研究業績

研究業績

2016年
  • Functional profiling of asymmetrically-organized human CCT/TRiC chaperonin. Kazutaka Araki, Atsushi Suenaga, Hidewo Kusano, Riko Tanaka, Tomohisa Hatta, Tohru Natsume and Kazuhiko Fukui, Biochemical and Biophysical Research Communications, Vol. 481, 232-238, 2016.
  • Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations. Noriaki Okimoto, Atsushi Suenaga and Makoto Taiji, Journal of Biomolecular Structure and Dynamics, in press.
  • All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations. Yutaka Kuroda, Atsushi Suenaga, Yuji Sato, Satoshi Kosuda and Makoto Taiji, Scientific Reports, Vol. 6, 19479, 2016.
2014年
  • Ion selectivity mechanism of Escherichia coli OmpF porin: a molecular dynamics simulation/free energy calculation study. Yasuhiro Matsuura, Ichiro Yamato, Tadashi Ando and Atsushi Suenaga, Journal of Computational Chemistry Japan, Vol. 13, 278-291, 2014.
2012年
  • Ligand diffusion on protein surface observed molecular dynamics simulation. Dmitry Nerkh, Noriaki Okimoto, Atsushi Suenaga and Makoto Taiji, The Journal of Physical Chemistry Letters, Vol. 3, 3476-3479, 2012.
  • Experimental identification and theoretical analysis of a thermally stabilized green fluorescent protein variant. Saori Akiyama, Atsushi Suenaga, Takayuki Kobayashi, Tetsuya Kamioka, Makoto Taiji and Yutaka Kuroda, Biochemistry, Vol. 51, 7974-7982, 2012.
  • An efficient computational method for calculating ligand binding affinities. Atsushi Suenaga, Noriaki Okimoto, Yoshinori Hirano and Kazuhiko Fukui, PLoS ONE, Vol. 7 (8), e42846, 2012.
  • Calculating the Na+ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation. Zahed Muhammed, Satoshi Arai, Shinya Saijo, Ichiro Yamato , Takeshi Murata and Atsushi Suenaga, Journal of Molecular Graphics and Modeling, Vol. 37, 59-66, 2012.
  • Blockade of Inflammatory Responses by a Small-Molecule Inhibitor of the Rac Activator DOCK2. Akihiko Nishikimi, Takehito Uruno, Xuefeng Duan, Qinhong Cao, Yuji Okamura, Takashi Saitoh, Nae Saitoh, Shunsuke Sakaoka, Yao Du, Atsushi Suenaga, Mutsuko Kukimoto-Niino, Kei Miyano, Kazuhito Gotoh, Takayoshi Okabe, Fumiyuki Sanematsu, Yoshihiko Tanaka, Hideki Sumimoto, Teruki Honma, Shigeyuki Yokoyama, Tetsuo Nagano, Daisuke Kohda, Motomu Kanai and Yoshinori Fukui, Chemistry & Biology, Vol. 19, 488-497, 2012.
2010年
  • 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 Suzuzki, Makoto Taiji, Masayoshi Itoh, Yoshihide Hayashizaki and Takehisa Matsuda, Biomaterials, Vol. 31, 58-66, 2010.
2009年
  • 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, Testu Narumi and Makoto Taiji, PLoS Computational Biology, Vol. 5 (10), e1000528, 2009.
  • Mutation of epidermal growth factor receptor is associated with MIG6 expression to modulate the signaling titer. Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Atsushi Suenaga, Kaori Ide, Noriko Yumoto, Yoshimi Naruo, Kaoru Takahashi, Yuko Saeki, Makoto Taiji, Hiroshi Tanaka, Shih-Feng Tsai 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年
  • 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.
2007年
  • Folding dynamics of 10-residues -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.
  • 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年
  • 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.
  • 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.
  • 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.
2005年
  • 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年
  • 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年
  • 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.
  • Molecular dynamics study on Class A -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.
  • 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.
  • 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.
  • 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, in CD-ROM
2002年
  • Protein Explorer: A Petaflops Special-Purpose Computer for Molecular Dynamics Simulations. Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada and Akihiko Konagaya, Genome Informatics, Vol. 13, 461-462, 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.
2000年
  • Funstional mapping againt Escherichia coli for the broad-spectrum antimicrobial peptide, thanatin, based on an In Vivo monitoring. Seichi Taguchi, Kanako Kuwasako, Atsushi Suenaga, Miyuki Okada and Haruo Momose, Journal of Biochemistry (Tokyo), Vol. 128, 745-754, 2000.
  • Molecular dynamics simulation of trp-repressor/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.
1998年
  • 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.