Publications (2004, 2005)

[Research Papers] [Presentations in Academic Meetings]

Research Papers

  1. N. Funasaki, M. Fukuba, T. Kitagawa, M. Nomura, S. Ishikawa, S. Hirota and S. Neya : Two-Dimensional NMR Study on the Structures of Micelles of Sodium Taurocholate. J. Phys. Chem. B, 108, 438-443 (2004)
  2. S. Neya, T. Hoshino, M. Hata and N. Funasaki : Influence of Metallo Core Variation on 1-Methylimidazole Ligation to the Iron(III) in Porphyrin, Porphycene, Corrphycene, and Hemiporphycene. Chem. Lett., 33, 114-115 (2004)
  3. N. Funasaki, T. Sumiyoshi, S. Ishikawa and S. Neya : Solution Structures of 1:1 Complexes of Oxyphenonium Bromide with β- and γ-Cyclodextrins. Mol. Pharmaceutics, 1, 166-172 (2004)
  4. H. Ogata, T. Fukuda, K. Nakai, Y. Fujimura, S. Neya, P. A. Stuzhin and N. Kobayashi : Absorption, Magnetic Circular Dichroism, IR Spectra, Electrochemistry, and Molecular Orbital Calculations of Monoaza- and Opposite Diazaporphyrins. Eur. J. Inorg. Chem., 2004, 1621-1629 (2004)
  5. K. Mori, M. Hata, S. Neya and T. Hoshino : MD Simulation of Asymmetric Phospholipid Bilayers with Ions and Cholesterols. Chem-Bio Inform. J., 4, 15-26 (2004)
  6. N. Funasaki, S. Ishikawa, S. Hirota, S. Neya and T. Nishimoto : Structure and Ethanol Complexation of Cyclic Tetrasaccharide in Aqueous Solution Studied by NMR and Molecular Mechanics. Chem. Pharm. Bull., 52, 708-713 (2004)
  7. N. Funasaki, S. Ishikawa, and S. Neya : 1:1 and 1:2 Complexes between Long-Chain Surfactant and α-Cyclodextrin Studied by NMR. J. Phys. Chem. B, 108, 9593-9598 (2004)
  8. M. Hata, Y. Hirano, T. Hoshino, R. Nishida and M. Tsuda : Theoretical Study on Compound I Formation in Monooxygenation Mechanism by Cytochrome P450. J. Phys. Chem. B, 108, 11189-11195 (2004)
  9. T. Hoshino, M. Hata, S. Neya and H. Morinaga : Adhesion Mechanism of Metal Impurities on Si Wafers in Alkali Solution. J. Electrochem. Soc., 151, G590-G597 (2004)
  10. T. Osakabe, Y. Fujii, M. Hata, M. Tsuda, S. Neya, T. Hoshino : Quantum Chemical Study on Base Excision Mechanism of 8-Oxoguanine DNA Glycosylase: Substrate-Assisted Catalysis of the N-Glycosidic Linkage Cleavage Reaction. Chem-Bio Inform J., 4, 73-92 (2004)
  11. Y. Mie, C. Yamada, G. P.-J. Hareau, S. Neya, T. Uno, N. Funasaki, K. Nishiyama and I. Taniguchi : Functional Evaluation of Heme Vinyl Groups in Myoglobins with Symmetric Protoheme Isomers. Biochemistry, 43, 13149-13155 (2004)
  12. S. Neya, J. Quan, T. Hoshino, M. Hata and N. Funasaki : Convenient Synthesis of Porphine from β-Tetra(tert-butyl)porphyrin. Tetrahedron Lett., 45, 8629-8630 (2004)
  13. A. Tsuneshige, K. Kanaori, U. Samuni, D. Danstker, J. M. Friedman, S. Neya, L. Giangiacomo and T. Yonetani : Semihemoglobins, High Oxygen Affinity Dimeric Forms of Human Hemoglobin Respond Efficiently to Allosteric Effectors without Forming Tetramers. J. Biol. Chem., 279, 48959-48967 (2004)
  14. N. Pan, Y. Bian, T. Fukuda, M. Yokoyama, R. Li, S. Neya, J. Jiang and N. Kobayashi : Homoleptic Lanthanide Triple-Deckers of 5,15-Diazaporphyrin with D2h Symmetry. Inorg. Chem., 43, 8242-8244 (2004)
  15. Y. Sato, M. Hata, S. Neya and T. Hoshino : Computational Analysis on the Transient Movement of Helices in Sensory Rhodopsin II. Protein Sci., 14, 183-192 (2005)
  16. H. Ode, M. Ota, S. Neya, M. Hata, W. Sugiura and T. Hoshino: Resistant Mechanism against Nelfinavir of Human Immunodeficiency Virus Type 1 Proteases. J. Phys. Chem. B, 109, 565-574 (2005)
  17. Y. Mie, C. Yamada, T. Uno, S. Neya, F. Mizutani, K. Nishiyama and I. Taniguchi : Notable Deuterium Effect on the Electron Transfer Rate of Myoglobin. Chem. Commun., 250-252 (2005)
  18. S. Neya, C.-K. Chang, D. Okuno, T. Hoshino, M. Hata and N. Funasaki : Control of Iron(III) Spin-State in the Model Complexes of Azide Hemoprotein by Porphycene, Corrphycene, and Hemiporphycene Macrocycles. Inorg. Chem., 44, 1193-1195 (2005)
  19. J. Hasegawa, K. Takata, T. Miyahara, S. Neya, M. J. Frisch, H. Nakatsuji : Excited States of Porphyrin Isomers and Porphycene Derivatives: A SAC-CI Study. J. Phys. Chem. B, 109, 3187-3200 (2005)
  20. M. Hata, Y. Hirano, T. Hoshino, R. Nishida, M. Tsuda : Theoretical Study on Monooxygenation Mechanism by Cytochrome P450: An Ultimate Species in the Substrate Oxidation Process. J. Mol. Struct. (THEOCHEM), 722, 133-137 (2005)
  21. N. Funasaki, M. Fukuba, T. Kitagawa, M. Nomura, S. Ishikawa, S. Hirota, S. Neya: Reply to the Comment on “Two-Dimensional NMR Study on the Structures of Micelles of Sodium Taurocholate." J. Phys. Chem. B, 109, 9851-9852 (2005)
  22. M. Hata, Y. Tanaka, Y. Fujii, S. Neya, T. Hoshino: A Theoretical Study on the Substrate Deacylation Mechanism of Class C β-Lactamase. J. Phys. Chem. B , 109, 16153-16160 (2005)
  23. Y. Hirano, N. Shinmoto, M. Hata, M. Tsuda, T. Hoshino: Quantum Chemical Study on the Deacylation Step of Human Chymase. J. Mol. Struct. (THEOCHEM), 757, 19-27 (2005)
  24. K. Nishiyama, T. Watanabe, T. Hoshino, I. Ohdomari: Analysis of Interactions between Green Fluorescent Protein and Si Substrates Using Molecular Dynamics Simulations. Jpn. J. Appl. Phys., 44, 8210-8215 (2005)
  25. K. Mori, M. Hata, S. Neya, T. Hoshino: Common Semiopen Conformations of Mg2+-free Ras, Rho, Rab, Arf, and Ran Proteins Combined with GDP and Their Similarity with GEF-bound Forms. J. Am. Chem. Soc., 127, 15127-15137 (2005)
  26. K. Iwamoto, H. Ode, M. Ohta, T. Misu, M. Hata, S. Neya and T. Hoshino: Estimation of Ligand Receptor Binding Affinity from Fluctuation of Their Interface. Jpn. J. Appl. Phys., 44, L1370-L1372 (2005)

Presentations in Academic Meetings

  1. A. Tsuneshige, K. Kanaori, L. Giangiacomo, EmilIa Chiancone, S. Neya and T. Yonetani : Semihemoglobins: High Oxygen Affinity Dimeric Models of Human Hemoglobin Respond Efficiently to Allosteric Effectors without Forming Tetramers. 48th Annual Meeting of American Biophysical Society, Baltimore, USA (2004)
  2. I. Ishii, Y. Kobayashi, M. Hata, N. Ariyoshi and M. Kitada : Theoretical Calculation of Triazolam Hydroxylation and Endogenous Steroid Inhibition in CYP3A4. 2nd Pharmaceutical Sciences World Congress (PSWC2004), Kyoto, Japan, Abstracts, 132 (2004)
  3. M. Kitada, M. Hata, N. Torimoto, N. Ariyoshi and I. Ishii : Lysine Residues Presented in Outer Side of Three-dimensional Modeling May Be Important in Occurrence of CYP3A7 Activities. 2nd Pharmaceutical Sciences World Congress (PSWC2004), Kyoto, Japan, Abstracts, 156 (2004)
  4. Y. Ohgo, S. Neya, M. Takahashi, M. Takeda and M. Nakamura : Molecular Structure and Physicochemical Properties of Diazaporphyrin Iron(III) Complexes. Third International Conference on Porphyrins and Phthalocyanines (ICPP-3), New Orleans, USA, Abstracts, 785 (2004)
  5. H. Ishikawa, M. Hata, Y. Fujii, T. Hoshino and S. Neya : Deacylation Mechanism of Class D β-Lactamase. 44th Interscience Conference on Antimicrobial Agents and Chemotherapy, Washington, DC, USA, ABSTRACTS, 74 (2004)
  6. H. Ode, S. Neya, M. Hata, W. Sugiura and T. Hoshino : Insight into the Resistant Mechanism against HIV-1 Protease Inhibitor through Molecular Dynamics Simulations. International Symposium on Molecular Nano-Engineering and Its Development into Microsystems - Semiconductor Nanotechnology -, Tokyo, Japan, 60-61 (2004)
  7. T. Hattori, M. Yokoyama, H. Sato and T. Hoshino : Computational Identification of HIV-1 Specific CTL Epitopes. International Symposium on Molecular Nano-Engineering and Its Development into Microsystems - Semiconductor Nanotechnology -, Tokyo, Japan, 62-63 (2004)
  8. Y. Syoji, H. Fuji, Y. Yokomaku and T. Hoshino : Establishment of Human Immunodeficiency Virus Type1 Protease Activity Assay. International Symposium on Molecular Nano-Engineering and Its Development into Microsystems - Semiconductor Nanotechnology -, Tokyo, Japan, 64-65 (2004)
  9. H. Fuji, Y. Yokomaku, Y. Syoji, T. Narita, K. Miyauchi, Z. Matsuda, H. Sato, H. Hoshino and T. Hoshino : Construction of HIV-1 env Clone Library -Rapid Cloning and Expression of HIV-1 env, and Production of Recombinant HIV-1-. International Symposium on Molecular Nano-Engineering and Its Development into Microsystems - Semiconductor Nanotechnology -, Tokyo, Japan, 66-67 (2004)
  10. K. Nishiyama, T. Watanabe, T. Hoshino and I. Ohdomari : Molecular Dynamics Simulation on Interactions between Biomolecules and Semiconductor Surfaces. International Symposium on Molecular Nano-Engineering and Its Development into Microsystems - Semiconductor Nanotechnology -, Tokyo, Japan, 68-69 (2004)
  11. D. Katagiri, H. Ode, H. Ishikawa, T. Hattori, Y. Syoji, H. Fuji and T. Hoshino: Ab initio Protein Structure Prediction. 6th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP 6), Gaeta, Italy (2004)
  12. D. Katagiri, H. Ode, H. Ishikawa, T. Hattori, Y. Syoji, H. Fuji and T. Hoshino: Ab initio Protein Structure Prediction. 2nd Student Addendum Conference to Critical Assessment of Techniques for Protein Structure Prediction (SAC-CASP6), Gaeta, Italy (2004)
  13. S. Neya, T. Hoshino and M. Hata: Regulation of Geometric Stability and Spin-State of Iron(III) by Isomeric Porphyrinoids. 12th International Conference on Biological Inorganic Chemistry (ICBIC-12), Michigan, USA, Abstract-CD, 2BLR-154 (2005)
  14. A. Wongmekiat, Y. Tozuka, S. Neya and K. Yamamoto: Preparation of Drug Nanoparticles by Co-griding with Cyclodextrins: Factors Affecting Nanoparticle Formation Mechanism. 2005 Annual Meeting of American Association of Pharmaceutical Scientists, Baltimore, USA, Abstract-CD, radDE963 (2005)
  15. H. Ode, S. Neya, M. Hata, W. Sugiura and T. Hoshino : Molecular Dynamics Simulations of HIV-1 Protease -Insight into the Multi-drug Resistance Conferred by Non-active Site Mutation L90M-. 25th International CBI Conference, Yokohama, Japan, Proceedings, 44 (2005)
  16. K. Mori, T. Takaoka, K. Iwamoto, M. Hata, S. Neya, T. Hoshino : GLYMM: A Program for Modeling a 3D Structure of a Carbohydrate Chain and a Lipid Membrane: the Application to Molecular Dynamics Simulations of Glycolipid (GM1) Membranes. 25th International CBI Conference, Yokohama, Japan, Proceedings, 45 (2005)
  17. T. Hoshino, K. Nishiyama, T. Tanii, T. Watanabe, I. Ohdomari : Specific Adhesion of Biomolecules on the Nano-patterning Region of a Solid Surface. 2005 Symposium on Nanoscale Materials, Processes and Devices (2005 Joint Symposium of Standford Univ. & Waseda Univ.), Hawaii, USA (2005)
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