Announcement original work dissertation

Center for Quantum Life Sciences (QuLiS)


List of Announcement of Fiscal Year 2004

› @Result of research of Fiscal Year 2004


Computations of Molecular Interactions and Reactivity group
iMembers: AIDA, Misako; IWATA, Suehiro; MATSUBARA, Toshiaki; SAKAE, Yoshitake; HARADA, Takanorij
iPostdoctoralFShaheda A. Wahabj


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

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

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

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

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

Toshiaki Matsubara, gDensity 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,h Journal of Molecular Structure (THEOCHEM), 676, 177-184 (2004).

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

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



Structural design, Predict and Synthesis group
iMembers: YOSHIDA, Hiroshi; KOJIMA, Satoshij
iPostdoctoralFTAKASU, Yuichi; AKAI, Nobuyukij

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

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

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

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

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

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

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

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

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

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

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

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

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






Protein Informatics group
iMembers: IDE, Hiroshi; IZUMI, Shunsuke; KATAYANAGI, Katsuoj
iPostdoctoralFYAMAMOTO, Tatsuyaj

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

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

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

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

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

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

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

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

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



Biological system Informatics group
iMembers : TANAKA, Nobukazu; OZAWA, Koichiro; KOTAKE, Yaichirou; KATSUMOTO, Yukiteruj
iPostdoctoral : Adchara Padermshokej
(Visiting Professor : SAITO, Hajime)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Hazime Saito, Satoru Yamaguchi, H. Okuda, A. Shiraishi and Satoru Tuzi, gDynamic Aspect of Bacteriorhodopsin as a Typical Membrane Protein as Revealed by Site-directed Solid-state 13C NMR,h 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, gSite-directed 13C Solid-state NMR Studies on Membrane Proteins: Strategy and Goals toward Revealing Conformation and Dynamics as Illustrated for 13C-Labeled Bacteriorhodopsin,h Magnetic Resonance in Chemistry, 42, 218-230 (2004).

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

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

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

Satoru Yamaguchi, Kazumi Shimono, Yuki Sudo, Satoru Tuzi, Akira Naito and Hazime Saito, gConformation 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),h Biophysical Journal, 86, 3131-3140 (2004).

A. Kira, M. Tanio, Satoru Tuzi and Hazime Saito, gSignificance 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,h 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, gDirect Evidence of Interaction of a Green Tea Polyphenol Epiglloccatechin Gallae, with Lipid Bilayers by Solid-state Nuclear Magnetic Resonance,h Biosci. Biotechnol.Biochem., 68, 1743-1747 (2004).

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

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

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

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

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


Calculator and Information group
iMembers: KAMINUMA, Tsuguchika; ISHINO, Yoko; MORIMOTO, Yasuhikoj


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

Tsuguchika Kaminuma, gLessons Learned in Building a Global Information Network on Chemicals (GINC),h Toxicology and Applied Pharmacology, in press.



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