个人简介

Kotaro Nakanishi received his B.S. degree from Tokyo University of Science in 2000, where he was involved in the research of the allosteric mechanism of lactate dehydrogenase. He received his M.S. degree from the University of Tokyo in 2003, where he studied the recognition mechanism of arginine tRNA-specific ribonuclease, colicin D. After working in industry, Kotaro returned to academic life, and obtained his D.Sc. in 2007 from Tokyo Institute of Technology, where he used X-ray crystallography and biochemistry to study aminoacyl-tRNA synthetase and tRNA modification enzyme with Osamu Nureki. In 2008, he joined the laboratory of Dinshaw Patel in the Memorial Sloan-Kettering Cancer Center. His work there resulted in the determination of the crystal structures of Argonaute and Dicer. He was awarded Japan Society for the Promotion of Science (JSPS) for Young Scientist, JSPS for Research Abroad, and Human Frontier Science Program for Long-term Fellow. In recognition of his works, Kotaro received the RNA Society/Scaringe Award in 2012 and the Young Scientists’ Prize of the Commendation for Science and Technology by the Japanese Minister of Education, Culture, Sports, Science and Technology in 2013. He joined the Department of Chemistry & Biochemistry of Ohio State University in August of 2013.

研究领域

Biochemistry

We study the structure of macromolecules in order to understand their mechanisms of recognition. We are able to recognize others through our five senses, sight, hearing, taste, smell and touch. Although the senses are sophisticated systems to understand objects, they sometimes lead us to misunderstandings. For example, we see a friend walking in front of us and say, “Hi John!” But then we realize it is actually someone else. How about macromolecules in our body? Needless to say, they have neither eyes, ears, mouth, nor nose. But they behave as if they have a sense of touch to distinguish the right partner from others. Touch itself seems to be a primitive but robust system to avoid such above-mentioned miscommunications because macromolecules fully exploit their own structure designed for the specific shape of the substrate, inhibitor, other subunit, binding partner, etc. Basically unless the object snugly fits, macromolecules don’t acknowledge that it is the proper one. They communicate with each other through their unique structures. Through the use of X-ray crystallography we can gain an understanding of how these structures determine events at the atomic resolution.

近期论文

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Nakanishi, K.*, Ascano, M.*, Gogakos, T., Ishibe-Murakami, S., Serganov, A.A., Briskin, D., Morozov, P., Tuschl, T., & Patel D.J. (2013) Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity. Cell Rep. 3, 1893-1900. Shen, J., Xia, W., Khotskaya, Y.B., Huo, L., Nakanishi, K., Lim, S.O., Du, Y., Wang, Y., Chang, W.C., Chen, C.H., Hsu, J.L., Lam, Y.C., James, B.P., Liu, C.G., Liu, X., Patel, D.J., & Hung, MC. (2013) EGFR Modulates miRNA Maturation in Response to Hypoxia through Phosphorylation of Ago2. Nature 497, 383-387. Nakanishi, K.*, Weinberg, D.E.*, Bartel, D.P., & Patel, D.J. (2012) Structure of yeast Argonaute with guide RNA. Nature 486, 368-374. Weinberg, D.E.*, Nakanishi, K.*, Patel, D.J., & Bartel, D.P. (2011) The inside-out mechanism of Dicers from budding yeasts. Cell 146, 262-276. Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R., & Nureki, O. (2009) Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 461, 1144-1148. Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., & Nureki, O. (2005) Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat. Struct. Mol. Biol. 12, 931-932. Nakanishi, K., Fukai, S., Ikeuchi, Y., Soma, A., Sekine, Y., Suzuki, T., & Nureki, O. (2005) Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc. Natl. Acad. Sci. U. S. A. 24, 7487-7492. Nakanishi, K., & Nureki, O. (2005) Recent progress of structural biology of tRNA processing and modification. Mol. Cells. 19, 157-166. Yajima, S., Nakanishi, K., Takahashi, K., Ogawa, T., Hidaka, M., Kezuka, Y., Nonaka, T., Ohsawa, K., & Masaki, H. (2004) Relation between tRNase activity and the structure of colicin D according to X-ray crystallography. Biochem. Biophys. Res. Commun. 24, 966-973.