2004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：Shaheda A. Wahab）

Misako Aida and Michel Dupuis, “Fundamental absorption frequency from quasi-classical direct ab initio molecular dynamics: Diatomic Molecule,” Chemical Physics Letters, 401, 170-174 (2005).

Masato Tanaka and Misako Aida, “An Ab Initio MO Study on Orbital Interaction and Charge Distribution in Alkali Metal Aqueous Solution: Li⁺, Na⁺ and K⁺,” Journal of Solution Chemistry, 33 (6-7), 887-901(2004).

Takeshi Nagata and Suehiro Iwata, “Perturbation expansion theory corrected from basis set superposition error I. Locally projected excited orbitals and single excitations,” Journal of Chemical Physics, 120, 3555-3563 (2004).

Takeshi Nagata, Mutsumi Aoyagi and Suehiro Iwata, “Noble gas clusters doped with a metal ion I. Ab initio studies of Na⁺Ar_n,” Journal of Physical Chemistry A, 108, 683-690 (2004).

Suehiro Iwata and Fenwu Chen, “Theoretical study of photoabsorption cross section of water cluster anions: The size and isomer dependences,” Journal of Electron Spectroscopy and Related Phenomina, 142, 277-281 (2005).

Toshiaki Matsubara, “Density Functional Study of the Electronic Structure of the New Type of Ion Clusters X(O₂)₂ and X(NO)₂ (X=H^-, H⁺, Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, Ca²⁺) with the Cyclic Form,” Journal of Molecular Structure (THEOCHEM), 676, 177-184 (2004).

Yoshitake Sakae and Yuko Okamoto, “Protein force-field parameters optimized with the Protein Data Bank.I. Force-field optimizations,” Journal of Theoretical and Computational Chemistry, 3, 339-358 (2004).

Yoshitake Sakae and Yuko Okamoto, “Protein force-field parameters optimized with the Protein Data Bank.II. Comparisons of force fields by folding simulations of short peptides,” Journal of Theoretical and Computational Chemistry, 3, 359-378 (2004).

構造設計予測合成グループ
（メンバー：吉田 弘・小島 聡志）
（博士研究員：高須 雄一・赤井 伸行）

Keijiro Taga, Y. Jibu, S. Hamada, Y. Yamamoto, T.Yoshida, N. Shida, Hiroshi Yoshida, Keiichi Ohno and Hiroatsu Matsuura, “Density Functional Study of n-Propyltrichlorogermane and n-Propyltrichlorostannane,” Journal of Molecular Structure, 694(1-3), 63-71 (2004).

Nobuyuki Akai, Daisuke Negishi, Satomi Kudoh, Masao Takayanagi and Munetaka Nakata, “Infrared spectrum and molecular structure of lowest electronically excited triplet state of 1,4-dicyano-2,3,5,6-tetrafluorobenzene in low-temperature matrices,” Journal of Molecular Structure, 688, 177-183 (2004).

Mitsuhiro Nagata, Yoshisuke Futami, Nobuyuki Akai, Satomi Kudoh and Munetaka Nakata, “Structure and infrared spectrum of 2-hydroxyphenyl radical, ” Chemical Physics Letters, 392, 259-264 (2004).

Nobuyuki Akai, Satomi Kudoh and Munetaka Nakata, “Matrix-isolation infrared spectrum and optimized structure of 2,3-dicyanonaphthalene in the T₁ state,” Chemical Physics Letters, 392, 480-485 (2004).

Nobuyuki Akai, Satomi Kudoh and Munetaka Nakata, “Hydrogen-atom migration and Wolff rearrangement in photolysis of chlorohydroquinone to produce p-benzoquinone and 3-hydroxy-2,4-cyclopentadiene-1-ylidenemethanone,” Journal of Photochemistry and Photobiology A, 169, 47-55 (2005).

Kenji Ujike, Nobuyuki Akai, Satomi Kudoh and Munetaka Nakata,” Photoisomerization and photocyclization of 3,5-cyclohexadiene-1,2-diimine and its methyl-substituted derivatives in low-temperature argon matrices,” Journal of Molecular Structure, 735-736, 335-342 (2005).

Satoshi Kojima, Kyoko Hiroike and Katsuo Ohkata, “Stereoselective synthesis of activated cyclopropanes with an a-pyridinium acetamide bearing an 8-phenylmenthyl group as the chiral auxiliary,” Tetrahedron Letters, 45, 3565-3568 (2004).

Yoshifumi Kanosue, Satoshi Kojima and Katsuo Ohkata, “Influence of solvent viscosity on the rate of hydrolysis of dipeptides by carboxypeptidase Y,” Journal of Physical Organic Chemistry, 17, 448-457 (2004).

Yoshifumi Kanosue, Satoshi Kojima, Y. Hiraga and Katsuo Ohkata, “Relationship between the hydrophobicity of dipeptides and the Michaelis-Menten constant K_m of their hydrolysis by carboxypeptidase-Y and carboxypeptidase-A,” Bulletin of the Chemical Society of Japan, 77, 1187-1193 (2004).

Satoshi Kojima, T. Fukuzaki, Atsushi Yamakawa and Y. Murai, “Highly Z-selective synthesis of b-monosubstituted-a, b-unsaturated cyanides using the Peterson reaction,” Organic Letters, 6, 3917-3920 (2004).

Satoshi Kojima, Tsugihiko Hidaka and Y. Ohba, “Synthesis of b-monosubstituted a,b-unsaturated amides with Z-selectivity using diphenylphosphonoacetamides,” Heteroatom Chemistry, 15, 515-523 (2004).

Katsuo Ohkata, Yukiko Tamura, B. B. Shetuni, Ryukichi Takagi, Wataru Miyanaga, Satoshi Kojima and L. A. Paquette, “Stereoselectivity control by oxaspiro rings during Diels-Alder cycloadditions to cross-conjugated cyclohexadienones: The syn oxygen phenomenon,” Journal of the American Chemical Society, 126, 16783-16792 (2004).

Satoshi Kojima, Tsugihiko Hidaka and Atsushi Yamakawa, “Application of organocerium reagents for the efficient conversion of Z-a,b-unsaturated Weinreb amides to Z-a,b-unsaturated ketones,” Chemistry Letters, 34, 470-471 (2005).

蛋白質情報グループ
（メンバー：井出 博・泉 俊輔・片柳 克夫）
（博士研究員：山本 竜也）

Mayumi Matsubara, Tamon Tanaka, Hiroaki Terato, Eiji Ohmae, Shunsuke Izumi, Katsuo Katayanagi and Hiroshi Ide, “Mutational analysis of the damage-recognition and catalytic　mechanism of human SMUG1 DNA glycosylase,” Nucleic Acid Research, 32, 5291-5302 (2004).

Tatsuya Yamamoto, Shunsuke Izumi and Kunihiko Gekko, “Mass Spectrometry on Segment-Specific Hydrogen Exchange of Dihydrofolate Reductase,” The Journal of Biochemistry, 135, 17-24 (2004).

Tatsuya Yamamoto, Shunsuke Izumi and Kunihiko Gekko, “Mass Spectrometry on Hydrogen/Deuterium Exchange of Dihydrofolate Reductase: Effects of Ligand Binding,” The Journal of Biochemistry, 135, 663-671 (2004).

Tatsuya Yamamoto, Eiji Ohmae and Kunihiko Gekko, “Mass Spectrometry of Hydrogen/Deuterium Exchange of Escherichia coli Dihydrofolate Reductase: Effects of Loop Mutations,” The Journal of Biochemistry, 135, 487-494 (2004).

Laurent Gros, Alexander A. Ishchenko, Hiroshi Ide, Rhoderick H. Elder and Murat K. Saparbaev, “The major human AP endonuclease (Ape1) is involved in the nucleotide incision repair pathway,” Nucleic Acids Research, 32, 73-81 (2004).

Mohammed Mohsin Ali, Satofumi Kurisu, Yoshihiro Yoshioka, Hiroaki Terato, Yoshihiko Ohyama, Kihei Kubo and Hiroshi Ide, “Detection of endonuclease III- and 8-oxoguanine glycosylase-sensitive base modifications in gamma-irradiated DNA and cells by the aldehyde reactive probe (ARP) assay,” Journal of Radiation Research, 45, 229-237 (2004).

Atsushi Katafuchi, Toshiaki Nakano, AyAya Masaoka, Hiroaki Terato, Shigenori Iwai, Fumio Hanaoka and Hiroshi Ide, “Differential specificity of human and Escherichia coli endonuclease III and VIII homologues for oxidative base lesions,” Journal of Biological Chemmistry, 279, 14464-14471 (2004).

Tomoaki Yamasaki, Shunsuke Izumi, Hiroshi Ide and Yoshihiko Ohyama, “Identification of a novel rat microsomal vitamin D3 25-hydroxylase,” Journal of Biological Chemmistry, 279, 22848-22856 (2004).

Alexander A. Ishchenko, Hiroshi Ide, D. Ramotar, G. Nevinsky and Murat K. Saparbaev, “Alpha-anomeric deoxynucleotides, anoxic products of ionizing radiation, are substrates for the endonuclease IV-type AP endonucleases,” Biochemistry, 43, 15210-15216 (2004).

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：齋藤 肇）

Yaichiro Kotake, Katsuhiro Okuda, Machiko Kamizono, Naoki Matsumoto, Takao Tanahashi, Hiroshi Hara, Dominique Capparos-Lefebvre and Shigeru Ohta, “Detection and determination of reticuline and N-methylcoculaurine in the Annonaceae family using liquid chromatography-tandem mass spectrometry,” Journal of Chromatography B Analytical Technologies in the Biomedical and Life Sciences, 806, 75-78 (2004).

Yukiteru Katsumoto, Takeyuki Tanaka and Yukihiro Ozaki, “Relationship between the Coil-Globule Transition of an Aqueous Poly(N-isopropylacrylamide) Solution and Structureal Changes in Local Conformations of the Polymer,” Macromolecular Symposia, 205, 209-223 (2004).

T. Kimura, K. Ishihara, Koichiro Ozawa and M. Sasa, “Augmentation of serotonin-induced inhibition of neuronal activity in the hippocampus following repeated treatment with methamphetamine, ” Annals of the New York Academy of Sciences, 1025, 242-247 (2004).

Katsuhito Nagano, Etsuko Suzaki, Yuko Nagano, Katsuko Kataoka and Koichiro Ozawa, “Early apoptosis signals in hindlimb unloading-induced muscle atrophy,” Jounal of Pharmacological Sciences, 94, 142 (2004).

Kimiko Ihara, Hiriroko Unei, Kenji Kihira, Hiroshi Iwasaki, Koichi Kanigawa and Koichiro Ozawa, “Energy metabolism and nutritional support in the early phase of severely burned patients,” Japanese Journal of Burn Injury, 23, 223-230 (2004).

Hiroshi Moriuchi, Chiho Okamoto, Ryuichi Nishihama, Ichiro Yamashita, Yasunori Machida and Nobukazu Tanaka, “Nuclear localization and interaction of RolB with plant 14-3-3 proteins correlates with induction of adventitious roots by the oncogene rolB,” The Plant Journal, 38, 260-275 (2004).

Hiroshi Moriuchi, Yuki Fujikawa, Mohammed Aly Mohammed Aly, Hirofumi Saneoka, Khonosuke Fujita, Ichiro Yamashita and Nobukazu Tanaka, “Hairy root-mediated transgenic-plant regeneration in Egyptian clover (Trifolium alexandrinum L.),” Plant Biotechnology, 21, 165-168 (2004).

Nobukazu Tanaka, Kenji Suzuki and Ichiro Yamashita, “ Evidence of horizontal gene transfer from Agrobacterium rhizogenes to tobacco plants during evolutionary process,” Endocytobiosis and Cell Research, 15, 151-162 (2004).

Kazuo Yoshida, Misugi Uraji, Yoshiyuki Hattori, Kazuki Moriguchi, Katunori Suzuki, Nobukazu Tanaka and Akira Kato, “ Genome structure and evolution of giant plant pathogenic plasmids in Agrobacterium tumefaciens and Agrobacterium rhizogenes,” Endocytobiosis and Cell Research, 15, 371-378 (2004).

Yaichiro Kotake, Ryota Taguchi, Katsuhiro Okuda, Yoko Sekiya, Yoshikazu Tasaki, Masaaki Hirobe and Shigeru Ohta, “Neuroprotective effect of 1-methyl-1,2,3,4-tetrahydroisoquinoline on cultured rat mesencephalic neurons in the presence or absence of various neurotoxins,” Brain Research, 1033, 143-150 (2005).

Adchara Padermshoke, Yukiteru Katsumoto, Harumi Sato, Sanong Ekgasit, Isao Noda and Yukihiro Ozaki, “Surface Melting and Crystallization Behavior of Polyhydroxyalkanoates Studied by Attenuated Total Reflection Infrared Spectroscopy,” Polymer, 45(19), 6547-6554 (2004).

Adchara Padermshoke, Harumi Sato, Yukiteru Katsumoto, Sanong Ekgasit, Isao Noda and Yukihiro Ozaki, “Crystallization Behavior of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) Studied by 2D IR Correlation Spectroscopy,” Polymer, 45(21), 7159-7165 (2004).

Adchara Padermshoke, Harumi Sato, Yukiteru Katsumoto, Sanong Ekgasit, Isao Noda and Yukihiro Ozaki, “Thermally Induced Phase Transition of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) Investigated by Two-Dimensional Infrared Correlation Spectroscopy,” Vibrational Spectroscopy, 36(2), 269-277 (2004).

Adchara Padermshoke, Yukiteru Katsumoto, Harumi Sato, Sanong Ekgasit, Isao Noda and Yukihiro Ozaki, “Melting Behavior of Poly(3-hydroxybutyrate) Investigated by Two-Dimensional Infrared Correlation Spectroscopy,” Spectrochimica Acta A, 61, 541-550 (2005).

Harumi Sato, Masayuki Nakamura, Adchara Padermshoke, Hiroshi Yamaguchi, Hikaru Terauchi, Sanong Ekgasit, Isao Noda and Yukihiro Ozaki, “Thermal Behavior and Molecular Interaction of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) Studied by Wide-Angle X-ray Diffraction,” Macromolecules, 37, 3763-3769 (2004).

Harumi Sato, Rumi Murakami, Adchara Padermshoke, Fuminobu Hirose, Kenichi Senda, Isao Noda and Yukihiro Ozaki, “Infrared Spectroscopy Studies of CH…O Hydrogen Bondings and Thermal Behavior of Biodegradable Polyhydroxyalkanoate,” Macromolecules, 37, 7203-7213 (2004).

Hazime Saito, Satoru Yamaguchi, H. Okuda, A. Shiraishi and Satoru Tuzi, “Dynamic Aspect of Bacteriorhodopsin as a Typical Membrane Protein as Revealed by Site-directed Solid-state ¹³C NMR,” Solid State Nuclear Magnetic Resonance, 25, 5-14 (2004).

Hazime Saito, J. Mikami, Satoru Yamaguchi, M. Tanio, A. Kira, Tadashi Arakawa, Kazutoshi Yamamoto and Satoru Tuzi, “Site-directed ¹³C Solid-state NMR Studies on Membrane Proteins: Strategy and Goals toward Revealing Conformation and Dynamics as Illustrated for ¹³C-Labeled Bacteriorhodopsin,” Magnetic Resonance in Chemistry, 42, 218-230 (2004).

Akira Naito , Miya Kamihira, R. Inoue and Hazime Saito, “Structural Diversity of Amyloid Fibril Formed in Human Calcitonin as Viewed from Site-directed ¹³C Solid State NMR Spectroscopy,” Magnetic Resonance in Chemistry, 42, 247-257 (2004).

Hazime Saito, Satoru Yamaguchi, K. Ogawa, M. Marquez, C. Sanz and E.Padros, “Glutamic Acid Residue(s) of Bacteriorhdopsin at the extracellular Surface as Determinants for Conformation and Dynamics as Revealed by Site-directed Solid-state ¹³C NMR,” Biophys. J., 86, 1673-1681 (2004).

Satoru Yamaguchi, Satoru Tuzi, J. U. Bowie and Hazime Saito, “Secondary Structure and Backbone Dynamics of Eschelicia coli Diacylglycerol Kinase, as Revealed by Site-directed Solid-state ¹³C NMR,” Biochim. Biophys. Acta, 1698, 97-105 (2004).

Satoru Yamaguchi, Kazumi Shimono, Yuki Sudo, Satoru Tuzi, Akira Naito and Hazime Saito, “Conformation and Dynamics of [3-¹³C]Ala-, [1-¹³C]Val-labeled Truncated pharaonis Transducer, pHtrII (1-159) as Revealed by Site-directed 13C Solid-state NMR: Their Changes due to Association with Phoborhodopsin (Sensory R hodopsin II),” Biophysical Journal, 86, 3131-3140 (2004).

A. Kira, M. Tanio, Satoru Tuzi and Hazime Saito, “Significance of low-frequency local fluctuation motions in the transmembrane B and C ?-helices of bacteriorhodopsin, to facilitate efficient proton uptake from the cytoplasmic surface, as revealed by site-directed solid-state ¹³C NMR,” European Biophysics Journal, 33, 580-588 (2004).

S. Kumazawa, K. Kajiya, Akira Naito , Hazime Saito, Satoru Tuzi, M. Tanio, M. Suzuki, F. Nanjo, E. Suzuki and T. Nakayama, “Direct Evidence of Interaction of a Green Tea Polyphenol Epiglloccatechin Gallae, with Lipid Bilayers by Solid-state Nuclear Magnetic Resonance,” Biosci. Biotechnol.Biochem., 68, 1743-1747 (2004).

Hazime Saito, “Dynamic Picture of Membrane Proteins in Two-dimensional Crystal, Lipid Bilayer and Detergent as Revealed by Site-Directed Solid-state ¹³C NMR,” Chemistry and Physics of Lipids, 132, 101-112 (2004).

Hazime Saito, “Conformational and Dynamics Aspects of Polysaccharide Gels by High-Resolution Solid-State NMR In “Polysaccharides: Structural Diversity and Functional Versatility,” ed. by S. Dumitriu,” Marcel Dekker, Inc., (2004).

Adchara Padermshoke, Harumi Sato, Yukiteru Katsumoto, Sanong Ekgasit, Isao Noda and Yukihiro Ozaki, “Thermally induced phase transition of poly(3-hydroxybutyrate-co-3- -hydroxyhexanoate) investigated by two-dimensional infrared correlation spectroscopy,” Vibrational Spectroscopy, 36, 241-249 (2004).

Md Ruhul Matin, Shaheda A. Wahab, Yukiteru Katsumoto, Hiroatsu Matsuura and Keiichi Ohno, “Thermal Stability of the Hydration Structure of Short-chain Poly(oxyethylene) in Carbon Tetrachloride: An Infrared Spectroscopic Observation of the Breakdown of Hydrogen Bonds,” Chemistry Letters, 34, 502-503 (2005).

Keiichi Ohno, Hiroshi Takao, Takashi Masuda and Yukiteru Katsumoto, “Two Characteristic H-bonded O-H stretching Bands for the Compounds Containing Ether Oxygen and Hydroxyl Oxygen,” Chemistry Letters, 34, 250-251 (2005).

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）

神田 毅， 杉原 厚吉， 森本 康彦，「幾何アルゴリズム加速のための混合演算に関する研究」，応用数理学会論文誌，14（2），117-150（2004）

Kaori Fukuzawa, Kazuo Kitaura, Masami Uebayasi, Kotoko Nakata, Tsuguchika Kaminuma and Tatsuya Nakano, “Ab initio Quantum Mechanical Study of the Binding Energies of Human Estrogen Receptor with its Ligands: An application of Fragment of Molecualr Orbital Method,” Journal of Computational Chemistry, 26, 1-10 (2005).

Tsuguchika Kaminuma, “Lessons Learned in Building a Global Information Network on Chemicals (GINC),” Toxicology and Applied Pharmacology, in press.