発表原著論文

量子生命科学プロジェクト研究センター
Center for Quantum Life Sciences (QuLiS)


2007年度業績リスト

○　原著論文


機能設計予測グループ
（メンバー：相田 美砂子・岩田 末廣・松原 世明・榮 慶丈・原田 隆範）
（博士研究員：吉田 智喜，Jiong Ran）

Maihemutijiang Jieli, Toshiko Miyake and Misako Aida, “Enumeration of Topology-Distinct Structures and Possible Stable Structures of Protonated Water Clusters, H3O+(H2O)n−1 (n≤5),” Bulletin of the Chemical Society of Japan, 80(11), 2131-2136 (2007).

Jun Nakazawa, Yoshitake Sakae, Misako Aida, and Yoshinori Naruta, “Kinetic Investigations of the Process of Encapsulation of Small Hydrocarbons into a Cavitand-Porphyrin,” Journal of Organic Chemistry, 72(25), 9448-9455 (2007).

Toshiaki Matsubara, Michel Dupuis and Misako Aida, “Ab initio ONIOM-Molecular dynamics (MD) study on the deamination reaction by cytidine deaminase,” Journal of Physical Chemistry B, 111, 9965-9974 (2007).

Masashi Furukawa, Hiroyuki S. Kato, Masateru Taniguchi, Tomoji Kawai, Takaki Hatsui, Nobuhiro Kosugi, Tomoki Yoshida, Misako Aida, and Maki Kawai, “Electronic states of the DNA polynucleotides poly(dG)-poly(dC) in the presence of iodine,” Physical Review B, 75, 045119 (2007).

Toshiaki Matsubara, Michel Dupuis and Misako Aida, “The ONIOM molecular dynamics method for biochemical applications:cytidine deaminase,” Chemical Physics Letters, 437(1-3), 138-142 (2007).

Nobuyuki Akai, Keiichi Ohno and Misako Aida, “Photochemistry of 2-(methylamino) pyridine in a low-temperature argon matrix: Amino-imino tautomerism and rotational isomerism,” Journal of Photochemistry and Photobiology A: Chemistry, 187, 113-118(2007).

Tomoki Yoshida and Misako Aida, “BSSE-corrected Three-body Interaction Energy in the Recognition of GC Base Pair by Asparagine,” Chemistry Letters, 36(1), 124-125(2007).

Masayuki Ohisa, Hiroshi Yamataka, Michel Dupuis and Misako Aida, “Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method,” Physical Chemistry Chemical Physics, 2008, 10, 844-849.

Tomonori Yamada, Misako Aida, “Fundamental absorption frequencies and mean structures at vibrational ground state from quasi-classical direct ab initio MD: Triatomic molecule,” Chemical Physics Letters, 2008, 452(4-6), 315-320.


構造設計予測合成グループ
（メンバー：井上 克也・江幡 孝之・石橋 孝章・小島 聡志）
（博士研究員：永原 哲彦）

Ryukichi Takagi, Yukiko Miwa, Takashi Nerio, Yuta Inoue, Shuji Matsumura, and Katsuo Ohkata, “Stereochemical investigation on the construction of poly-functionalized bicyclo[3.3.1]nonenones by successive Michael reactions of 2-cyclohexenones,” Organic and Biomolecular Chemistry, 5(2), 286-300 (2007).

Kohichi Kashiwagi, Ryoji Sugise, Toshihiro Shimakawa, Tunao Matuura, and Masashi Shirai, “Linear relationship between activity of a new Ru-catalyst and acidity of substituted benzoic acids in the dimerization of acrylonitrile,” Chemistry Letters 35(2), 186-187 (2006).

Kohichi Kashiwagi, Ryoji Sugise, Toshihiro Shimakawa, Tunao Matuura, and Masashi Shirai, “Ruthenium-catalyzed dimerization of acrylonitrile in the presence of carboxylic acids,” Journal of Molecular Catalysis A: Chemistry 264(1-2), 9-16 (2007).

Kohichi Kashiwagi, Ryoji Sugise, Toshihiro Shimakawa, Tunao Matuura, and Masashi Shirai, “Improvement of catalyst activity in the Ru-catalyzed dimerization of acrylonitrile by using diphenyl ether as a solvent,” Chemistry Letters 36(11), 1384-1385 (2007).

Kohichi Kashiwagi, Ryoji Sugise, Toshihiro Shimakawa, Tunao Matuura, and Masashi Shirai, “Elucidation of inhibitors in the dimerization of acrylonitrile using [RuCl2(DMSO)4/CH3CH2COONa/DMSO/o-benzoylbenzoic acid] as catalyst,” Journal of Molecular Catalysis A: Chemistry, in press (on line Feb. 19, 2008).

Xin-Dong Jiang, Ken-ichiro Kakuda, Shiro Matsukawa, Hideaki Yamamichi, Satoshi Kojima, and Yohsuke Yamamoto “Synthesis and application of a bidentate ligand based on decafluoro-3-phenyl-3-pentanol: steric effect of pentafluoroethyl groups on the stereomutation of O-equatorial C-apical spirophosphoranes,” Chemistry an Asian Journal, 2(2), 314-323 (2007).

Kazuhisa Tanabe, Ayako Fujie, Naoki Ohmori, Yoshikazu Hiraga, Satoshi Kojima, and Katsuo Ohkata, “Studies on ring-closing metathesis for the 11-membered ring system for the synthesis of daphnezomine C,” Bulletin of the Chemical Society of Japan, 80(8), 1597-1604 (2007).

Xin-Dong Jiang, Shiro Matsukawa, Hideaki Yamamichi, Ken-ichiro Kakuda, Satoshi Kojima, and Yohsuke Yamamoto, “Stereomutation and experimental determination of the relative stability of diastereomeric O-equatorial anti-apicophilic spirophosphoranes,” European Journal of Organic Chemistry, (8), 1392-1405 (2008).

Satoshi Kojima, Masaaki Nakamoto, and Kin-ya Akiba, “Stereospecific pseudorotation of diastereomeric anti-apicophilic spirophosphoranes: a novel stereochemical transformation involving 10-P-5 phosphoranes,” European Journal of Organic Chemistry, (10), 1715-1722 (2008).

Satoshi Kojima, Takashi Chabayashi, Yasuhiro Umeda, Akihisa Iwamoto, Kazuhisa Tanabe, and Katsuo Ohkata, “Stereoselective synthesis of a novel chiral piperazine,” Heterocycles, in press (on line Feb. 22, 2008).

Laser spectroscopic study on the conformations and the hydrated structures of benzo-18-crown-6-ether and dibenzo-18-crown-6-ether in supersonic jets, Ryoji Kusaka, Yoshiya Inokuchi, and Takayuki Ebata, Phys. Chem. Chem. Phys., 2007, 9(32), 4452-4459.

Conformation of L-tyrosine studied by fluorescence-detected UV-UV and IR-UV double-resonance spectroscopy, Yoshiya Inokuchi, Yusuke Kobayashi, Takafumi Ito, and Takayuki Ebata, J. Phys. Chem. A, 2007, 111, 3209-3215.

Electronic spectra of jet-cooled calix[4]arene and its van der Waals clusters: Encapsulation of a neutral atom in a molecular bowl, Takayuki Ebata, Yuki Hodono, Takafumi Ito, and Yoshiya Inokuchi, J. Chem. Phys. 2007, 126, 141101-1-141101-4.

Picosecond IR-UV pump-probe spectroscopic study on the vibrational energy flow in isolated molecules and clusters, Yuji Yamada, Yukiteru Katsumoto and Takayuki Ebata, Phys. Chem. Chem. Phys., 2007, 9, 1170-1185.

Spin Transition at the Mesophase Transition Temperature in a Cobalt(II) Compound with Branched Alkyl Chains, Shinya Hayami, Reiko Moriyama, Aya Shuto, Yonezo Maeda, Kazuchika Ohta, and Katsuya Inoue, Inorg. Chem., 2007, 46, 7692-7694.

Effect of pressure on a chiral two-dimensional ferrimagnet, K. Iriguchi, Y. Komorida, I. Akiyama, M. Mito, J. Kishine, H. Deguchi, Y. Yoshida, K. Inoue, J. Phys. Soc. Jpn., 2007, 76, Suppl. A, 192-193.

Field-Induced Ferrimagnetic State in a Molecule-Based Magnet Consisting of a Co II Ion and a Chiral Triplet Bis(nitroxide) Radical, Youhei Numata, Katsuya Inoue, Nikolai Baranov, Mohamedally Kurmoo, and Koichi Kikuchi, J. Am. Chem. Soc., 2007, 129, 9902-9909.

Chiral Effects on Magnetic Properties for Chiral and Racemic WV?CuII Prussian Blue Analogues, Hiroyuki Higashikawa, Kazuki Okuda, Jun-ichiro Kishine, Naoji Masuhara, and Katsuya Inoue, Chemistry Letters, 2007, 36(8), 1022-1023.

Metal-organic frameworks from copper dimers with cis- and trans-1,4-cyclohexanedicarboxylate and cis,cis-1,3,5-cyclohexanetricarboxylate, Kumagai H, Akita-Tanaka M, Inoue K, Takahashi K, Kobayashi H, Vilminot S, Kurmoo M, Inorg. Chem., 2007, 46, 5949-5956.

Spin-crossover iron(II) compounds with liquid-crystal properties, Shinya Hayami, Natsuko Motokawa, Aya Shuto, Reiko Moriyama, Naoji Masuhara, Katsuya Inoue and Yonezo Maeda, Polyhedron, 2007, 26, 2375-2380.

Dual-function Molecular Crystal Containing the Magnetic Chain Anion [FeIII(C2O4)Cl2-]n, Bin Zhang, Zheming Wang, Yan Zhang, Hayao Kobayashi, Mohamedally Kurmoo, Takehiko Mori, Francis L. Pratt, Kastuya Inoue, Daoben Zhu, Polyhedron, 2007, 26, 1800-1804.

Guest-Induced Chirality in the Ferrimagnetic Nanoporous Diamond Framework Mn3(HCOO)6, Zhang, Bin, Wang, Zheming, Kurmoo, Mohamedally, Gao, Song, Inoue, Katsuya, Kobayashi, Hayao, Advanced Functional Materials, 2007, 17, 577-584.

Photoinduced Spin Transition for Iron(II) Compounds with Liquid-Crystal Properties, Shinya Hayami, Natsuko Motokawa, Aya Shuto, Naoji Masuhara, Takehiro Someya, Yoshihiro Ogawa, Katsuya Inoue, and Yonezo Maeda, Inorganic Chemistry, 2007, 46, 1789-1794.

Magnetic properties of a spin-1 ladder under pressure, Hosokoshi Y, Konishi Y, Nishihara S, Inoue K, J, Mag. Mag. Mat., 2007, 310, E420-E422.

Magnetic phase diagram of the quasi-two-dimensional S=1 antiferromagnet F2PNNNO, Tsujii H, Andraka B, Hosokoshi Y, Inoue K, Takano Y, J, Mag. Mag. Mat., 2007, 310, E415-E417.

Synthesis, crystal structure and magnetic properties of a cyclic dimer of [{Co(hfac)2}?BNOt-Bu]2, Y. Numata, K. Inoue, J, Mag. Mag. Mat., 2007, 310, 1847-1848.

Spin-density distribution in the partially magnetized organic quantum magnet F2PNNNO, Zheludev, A., Garlea, V. O., Nishihara, S., Hosokoshi, Y., Cousson, A., Gukasov, A., Inoue, K., Phys. Rev. B, 2007, 75, 104427.

Studies for Direction Dependences of Magnetizations and Magnetic Structure of Chiral Molecule-Based Metamagnet, [Mn(hfac)2]･BNO*, Youhei Numata, Katsuya Inoue, Chem. lett., 2007, 36, 534-535.

Millimeter Wave ESR Measurements on the Two Dimensional Chiral Molecule-Based Ferrimagnet [Cr(CN)6] [Mn(R)-pnH(H2O)](H2O), T. Fujita, S. Mitsudo, M. Toda, T. Idehara, M. Chiba, K. Inoue, and M. Motokawa, AIP Conference Proceedings, 2007, 850, 1055-1056.

Chiral Magnetic Ordering and Commensurate-to-incommensurate Transition in CuB2O4, Y. Kousaka, S. Yano, J. Kishine, Y. Yoshida, K. Inoue, and J. Akimitsu, J. Magn. Magn. Mater, 2007, 310, 463.




蛋白質情報グループ
（メンバー：井出 博・楯　真一・泉 俊輔・片柳 克夫）

Anisotropic nuclear spin interactions for the morphology analysis of proteins in solution by NMR spectroscopy, S. Tate, Analytical Sciences, 24(1), 39-50 (2008).

Chimeric structural stabilities in the coiled-coil structure of the NECK domain in human lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1), T. Ishigaki, I. Ohki, N. Utsunomiya-Tate, S. Tate, J. Biochemistry, 141(6), 855-866 (2007).

Nucleotide Excision Repair and Homologous Recombination Systems Commit Differentially to the Repair of DNA-Protein Crosslinks, T. Nakano, S. Morishita, A. Katafuchi, M. Matsubara, Y. Horikawa, H. Terato, A.M.H. Salem, S. Izumi, S. P. Pack, K. Makino, H. Ide, Molecular Cell, 28(1), 147-158 (2007).

Post-translational palmitoylation and glycosylation of Wnt-5a are necessary for its signaling, M. Kurayoshi, H. Yamamoto, S. Izumi, A. Kikuchi, Biochemical Journal, 402, 515-523 (2007).



生体系情報グループ
（メンバー：田中 伸和・小澤 孝一郎・古武 弥一郎・勝本 之晶）
（博士研究員：Adchara Padermshoke）
（客員教授：齊藤 肇）

Izuru Kawamura, Naoki Kihara, Masato Ohmine, Katsuyuki Nishimura, Satoru Tuzi, Hazime Saito, and Akira Naito, “Two different Backbone Conformations at Tyr185 in Bacteriorhodopsin Corresponding to Retinal Configurations in the Dark, Light, and Pressure Adapted State,” Journal of American Chemical Society, 129, 1016-1017 (2007).

Izuru Kawamura, Yoichi Ikeda, Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Satoru Yamaguchi, Satoru Tuzi, Hazime Saito, Naoki Kamo, and Akira Naito, “Participation of the Surface Structure of Pharaonis Phoborhodopsin, ppR and Its A149S and A149V Mutants, Consisting of the C-terminal ?-helix and E-F loop, in the Complex-formation with the Cognate Transducer pHtrII, as Revealed by Site-directed 13C Solid-state NMR,” Photochem. Photobiol. 83, 339-345 (2007).

Izuru Kawamura, Yoshiaki Degawa, Satoru Yamaguchi, Katsuyuki Nishimura, Satoru Tuzi, Hazime Saito and Akira Naito, “Pressure induced isomerization of retinal on bacteriorhodopsin as disclosed by Fast Magic Angle, Spinning NMR,” Photochemistry and Photobiology, 83, 346-350 (2007).

Izuru Kawamura, M. Ohmine, J. Tanabe, Satoru Tuzi, Hazime Saito, and Akira Naito, “Dynamic Aspects of Extracellular Loop Region as a Proton release Pathway of Bbacteriorhodopsin Studied by Relaxation Time Measurements by Solid State NMR,” Biochimica et Biophysica Acta, 1768, 3090-3097 (2007).

Izuru Kawamura, H. Yoshida, Y. Ikeda, Chise Hasegawa, Satoru Yamaguchi, Yuki Sudo, Satoru Tuzi, Hazime Saito, Naoki Kamo and Akira Naito, “Dynamics Changes Leading to Signal Transduction in the Terminal and Cytoplasmic α-Helical Regions of Pharaonis Phoborhodopsin and Its D75N Mutant Complexed with pHtrII by Site-directed Solid State 13C NMR,” Photochemistry and Photobiology, in press.
Published article online: 18-Mar-2008 doi: 10.1111/j.1751-1097.2008.00327.x

Toru Hosoi, Kanae Hyoda, Yasunobu Okuma, Yasuyuki Nomura and Koichiro Ozawa, “Akt up- and down-regulation in response to endoplasmic reticulum stress,” Brain Research, 1152, 27-31 (2007) Hiromi Katoh, Michiko Yoshii and Koichiro Ozawa, “Comparative study drug efficacy and additives between generic drugs and original drugs," YAKUGAKU ZASSHI 127, 2035-2044 (2007)

Michiko Yoshii, Naomi Iwasa, Ai Tarao, Fumi Tanaka and Koichiro Ozawa, “The effect of bile acid analogues on histamine release from RBL-2H3 cells,” YAKUGAKU ZASSHI, 127 Suppl. 5, 117-118 (2007)

Miya Honda, Toru Hosoi, Misae Takakuwa, Yasunobu Okuma, Yasuyuki Nomura and Koichiro Ozawa, “Possible involvement of endoplasmic reticulum stress in the immune function,” Journal of Pharmacological Sciences, 106, 127P (2008)

Koichiro Ozawa, Kenta Korematsu, Toru Hosoi, Naohiro Horie and Yasuyuki Nomura, “Possible involvement of endoplasmic reticulum stress in the immune function,” Journal of Pharmacological Sciences, 106, 132P (2008)

Toru Hosoi, Miyako Sasaki, Chie Hashimoto, Tsuyoshi Miyahara, Suguru Matsuo, Michiko Yoshii and Koichiro Ozawa, “Mechanism of endoplasmic reticulum stress-induced leptin resistance,” Journal of Pharmacological Sciences, 106, 134P (2008)

Shinsuke Ino, Toru Hosoi, Fumie Ohnishi, Michiko Yoshii and Koichiro Ozawa, “Inhibitory effect of the drug containing purine skelton on IgE-induced histamine release,” Journal of Pharmacological Sciences, 106, 199P (2008)

Y. Katsumoto, T. Tanaka, K. Ihara, M. Koyama, and Y. Ozaki, “Contribution of Intramolecular C=OoooH-N Hydrogen Bonding to the Solvent-Induced Reentrant Phase Separation of Poly(N-isopropylacrylamide)” J. Phys. Chem. B, 111(44), 12730-12737 (2007).

K. Shin-ya, H. Sugeta, S. Shin, Y. Hamada, Y. Katsumoto, and K. Ohno, “Absolute Configuration and Conformation Analysis of 1-Phenylethanol by Matrix-Isolation Infrared and Vibrational Circular Dichroism Spectroscopy Combined with Density Functional Theory Calculation,” J. Phys. Chem. A, 111(35), 8598-8605 (2007).

K. Shin-ya, O. Takahashi, Y. Katsumoto, and K. Ohno, “Conformational stability of propylbenzene and benzyl methyl ether connected with CHoooπ interaction studied by matrix-isolation infrared spectroscopy and theoretical calculations,” J. Mol. Struct., 827(1-3), 155-164 (2007).

Badejo, A.A., Tanaka, N. and Esaka, “M. Analysis of GDP-D-mannose pyrophosphrylase gene promoter from acerola (Malpighia glabra) and increase in ascorbate content of transgenic tobacco expressing the acelora gene,” Plant Cell Physiol., 49, 126-132 (2008).

Yaichiro Kotake, Yoko Sekiya, Katsuhiro Okuda and Shigeru Ohta, “Cytotoxicity of 17 tetrahydroisoquinoline derivatives in SH-SY5Y human neuroblastoma cells is related to mitochondrial NADH-ubiquinone oxidoreductase inhibition,” Neurotoxicology, 28, 27-32 (2007).

Yusuke Nakatsu, Yaichiro Kotake and Shigeru Ohta, “Concentration dependence of the mechanisms of tributyltin-induced apoptosis,” Toxicological Sciences, 97, 438-447 (2007).

Yusuke Nakatsu, Yaichiro Kotake, Atsuko Hino and Shigeru Ohta, “Activation of AMP-activated protein kinase by tributyltin induces neuronal cell death,” Toxicology and Applied Pharmacology, in press.

計算機情報グループ
（メンバー：神沼 二眞・石野 洋子・森本 康彦・大倉 和博）

Y. Ishino and H. Taniguchi, An a posteriori calibration method for improving protein identification accuracy in proteomics using electrospray ionization time-of-flight tandem mass spectrometry, Rapid Commun Mass Spectrom., in press.

Y. Ishino, H. Okada, M. Ikeuchi, H. Taniguchi: Mass Spectrometry-based Prokaryote Gene Annotation, Proteomics, 7, 4053-4065, (2007).





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