Peer-reviewed Papers

2024

• Suguru Fujita, Tohru Terada (2024). “Enhanced prediction of protein functional identity through the integration of sequence and structural features” Computational and Structural Biotechnology Journal, 23, 4124–4130.
• Takayoshi Awakawa, Takahiro Mori, Lena Barra, Yusef Ahmed, Richiro Ushimaru, Yaojie Gao, Naruhiko Adachi, Toshiya Senda, Tohru Terada, Dean J. Tantillo & Ikuro Abe (2024). “The structural basis of pyridoxal-5′-phosphate-dependent β-NAD-alkylating enzymes” Nature Catalysis, 7, 1099–1108.
• Kazutoshi Tani, Saori Maki-Yonekura, Ryo Kanno, Tatsuki Negami, Tasuku Hamaguchi, Malgorzata Hall, Akira Mizoguchi, Bruno M. Humbel, Tohru Terada, Koji Yonekura & Tomoko Doi (2024). “Structure of endothelin ET_B receptor–G_i complex in a conformation stabilized by unique NPxxL motif” Communications Biology, 7, 1303 (13 pages).
• Masato Homma, Takatoshi Wakabayashi, Yoshitaka Moriwaki, Nanami Shiotani, Takumi Shigeta, Kazuki Isobe, Atsushi Okazawa, Daisaku Ohta, Tohru Terada, Kentaro Shimizu, Masaharu Mizutani, Hirosato Takikawa, and Yukihiro Sugimoto (2024). “Insights into stereoselective ring formation in canonical strigolactone: Identification of a dirigent domain-containing enzyme catalyzing orobanchol synthesis” Proceedings of the National Academy of Sciences of the United States of America, 121, e2313683121 (11 pages).
• Atsushi Yamagata, Kaori Ito, Takehiro Suzuki, Naoshi Dohmae, Tohru Terada, and Mikako Shirouzu (2024). “Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A” Nature Communications, 15, 3027 (13 pages).
• Fan Zhao, Yoshitaka Moriwaki, Tomohiro Noguchi, Kentaro Shimizu, Tomohisa Kuzuyama, and Tohru Terada (2024). “QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6” Biochemistry, 63, 806–814.

2023

• Tina Lusiany, Tohru Terada, Jun-ichi Kishikawa, Mika Hirose, David Virya Chen, Fuminori Sugihara, Hendra Saputra Ismanto, Floris J. van Eerden, Songling Li, Takayuki Kato, Hisashi Arase, Matsuura Yoshiharu, Masato Okada, Daron M. Standley (2023). “Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies” Viruses, 15, 2421 (12 pages).
• Kazue Terasawa, Tatsuro Seike, Kensaku Sakamoto, Kazumasa Ohtake, Tohru Terada, Takanori Iwata, Tetsuro Watabe, Shigeyuki Yokoyama, Miki Hara-Yokoyama (2023). “Site-specific photo-crosslinking/cleavage for protein?protein interface identification reveals oligomeric assembly of lysosomal-associated membrane protein type 2A in mammalian cells” Protein Science, 32,e4823 (16 pages).
• Tomoki Sawa, Yoshitaka Moriwaki, Hanting Jiang, Kohji Murase, Seiji Takayama, Kentaro Shimizu, Tohru Terada (2023). “Comprehensive computational analysis of the SRK–SP11 molecular interaction underlying self-incompatibility in Brassicaceae using improved structure prediction for cysteine-rich proteins” Computational and Structural Biotechnology Journal, 21, 5228-5239.
• Tatsuki Negami, Tohru Terada (2023). “Calculations of the binding free energies of the Comprehensive in vitro Proarrhythmia Assay (CiPA) reference drugs to cardiac ion channels” Biophysics and Physicobiology, 20, e200016 (15 pages).
• Wenchao Zhu, Shiori Takeuchi, Shosei Imai, Tohru Terada, Takumi Ueda, Yusuke Nasu, Takuya Terai & Robert E. Campbell (2023). “Chemigenetic indicators based on synthetic chelators and green fluorescent protein” Nature Chemical Biology, 19, 38–44.

2022

• Shohei Nosaki, Nobutaka Mitsuda, Shingo Sakamoto, Kazuki Kusubayashi, Ayumi Yamagami, Yuqun Xu, Thi Bao Chau Bui, Tohru Terada, Kenji Miura, Takeshi Nakano, Masaru Tanokura & Takuya Miyakawa (2022). “Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout” Nature Plants, 8, 1440–1452.
• Atsushi Yamagata, Yoshiko Murata, Kosuke Namba, Tohru Terada, Shuya Fukai & Mikako Shirouzu (2022). “Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter” Nature Communications, 13, 7180 (12 pages).
• Kano Hasegawa, Yoshitaka Moriwaki, Tohru Terada, Cao Wei and Kentaro Shimizu (2022). “Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides” Journal of Bioinformatics and Computational Biology, 20, 2250026 (23 pages).
• Shohei Yamaguchi, Haruka Nakashima, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu (2022). “Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning” Computational Biology and Chemistry, 100, 107744 (12 pages).
• Pi-Cheng Tsai, Joydeep Chakraborty, Chiho Suzuki-Minakuchi, Tohru Terada, Tatsurou Kotake, Jun Matsuzawa, Kazunori Okada, Hideaki Nojiri (2022). “The α- and β-Subunit Boundary at the Stem of the Mushroom-Like α3β3-Type Oxygenase Component of Rieske Non-Heme Iron Oxygenases Is the Rieske-Type Ferredoxin-Binding Site” Applied and Environmental Microbiology, 88, e00835-22 (16 pages).
• Miho Watanabe-Takahashi, Miki Senda, Ryunosuke Yoshino, Masahiro Hibino, Shinichiro Hama, Tohru Terada, Kentaro Shimizu, Toshiya Senda & Kiyotaka Nishikawa (2022). “A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin” Scientific Reports, 12, 11443 (13 pages).
• Xiaoyu Yang, Natsuko I Kobayashi, Yoshiki Hayashi, Koichi Ito, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu, Motoyuki Hattori, Ren Iwata, Hisashi Suzuki, Tomoko M Nakanishi, Keitaro Tanoi (2022). “Mutagenesis analysis of GMN motif in Arabidopsis thaliana Mg²⁺ transporter MRS2-1” Bioscience, Biotechnology & Biochemistry, 86, 870–874.
• Peng Cao, Laura Bracun, Atsushi Yamagata, Bern M. Christianson, Tatsuki Negami, Baohua Zou, Tohru Terada, Daniel P. Canniffe, Mikako Shirouzu, Mei Li & Lu-Ning Liu (2022). “Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex” Nature Communications, 13, 1977 (12 pages).
• Tomohiro Noguchi, Shota Isogai, Tohru Terada, Makoto Nishiyama, and Tomohisa Kuzuyama (2022). “Cryptic Oxidative Transamination of Hydroxynaphthoquinone in Natural Product Biosynthesis” Journal of the American Chemical Society, 144, 5435–5440.
• Maki Kuzuya, Hidemi Hirano, Kenichi Hayashida, Masakatsu Watanabe, Kazumi Kobayashi, Tohru Terada, Md. Iqbal Mahmood, Florence Tama, Kazutoshi Tani, Yoshinori Fujiyoshi, and Atsunori Oshima (2022). “Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids” Science Signaling, 15, eabg6941 (10 pages).
• Hayama Tsutsumi, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu, Kazuo Shin-ya, Yohei Katsuyama, Yasuo Ohnishi (2022). “Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase” Angewandte Chemie International Edition, 61, e202111217 (9 pages).
• Evgeniia Borisova, Ken Nishimura, Yuri An, Miho Takami, Jingyue Li, Dan Song, Mami Matsuo-Takasaki, Dorian Luijkx, Shiho Aizawa, Akihiro Kuno, Eiji Sugihara, Taka-aki Sato, Fumiaki Yumoto, Tohru Terada, Koji Hisatake, Yohei Hayashi (2022). “Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency” iScience, 25, 103525 (26 pages).

2021

• Toma Kashima, Kouki Okumura, Akihiro Ishiwata, Machika Kaieda, Tohru Terada, Takatoshi Arakawa, Chihaya Yamada, Kentaro Shimizu, Katsunori Tanaka, Motomitsu Kitaoka, Yukishige Ito, Kiyotaka Fujita, Shinya Fushinobu (2021). “Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family” Journal of Biological Chemistry, 297, 101324 (17 pages).
• Ryosuke Miyata, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu (2021). “Prediction and analysis of antifreeze proteins” Heliyon, 7, e07953 (8 pages).
• Tetsuhiro Ogawa, Kazutoshi Takahashi, Wataru Ishida, Toshihiro Aono, Makoto Hidaka, Tohru Terada, Haruhiko Masaki (2021). “Substrate recognition mechanism of tRNA-targeting ribonuclease, colicin D, and an insight into tRNA cleavage-mediated translation impairment” RNA Biology, 18, 1193–1205.
• Laura Bracun, Atsushi Yamagata, Bern M. Christianson, Tohru Terada, Daniel P. Canniffe, Mikako Shirouzu and Lu-Ning Liu (2021). “Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution” Science Advances, 7, eabf8864 (11 pages).
• Keisuke Yanagisawa, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu (2021). “EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation” Journal of Chemical Information and Modeling, 61, 2744–2753
• Mimin Zhang, Peng Lu, Tohru Terada, Miaomiao Sui, Haruka Furuta, Kilico Iida, Yukie Katayama, Yi Lu, Ken Okamoto, Michio Suzuki, Tomiko Asakura, Kentaro Shimizu, Fumihiko Hakuno, Shin-Ichiro Takahashi, Norimoto Shimada, Jinwei Yang, Tsutomu Ishikawa, Jin Tatsuzaki & Koji Nagata (2021). “Quercetin 3,5,7,3′,4′-pentamethyl ether from Kaempferia parviflora directly and effectively activates human SIRT1” Communications Biology, 4, 209 (14 pages).
• Shohei Nosaki, Tohru Terada, Akira Nakamura, Kei Hirabayashi, Yuqun Xu, Thi Bao Chau Bui, Takeshi Nakano, Masaru Tanokura & Takuya Miyakawa (2021). “Highlighting the potential utility of MBP crystallization chaperone for Arabidopsis BIL1/BZR1 transcription factor-DNA complex” Scientific Reports, 11, 3879 (9 pages).

2020

• Masayuki Miyake, Tohru Terada, Michiko Shimokawa, Naohisa Sugimoto, Takatoshi Arakawa, Kentaro Shimizu, Kiyohiko Igarashi, Kiyotaka Fujita, Shinya Fushinobu (2020). “Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum” FEBS Journal, 287, 5114–5129.
• Kohji Murase, Yoshitaka Moriwaki, Tomoyuki Mori, Xiao Liu, Chiho Masaka, Yoshinobu Takada, Ryoko Maesaki, Masaki Mishima, Sota Fujii, Yoshinori Hirano, Zen Kawabe, Koji Nagata, Tohru Terada, Go Suzuki, Masao Watanabe, Kentaro Shimizu, Toshio Hakoshima & Seiji Takayama (2020). “Mechanism of self/nonself-discrimination in Brassica self-incompatibility” Nature Communications, 11, 4916 (11 pages).
• Yuichi Yokoyama, Tohru Terada, Kentaro Shimizu, Kouki Nishikawa, Daisuke Kozai, Atsuhiro Shimada, Akira Mizoguchi, Yoshinori Fujiyoshi & Kazutoshi Tani (2020). “Development of a deep learning-based method to identify “good” regions of a cryo-electron microscopy grid” Biophysical Reviews, 12, 349–354.
• Takashi Yasukawa, Aya Tsutsui, Chieri Tomomori-Sato, Shigeo Sato, Anita Saraf, Michael P. Washburn, Laurence Florens, Tohru Terada, Kentaro Shimizu, Ronald C. Conaway, Joan W. Conaway, Teijiro Aso (2020). “NRBP1-Containing CRL2/CRL4A Regulates Amyloid β Production by Targeting BRI2 and BRI3 for Degradation” Cell Reports, 30, 3478–3491.
• Batuujin Burendei, Ruriko Shinozaki, Masakatsu Watanabe, Tohru Terada, Kazutoshi Tani, Yoshinori Fujiyoshi and Atsunori Oshima (2020). “Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids” Science Advances, 6, eaax3157 (10 pages).
• Tatsuki Negami, Kentaro Shimizu, Tohru Terada (2020). “Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding” Chemical Physics Letters, 742, 137144 (6 pages).
• Takatoshi Arakawa, Yuta Sato, Masayuki Yamada, Jumpei Takabe, Yoshitaka Moriwaki, Noriya Masamura, Masahiro Kato, Morihiro Aoyagi, Takahiro Kamoi, Tohru Terada, Kentaro Shimizu, Nobuaki Tsuge, Shinsuke Imai, Shinya Fushinobu (2020). “Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase” ACS Catalysis, 10, 9–19.

2019

• Yoshitaka Moriwaki, Mirai Yato, Tohru Terada, Seiji Saito, Noriyuki Nukui, Takumi Iwasaki, Tatsunari Nishi, Yuko Kawaguchi, Ken Okamoto, Takatoshi Arakawa, Chihaya Yamada, Shinya Fushinobu, Kentaro Shimizu (2019). “Understanding the Molecular Mechanism Underlying the High Catalytic Activity of p-Hydroxybenzoate Hydroxylase Mutants for Producing Gallic Acid” Biochemistry, 58, 4543–4558.
• Peng Lu, Yoshitaka Moriwaki, Mimin Zhang, Yukie Katayama, Yi Lu, Ken Okamoto, Tohru Terada, Kentaro Shimizu, Mengyao Wang, Takehiro Kamiya, Toru Fujiwara, Tomiko Asakura, Michio Suzuki, Etsuro Yoshimura and Koji Nagata (2019). “Functional characterisation of two ferric-ion coordination modes of TtFbpA, the periplasmic subunit of an ABC-type iron transporter from Thermus thermophilus HB8” Metallomics, 11, 2078–2088.
• Tatsuki Negami, Mitsugu Araki, Yasushi Okuno, and Tohru Terada (2019). “Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs” Scientific Reports, 9, 16586 (12 pages).
• Zihan Tian, Cao Wei, Yutaka Moriwaki, Tohru Terada, Shugo Nakamura, Kazuya Sumikoshi, Fang Chun, and Kentaro Shimizu (2019). “Prediction of protein–metal ion-binding sites using sequence homology and machine-learning methods” Advanced Bioinformatics & Chemistry, 1, 025–036.
• Nobukiyo Tanaka, Masahiro Nakajima, Megumi Narukawa-Nara, Hiroki Matsunaga, Shinji Kamisuki, Hiroki Aramasa, Yuta Takahashi, Naohisa Sugimoto, Koichi Abe, Tohru Terada, Akimasa Miyanaga, Tetsuro Yamashita, Fumio Sugawara, Takashi Kamakura, Shiro Komba, Hiroyuki Nakai and Hayao Taguchi (2019). “Identification, characterization, and structural analyses of a fungal endo-β-1,2-glucanase reveal a new glycoside hydrolase family” Journal of Biological Chemistry, 294, 7942–7965.
• Kazunori Hirayama, Yuuki Fujiwara, Tohru Terada, Kentaro Shimizu, Keiji Wada, Tomohiro Kabuta (2019). “Virtual screening identification of novel chemical inhibitors for aberrant interactions between pathogenic mutant SOD1 and tubulin” Neurochemistry International, 126, 19–26.

2018

• Kumar Nagarathinam, Yoshiko Nakada-Nakura, Christoph Parthier, Tohru Terada, Narinobu Juge, Frank Jaenecke, Kehong Liu, Yunhon Hotta, Takaaki Miyaji, Hiroshi Omote, So Iwata, Norimichi Nomura, Milton T. Stubbs, Mikio Tanabe (2018). “Outward open conformation of a Major Facilitator Superfamily multidrug/H⁺ antiporter provides insights into switching mechanism” Nature Communications, 9, 4005 (9 pages).
• Atsushi Yamagata, Sakurako Goto-Ito, Yusuke Sato, Tomoko Shiroshima, Asami Maeda, Masahiko Watanabe, Takashi Saitoh, Katsumi Maenaka, Tohru Terada, Tomoyuki Yoshida, Takeshi Uemura, Shuya Fukai (2018). “Structural insights into modulation and selectivity of transsynaptic neurexin–LRRTM interaction” Nature Communications, 9, 3964 (11 pages).
• Koichi Abe, Naoki Sunagawa, Tohru Terada, Yuta Takahashi, Takatoshi Arakawa, Kiyohiko Igarashi, Masahiro Samejima, Hiroyuki Nakai, Hayao Taguchi, Masahiro Nakajima and Shinya Fushinobu (2018). “Structural and thermodynamic insights into β-1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua” Journal of Biological Chemistry, 293, 8812–8828.
• Kei Moritsugu, Tohru Terada, Hironori Kokubo, Satoshi Endo, Toshimasa Tanaka, and Akinori Kidera (2018). “Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion ” Journal of Chemical Physics, 149, 072314 (12 pages).
• Yasuhiro Matsunaga, Tsutomu Yamane, Tohru Terada, Kei Moritsugu, Hiroshi Fujisaki, Satoshi Murakami, Mitsunori Ikeguchi, Akinori Kidera (2018). “Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB” eLife, 7, e31715 (19 pages).
• Kentaro Shimizu, Wei Cao, Gull Saad, Michiru Shoji, Tohru Terada (2018). “Comparative analysis of membrane protein structure databases” Biochimica et Biophysica Acta (BBA) - Biomembranes, 1860, 1077–1091.

2017

• Yifan Tang, Cao Wei, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Koji Kadota, Kentaro Shimizu (2017). “Predicting protein-protein interactions using sequence homology and machine-learning methods” Research Journal of Life Sciences, Bioinformatics, Pharmaceutical and Chemical Sciences, 3(3), 1–26.
• Kei Moritsugu, Tohru Terada, and Akinori Kidera (2017). “Free-Energy Landscape of Protein–Ligand Interactions Coupled with Protein Structural Changes” Journal of Physical Chemistry B, 121, 731–740.
• Masaki Banno, Yusuke Komiyama, Wei Cao, Yuya Oku, Kokoro Ueki, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Kentaro Shimizu (2017). “Development of a sugar-binding residue prediction system from protein sequences using support vector machine” Computational Biology and Chemistry, 66, 36–43.

2016

• Chiho Suzuki-Minakuchi, Kohei Kawazuma, Jun Matsuzawa, Delyana Vasileva, Zui Fujimoto, Tohru Terada, Kazunori Okada, Hideaki Nojiri (2016). “Structural similarities and differences in H-NS family proteins revealed by the N-terminal structure of TurB in Pseudomonas putida KT2440” FEBS Letters, 590, 3583–3594.
• Marie Kubota, Kaoru Takeuchi, Shumpei Watanabe, Shinji Ohno, Rei Matsuoka, Daisuke Kohda, Shin-ichi Nakakita, Hiroaki Hiramatsu, Yasuo Suzuki, Tetsuo Nakayama, Tohru Terada, Kentaro Shimizu, Nobutaka Shimizu, Mitsunori Shiroishi, Yusuke Yanagi, and Takao Hashiguchi (2016). “Trisaccharide containing α2,3-linked sialic acid is a receptor for mumps virus” Proceedings of the National Academy of Science of the United States of America, 113, 11579–11584.
• Shunsuke Shigemitsu, Wei Cao, Tohru Terada, Kentaro Shimizu (2016). “Development of a prediction system for tail-anchored proteins” BMC Bioinformatics, 17, 378 (11 pages).
• Kei Moritsugu, Tohru Terada, Akinori Kidera (2016). “Multiscale enhanced sampling for protein systems: An extension via adiabatic separation” Chemical Physics Letters, 661, 279–283.
• Wayne K. Dawson, Ryota Jono, Tohru Terada, Kentaro Shimizu (2016). “Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center” PLoS ONE, 11, e0162031 (41 pages).
• Hiroto Tsujikawa, Kenta Sato, Cao Wei, Gul Saad, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Kentaro Shimizu (2016). “Development of a protein–ligand-binding site prediction method based on interaction energy and sequence conservation” Journal of Structural and Functional Genomics, 17, 39–49.
• Kokoro Ueki, Kenta Sato, Shugo Nakamura, Tohru Terada, Kazuya Sumikoshi, Kentaro Shimizu (2016). “Development of a computational method for lipid-binding protein prediction” Research Journal of Life Sciences, Bioinformatics, Pharmaceutical and Chemical Sciences, 1, 223–236.

2015

• Yoshitaka Moriwaki, Tohru Terada, Kouhei Tsumoto, Kentaro Shimizu (2015). “Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations” PLoS ONE, 10, e0145125 (15 pages).
• Zuoqi Gai, Asuka Matsuno, Koji Kato, Sanae Kato, Md Rafiqul Islam Khan, Takeshi Shimizu, Takeya Yoshioka, Yuki Kato, Hideki Kishimura, Gaku Kanno, Yoshikatsu Miyabe, Tohru Terada, Yoshikazu Tanaka, Min Yao (2015). “Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Å Resolution” Structure, 23, 2204–2212.
• Kayako Ogi, Haruyuki Yamashita, Tohru Terada, Ryousuke Homma, Akiko Shimizu-Ibuka, Etsuro Yoshimura, Yoshiro Ishimaru, Keiko Abe, and Tomiko Asakura (2015). “Long-Chain Fatty Acids Elicit a Bitterness-Masking Effect on Quinine and Other Nitrogenous Bitter Substances by Formation of Insoluble Binary Complexes” Journal of Agricultural and Food Chemistry, 63, 8493–8500.
• Masayuki Yarimizu, Cao Wei, Yusuke Komiyama, Kokoro Ueki, Shugo Nakamura, Kazuya Sumikoshi, Tohru Terada, and Kentaro Shimizu (2015). “Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine” Advances in Bioinformatics, 2015, 528097 (5 pages).
• Taichi Koizumi, Tohru Terada, Ken-ichiro Nakajima, Masaki Kojima, Seizo Koshiba, Yoshitaka Matsumura, Kohei Kaneda, Tomiko Asakura, Akiko Shimizu-Ibuka, Keiko Abe, and Takumi Misaka (2015). “Identification of key neoculin residues responsible for the binding and activation of the sweet taste receptor” Scientific Reports, 5, 12947 (11 pages).
• Masanori Komatsu, Yoichi Sato, Tatsuki Negami, Tohru Terada, Osamu Sasaki, Jumpei Yasuda, Aisaku Arakawa, Chikara Yoshida, Hideaki Takahashi, Aduli E. O. Malau-Aduli, Keiichi Suzuki, and Kentaro Shimizu (2015). “Overdominance Effect of the Bovine Ghrelin Receptor (GHSR1a)-DelR242 Locus on Growth in Japanese Shorthorn Weaner Bulls: Heterozygote Advantage in Bull Selection and Molecular Mechanisms” G3: Genes, Genomes, Genetics, 5, 271–279.

2014

• Kei Moritsugu, Tohru Terada, Akinori Kidera (2014). “Multiscale enhanced sampling driven by multiple coarse-grained models” Chemical Physics Letters, 616–617, 20–24.
• Kei Moritsugu, Tohru Terada, Akinori Kidera (2014). “Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling” PLoS Computational Biology, 10, e1003901.
• Tatsuki Negami, Kentaro Shimizu, and Tohru Terada (2014). “Coarse-Grained Molecular Dynamics Simulations of Protein–Ligand Binding” Journal of Computational Chemistry, 35, 1835–1845.
• Chiho Suzuki, Kohei Kawazuma, Shoichiro Horita, Tohru Terada, Masaru Tanokura, Kazunori Okada, Hisakazu Yamane, Hideaki Nojiri (2014). “Oligomerization Mechanisms of an H-NS Family Protein, Pmr, Encoded on the Plasmid pCAR1 Provide a Molecular Basis for Functions of H-NS Family Members” PLoS ONE, 9, e105656.
• Kengo Inoue, Yusuke Usami, Yuji Ashikawa, Haruko Noguchi, Takashi Umeda, Aiko Yamagami-Ashikawa, Tadafumi Horisaki, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Hiroshi Habe, Hisakazu Yamane, Zui Fujimoto and Hideaki Nojiri (2014). “Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase” Applied and Environmental Microbiology, 80, 2821–2832.

2013

• Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, and Kentaro Shimizu (2013). “Heme Binding Mechanism of Structurally Similar Iron-Regulated Surface Determinant Near Transporter Domains of Staphylococcus aureus Exhibiting Different Affinities for Heme” Biochemistry, 52, 8866–8877.
• Nhuan T. Vu, Yoshitaka Moriwaki, Jose M. M. Caaveiro, Tohru Terada, Hiroshi Tsutsumi, Itaru Hamachi, Kentaro Shimizu, and Kouhei Tsumoto (2013). “Selective binding of antimicrobial porphyrins to the heme-receptor IsdH-NEAT3 of Staphylococcus aureus” Protein Science, 22, 942–953.

2012

• Satoshi Yamasaki, Tohru Terada, Hidetoshi Kono, Kentaro Shimizu, and Akinori Sarai (2012). “A new method for evaluating the specificity of indirect readout in protein-DNA recognition” Nucleic Acids Research, 40, e129 (7 pages).
• Tohru Terada, Akinori Kidera (2012). “Comparative Molecular Dynamics Simulation Study of Crystal Environment Effect on Protein Structure” Journal of Physical Chemistry B, 116, 6810–6818.
• Yasuhiro Matsunaga, Hiroshi Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, Akinori Kidera (2012). “Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase” PLoS Computational Biology, 8, e1002555.
• Kei Moritsugu, Tohru Terada, Akinori Kidera (2012). “Disorder-to-Order Transition of an Intrinsically Disordered Region of Sortase Revealed by Multiscale Enhanced Sampling” Journal of the American Chemical Society, 134, 7094–7101.
• Yoko Chiba, Tohru Terada, Masafumi Kameya, Kentaro Shimizu, Hiroyuki Arai, Masaharu Ishii, Yasuo Igarashi (2012). “Mechanism for folate-independent aldolase reaction catalyzed by serine hydroxymethyltransferase” FEBS Journal, 279, 504–514.

2011

• Ayako Koizumi, Asami Tsuchiya, Ken-ichiro Nakajima, Keisuke Ito, Tohru Terada, Akiko Shimizu-Ibuka, Loïc Briand, Tomiko Asakura, Takumi Misaka, and Keiko Abe (2011). “Human sweet taste receptor mediates acid-induced sweetness of miraculin” Proceedings of the National Academy of Sciences of the United States of America, 108, 16819–16824.
• Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu (2011). “Protein-Protein Docking Using Multi-layered Spherical Basis Functions” Proceedings of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics, (International Proceedings of Chemical, Biological and Environmental Engineering, 5), 342–347.
• Wei Cao, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Kentaro Shimizu (2011). “Prediction of N-myristoylation modification of proteins by SVM” Bioinformation, 6, 204–206.
• Mizuki Morita, Tohru Terada, Shugo Nakamura and Kentaro Shimizu (2011). “BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states” BMC Research Notes, 4, 143.
• Ken-ichiro Nakajima, Kanako Yokoyama, Taichi Koizumi, Ayako Koizumi, Tomiko Asakura, Tohru Terada, Katsuyoshi Masuda, Keisuke Ito, Akiko Shimizu-Ibuka, Takumi Misaka, Keiko Abe (2011). “Identification and Modulation of the Key Amino Acid Residue Responsible for the pH Sensitivity of Neoculin, a Taste-Modifying Protein” PLoS ONE, 6, e19448.

2010

• Takashi Hagiwara, Seiji Saito, Yoshifumi Ujiie, Kensaku Imai, Masanori Kakuta, Koji Kadota, Tohru Terada, Kazuya Sumikoshi, Kentaro Shimizu, Tatsunari Nishi (2010). “HPLC Retention time prediction for metabolome analysis” Bioinformation, 5, 255–258.
• Kei Moritsugu, Tohru Terada, and Akinori Kidera (2010). “Scalable free energy calculation of proteins via multiscale essential sampling” Journal of Chemical Physics, 133, 224105.
• Kei Urano, Takaaki Daimon, Yutaka Banno, Kazuei Mita, Tohru Terada, Kentaro Shimizu, Susumu Katsuma, and Toru Shimada (2010). “Molecular defect of isovaleryl-CoA dehydrogenase in the skunk mutant of silkworm, Bombyx mori” FEBS Journal, 277, 4452–4463.
• Seizi Someya, Masanori Kakuta, Mizuki Morita, Kazuya Sumikoshi, Wei Cao, Zhenyi Ge, Osamu Hirose, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu (2010). “Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines” Advances in Bioinformatics, 2010, 289301.
• Ryota Jono, Yuusuke Watanabe, Kentaro Shimizu, and Tohru Terada (2010). “Multicanonical Ab Initio QM/MM Molecular Dynamics Simulation of a Peptide in an Aqueous Environment” Journal of Computational Chemistry, 31, 1168–1175.

2009

• Yuji Morita, Ken-ichiro Nakajima, Kisho Iizuka, Tohru Terada, Akiko Shimizu-Ibuka, Keisuke Ito, Ayako Koizumi, Tomiko Asakura, Takumi Misaka, and Keiko Abe (2009). “pH-dependent structural change of neoculin in special reference to its taste-modifying activity” Bioscience, Biotechnology, and Biochemistry, 73, 2552–2555.
• Wei Cao, Jun-ichi Maruyama, Katsuhiko Kitamoto, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2009). “Using a new GPI-anchored-protein identification system to mine the protein databases of Aspergillus fumigatus, Aspergillus nidulans, and Aspergillus oryzae” The Journal of General and Applied Microbiology, 55, 381–393.
• Satoshi Yamasaki, Tohru Terada, Kentaro Shimizu, Hidetoshi Kono, and Akinori Sarai (2009). “A generalized conformational energy function of DNA derived from molecular dynamics simulations” Nucleic Acids Research, 37, e135.
• Tokiha Masuda, Yutaka Ito, Tohru Terada, Takehiko Shibata, and Tsutomu Mikawa (2009). “A non-canonical DNA structure enables homologous recombination in various genetic systems” Journal of Biological Chemistry, 284, 30230–30239.
• Kengo Inoue, Yuji Ashikawa, Takashi Umeda, Mitsuru Abo, Junichi Katsuki, Yusuke Usami, Haruko Noguchi, Zui Fujimoto, Tohru Terada, Hisakazu Yamane, and Hideaki Nojiri (2009). “Specific interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase” Journal of Molecular Biology, 329, 436–451.
• Wei Cao, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Katsuhiko Kitamoto, and Kentaro Shimizu (2009). “Computational protocol for screening GPI-anchored proteins” Proceedings of the First International Conference on Bioinformatics and Computational Biology (S. Rajasekaran, ed.), New Orleans, USA, published in Lecture Notes in Bioinformatics, 5462, 164–175.
• Tadaomi Furuta, Kentaro Shimizu, Tohru Terada (2009). “Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures” Chemical Physics Letters, 472, 134–139.

2008

• Hiromasa Uchimura, Tadafumi Horisaki, Takashi Umeda, Haruko Noguchi, Yusuke Usami, Li Li, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Tetsuo Takemura, Hiroshi Habe, Kazuo Furihata, Toshio Omori, Hisakazu Yamane, and Hideaki Nojiri (2008). “Alteration of the Substrate Specificity of the Angular Dioxygenase Carbazole 1,9a-Dioxygenase” Bioscience, Biotechnology, and Biochemistry, 72, 3237–3248.
• Tohru Terada, Daisuke Satoh, Tsutomu Mikawa, Yutaka Ito, Kentaro Shimizu (2008). “Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation” Proteins: Structure, Function, and Bioinformatics, 73, 621–631.
• Tohru Terada and Kentaro Shimizu (2008). “A comparison of generalized Born methods in folding simulations” Chemical Physics Letters, 460, 295–299.
• Akiko Shimizu-Ibuka, Yuji Nakai, Keisuke Nakamori, Yuji Morita, Ken-ichiro Nakajima, Koji Kadota, Hirohito Watanabe, Satoshi Okubo, Tohru Terada, Tomiko Asakura, Takumi Misaka, and Keiko Abe (2008). “Biochemical and Genomic Analysis of Neoculin Compared to Monocot Mannose-Binding Lectins” Journal of Agricultural and Food Chemistry, 56, 5338–5344.
• Ken-ichiro Nakajima, Yuji Morita, Ayako Koizumi, Tomiko Asakura, Tohru Terada, Keisuke Ito, Akiko Shimizu-Ibuka, Jun-ichi Maruyama, Katsuhiko Kitamoto, Takumi Misaka, and Keiko Abe (2008). “Acid-induced sweetness of neoculin is ascribed to its pH-dependent agonistic-antagonistic interaction with human sweet taste receptor” The FASEB Journal, 22, 2323–2330.
• Ryuichiro Ishitani, Tohru Terada, Kentaro Shimizu (2008). “Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations” Molecular Simulation, 34, 327–336.

2007

• Keisuke Ito, Tomiko Asakura, Yuji Morita, Ken-ichiro Nakajima, Ayako Koizumi, Akiko Shimizu-Ibuka, Katsuyoshi Masuda, Masaji Ishiguro, Tohru Terada, Jun-ichi Maruyama, Katsuhiko Kitamoto, Takumi Misaka, and Keiko Abe (2007). “Microbial production of sensory-active miraculin” Biochemical and Biophysical Research Communications, 360, 407–411.
• Satoshi Yamasaki, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu (2007). “Mechanism of the Difference in the Binding Affinity of E. coli tRNA^Gln to Glutaminyl-tRNA Synthetase Caused by Noninterface Nucleotides in Variable Loop” Biophysical Journal, 92, 192–200.

2006

• Ryota Jono, Kentaro Shimizu, and Tohru Terada (2006). “A multicanonical ab initio molecular dynamics method: Application to conformation sampling of alanine tripeptide” Chemical Physics Letters, 432, 306–312.
• Wei Cao, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2006). “Insight of the Signal Motif of GPI-(like)-anchored Proteins by using SVM” Proceedings of 2006 International Conference on Bioinformatics & Computational Biology, Editors: Hamid R. Arabnia and Homayoun Valafar, Las Vegas, USA, 541–546.
• Koji Kadota, Jiazhen Ye, Yuji Nakai, Tohru Terada, and Kentaro Shimizu (2006). “ROKU: a novel method for identification of tissue-specific genes” BMC Bioinformatics, 7, 294.
• Ryuichiro Ishitani, Kentaro Shimizu, and Tohru Terada (2006). “Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides” Journal of Chemical Physics, 124, 214902.
• Daisuke Satoh, Kentaro Shimizu, Shugo Nakamura, Tohru Terada (2006). “Folding free-energy landscape of a 10-residue mini-protein, chignolin” FEBS Letters, 580, 3422–3426.
• Akiko Shimizu-Ibuka, Yuji Morita, Tohru Terada, Tomiko Asakura, Ken-ichiro Nakajima, So Iwata, Takumi Misaka, Hiroyuki Sorimachi, Soichi Arai, and Keiko Abe (2006). “Crystal Structure of Neoculin: Insights into its Sweetness and Taste-modifying Activity” Journal of Molecular Biology, 359, 148–158.

2005

• Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu (2005). “A Fast Protein-Protein Docking Algorithm Using Series Expansion in Terms of Spherical Basis Functions” Genome Informatics, 16(2), 161–173.
• Hideaki Nojiri, Yuji Ashikawa, Haruko Noguchi, Jeong-Won Nam, Masaaki Urata, Zui Fujimoto, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Takako Yoshida, Hiroshi Habe, and Toshio Omori (2005). “Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase” Journal of Molecular Biology, 351, 355–370.
• Kazuhiko Arima, Kazuo Sato, Go Tanaka, Sachiko Kanaji, Tohru Terada, Eijiro Honjo, Ryota Kuroki, Yo Matsuo, and Kenji Izuhara (2005). “Characterization of the Interaction between Interleukin-13 and Interleukin-13 Receptors” Journal of Biological Chemistry, 280, 24915–24922.
• Xuesong Dong, Shinya Fushinobu, Eriko Fukuda, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Hideaki Nojiri, Toshio Omori, Hirofumi Shoun, and Takayoshi Wakagi (2005). “Crystal Structure of the Terminal Oxygenase Component of Cumene Dioxygenase from Pseudomonas fluorescens IP01” Journal of Bacteriology, 187, 2483–2490.

2004

• Akira Nomoto, Wataru Kaneko, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2004). “Programming Environment Based on Distributed Shared Arrays for High-Performance Scientific Computing” Proceedings of the 2004 Symposium on Applications and the Internet-Workshops (SAINT 2004 Workshops), 630–636.
• Takanori Ishizuka, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2004). “Improvement of accuracy of free-energy landscapes of peptides calculated with generalized Born model by using numerical solutions of Poisson's equation” Chemical Physics Letters, 393, 546–551.

2003

• Takashi Ishida, Takeshi Nishimura, Makoto Nozaki, Tsuyoshi Inoue, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2003). “Development of an ab initio protein structure prediction system ABLE” Genome Informatics, 14, 228–237.
• Tohru Terada, Yo Matsuo, and Akinori Kidera (2003). “A method for evaluating multicanonical potential function without iterative refinement: Application to conformational sampling of a globular protein in water” Journal of Chemical Physics, 118, 4306–4311.
• Takafumi Uchida, Mari Takamiya, Morito Takahashi, Hitoshi Miyashita, Hisafumi Ikeda, Tohru Terada, Yo Matsuo, Mikako Shirouzu, Shigeyuki Yokoyama, Fumihiro Fujimori, and Tony Hunter (2003). “Pin1 and Par14 Peptidyl Prolyl Isomerase Inhibitors Block Cell Proliferation” Chemistry & Biology, 10, 15–24.

2002

• Tohru Terada and Akinori Kidera (2002). “Generalized form of the conserved quantity in constant-temperature molecular dynamics” Journal of Chemical Physics, 116, 33–41.

1996–2001 (Experimental studies)

• Tohru Terada, Mikako Shirouzu, Yasuhiro Fukumori, Fumihiro Fujimori, Yutaka Ito, Takanori Kigawa, Shigeyuki Yokoyama, and Takafumi Uchida (2001). “Solution Structure of the Human Parvulin-like Peptidyl Prolyl cis/trans Isomerase, hPar14” Journal of Molecular Biology, 305, 917–926.
• Tohru Terada, Yutaka Ito, Mikako Shirouzu, Masaru Tateno, Kyoko Hashimoto, Takanori Kigawa, Toshikazu Ebisuzaki, Koji Takio, Takehiko Shibata, Shigeyuki Yokoyama, Brian O. Smith, Ernest D. Laue, and Jonathan A. Cooper (1999). “Nuclear Magnetic Resonance and Molecular Dynamics Studies on the Interactions of the Ras-binding Domain of Raf-1 with Wild-type and Mutant Ras Proteins” Journal of Molecular Biology, 286, 219–232.
• Takashi Yabuki, Takanori Kigawa, Naoshi Dohmae, Koji Takio, Tohru Terada, Yutaka Ito, Ernest D. Laue, Jonathan A. Cooper, Masatsune Kainosho, Shigeyuki Yokoyama (1998). “Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis” Journal of Biolomecular NMR, 11, 295–306.
• Hideki Aihara, Yutaka Ito, Hitoshi Kurumizaka, Tohru Terada, Shigeyuki Yokoyama, and Takehiko Shibata (1997). “An Interaction between a Specific Surface of the C-terminal Domain of RecA Protein and Double-stranded DNA for Homologous Pairing” Journal of Molecular Biology, 274, 213–221.
• Yutaka Ito, Kazuhiko Yamasaki, Junji Iwahara, Tohru Terada, Akihide Kamiya, Mikako Shirouzu, Yutaka Muto, Gota Kawai, Shigeyuki Yokoyama, Ernest D. Laue, Markus Waelchli, Takehiko Shibata, Susumu Nishimura, and Tatsuo Miyazawa (1997). “Regional Polysterism in the GTP-Bound Form of the Human c-Ha-Ras Protein” Biochemistry, 36, 9109–9119.
• Satoko Akashi, Mikako Shirouzu, Tohru Terada, Yutaka Ito, Shigeyuki Yokoyama, and Koji Takio (1997). “Characterization of the Structural Difference between Active and Inactive Forms of the Ras Protein by Chemical Modification Followed by Mass Spectrometric Peptide mapping” Analytical Biochemistry, 248, 15–25.
• Brian O. Smith, Yutaka Ito, Andrew Raine, Sarah Teichmann, Liat Ben-Tovim, Daniel Nietlispach, R. William Broadhurst, Tohru Terada, Mark Kelly, Hartmut Oschkinat, Takehiko Shibata, Shigeyuki Yokoyama, and Ernest D. Laue (1996). “An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types” Journal of Biomolecular NMR, 8, 360–368.