Publications

発表論文・著書等

• Hiro Nakamura, Hiroshi Murakami, Ichiro Yamato, and Yasuhiro Anraku: Nucleotide sequence of cybB, the gene for cytochrome b₅₆₁ in Escherichia coli K-12.
  Mol. Gen. Genet. 212, 1-5 (1988)

• Kentaro Hanada, Ichiro Yamato, and Yasuhiro Anraku: Solubilization and reconstitution of proline carrier in Escherichia coli; quantitative analysis and optimal conditions.
  Biochim. Biophys. Acta 939 282-288 (1988)

• Kentaro Hanada, Ichiro Yamato, and Yasuhiro Anraku: Purification and reconstitution of Escherichia coli proline carrier using a site specifically cleavable fusion protein.
  J. Biol. Chem. 263, 7181-7185 (1988)

• Ichiro Yamato, Hiro Nakamura, Hiroshi Murakami, and Yasuhiro Anraku: Mapping and disruption of the cybB gene coding for cytochrome b₅₆₁ in E. coli.
  FEMS Microbiol. Lett. 56, 21-28 (1988)

• Toshifumi Nakao, Ichiro Yamato, and Yasuhiro Anraku: Mapping of the multiple regulatory sites for putP and putA expression in the putC region of Escherichia coli.
  Mol. Gen. Genet. 214, 379-388 (1988)

• Minako Ohsawa, Tatsushi Mogi, Hiroshi Yamamoto, Ichiro Yamato, and Yasuhiro Anraku: Proline carrier mutant in Escherichia coli K-12 with altered cation sensitivity of substrate binding activity: Cloning, biochemical characterization and identification of the mutation.
  J. Bacteriol. 170, No. 11, 5185-5191 (1988)

• Malcolm G. P. Page, Jurg P. Rosenbusch, and Ichiro Yamato: The effects of pH on proton sugar symport activity of the lactose permease purified from Escherichia coli.
  J. Biol. Chem. 263, No. 31, 15897-15905 (1988)

• Ichiro Yamato, and Yasuhiro Anraku: Site-specific alteration of cysteine-281, cysteine-344, and cysteine-349 in the proline carrier of Escherichia coli.
  J. Biol. Chem. 263, No. 31, 16055-16057 (1988)

• 山登一郎： 生体膜
  分子設計技術（第４章第１節７．）、pp.270-277 (1988)（編集：岡田正和、菅野卓雄、米沢貞次郎、 山岸俊一、太田隆久）サイエンスフォーラム社、東京

• Yasuhiro Anraku, Kentaro Hanada, and Ichiro Yamato: Molecular structure and energy coupling mechanism of the Escherichia coli proline carrier.
  Molecular Basis of Biomembrane Transport, pp.25-32 (1988) (Ed. by F. Palmieri and E. Quagliariello) Elsevier Scientific Publishers, Amsterdam

• Ichiro Yamato, and Yasuhiro Anraku: Dependence on pH of substrate binding to a mutant lactose carrier, lacY^unc, in Escherichia coli: A model for H⁺/lactose symport.
  Biochem. J. 258, 389-396 (1989)

• Yutaka Deguchi, Ichiro Yamato, and Yasuhiro Anraku: Molecular cloning of gltS and gltP encoding glutamate carriers of Escherichia coli B.
  J. Bacteriol. 171, No. 3, 1314-1319 (1989)

• Yuto Komeiji, Kentaro Hanada, Ichiro Yamato, and Yasuhiro Anraku: Orientation of the carboxyl terminus of the Na⁺/proline symport carrier in Escherichia coli.
  FEBS Lett. 256, No. 1/2, 135-138 (1989)

• 山登一郎： 生体物質の持つ特異性を利用した分離技術
  Sut Bulletin 1, 57-59 (1989)

• Ichiro Yamato, and Yasuhiro Anraku: Mechanism of Na⁺/proline symport in Escherichia coli: Reappraisal of the effect of cation binding to the Na⁺/proline symport carrier.
  J. Membrane Biol. 114, 143-151 (1990)

• Ichiro Yamato, Minako Ohsawa, and Yasuhiro Anraku: Defective cation-coupling mutants of Escherichia coli Na⁺/proline symport carrier. Characterization and localization of mutations.
  J. Biol. Chem. 265, No. 5, 2450-2455 (1990)

• Hiro Nakamura, Ichiro Yamato, Yasuhiro Anraku, L. Lemieux, and Robert B. Gennis: Expression of cyoA and cyoB demonstrates that the CO-binding heme component of the Escherichia coli cytochrome o complex is in subunit I.
  J. Biol. Chem. 265, No. 19, 11193-11197 (1990)

• Jun Minagawa, Hiro Nakamura, Ichiro Yamato, Tatsushi Mogi, and Yasuhiro Anraku: Transcriptional regulation of the cytochrome o complex in Escherichia coli. Gene expression and molecular characterization of the promoter.
  J. Biol. Chem. 265, No. 19, 11198-11203 (1990)

• Yutaka Deguchi, Ichiro Yamato, and Yasuhiro Anraku: Nucleotide sequence of gltS, the Na⁺/glutamate symport carrier gene of Escherichia coli.
  J. Biol. Chem. 265, No. 35, 21704-21708 (1990)

• 山登一郎： 大腸菌プロリン輸送系の研究
  生化学　62、1020ｰ1030 (1990)

• 山登一郎： 糖・アミノ酸の輸送と輸送タンパク質
  生体膜工学（第６章）pp.137-156 (1991)（編集：二井將光）丸善株式会社、東京

• Shin-ichi Kajie, Ritsuro Ideta, Ichiro Yamato, and Yasuhiro Anraku: Molecular cloning and DNA sequence of dniR, a gene affecting anaerobic expression of the Escherichia coli hexaheme nitrite reductase.
  FEMS Microbiol. Lett. 83, 205-212 (1991)

• Yoshimi Kakinuma, Kazuei Igarashi, Kiyoshi Konishi, and Ichiro Yamato: Primary structure of the α-subunit of vacuolar-type Na⁺-ATPase in Enterococcus hirae Amplification of a 1000-bp fragment by polymerase chain reaction.
  FEBS Lett. 292, No. 1/2, 64-68 (1991)

• Yuto Komeiji, Masami Uebayasi, Jun-ichiro Someya, and Ichiro Yamato: Molecular dynamics simulation of trp-aporepressor in a solvent.
  Prot. Engng. 4, No. 8, 871-875 (1991)

• Ichiro Yamato: Ordered binding model as a general mechanistic mechanism for secondary active transport systems.
  FEBS Lett. 298, No. 1, 1-5 (1992)

• Kentaro Hanada, Takashi Yoshida, Ichiro Yamato, and Yasuhiro Anraku: Sodium ion and proline binding sites in the Na^＋/proline symport carrier of Escherichia coli.
  Biochim. Biophys. Acta 1105, No. 1, 61-66 (1992)

• Ichiro Yamato: Membrane assembly of lactose permease of Escherichia coli.
  J. Biochem. 111, No. 4, 444-450 (1992)

• Mayumi Arai, Keietsu Abe, and Ichiro Yamato: Purification and characterization of the HPr protein of Pediococcus halophilus.
  Biochem. Int. 27, No. 2, 275-279 (1992)

• 山登一郎： 変異株の分離・細菌
  新生化学実験講座第６巻生体膜と膜輸送、 pp.203-214 (1992)（編集：水島昭二、田川邦夫、安楽泰宏、 二井將光、永井克孝）東京化学同人、東京

• 山登一郎： 二次性能動輸送機構の統一的モデル
  生物物理　32, No. 4, 174-179 (1992)

• Ichiro Yamato, and Yasuhiro Anraku: Na^＋/substrate symport in prokaryotes.
  In Alkali cation transport systems in prokaryotes, p.53-p.76 (1992) (ed. by E. P. Bakker) CRC Press, Florida, USA

• 山登一郎： プロリン／Ｎａ^＋シンポート
  新生化学実験講座第６巻生体膜と膜輸送、pp.497-501 (1992)（編集：水島昭二、田川邦夫、安楽泰宏、 二井將光、永井克孝） 東京化学同人、東京

• 山登一郎： ＡＴＰ共役輸送
  新生化学実験講座第６巻生体膜と膜輸送、pp.521-529 (1992)（編集：水島昭二、田川邦夫、安楽泰宏、 二井將光、永井克孝）東京化学同人、東京

• Yuto Komeiji, Masami Uebayasi, Jun-ichiro Someya, and Ichiro Yamato: Free energy perturbation calculation on a Trp-binding mutant (Ser８８→Cys) of the trp-repressor.
  Prot. Engng. 5, No. 8, 759-767 (1992)

• Yuto Komeiji, Masami Uebayasi, Jun-ichiro Someya, and Ichiro Yamato: A molecular dynamics study of solvent behavior around a protein.
  Proteins: Structure, Function, and Genetics 16, 268-277 (1993)

• Kazuma Takase, Ichiro Yamato, and Yoshimi Kakinuma: Cloning and sequencing of the genes coding for the A and B subunits of vacuolar-type Na^＋-ATPase from Enterococcus hirae. Coexistence of V- and F-type ATPases in one bacterial cell.
  J. Biol. Chem. 268, No. 16, 11610-11616 (1993)

• Yuto Komeiji, Nobuo Honda, and Ichiro Yamato: Helix propensity of Ala and Val: a free energy perturbation study.
  Biophys. Chem. 47, 113-121 (1993)

• 山登一郎： 特異的生体反応の分子論的解明．
  CBI News 13, No. 3, 1-2 (1993)

• 山登一郎、古明地勇人： タンパク質分子シミュレーション（分子動力学法）の応用．分子動力学計算を用いたタンパク質の構造と 機能の研究．
  CICSJ Bulletin 11, No. 4, 10-13 (1993)

• Yoshimi Kakinuma, Shizuko Kakinuma, Kazuma Takase, Kiyoshi Konishi, Kazuei Igarashi, and Ichiro Yamato: A gene encoding the 16-kDa proteolipid subunit of Enterococcus hirae Na^＋-ATPase complex.
  Biochem. Biophys. Res. Commun. 195, No. 2, 1063-1069 (1993)

• Ichiro Yamato: Ordered binding model as a general tight coupling mechanism for bioenergy transduction --- A hypothesis.
  Proc. Japan Acad. 69, No. 8, 218-223 (1993)

• Ichiro Yamato, Masanori Kotani, Yumiko Oka, and Yasuhiro Anraku: Site-specific alteration of arginine-376, the unique positively charged amino acid residue in mid-membrane spanning regions of the proline carrier of Escherichia coli.
  J. Biol. Chem. 269, No. 8, 5720-5724 (1994)

• 山登一郎： 二次性能動輸送過程のエネルギー共役機構．
  薬学研究の進歩（薬学研究奨励財団）１０巻、p.175-p.185 (1994)

• Kazuma Takase, Shizuko Kakinuma, Ichiro Yamato, Kiyoshi Konishi, Kazuei Igarashi, and Yoshimi Kakinuma: Sequencing and characterization of the ntp gene cluster for vacuolar type Na^＋-translocating ATPase of Enterococcus hirae.
  J. Biol. Chem. 269, No. 15, 11037-11044 (1994)

• 山登一郎： タンパク質をデザインするー生命科学における第２の暗号解読問題．
  Sut Bulletin 8, 36-41 (1994)

• Yuto Komeiji, Izumi Fujita, Nobuo Honda, Masaru Tsutsui, Takahiko Tamura, and Ichiro Yamato: Glycine-85 of the trp-repressor of E. coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches.
  Prot. Engng. 7, No. 10, 1239-1247 (1994)

• Yuto Komeiji, Masami Uebayasi, and Ichiro Yamato: Molecular dynamics simulations of trp apo- and holorepressors: domain structure and ligand- protein interaction.
  Proteins: Structure, Function, and Genetics 20, 248-258 (1994)

• 丸山明子、前場良太、島崎弘幸、山登一郎、樽谷修、植田伸夫： 酸化ＬＤＬのスーパーオキサイド産生能及び好中球からのスーパーオキサイド産生誘導能．
  帝京医学雑誌 17, No. 6, 511-521 (1994)

• 山田芽由美、前場良太、島崎弘幸、山登一郎、樽谷修、上田伸夫： 酸化ＬＤＬのスーパーオキシド産生機構．
  帝京医学雑誌　18, No. 4, 369-380 (1995)

• Izumi Fujita, Yuto Komeiji, and Ichiro Yamato: Threonine 81 of the trp repressor of Escherichia coli plays an auxiliary role in the formation of the corepressor binding pocket.
  Prot. Engng. 8, No. 9, 935-938 (1995)

• Takeshi Murata, Kazuma Takase, Ichiro Yamato, Kazuei Igarashi, and Yoshimi Kakinuma: The ntpJ gene in the Enterococcus hirae ntp operon encodes a component of KtrII potassium transport system functionally independent of vacuolar Na⁺-ATPase.
  J. Biol. Chem. 271, No. 17, 10042-10047 (1996)

• Nobuo Honda, Yuto Komeiji, Masami Uebayasi, and Ichiro Yamato: Computational design of a substrate specificity mutant of a protein.
  Proteins: Structure, Function, and Genetics 26, 459-464 (1996)

• Takeshi Murata, Ichiro Yamato, Kazuei Igarashi, and Yoshimi Kakinuma: Intracellular Na^＋ regulates transcription of the ntp operon encoding a vacuolar-type Na^＋- translocating ATPase in Enterococcus hirae.
  J. Biol. Chem. 271, No. 39, 23661-23666 (1996)

• 山登一郎： 微生物の構造と生理．
  生物工学基礎コース、微生物工学、pp.38-57 (1997)（編集：百瀬春生）丸善株式会社、東京

• Atsushi Suenaga, Ichiro Yamato, and Minoru Saito: Molecular dynamics simulation of outer membrane porins in Escherichia coli.
  Progress in Cell Research, Vol.6: Molecular Biophysics of Ion Channels, pp.217-232 (1997) (eds. M. Sokabe and A. Auerbach) Elsevier Sci. Pub., Amsterdam

• Takeshi Murata, Kazuma Takase, Ichiro Yamato, Kazuei Igarashi, and Yoshimi Kakinuma: Purification and reconstitution of Na^＋-translocating vacuolar ATPase from Enterococcus hirae.
  J. Biol. Chem. 272, No. 40, 24885-24890 (1997)

• Atsushi Suenaga, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro, and Ichiro Yamato: Molecular dynamics simulation of unfolding of histidine-containing phosphocarrier protein in water.
  J. Chem. Software 4, No.4, 127-142 (1998)

• Atsushi Suenaga, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro, Minoru Saito, and Ichiro Yamato: Computational observation of an ion permeation process through a channel protein.
  Bioscience Reports 4, No.1, 39-48 (1998)

• Yasuo Takeda, Kazuma Takase, Ichiro Yamato, and Keietsu Abe: Sequencing and characterization of xyl operon of a Gram-positive bacterium, Tetragenococcus halophila.
  Applied and Environmental Microbiology 64, No.7, 2513-2519 (1998)

• 山登一郎： 　　 生物工学分野の計算機利用教育.
  私情協ジャーナル 7, No.2, 2-3 (1998)

• Keietsu Abe, Takeshi Higuchi, and Ichiro Yamato: 　　 Xylose transport insensitive to catabolite inhibition by phosphoenolpyruvate:sugar phospho- transferase system in Tetragenococcus halophila.
  Biosci. Biotechnol. Biochem. 62, No.9, 1676-1683 (1998)

• Takeshi Murata, Kazuma Takase, Ichiro Yamato, Kazuei Igarashi, and Yoshimi Kakinuma: Properties of the V₀V₁ Na⁺-ATPase from Enterococcus hirae and Its V₀ moiety.
  J. Biochem (Tokyo) 125, No.2, 414-421 (1999)

• Yoshimi Kakinuma, Ichiro Yamato, and Takeshi Murata: Structure and function of vacuolar Na⁺-translocating ATPase in Enterococcus hirae.
  J. Bioenerg. Biomembr. 31, No.1, 7-14 (1999)

• Kazuma Takase, Ichiro Yamato, Kazuei Igarashi, and Yoshimi Kakinuma: Indispensable glutamic acid residue-139 of NtpK proteolipid in the reaction of vacuolar Na⁺-translocating ATPase in Enterococcus hirae.
  Biosci. Biotechnol. Biochem. 63, No.6, 1125-1129 (1999)

• Miho Ikegami, Miyuki Kawano, Kazuma Takase, Ichiro Yamato, Kazuei Igarashi, and Yoshimi Kakinuma: Enterococcus hirae vacuolar ATPase is expressed in response to pH as well as sodium.
  FEBS Lett. 454, No.1-2, 67-70 (1999)

• Takeshi Murata, Kazuei Igarashi, Yoshimi Kakinuma, and Ichiro Yamato: Na⁺ binding of V-type Na⁺-ATPase in Enterococcus hirae.
  J. Biol. Chem. 275, No.18, 13415-13419 (2000)

• Atsushi Suenaga, Chieko Yatsu, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro, and Ichiro Yamato: Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein-DNA interaction.
  Journal of Molecular Structure 526, No.1-3, 209-218 (2000)

• Takeshi Murata, Miyuki Kawano, Kazuei Igarashi, Ichiro Yamato, and Yoshimi Kakinuma: Catalytic properties of Na⁺-translocating V-ATPase in Enterococcus hirae.
  Biochim. Biophys. Acta 1505, No.1, 75-81 (2001)

• Takeshi Murata, Yoshimi Kakinuma, and Ichiro Yamato: ATP-dependent affinity change of Na⁺ binding sites of V-ATPase in Enterococcus hirae.
  J. Biol. Chem. 276, No.51, 48337-48340 (2001)

• Kenji Tabata, Mariko Kajiyama, Tomohiro Hiraishi, Hideki Abe, Ichiro Yamato, and Yoshiharu Doi: Purification and characterization of poly(aspartic acid) hydrolase from Sphingomonas sp. KT-1.
  Biomacromolecules 2, No.4, 1155-1160 (2001)

• Toshiyuki Meguro and Ichiro Yamato: New structure deformation algorithm of Monte Carlo simulation of protein folding.
  J. Comput. Chem., Jpn., 1, No.1, 9-22(2002)

• Miyuki Kawano, Kazuei Igarashi, Ichiro Yamato and Yoshimi Kakinuma: Arginine residue at position 573 in Enterococcus hirae V-ATPase NtpI subunit plays a crucial role in Na⁺ translocation.
  J. Biol. Chem., 277, No.27, 24405-24410 (2002)

• Seiichi Taguchi, Hirofumi Nakamura, Tomohiro Hiraishi, Ichiro Yamato and Yoshiharu Doi: In vitro evolution of a polyhydroxybutyrate synthase by intragenic suppression-type mutagenesis.
  J. Biochem., 131, No.6, 801-806 (2002)

• Tadashi Ando, Toshiyuki Meguro and Ichiro Yamato: Development of an atomistic Brownian dynamics algorithm with implicit solvent model for long time simulation.
  J. Comput. Chem., Jpn., 1, No.3, 103-110 (2002)

• Takeshi Murata, Yasushi Yoshikawa, Toshiaki Hosaka, Kazuma Takase, Yoshimi Kakinuma, Ichiro Yamato and Takeshi Kikuchi: Nucleotide binding sites in V-type Na⁺-ATPase from Enterococcus hirae.
  J. Biochem., 132, No.5, 789-794 (2002)

• Ryo Ohashi, Jose M. Otero, Adam Chwistek, Ichiro Yamato and Jean-Francois P. Hamel: On-line purification of monoclonal antibodies using an integrated stirred-tank reactor/expanded-bed adsorption system.
  Biotechnol. Prog., 18, 1292-1300 (2002)

• Toshiyuki Meguro, Tadashi Ando and Ichiro Yamato: Development of multifunctional object-oriented program library for molecular simulation and structure analysis.
  J. Comput. Chem., Jpn., 2, No. 1, 7-16 (2003)

• Tomohiro Hiraishi, Mariko Kajiyama, Kenji Tabata, Ichiro Yamato and Yoshiharu Doi: Genetic analysis and characterization of poly(aspartic acid) hydrolase-1 from Sphingomonas sp. KT-1.
  Biomacromolecules, 4, No.1, 80-86 (2003)

• Christophe Danelon, Atsushi Suenaga, Mathias Winterhalter and Ichiro Yamato: Molecular origin of the cation selectivity in OmpF porin: Single channel conductances versus free energy calculation.
  Biophys. Chem., 104, 591-603 (2003)

• Takeshi Murata, Ignacio Arechaga, Ian M. Fearnley, Yoshimi Kakinuma, Ichiro Yamato and John E. Walker: The membrane domain of the Na⁺-motive V-ATPase from Enterococcus hirae contains a heptameric rotor.
  J. Biol. Chem., 278, No.23, 21162-21167 (2003)

• Tomohiro Hiraishi, Mariko Kajiyama, Kenji Tabata, Hideki Abe, Ichiro Yamato and Yoshiharu Doi: Biochemical and molecular characterization of poly(aspartic acid) hydrolase-2 from Sphingomonas sp. KT-1.
  Biomacromolecules, 4, No.5, 1285-1292 (2003)

• Toshiaki Hosaka, Toshiyuki Meguro, Ichiro Yamato and Yasuo Shirakihara: Crystal structure of Enterococcus hirae enolase at 2.8 A resolution.
  J. Biochem., 133, No.6, 817-823 (2003)

• Tadashi Ando, Toshiyuki Meguro and Ichiro Yamato: Multiple time step Brownian dynamics for long time simulation of biomolecules.
  Mol. Simul., 29, No.8, 471-478 (2003)

• Takeo Asaoka, Tadashi Ando, Toshiyuki Meguro and Ichiro Yamato: Development of a structure based protein function prediction method: Calcium binding protein.
  Chemo-Bio Informatics Journal, 3, No.3, 96-113 (2003)

• Toshiaki Hosaka, Takeshi Murata, Yoshimi Kakinuma and Ichiro Yamato: Identification of nucleotide binding sites in V-type Na⁺-ATPase from Enterococcus hirae.
  Biosci. Biotechnol. Biochem., 68, No.2, 293-299 (2004)

• Tomohiro Hiraishi, Mariko Kajiyama, Ichiro Yamato, and Yoshiharu Doi: Enzymatic hydrolysis of α- and β-oligo(L-aspartic acid)s by poly(aspartic acid) hydrolases-1 and 2 from Sphingomonas sp. KT-1.
  Macromolecular Bioscience, 4, 330-339 (2004)

• Tadashi Ando, Toshiyuki Meguro, and Ichiro Yamato: A new implicit solvent model for Brownian dynamics simulation: Solvent-accessible surface area dependent effective charge model.
  J. Comput. Chem., Jpn., 3, No. 4, 129-136 (2004)

• 山登一郎：編集室．
  理大　科学フォーラム，2004年7月号（241号）（編集後記）

• 山登一郎：自動ペプチド合成機（東京理科大学・話題の科学技術（20））.
  理大　科学フォーラム，2004年8月号（242号）（表紙裏）

• 山登一郎：発明・発見（DNAの二重らせん構造）．
  理大　科学フォーラム，2004年12月号（246号）（編集後記）

• Takeshi Murata, Ichiro Yamato, Yoshimi Kakinuma, Andrew G. W. Lestlie, and John E. Walker: Structure of the rotor of the V-type Na⁺-ATPase from Enterococcus hirae.
  Science, 308, No.5722, 654-659 (2005)

• 山登一郎：わが伝統とその挑戦（特集／入学おめでとう）．
  　　　理大　科学フォーラム，2005年4月号, 7-8（250号）

• Tadashi Ando and Ichiro Yamato: Free energy landscapes of two model peptides: α-Helical and β-hairpin peptides explored with Brownian dynamics simulation.
  Molecular Simul., 31, No.10, 683-693 (2005)

• 山登一郎：夏休みの読書「レ・ミゼラブル」ビクトル・ユゴー、「竜馬がゆく」「世に棲む日々」司馬遼太郎．
  　　　理大　科学フォーラム，2005年7月号，18-19（253号）

• 山登一郎：バイオ系研究室の今後の教育と研究ーゲノム・バイオ・ナノ・インフォマティクスー． （東京理科大学創立125周年記念巡回講演会）
  　　　理大　科学フォーラム，2005年11月号，16-17（257号）

• Takeshi Murata, Ichiro Yamato, and Yoshimi Kakinuma: 　　　Structure and mechanism of vacuolar Na⁺-translocating ATPase from Enterococcus hirae.
  J. Bioenerg. Biomembr., 37, No.6, 411-413 (2005)

• Ayumi Suzuki, Tadashi Ando, Ichiro Yamato, and Satoru Miyazaki: FCANAL: Structure based protein function prediction method. Application to enzymes and binding proteins.
  Chemo-Bio Informatics J., 5, No.3, 39-55 (2006)

• Toshiaki Hosaka, Kazuma Takase, Takeshi Murata, Yoshimi Kakinuma, and Ichiro Yamato: Deletion analysis of the subunit genes of V-type Na⁺-ATPase from Enterococcus hirae.
  J. Biochem., 139, No.6, 1045-1052 (2006)

• 安藤格士、山登一郎：ランジュバン・ブラウン動力学法.
  バイオインフォマティクス事典、p.634-p.636 (2006)、日本バイオインフォマティクス学会〈JSBi学会〉編集 （宮野 悟（委員長），江口 至洋（副委員長），金久 實，高木 利久，中井 謙太編集委員）共立出版、東京

• 末永敦、山登一郎：膜タンパク質のダイナミクス.
  バイオインフォマティクス事典、p.649-p.650 (2006)、日本バイオインフォマティクス学会〈JSBi学会〉編集 （宮野 悟（委員長），江口 至洋（副委員長），金久 實，高木 利久，中井 謙太編集委員）共立出版、東京

• 山登一郎：世界最小生体分子モーターの回転子．
  　　理大　科学フォーラム，2006年10月号，表紙および p.64-65（通巻268号）

• 山登一郎：編集後記．
  理大　科学フォーラム，2006年12月号（野田・諏訪オープンキャンパス特集），p.64（通巻270号）

• 山登一郎：発明・発見（生体高分子のX線結晶構造解析法の確立）
  理大　科学フォーラム，2006年12月号，p.30-31（通巻270号）

• 村田武士、山登一郎、柿沼喜己：V型Na⁺-ATPaseの膜内在性ローターリング の構造：結晶構造から見えてきた回転モーターのイオン透過機構．
  生物物理, 46, No.6, 336-340 (2006)

• Tadashi Ando, and Ichiro Yamato: Brownian Dynamics Approach to Protein Folding.
  Proceedings of International Symposium on Frontiers of Computational Science 2005 (FCS 2005), pp.181-186, Nagoya (2006)

• Koji Furukawa, Takeyuki Shimizu, Akikazu Murakami, Ryo Kono, Masatoshi Nakagawa, Takuma Sagawa, Ichiro Yamato, and Takachika Azuma: Strategy for affinity maturation of an antibody with high evolvability to (4-hydroxy-3- nitrophenyl) acetyl hapten.
  Molecular Immunology, 44, No.9, 2436-2445 (2007)

• 村田武士、山登一郎、柿沼喜己、横山謙： 　　V-ATPaseの新しい機能とその構造からみえてきたメカニズム．
  蛋白質核酸酵素，52，No.4, 335-341 (2007)

• Tadashi Ando, and Ichiro Yamato: Brownian dynamics approach to protein folding.
  Frontiers of computational science, p.157-p.163 (2007) (eds. Yukio Kaneda, Hiroshi Kawamura, and Masaki Sasai) (Proceedings of the International Symposium on Frontiers of Computational Science 2005 (FCS 2005), Nagoya), Springer, Heidelberg

• 山登一郎：編集後記．
  理大　科学フォーラム 2007年8月号（現代GP in 長万部キャンパス特集），p.64（通巻278号）

• 金完起、伊藤隆宏、山登一郎、安藤格士: 膜タンパク質ブラウン動力学シミュレーション法の開発.
  J. Comput. Chem., Jpn. 6, No.5, 253-262 (2007)

• Ichiro Yamato, Tadashi Ando, Ayumi Suzuki, Kazuo Harada, Seigo Itoh, Satoru Miyazaki, Naoki Kobayashi, and Masayuki Takeda: Toward in silico biology (from sequences to systems).
  Quantum Bio-Informatics (From Quantum Information to Bio-Informatics), eds L. Accardi, W. Freudenberg, & M. Ohya, p.440-p.455 (2007) (Proceedings of the International Symposium of Quantum Bio-Informatics Research Center 2007, Chiba), World Scientific, Singapore

• Takeshi Murata, Ichiro Yamato, Yoshimi Kakinuma, Mikako Shirouzu, John E. Walker, Shigeyuki Yokoyama, and So Iwata: Ion binding and selectivity of the rotor ring of the Na⁺- transporting V-ATPase.
  Proc. Natl. Acad. Sci. USA 105, No.25, 8607-8612 (2008)

• Misaki Yamamoto, Satoru Unzai, Shinya Saijo, Kazuki Ito, Kenji Mizutani, Chiyo Suno-Ikeda, Yukako Yabuki-Miyata, Takaho Terada, Mitsutoshi Toyama, Mikako Shirouzu, Takuya Kobayashi, Yoshimi Kakinuma, Ichiro Yamato, Shigeyuki Yokoyama, So Iwata, and Takeshi Murata: Interaction and stoichiometry of the peripheral stalk subunits, NtpE, NtpF and the N-terminal hydrophilic domain of NtpI, of Enterococcus hirae V-ATPase.
  J. Biol. Chem. 283, No.28, 19422-19431 (2008)

• 末永敦、梅津倫、安藤格士、山登一郎、村田武士、泰地真弘人： 分子動力学／自由エネルギー計算によるF-ATPase触媒部位への基質結合親和性の算出．
  J. Comput. Chem., Jpn. 7, No.3, 103-116 (2008)

• Tadashi Ando, and Ichiro Yamato: Basics of molecular simulation and its application to biomolecules.
  Quantum Bio-Informatics II. (From Quantum Information to Bio-Informatics) p.228-p.241 (2009) (eds L. Accardi, W. Freudenberg, & M. Ohya) (Proceedings of the International Symposium of Quantum Bio-Informatics Research Center 2008, Chiba) World Scientific, Singapore

• Tadashi Ando, Ichiro Yamato, Naoyuki Kobayashi, and Masayuki Takeda: TANPAKU: Protein structure prediction using volunteer computing.
  Distributed & grid computing ? Science Made Transparent for Everyone. Principles, Applications and Supporting Communities (2008) (Weber, M.H.W., ed) Rechenkraft.net, Marburg

• Satoshi Arai, Ichiro Yamato, Asuka Shiokawa, Shinya Saijo, Yoshimi Kakinuma, Yoshiko Ishizuka- Katsura, Mitsutoshi Toyama, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, and Takeshi Murata: Reconstitution in vitro of the catalytic portion (NtpA₃-B₃-D-G complex) of Enterococcus hirae V-type Na⁺-ATPase.
  Biochem. Biophys. Research Commun. 390, No.3, 698-702 (2009)

• Soracom Chardwiriyapreecha, Tomohiro Inoue, Naoko Sugimoto, Takayuki Sekito, Ichiro Yamato, Takeshi Murata, Michio Homma, and Yoshimi Kakinuma: Tributyltin sensitivity of vacuolar-type Na⁺-transporting ATPase from Enterococcus hirae.
  J. Toxicol. Sci. 34, 575-579 (2009)

• Khandoker Mohammad Mozaffor Hossain, Mohammad Takabbar Hossain, and Ichiro Yamato: Seroprevalence of Salmonella and Mycoplasma gallisepticum infection in chickens in Rajshahi and surrounding districts of Bangladesh.
  International Journal of Biology 2, No.2, 74-80 (2010)

• Khandoker Mohammad Mozaffor Hossain, Mohammad Yamin Ali, and Ichiro Yamato: Antibody levels against Newcastle Disease Virus in chickens in Rajshahi and surrounding districts of Bangladesh.
  International Journal of Biology 2, No.2, 102-106 (2010)

• Wankee Kim, Ichiro Yamato, and Tadashi Ando: Alanine-based peptides containing polar residues presumably favor α-helical structure entropically.
  Mol. Simul. 37, No.5, 379-385 (2011)

• Khandoker Mohammad Mozaffor Hossain, Satoshi Arai, Shinya Saijo, Yoshimi Kakinuma, Takeshi Murata, and Ichiro Yamato: Expression and purification of the central stalk subunits of sodium-translocating V-type ATPase from Enterococcus hirae.
  African J. Biotechnology 10, No.13, 2406-2413 (2011)

• Suhaila Rahman, Yoshiko Ishizuka-Katsura, Satoshi Arai, Shinya Saijo, Ichiro Yamato, Mitsutoshi Toyama, Noboru Ohsawa, Mio Inoue, Keiko Honda, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, and Takeshi Murata: Expression, purification and characterization of isoforms of peripheral stalk subunits of human V-ATPase.
  Protein Expression and Purification 78, 181-188 (2011)

• Miyuki Kawano-Kawada, Hiroko Takahashi, Kazuei Igarashi, Takeshi Murata, Ichiro Yamato, Michio Homma, and Yoshimi Kakinuma: Significance of the glutamate-139 residue of the V-type Na⁺-ATPase NtpK subunit in catalytic turnover linked with salt tolerance of Enterococcus hirae.
  J. Bacteriol. 193, No.14, 3657-3661 (2011)

• Anowarul Amin, Tadashi Ando, Shinya Saijo, and Ichiro Yamato: Role of Asp187 and Gln190 in Na⁺/proline symporter (PutP) of Escherichia coli.
  J. Biochem. 150, No.4, 395-402 (2011)

• Irina Basieva, Andrei Khrennikov, Masanori Ohya, and Ichiro Yamato: Quantum-like interference effect in gene expression: glucose-lactose destructive interference.
  Systems and Synthetic Biology 5, No.1, 59-68 (2011)

• Suhaila Rahman, Satoshi Arai, Shinya Saijo, Ichiro Yamato, and Takeshi Murata: Sarkosyl is a good regeneration reagent for studies on V-ATPase subunit interactions in Biacore experiments.
  Anal. Biochem. 418, 301-303 (2011)

• Kenji Mizutani, Misaki Yamamoto, Ichiro Yamato, Yoshimi Kakinuma, Mikako Shirouzu, John E. Walker, Shigeyuki Yokoyama, So Iwata, and Takeshi Murata: Structure of the Na⁺ unbound rotor ring modified with N,N'-Dicyclohexylcarbodiimide of the Na⁺- transporting V-ATPase.
  Proc. Natl. Acad. Sci. U. S. A. 108, 13474-13479 (2011)

• Shinya Saijo, Satoshi Arai, Khandoker Mohammad Mozaffor Hossain, Ichiro Yamato, Kano Suzuki, Yoshimi Kakinuma, Yoshiko Ishizuka-Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, and Takeshi Murata: Crystal structure of the central axis DF complex of the prokaryotic V-ATPase.
  Proc. Natl. Acad. Sci. U. S. A. 108, 19955-19960 (2011)

• 山登一郎： 高齢化とヒトの幸せ（薬学への期待）
  　 　薬奨ニュース No.12 (2011)

• Kengo Hanaya, Miho Suetsugu, Shinya Saijo, Ichiro Yamato, Shin Aoki: Potent inhibition of dinuclear Zinc(II) peptidase, an aminopeptidase from Aeromonas proteolytica, by 8-quinolinol derivatives: Inhibitor design based on Zn²⁺ fluorophores, kinetic, and X-ray crystallographic study.
  J. Biological Inorganic Chemistry 17, No.4, 517-529 (2012)

• Zahed Muhammed, Satoshi Arai, Shinya Saijo, Ichiro Yamato, Takeshi Murata, Atsushi Suenaga: Calculating the Na⁺ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation.
  J. Mol. Graph. Model. 37, 59-66 (2012)

• Masanari Asano, Irina Basieva, Andrei Khrennikov, Masanori Ohya, Yoshiharu Tanaka, Ichiro Yamato: Quantum-like model of glucose effect on Escherichia coli growth.
  In Foundations of probability and physics-6, p.507-p.511 (Ed. Mauro D'Ariano, Shao-Ming Fei, Emmanuel Haven, Beatrix Hiesmayr, Gregg Jaeger, Andrei Khrennikov, Jan-Ake Larsson) American Institute of Physics, Conference proceedings, 14-16 June 2011, Vaxjo, Sweden

• Masanari Asano, Irina Basieva, Andrei Khrennikov, Masanori Ohya, Yoshiharu Tanaka, Ichiro Yamato: Quantum-like model for the adaptive dynamics of the genetic regulation of E.coli's metabolism of glucose/lactose.
  Systems and Synthetic Biology 6, No.1-2, 1-7 (2012)

• Miyuki Kawano-Kawada, Tomoko Iwaki, Toshiaki Hosaka, Takeshi Murata, Ichiro Yamato, Michio Homma, and Yoshimi Kakinuma: Mutagenesis of the residues forming an ion-binding pocket of the NtpK subunit of Enterococcus hirae V-ATPase.
  J. Bacteriol. 194, No.17, 4546-4549 (2012)

• Masanari Asano, Irina Basieva, Andrei Khrennikov, Masanori Ohya, Yoshiharu Tanaka, and Ichiro Yamato: Quantum-like model of diauxie in E. coli: Operational description of precultivation effect.
  J. Theoretical Biol. 314, 130-137 (2012)

• Satoshi Arai, Shinya Saijo, Kano Suzuki, Kenji Mizutani, Yoshimi Kakinuma, Yoshiko Ishizuka- Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, Ichiro Yamato, and Takeshi Murata: Rotation mechanism of Enterococcus hirae V₁-ATPase based on asymmetric crystal structures.
  Nature 493, No.7434, 703-707 (2013)

• Suhaila Rahman, Ichiro Yamato, Shinya Saijo, Kenji Mizutani, Yoshiko Ishizuka-Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, and Takeshi Murata: Subunit-subunit interaction properties revealed at the peripheral stalk of human V-ATPase.
  PLoS One, 8(2), e55704 (2013)

• Ichiro Yamato: From structure and function of proteins toward in silico biology.
  Quantum Bio-Informatics V. (From Quantum Information to Bio-Informatics) p.473- p.485 (2013) (eds L. Accardi, W. Freudenberg, & M. Ohya) (Proceedings of the International Symposium of Quantum Bio-Informatics Research Center 2011, Chiba) World Scientific, Singapore

• Masanori Asano, Masanori Ohya, Yoshiharu Tanaka, Ichiro Yamato, Irina Basieva, and Andrei Khrennikov: A mathematical treatment of joint and conditional probability.
  Quantum Bio-Informatics V. (From Quantum Information to Bio-Informatics) p.69- p.84 (2013) (eds L. Accardi, W. Freudenberg, & M. Ohya) (Proceedings of the International Symposium of Quantum Bio-Informatics Research Center 2011, Chiba) World Scientific, Singapore

• Satoshi Iriyama, Masanori Ohya, and Ichiro Yamato: Quantum algorithm for protein folding and its computational complexity.
  Quantum Bio-Informatics V. (From Quantum Information to Bio-Informatics) p.193- p.202 (2013) (eds L. Accardi, W. Freudenberg, & M. Ohya) (Proceedings of the International Symposium of Quantum Bio-Informatics Research Center 2011, Chiba) World Scientific, Singapore

• Masanari Asano, Irina Basieva, Andrei Khrennikov, Masanori Ohya and Ichiro Yamato: Non-Kolmogorovian approach to the context-dependent systems breaking the classical probability law.
  Foundations of Physics DOI 10.1007/s10701-013-9725-5 (2013)

• Masanari Asano, Irina Basieva, Andrei Khrennikov, Masanori Ohya, Yoshiharu Tanaka and Ichiro Yamato: A model of epigenetic evolution based on theory of open quantum systems.
  Systems and Synthetic Biology 7, No. 4, DOI 10.1007/s11693-013-9109-2 (2013)

• Md. Jahangir Alam, Satoshi Arai, Shinya Saijo, Kano Suzuki, Kenji Mizutani, Yoshiko Ishizuka- Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, Yoshimi Kakinuma, Ichiro Yamato, and Takeshi Murata: Loose binding of the DF axis with the A₃B₃ complex stimulates the initial activity of Enterococcus hirae V₁-ATPase.
  PLoS ONE 8(9): e74291. doi:10.1371 (2013)

• 増保安彦、山登一郎： 　　２１世紀のホモ・サピエンス（原始のホモ・サピエンスに、 ヒトのあるべき姿を視る） (Copyrights Reserved)
  　　エース出版、146ページ (2013)

• Yoshihiro Minagawa, Hiroshi Ueno, Mayu Hara, Yoshiko Ishizuka-Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, Ichiro Yamato, Erio Muneyuki, Hiroyuki Noji, Takeshi Murata, and Ryota Iino: Basic properties of rotary dynamics of Enterococcus hirae V₁-ATPase.
  J. Biol. Chem. 288, 32700-32707 (doi: 10.1074/jbc.M113.506329) (2013)

• 安藤格士、伊東聖剛，山登 一郎： 生化学データに基づくシステムシミュレータの開発 ‐大腸菌二段増殖のシミュレーション‐
  J. Comp. Chem. J. 12, No. 4, 204-214 (2013)

• Md. Jahangir Alam, Ichiro Yamato, Satoshi Arai, Shinya Saijo, Kenji Mizutani, Yoshiko Ishizuka- Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, Yoshimi Kakinuma and Takeshi Murata: Mutant LV476-7AA of A-subunit of Enterococcus hirae V₁-ATPase: High affinity of A₃B₃ complex to DF axis and low ATPase activity.
  SpringerPlus 2:689. doi:10.1186/2193-1801-2-689 (2013)

• 西條慎也、山登一郎、村田武士： 　　X線結晶構造解析から明らかになる腸球菌Na⁺輸送性V-ATPaseの回転メカニズム．
  　　PFNews 31, No.3, 23-27 (2013)

• Hiroshi Ueno, Yoshihiro Minagawa, Mayu Hara, Suhaila Rahman, Ichiro Yamato, Eiro Muneyuki, Hiroyuki Noji, Takeshi Murata, and Ryota Iino: Torque generation of Enterococcus hirae V-ATPase.
  J. Biol. Chem. 289, 31212-31223 (2014)

• Yasuhiro Matsuura, Tadashi Ando, Atsushi Suenaga and Ichiro Yamato: Ion selectivity mechanism of Escherichia coli OmpF porin: A molecular dynamics simulation/free energy calculation study.
  Journal of Computer Chemistry, Japan 13, No.5, 278-291 (2014)

• Masanari Asano, Andrei Khrennikov, Masanori Ohya, Yoshiharu Tanaka and Ichiro Yamato: Quantum adaptivity in biology: From genetics to cognition. p.1-p.173 (2015) Springer Netherlands, Dordrecht. ISBN 978-94-017-9818-1

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