and locations of the retinal-binding pocket, indicating that their functional differentiation is regulated by differences in more detailed structures, including the amino acid side chain(s), ions and water molecules. Thus, despite their high similarity in structure, the question arises of how these proteins can function so differently? We are focusing on three research topics as follows; 1) Discovery of novel retinal proteins from the nature, 2) Structural and functional characterization of the retinal proteins with biophysical techniques, 3) Development of the retinal protein-based optical tools (see Figure). 

Figure

Recent Research Progress

1. We found and investigated a novel microbial rhodopsin derived from the extreme thermophilic bacterium Thermus thermophilus which lives in a hot spring at around 75?C (Tsukamoto et al., 2013). 2. We determined color discriminating retinal configurations in sensory rhodopsin I (Yomoda et al., in press). 3. We successfully produced a blue-shifted light-driven proton pump for neural silencing (Sudo et al., 2013).

Selected Recent Publications

  1. Sudo Y., and *Spudich, J.L. Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor. Proc. Natl. Acad. Sci. USA 103, 16129-16134 (2006)
  2. *Sudo,Y., Ihara K., Kobayashi S., Suzuki D., Irieda H., Kikukawa T., Kandori H., and Homma, M. A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties. J. Biol. Chem. 286, 5967-5976 (2011a)
  3. *SudoY., Yuasa Y., Shibata J., Suzuki D., and Homma M. Spectral tuning in sensory rhodopsin I from Salinibacter ruber. J. Biol. Chem. 286, 11328-11336 (2011b)
  4. Irieda H., Morita T., Maki K., Homma M., Aiba H., and *Sudo Y. Photo-induced regulation of the chromatic adaptive gene expression by Anabaena sensory rhodopsin. J. Biol. Chem. 287, 32485-32493 (2012)
  5. *Sudo Y., Okazaki A., Ono H., Yagasaki J., Sugo S., Kamiya M., Reissig L., Inoue K., Ihara K., Kandori H., Takagi S., and Hayashi, S. A blue-shifted light-driven proton pump for neural silencing. J. Biol. Chem. 288, 20624-20632 (2013)
  6. Tsukamoto T., Inoue K., Kandori H., and *Sudo Y. Thermal and spectroscopic characterization of a proton pumping rhodopsin from an extreme thermophile. J. Biol. Chem. 288, 21581-21592 (2013)
  7. Yomoda H., Makino Y., Tomonaga Y., Hidaka T., Kawamura I., Okitsu T., Wada A., *Sudo Y., and *Naito, A. Color discriminating retinal configurations of sensory rhodopsin I by photo-irradiation solid state NMR spectroscopy. Angew. Chem. Int. Ed. in press.