業績

- 査読有り論文 -

2010

• Reversible hydrogel formation driven by protein-peptide-specific interaction and chondrocyte entrapment. Fuyu Ito, Kengo Usui, Daigo Kawahara, Atsushi Suenaga, Tei Maki, Satoru Kidoaki, Harukazu Suzuki, Makoto Taiji, Masayoshi Itoh, Yoshihide Hayashizaki and Takehisa Matsuda, Biomaterials, Vol. 31, 58-66, 2010.

2009

• High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations. Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi and Makoto Taiji, PLoS Computational Biology, Vol. 5 (10), e1000528 2009.
• Mutation of epidermal growth factor receptor is associated with MIG6 expression. Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Atsushi Suenaga, Kaori Ide, Noriko Yumoto, Yoshimi Naruo, Kaoru Takahashi, Yuko Saeki, Makoto Taiji, Hiroshi Tanaka, Tsai Shih-Feng and Mariko Hatakeyama, FEBS Journal, Vol. 276, 5239-5251, 2009.
• Structural and functional basis of an essential role for CRKL in an FGF8-induced feedforward loop. Ji-Heui Seo, Atsushi Suenaga, Mariko Hatakeyama, Makoto Taiji and Akira Imamoto, Molecular and Cellular Biology, Vol.29, 3076-3087, 2009.
• Nanoscale elongating control of the self-assembled protein filament with the cycteine-introduced building blocks. Kengo Usui, Tei Maki, Fuyu Ito, Atsushi Suenaga, Satoru Kidoaki, Masayoshi Ito, Makoto Taiji, Takehisa Matsuda, Yoshihide Hayashizaki and Harukazu Suzuki, Protein Science, Vol.18, 960-969, 2009.
• Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor. Atsushi Suenaga, Mariko Hatakeyama, Anatoly B. Kiyatkin, Ravi Radhakrishnan, Makoto Taiji and Boris N. Kholodenko, Biophysical Journal, Vol.96, 2278-2288, 2009.

2008

• Estimation of ligand binding free energies of F-ATPase by using molecular dynamics/free energy calculation. Atsushi Suenaga, Osamu Umezu, Tadashi Ando, Ichiro Yamato, Takeshi Murata and Makoto Taiji, Journal of Computer Chemistry Japan, Vol. 7, 103-116, 2008. (Corresponding author)

2007

• Folding dynamics of 10-residues beta-hairpin peptide chignolin. Atsushi Suenaga, Tetsu Narumi, Noriyuki Futatsugi, Ryoko Yanai, Yousuke Ohno, Noriaki Okimoto and Makoto Taiji, Chemistry – An Asian Journal, Vol. 2, 591-598, 2007. (Corresponding author)
• Crystal structure of the Rac activator, Asef, reveals its autoinhibitory mechanism. Kazutaka Murayama, Mikako Shirouzu, Yoshihiro Kawasaki, Miyuki Kato-Murayama, Kyoko Hanawa-Suetsugu, Ayako Sakamoto, Yasuhiro Katsura, Atsushi Suenaga, Mitsutoshi Toyama, Takaho Terada, Makoto Taiji, Tetsu Akiyama and Shigeyuki Yokoyama, The Journal of Biological Chemistry, Vol. 282, 4238-4242, 2007.

2006

• A 185 TFLOPS Simulation of Amyloid-forming Peptides from Yeast Prion Sup35 with the Special-purpose Computer System MDGRAPE-3. Tetsu Narumi, Yousuke Ohno, Noriaki Okimoto, Takahiro Koishi, Atsushi Suenaga, Noriyuki Futatsugi, Ryoko Yanai, Ryutaro Himeno, Shigenori Fujikawa, Makoto Taiji, Proceedings of Supercomputing 2006, in CD-ROM, 2006.
• Structure and dynamics of RNA polymerase II elongation complex. Atsushi Suenaga, Noriaki Okimoto, Noriyuki Futatsugi, Yoshinori Hirano, Tetsu Narumi, Yousuke Ohno, Ryoko Yanai, Takatsugu Hirokawa, Toshikazu Ebisuzaki, Akihiko Konagaya and Makoto Taiji, Biochemical and Biophysical Research Communications, Vol. 343, 90-98, 2006. (Corresponding author)
• Bead-like passage of chloride ions through ClC chloride channels. Atsushi Suenaga, Jay Z. Yeh, Makoto Taiji, Akira Toyama, Hideo Takeuchi, Mingyu Son, Kazuyoshi Takayama, Masatoshi Iwamoto, Ikuro Sato, Toshio Narahashi, Akihiko Konagaya and Kunihiko Goto, Biophysical Chemistry, Vol. 120, 36-43, 2006.

2005

• Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides. Atsushi Suenaga, Naoki Takada, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Kentaro Tomii, Noriaki Okimoto, Noriyuki Futatsugi, Tetsu Narumi, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya and Makoto Taiji, The Journal of Biological Chemistry, Vol. 280, 1321-1326, 2005.

2004

• Nanoscale hydrophobic interaction and nanobubble nucleation. Takahiro Koishi, Soohaeng Yoo, Kenji Yasuoka, Xiao Cheng Zeng, Tetsu Narumi, Rutaro Susukita, Atsushi Kawai, Hideaki Furusawa, Atsushi Suenaga, Noriaki Okimoto, Noriyuki Futatsugi and Toshikazu Ebisuzaki, Physical Review Letters, Vol. 93, 185701, 2004.
• Cooperative motions of protein and hydration water molecules: molecular dynamics study of Scytalone dehydratase. Noriaki Okimoto, Takashi Nakamura, Atsushi Suenaga, Noriyuki Futatsugi, Yoshinori Hirano, Isamu Yamaguchi and Toshikazu Ebisuzaki, Journal of the American Chemical Society, Vol. 126, 13132-13139, 2004.
• Tyr317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation sites as revealed by molecular dynamics simulations. Atsushi Suenaga, Anatoly B. Kiyatkin, Mariko Hatakeyama, Noriyuki Futatsugi, Noriaki Okimoto, Yoshinori Hirano, Tetsu Narumi, Atsushi Kawai, Ryutaro Susukita, Takahiro Koishi, Hideaki Furusawa, Kenji Yasuoka, Naoki Takada, Yousuke Ohno, Makoto Taiji, Toshikazu Ebisuzaki, Jan B. Hoek, Akihiko Konagaya and Boris N. Kholodenko, The Journal of Biological Chemistry, Vol. 279, 4657-4662, 2004.

2003

• Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution. Jun Hoseki, Akihiro Okamoto, Naoki Takada, Atsushi Suenaga, Noriyuki Funatsugi, Akihiko Konagaya, Makoto Taiji, Takato Yano, Seiki Kuramitsu, and Hiroyuki Kagamiyama, Biochemistry, Vol. 42, 14469-14475, 2003.
• Protein Explorer: a petaflops special-purpose computer system for moleculr dynamics simulations. Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada and Akihiko Konagaya, In Proceedings of Supercomputing 2003, IEEE Computer Society, 2003, in CD-ROM.
• Molecular dynamics study on Class A beta-lactamase: The hydrogen bond network among the functional groups the penicillin G and the side chains of the conserved residues in the active site. Yasuyuki Fujii, Noriaki Okimoto, Masayuki Hata, Tetsu Narumi, Kenji Yasuoka, Ryutarou Susukita, Atsushi Suenaga, Noriyuki Futatsugi, Takahiro Koishi, Hideaki Furusawa, Atsushi Kawai, Toshikazu Ebisuzaki, Saburo Neya and Tyuji Hoshino, Journal of Physical Chemistry B, Vol. 107, 10274-10283, 2003.
• Replica-exchange molecular dynamics simulations for a small-sized protein folding with implicit solvent. Atsushi Suenaga, Journal of Molecular Structure (THEOCHEM), Vol. 634, 235-241, 2003. (Corresponding author)
• Molecular origin of the cation selectivity in OmpF porin: single channel conductances versus free energy calculation. Christophe Danelon, Atsushi Suenaga, Mathias Winterhalter and Ichiro Yamato, Biophysical Chemistry, Vol. 104, 591-603, 2003.
• Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides. Atsushi Suenaga, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Noriyuki Futatsugi, Tetsu Narumi, Kazuhiko Fukui, Takaho Terada, Makoto Taiji, Mikako Shirouzu, Shigeyuki Yokoyama and Akihiko Konagaya, Biochemistry, Vol. 42, 5195-5200, 2003. (Corresponding author)
• Molecular Dynamics Simulations of Prion Proteins - Effect of Ala117 → Val mutation- Noriaki Okimoto, Kazunori Yamanaka, Atsushi Suenaga, Yoshinori Hirano, Noriyuki Futatsugi, Tetsu Narumi, Kenji Yasuoka, Ryutaro Susukita, Takahiro Koishi, Hideaki Furusawa, Atsushi Kawai, Masayuki Hata, Tyuji Hoshino, and Toshikazu Ebisuaki, Chem-Bio Informatics Journal, Vol.3  No.1, 1-11, 2003.

2002

• Computational studies on Prion proteins: effect of Ala117 → Val mutation. Noriaki Okimoto, Kazunori Yamanaka, Atsushi Suenaga, Masayuki Hata and Tyuji Hoshino, Biophysical Journal, Vol. 82, 2746-2757, 2002.
• Refolding molecular dynamics simulations of small- and middle-sized proteins in an explicit solvent. Atsushi Suenaga, Noriaki Okimoto and Toshikazu Ebisuzaki, Molecular Simulation, Vol. 28, 337-357, 2002. (Corresponding author)

2001

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2000

• Molecular dynamics simulation of trp-reoressor/operator complex: Analysis of hydrogen bond patterns of protein-DNA interaction. Atsushi Suenaga, Chieko Yatsu, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro and Ichiro Yamato, Journal of Molecular Structure, Vol. 526, pp. 209-218, 2000.

1999

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1998

• Computational observation of an ion permeation through a channel protein. Atsushi Suenaga, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro, Minoru Saito and Ichiro Yamato, Bioscience Reports, Vol. 18, No. 1, pp. 39-48, 1998.
• Molecular dynamics simulation of unfolding of Histidine-containing phosphocarrier protein in water. Atsushi Suenaga, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro and Ichiro Yamato, The Journal of Chemical Software, Vol. 4, No. 4, pp. 127-142, 1998.

- その他 -

• 膜タンパク質のダイナミクス. 末永敦, バイオインフォマティックス事典, 共立出版, 日本バイオインフォマティックス学会編集, 649-650ページ, 2006年.
• Protein folding mechanism studied by molecular dynamics simulation, Atsushi Suenaga and Toshikazu Ebisuzaki, RIKEN Review, No. 25, pp. 101-103,1999.
• Molecular dynamics simulation of outer membrane porins in Escherichia coli. Atsushi Suenaga, Ichiro Yamato and Minoru Saito, Progress in Cell Research: Towards Molecular Biophysics of Ion Channels, Vol. 6, pp. 217-232, 1997.
• Molecular dynamics simulation of outer membrane porins in Escherichia coli. Atsushi Suenaga, Ichiro Yamato and Minoru Saito, Proceedings of the 19^th Taniguchi international symposium biophysics division, pp. 203-208, 1994.

- 受賞歴 -

• Strategy of structure-based peptide design. 山岸純也, 沖本憲明, 末永敦, 岡田眞里子, 今本公, 泰地真弘, 星野忠次. ポスター賞. 2010年CBI学会年会, 2010年.
• A 185 Tflops simulation of amyloid-forming peptides from Yeast prion sup35 with the special-purpose computer system MD-FRAPE3, Tetsu Narumi, Yousuke Ohno, Noriaki Okimoto, Takahiro Koishi, Atsushi Suenaga, Noriyuki Futatsugi, Ryoko Yanai, Ryutato Himeno, Shigenori Fujikawa, Mitsuru Ikei and Makoto Taiji. Gordon Bell Prize Honorable Mention: Peak Performance. Supercomputing 2006, 2006.
• RNAポリメラーゼの分子動力学シミュレーション. 末永敦, 優秀論文賞, 第三回CBI学会年会, 2002年.

- 競争的資金の獲得状況　-

• 理化学研究所 理事長ファンド、「柔らかい標的部位を持つタンパク質に対する計算機支援創薬研究」、平成２３年４月〜平成２５年３月、分担者（アドバイザー）：末永敦、代表者：本間光輝
• 科学研究費補助金、若手研究B、「計算科学・生化学的手法を用いたEGFレセプター高親和性人工リガンドの分子設計」、平成１９年度〜平成 ２０年度、代表者：末永 敦
• 大和日英基金（The Daiwa Anglo-Japanese Foundation）、重点助成（Daiwa Foundation Award）、"Chaos and complexity in the dynamics of molecular transitions during protein folding"、平成１８年１２月〜平成１９年１１月、共同研究者：末永敦、代表研究 者：Dmitry Nerukh（Cambridge University）
• 理化学研究所ゲノム科学総合研究センター長裁量費、RTKプロジェクト、「計算機シミュレーションを用いたEGFレセプター高親和性リガンド の設計」、平成１７年１０月〜平成１８年９月、担当者：末永敦、代表者：泰 地真弘人

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