Minoru Kubo

「Minoru Kubo」
Degree
Ph.D.
Position, Research site
Senior Research Scientist, RIKEN SPring-8 Center, RIKEN Harima Institute
URL
http://www.riken.jp/biometal/index-e.htm
Research Field
Vibrational spectroscopy

Original Papers

  1. "Takehiko Tosha, Takashi Nomura, Takuma Nishida, Naoya Saeki, Kouta Okubayashi, Raika Yamagiwa, Michihiro Sugahara, Takanori Nakane, Keitaro Yamashita, Kunio Hirata, Go Ueno, Tetsunari Kimura, Tamao Hisano, Kazumasa Muramoto, Hitomi Sawai, Hanae Takeda, Eiichi Mizohata, Ayumi Yamashita, Yusuke Kanematsu, Yu Takano, Eriko Nango, Rie Tanaka, Osamu Nureki, Osami Shoji, Yuka Ikemoto, Hironori Murakami, Shigeki Owada, Kensuke Tono, Makina Yabashi, Masaki Yamamoto, Hideo Ago, So Iwata, Hiroshi Sugimoto*, Yoshitsugu Shiro*, Minoru Kubo*" "Capturing an Initial Intermediate during the P450nor Enzymatic Reaction using Time-Resolved XFEL Crystallography and Caged-Substrate" Nat Commun. 2017 Nov 17;8(1):1585. doi: 10.1038/s41467-017-01702-1.
  2. Kubo, M., Nango, E., Tono, K., Kimura, T., Owada, S., Song, C., Mafune, F., Miyajima, K., Takeda, Y., Kohno, J., Miyauchi, N., Nakane, T., Tanaka, T., Nomura, T., Davidsson, J., Tanaka, R., Murata, M., Kameshima, T., Hatsui, T., Joti, Y., Neutze, R., Yabashi, M., Iwata, S. Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA. J Synchrotron Radiat. 2017 Sep 1;24(Pt 5):1086-1091. doi: 10.1107/S160057751701030X. Epub 2017 Aug 22.
  3. Shimada, A.†, Kubo, M.†, Baba, S.†, Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T. A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase Sci. Adv. (2017) Vol. 3, e1603042. (†equal contribution)
  4. Suga, M.†, Akita, F.†, Sugahara, M.†, Kubo, M.†, Nakajima, Y.†, Nakane, T., Yamashita, K., Umena, Y., Nakabayashi, M., Yamane, T., Nakano, T., Suzuki, M., Masuda, T., Inoue, S., Kimura, T., Nomura, T., Yonekura, S., Yu, L.-J., Sakamoto, T., Motomura, T., Chen, J.-H., Kato, Y., Noguchi, T., Tono, K., Joti, Y., Kamechima, T., Hatsui, T., Nango, E., Tanaka, R., Naitow, H., Matsuura, Y., Yamashita, A., Yamamoto, M., Nureki, O., Yabashi, M., Ishikawa, T., Iwata, S., Shen, J.-R. Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL Nature (2017) Vol. 543, 131-135. (†equal contribution)
  5. Nango, E., Royant, A.†, Kubo, M.†, Nakane, T., Kimura, T., Wickstrand, C., Tanaka, T., Tono, K., Song, C., Tanaka, R., Arima, T., Yamashita, A., Kobayashi, J., Hosaka, T., Mizohata, E., Nogly, P., Sugahara, M., Nam, D., Dods, R., Nomura, T., Shimamura, T., Im, D., Fujiwara, T., Yamanaka, Y., Jeon, B., Nishizawa, T., Oda, K., Fukuda, M., Andersson, R., Bath, P., Davidsson, J., Matsuoka, S., Kawatake, S., Murata, M., Nureki, O., Owada, S., Kameshima, T., Hatsui, T., Joti, Y., Schertler, G., Yabashi, M., Bondar, A.-N., Standfuss, J., Neutze, R., Iwata, S. A three dimensional movie of structural changes in bacteriorhodopsin. Science (2016) Vol. 354, 1552-1557. (†equal contribution)
  6. Nogly, P., Panneels, V., Nelson, G., Gati, C., Kimura, T., Milne, C., Milathianaki, D., Kubo, M., Wu, W., Conrad, C., Coe, J., Bean, R., Zhao, Y., Bath, P., Dods, R., Harimoorthy, R., Beyerlein, K. R., Rheinberger, J., James, D., DePonte, D., Li, C., Sala, L., Williams, G., Hunter, M., Koglin, J. E., Berntsen, P., Nango, E., Iwata, S., Chapman, H. N., Fromme, P., Frank, M., Abela, R., Boutet, S., Barty, A., White, T. A., Weierstall, U., Spence, J., Neutze, R., Schertler, G., Standfuss, J. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography Nat. Commun. (2016) Vol. 7, 12314 (9 pages).
  7. Otomo, A., Ishikawa, H., Mizuno, M., Kimura, T., Kubo, M., Shiro, Y., Aono, S., Mizutani, Y. A study of the dynamics of the heme pocket and C-helix in CooA upon CO dissociation using time-resolved visible and UV resonance Raman spectroscopy J. Phys. Chem. B (2016) Vol. 120, 7836-7843.
  8. M. Sakaguchi, T. Kimura, T. Nishida, T. Tosha, H. Sugimoto, Y. Yamaguchi, S. Yanagisawa, G. Ueno, H. Murakami, H. Ago, M. Yamamoto, T. Ogura, Y. Shiro*, M. Kubo* A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline. J. Synchrotron Rad. (2016) Vol. 23, 334-338
  9. Tano T, Okubo Y, Kunishita A, Kubo M, Sugimoto H, Fujieda N, Ogura T, Itoh S. Redox properties of a mononuclear copper(II)-superoxide complex. Inorg Chem. 2013 Sep 16;52(18):10431-7. doi: 10.1021/ic401261z. Epub 2013 Sep 5.
  10. Kubo, M., Nakashima, S., Yamaguchi, S., Ogura, T., Mochizuki, M., Kang, J., Tateno, M., Shinzawa-Itoh, K., Kato, K., Yoshikawa, S. :Effective pumping-proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system. J. Biol. Chem. (2013) 288, 30259-30269
  11. Sugimoto, H., Tatemoto, S., Toyota, K., Kubo, M., Ogura, T., Itoh, S. Oxo-sulfido- and oxo-selenido-molybdenum(VI) complexes possessing dithiolene ligand related to the active sites of hydroxylases of molybdoenzymes: Low temperature preparation and characterization. (2013) Chem. Commun. Vol. 49(39), 4358-60.
  12. Sugimoto, H., Hatakeda, K., Toyota, K., Tatemoto, S., Kubo, M., Ogura, T., Itoh, S. A new series of bis(ene-1,2-dithiolato)tungsten(IV), -(V), -(VI) complexes as reaction centre models of tungsten enzymes: preparation, crystal structures and spectroscopic properties. (2013) Dalton Trans. Vol. 42, 3059-3070.
  13. Yokoyama, A., Han, J. E., Cho, J., Kubo, M., Ogura, T., Siegler, M. A., Karlin, K. D., Nam, W. Chromium(IV) peroxo complex formation and its nitric oxide dioxygenase reactivity. (2012) J. Am. Chem. Soc. Vol. 134, 15269-15272.
  14. Kubo, M., Okuyama, O., Kitagawa, T., Shigeta, Y. DFT analysis of low-frequency heme vibrations in soluble guanylate cyclase: Raman mode enhancement by propionate-protein interactions. (2012) Chem. Lett. Vol. 41, 860-862.
  15. Kobayashi, Y., Okubo, K., Nomura, T., Kubo, M., Fujieda, N., Sugimoto, H., Fukuzumi, S., Goto, K., Ogura, T., Itoh, S. Copper(I)-dioxygen reactivity in a sterically demanding tripodal tetradentate tren ligand. Formation and reactivity of a mononuclear copper(II) end-on superoxo complex. (2012) Eur. J. Inorg. Chem. (29), 4574-4578 (Selected for Cover Picture).
  16. El-Mashtoly, S. F., Kubo, M., Gu, Y., Sawai, H., Nakashima, S., Ogura, T., Aono, S., Kitagawa, T. Site-specific protein dynamics in communication pathway from sensor to signaling domain of oxygen sensor protein, HemAT-Bs: Time-resolved ultraviolet resonance Raman study. (2012) J. Biol. Chem. Vol. 287, 19973-19984.
  17. El-Mashtoly, S. F., Kubo, M., Nakashima, S., Shimizu, T., Kitagawa, T. Structural dynamics of EcDOS heme domain revealed by time-resolved ultraviolet resonance Raman spectroscopy. (2011) J. Phys. Chem. Lett. Vol. 2, 2212-2217.
  18. Barabanschikov, A., Demidov, A., Kubo, M., Champion, P. M., Sage, J. T., Zhao, J., Sturhahn, W., Alp, E. E. Spectroscopic identification of reactive porphyrin motions. (2011) J. Chem. Phys. Vol. 135, 015101 (Selected for Cover Picture; Selected for Virtual J. Biol. Phys. Res.; Selected for Top 20 Most Downloaded Article in July 2011).
  19. Choi, Y. J., Cho, K.-B., Kubo, M., Ogura, T., Karlin, K. D., Cho, J., Nam, W. Spectroscopic and computational characterization of CuII-OOR (R = H or Cumyl) complexes bearing a Me6-tren ligand. (2011) Dalton Trans. Vol. 40, 2234-2241 (Special Issue, New Talent Asia).
  20. Cho, J., Woo, J., Han, J. E., Kubo, M., Ogura, T., Nam, W. Chromium(V)-oxo and chromium(III)-superoxo complexes bearing a macrocyclic TMC ligand in hydrogen atom abstraction reactions. (2011) Chem. Sci.. Vol. 2, 2057-2062.
  21. Aki, Y., Nagai, M., Nagai, Y., Imai, K., Aki, M., Sato, A., Kubo, M., Nagatomo, S., Kitagawa, T. Differences in coordination states of substituted tyrosine residues and quaternary structures among hemoglobin M probed by resonance Raman spectroscopy. (2010) J. Biol. Inorg. Chem. Vol. 15, 147-158.
  22. Benabbas, A., Ye, X., Kubo, M., Zhang, Z., Maes, E. M., Montfort, W. R., Champion, P. M. Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. (2010) J. Am. Chem. Soc. Vol. 132, 2811-2820.
  23. Sawant, S. C., Wu, X., Cho, J., Cho, K.-B., Kim, S. H., Seo, M. S., Lee, Y.-M., Kubo, M., Ogura, T., Shaik, S., Nam, W. Water as an oxygen source: Synthesis, characterization, and reactivity studies of a mononuclear nonheme manganese(IV) oxo complex. (2010) Angew. Chem. Int. Ed. Vol. 49, 8190-8194.
  24. Cho, J., Sarangi, R., Kang, H. Y., Lee, J. Y., Kubo, M., Ogura, T., Solomon, E. I., Nam, W. Synthesis, structural and spectroscopic characterization, and reactivities of mononuclear cobalt(III)-peroxo complexes. (2010) J. Am. Chem. Soc. Vol. 132, 16977-16986.
  25. Kim, S. H., Park, H., Seo, M. S., Kubo, M., Ogura, T., Klajn, J., Gryko, D. T., Valentine, J. S., Nam, W. Reversible O-O bond cleavage and formation between Mn(IV) peroxo and Mn(V) oxo corroles. (2010) J. Am. Chem. Soc. Vol. 132, 14030-14032.
  26. Nakane, D., Kuwasako, S., Tsuge, M., Kubo, M., Funahashi, Y., Ozawa, T., Ogura, T., Masuda, H. A square-planar Ni(II) complex with an N2S2 donor set similar to the active centre of nickel-containing superoxide dismutase and its reaction with superoxide. (2010) Chem. Commun. Vol. 46, 2142-2144.
  27. Tano, T., Doi, Y., Inosako, M., Kunishita, A., Kubo, M., Ishimaru, H., Ogura, T., Sugimoto, H., Itoh, S. Nickel(II) complexes of TPA ligands with 6-phenyl substituents PhnTPA. Structure and H2O2-reactivity. (2010) Bull. Chem. Soc. Jpn. Vol. 83, 530-538 (Selected Paper).
  28. Cho, J., Sarangi, R., Annaraj, J., Kim, S. Y., Kubo, M., Ogura, T., Solomon, E. I., Nam, W. Geometric and electronic structure and reactivity of a mononuclear “side-on” nickel(III)-peroxo complex. (2009) Nature Chem. Vol. 1, 568-572.
  29. Lee, Y.-M., Dhuri, S. N., Sawant, S. C., Cho, J., Kubo, M., Ogura, T., Fukuzumi, S., Nam, W. Water as an oxygen source in the generation of mononuclear nonheme iron(IV)-oxo complexes. (2009) Angew. Chem. Int. Ed. Vol. 48, 1803-1806.
  30. Honda, K., Cho, J., Matsumoto, T., Roh, J., Furutachi, H., Tosha, T. Kubo, M., Fujinami, S., Ogura, T., Kitagawa, T., Suzuki, M. New oxidation reactivity of a bis(mu-oxo)-dinickel(III) complex: Arene hydroxylation of the supporting ligand. (2009) Angew. Chem. Int. Ed. Vol. 48, 3304-3307.
  31. Inosako, M., Kunisita, A., Kubo, M., Ogura, T., Sugimoto, H., Itoh, S. (mu-eta2:eta2-disulfido)dinickel(II) complexes supported by 6-methyl-TPA ligands. (2009) Dalton Trans. 9410-9417 (Selected Paper for Cover Picture).
  32. Kunishita, A., Doi, Y., Kubo, M., Ogura, T., Sugimoto, H., Itoh, S. Ni(II)/H2O2 reactivity in bis[(pyridin-2-yl)methyl]amine tridentate ligand system. Aromatic hydroxylation reaction by bis(mu-oxo)dinickel(III) complex. (2009) Inorg. Chem. Vol. 48, 4997-5004.
  33. Kunishita, A., Kubo, M., Sugimoto, H., Ogura, T., Sato, K., Takui, T., Itoh, S. Mononuclear copper(II)-superoxo complexes that mimic the structure and reactivity of the active centers of PHM and DbetaM. (2009) J. Am. Chem. Soc. Vol. 131, 2788-2789.
  34. Kunishita, A., Kubo, M., Ishimaru, H., Ogura, T., Sugimoto, H., Itoh, S. H2O2-reactivity of copper(II) complexes supported by Tris[(pyridin-2-yl)methyl]amine ligands with 6-phenyl substituents. (2008) Inorg. Chem. Vol. 47, 12032-12039.
  35. Inosako, M., Kunishita, A., Shimokawa, C., Teraoka, J., Kubo, M., Ogura, T., Sugimoto, H., Itoh, S. Reaction of beta-diketiminate copper(II) complexes and Na2S2. (2008) Dalton Trans. 6250-6256.
  36. Kubo, M., Gruia, F., Benabbas, A., Barabanschikov, A., Montfort, W. R., Maes, E. M., Champion, P. M. Low frequency mode activity of heme: Femtosecond coherence spectroscopy of iron porphine halides and nitrophorin. (2008) J. Am. Chem. Soc. Vol. 130, 9800-9811.
  37. Gruia, F., Ionascu, D., Kubo, M., Ye, X., Dawson, J., Osborne, R. L, Sligar, S. G., Denisov, I., Das, A., Poulos, T. L., Terner, J., Champion, P. M. Low frequency dynamics of Caldariomyces fumago chloroperoxidase probed by femtosecond coherence spectroscopy. (2008) Biochemistry Vol. 47, 5156-5167.
  38. Gruia, F., Kubo, M., Ye, X., Ionascu, D., Lu, C., Poole, R. K., Yeh, S.-R., Champion, P. M. Coherence spectroscopy investigations of the low-frequency vibrations of heme: Effects of protein-specific perturbations. (2008) J. Am. Chem. Soc. Vol. 130, 5231-5244.
  39. Gruia, F., Kubo, M., Ye, X., Champion, P. M. Investigations of vibrational coherence in the low frequency region of ferric heme proteins. (2008) Biophys. J. Vol. 94, 2252-2268.
  40. Kubo, M., Uchida, T., Nakashima, S., Kitagawa, T. Construction of subnanosecond time-resolved, high-resolution UV resonance Raman measurement system and its application to reveal the dynamical structures of proteins. (2008) Appl. Spectrosc. Vol. 62, 30-37.
  41. Nishimura, M., Yoshimura, H., Ozawa, K., Yoshioka, S., Kubo, M., Kitagawa, T., Aono, S. Hydrogen bonding interaction on the heme-bound ligand in the heme-based O2 sensor protein. (2008) J. Porphyrins Phthalocyanines Vol. 12, 142-148.
  42. Gruia, F., Ye, X., Ionascu, D., Kubo, M., Champion, P. M. Low frequency spectral density of ferrous heme: Perturbations induced by axial ligation and protein insertion. (2007) Biophys. J. Vol. 93, 4404-4413.
  43. Kubo, M., Mori, Y., Otani, M., Murakami, M., Ishibashi, Y., Yasuda, M., Hosomizu, K., Miyasaka, H., Imahori, H., Nakashima, S. Ultrafast photoinduced electron transfer in directly-linked porphyrin-ferrocene dyads. (2007) J. Phys. Chem. A Vol. 111, 5136-5143.
  44. Kubo, M., Inagaki, S., Yoshioka, S., Uchida, T., Mizutani, Y., Aono, S., Kitagawa, T. Evidence for displacements of the C-helix by CO ligation and DNA binding to CooA revealed by UV resonance Raman spectroscopy. (2006) J. Biol. Chem. Vol. 281, 11271-11278.
  45. Kobayashi, K., Kubo, M., Yoshioka, S., Kitagawa, T., Kato, Y., Asano, Y., Aono, S. Systematic regulation of the enzyme activity of phenylacetaldoxime dehydratase by exogenous ligand. (2006) ChemBioChem Vol. 7, 2004-2009.
  46. Yoshimura, H., Yoshioka, S., Kobayashi, K., Ohta, T., Uchida, T., Kubo, M., Kitagawa, T., Aono, S. Specific hydrogen-bonding networks responsible for selective O2 sensing of the oxygen sensor protein HemAT from Bacillus subtilis. (2006) Biochemistry Vo. 45, 8301-8307.
  47. Kubo, M., Mori, Y., Otani, M., Murakami, M., Ishibashi, Y., Yasuda, M., Hosomizu, K., Miyasaka, H., Imahori, H., Nakashima, S. Coherent nuclear dynamics in ultrafast electron transfer in a porphyrin-ferrocene dyad. (2006) Chem. Phys. Lett. Vol. 429, 91-96.
  48. Shiga, H., Yamane, Y., Kubo, M., Sakurai, Y., Aso, H., Ito, E. Differentiation of immature oligodendrocytes is regulated by phosphorylation of cyclic AMP-response element binding protein by a protein kinase C signaling cascade. (2005) J. Neurosci. Res. Vol. 80, 767-776.
  49. Kubo, M., Shiomitsu, E., Odai, K., Sugimoto, T., Suzuki, H., Ito, E. Picosecond dynamics of the glutamate receptor in response to agonist-induced vibrational excitation. (2004) Proteins Vol. 54, 231-236.
  50. Kikuchi, H., Kubo, M., Watanabe, N., Suzuki, H. Computational method for calculating multidimensional Franck-Condon factors: Based on Sharp-Rosenstock's method. (2003) J. Chem. Phys. Vol. 119, 729-736.
  51. Kubo, M., Shiomitsu, E., Odai, K., Sugimoto, T., Suzuki, H., Ito, E. Agonist-specific vibrational excitation of glutamate receptor. (2003) J. Mol. Struct. (Theochem) Vol. 639, 117-128.
  52. Kubo, M., Shiomitsu, E., Odai, K., Sugimoto, T., Suzuki, H., Ito, E. Quantum chemical study of ligand-receptor electrostatic interactions in molecular recognition of the glutamate receptor. (2003) J. Mol. Struct. (Theochem) Vol. 634, 145-157.
  53. Odai, K., Sugimoto, T., Kubo, M., Ito, E. Theoretical research on structures of gamma-aminobutyric acid and glutamic acid in the aqueous condition. (2003) J. Biochem. Vol. 133, 335-342.
  54. Shiomitsu, E., Kubo, M., Suzuki, H., Ito, E. A thermodynamical study of the Schrodinger gear proposed in his clockwork hypothesis. (2002) Information Vol. 5, 491-502.
  55. Kubo, M., Odai, K., Sugimoto, T., Ito, E. Quantum chemical study of agonist-receptor vibrational interactions for activation of the glutamate receptor. (2001) J. Biochem. Vol. 129, 869-874.
  56. Odai, K., Sugimoto, T., Hatakeyama, D., Kubo, M., Ito, E. A theoretical study of electronic and structural states of neurotransmitters: gamma-aminobutyric acid and glutamic acid. (2001) J. Biochem. Vol. 129, 909-915.
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Reviews

  1. Kubo. M. Ligand-receptor interactions of the ionotropic glutamate receptor. SEIBUTSU BUTSURI (2006) 46, 93-97.
  2. Kubo, M., Ito, E. Structural dynamics of an ionotropic glutamate receptor. (2004) Proteins 56, 411-419.
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