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Design of Cyborg Proteins by Loop Region Replacement with Oligo(ethylene glycol): Exploring Suitable Mutations for Cyborg Protein Construction Using Machine Learning
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The difference in the cellular uptake of tocopherol and tocotrienol is influenced by their affinities to albumin. Scientific reports, 13, 7392-7392 (2023) [doi]
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A simple method for the creation of a bacteria-sized unilamellar liposome with different proteins localized to the respective sides of the membrane ACS Synthetic Biology, 12, 1437−1446 (2023) [doi]
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A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation Nature Communications, 13, 7262-7262 (2022) [doi]
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An ancestral function of strigolactones as symbiotic rhizosphere signals. Nature Communications, 13, 3974-3974 (2022) [doi]
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Regulation of axon arborization pattern in the developing chick ciliary ganglion: Possible involvement of caspase 3 Dev. Growth Differ., 59, 115-128 (2017) [PubMed]
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CXCL4 is a novel nickel-binding protein and augments nickel allergy Clin. Exp. Allergy, 2017, 1-10 (2017) [PubMed]
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Isolation and Biochemical Characterization of Mucus Proteins in Japanese Bunching Onion (Allium fistulosum) Green Leaves Food Sci. Technol. Res., 22, 235-243 (2016) [link]
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A dye-decolorizing peroxidase from Vibrio cholera. Biochemistry, 54, 6610-6621 (2015)
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Structural basis for pore-forming mechanism 1 of staphylococcal α-hemolysin. Toxicon, 108, 226-231 (2015)
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Crystal structure of the 3.8 MDa respiratory supermolecule hemocyanin at 3.0 angstrom resolution. Structure, 23, 2204-2212 (2015)
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Zinc ion-binding activity of an anti-ZnO VHH antibody, 4F2. Chem. Letters, 44, 1309-1311 (2015)
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Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin. J. Struct. Biol., 190, 379-382 (2015)
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Antioxidant Properties of Tripeptides Revealed by a Comparison of Six Different Assays. Food Sci. Technol. Res., 21, 685-693 (2015)
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Effect of Chum Salmon Egg Lectin on Tight Junctions in Caco-2 Cell Monolayers. Molecules, 20, 8094-8098 (2015)
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Isolation and Biochemical Characterization of Apios Tuber Lectin. Molecules, 20, 987-1002 (2015)
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Expression, purification and crystallization of a plant polyketide cyclase from Cannabis sativa.
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Structural basis for β-carboline alkaloid production by the microbial homodimeric enzyme McbB. Chem. & Biol., 22, 898-906 (2015)
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Structural basis for the formation of acylalkylpyrones from two β-ketoacyl units by the fungal type III polyketide synthase CsyB. J. Biol. Chem., 290, 5214-5225 (2015)
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A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin. Nature Chem. Biol., 11, 71-76 (2015)
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Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18S rRNA. J. Biol. Chem., 289, 35724-35730(2014)
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Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins. Nature Commun., 5, 4897 (2014)
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Structural and genomic DNA analysis of the putative TetR transcriptional repressor SCO7518 from Streptomyces coelicolor A3(2). FEBS Letters, 588, 4311-4318 (2014)
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Anchoring protein crystals to mounting loops with hydrogel using inkjet technology.Acta Cryst. D., D70 2794-2799 (2014)
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Nucleoid compaction by MrgAAsp56Ala/Glu60Ala does not contribute to staphylococcal cell survival against oxidative stress and phagocytic killing by macrophage. FEMS Microbiol. Letters, 360, 144-151 (2014)
Suzuki, T., Yamashita, K., Tanaka, Y., Tanaka, I., and Yao, M., Crystallization and preliminary X-ray crystallographic analysis of a bacterial Asn-transamidosome. Acta Cryst. F., F70, 790-793 (2014)
Asano, N., Atsuumi, H., Nakamura, A., Tanaka, Y., Tanaka, I., and Yao, M., Direct interaction between EFL1 and SBDS is mediated by an intrinsically disordered insertion domain. Biochem. Biophys. Res. Commun., 443, 1251-1256 (2014)
Naganuma T., Hoshino W., Shikanai Y., Sato R., Liu K., Sato S., Muramoto K., Osada M., Yoshimi K., Ogawa T., Novel Matrix Proteins of Pteria penguin Pearl Oyster Shell Nacre Homologous to the Jacalin-Related β-Prism Fold Lectins. PLos ONE, 9 e112326 (2014)
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Matsui T., Han X., Yu J., Yao M., Tanaka I., Structural Change in FtsZ Induced by Intermolecular Interactions between Bound GTP and the T7 loop. J. Biol. Chem., 289 3501-3509 (2014)
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Matsumoto, K., Tanaka, Y., Watanabe, T., Motohashi, R., Ikeda, K., Tobitani, K., Yao, M., Tanaka, I., and Taguchi, S., Directed evolution and structural analysis of NADPH-dependent acetoacetyl-CoA reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics. Appl. Env. Microb., 79, 6134-6139 (2013)
Gai, Z., Nakamura, A., Tanaka, Y., Hirano, N., Tanaka, I., and Yao, M., Crystal structure analysis, overexpression and refolding behavior of a DING protein with single mutation. J. Synchrotron Rad., 20, 854-858 (2013)
Chen, M., Yu, J., Tanaka, Y., Tanaka, M., Tanaka, I., and Yao, M., Crystal structure of dihydrouridine synthase C (DusC) from Escherichia coli. Acta Cryst. F., F69, 834-838 (2013)
Sugawara, T., Yamashita, D., Tanaka, Y., Kaneko, J., Kamio, Y., Tanaka, I., and Yao, M., Preliminary X-ray crystallographic study of staphylococcal α-hemolysin monomer. Acta Cryst. F., F69, 868-870 (2013)
Hayashi, T., Tanaka, Y., Sakai, N., Okada, U., Yao, M., Watanabe, N., Tamura, T., and Tanaka, I., SCO4008, a putative TetR transcriptional repressor from Streptomyces coelicolor A3(2), regulates transcription of sco4007 by multidrug recognition. J. Mol. Biol., 425, 3289-3300 (2013)
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Hayashi, T., Tanaka, Y., Sakai, N., Watanabe, N., Tamura, T., Tanaka, I., and Yao, M., Structural and genomic DNA analysis of a putative transcription factor SCO5550 from Streptomyces coelicolor A3(2): regulating the expression of gene sco5551 as a transcriptional activator with a novel dimer shape. Biochem. Biophys. Res. Commun., 435, 28-33 (2013)
Kita, S., Tanaka, Y., Hirano, N., Kimura, S., Suzuki, T., Suzuki, T., Yao, M., and Tanaka. I., Crystal structure of a putative methyltransferase SAV1081 from Staphylococcus aureus. Protein & Pept. Lett., 20, 530-537 (2013)
Yamamoto S., Tomiyama M., Nemoto R., Naganuma T., Ogawa T., Muramoto K., Effects of Food Lectins on the Transport System of Human Intestinal Caco-2 Cell Monolayers. Biosci. Biotechnol. Biochem., 77, 1917-1924 (2013)
Watanabe Y., Chang YH., Nakamura O., Naganuma T., Ogawa T., Muramoto K., Rhamnose-binding lectins induce respiratory burst activity in macrophage cells from rainbow trout. Fisheries Sci., 79, 513-519 (2013)
Mori T., Shimokawa Y., Matsui T., Kinjo K., Kato R., Noguchi H., Sugio S., Morita H., Abe I., Cloning and structure-function analyses of quinolone-and acridone-producing novel type III polyketide synthases from Citrus microcarpa. J. Biol. Chem., 288, 28845-28858 (2013)
Kawashima Y., Satoh M., Saito T., Matsui T., Nomura F., Matsumoto H., Kodera Y., Cyclic sample pooling using two‐dimensional liquid chromatography system enhances coverage in shotgun proteomics. Biomed. Chromatogr., 27, 691-694 (2013)
Saito T., Kawashima Y., Minamida S., Matsumoto K., Araki K., Matsui T., Satoh M., Nomura F., Iwamura M., Maeda T., Baba S., Kodera Y., Establishment and application of a high-quality comparative analysis strategy for the discovery and small-scale validation of low-abundance biomarker peptides in serum based on an optimized novel peptide extraction method. J. Electrophr., 57, 1-9 (2013)
Gai, Z., Kitagawa, Y., Tanaka, Y., Shimizu, N., Komoda, K., Tanaka, I., and Yao, M., The binding mechanism of eIF2{beta} with its partner proteins, eIF5 and eIF2B{epsilon}. Biochem. Biophys. Res. Commun., 423, 515-519 (2012)
Tsukamoto, K., Arimitsu, H., Ochi, S., Nakamura, K., Tanaka, Y., Nuemket, N., Taniguchi, K., Kozaki, S., and Tsuji, T., P19 embryonal carcinoma cells exhibit high sensitivity to botulinum type C and D/C mosaic neurotoxins. Microbiol. and Immunol., 56, 664-672 (2012)
Ui, M., Tanaka, Y., Araki, Y., Wada, T., Takei, T., Tsumoto, K., Endo, S., and Kinbara, K., Application of photoactive yellow protein as a photoresponsive module for controlling hemolytic activity of staphylococcal α-hemolysin. Chem. Commun.48, 4737-4739 (2012)
Miyafusa T, Caaveiro JM, Tanaka Y, Tsumoto K. Crystal Structure of Enzyme CapF of Staphylococcus aureus Reveals a Unique Architecture Composed of Two Functional Domains. Biochem J., 443, 671-680 (2012)
Yoshimura S., Komatsu M., Kaku K., Hori M., Ogawa T., Muramoto K., Kazama T., Ito Y., Toriyama K., Production of transgenic rice plants expressing Dioscprea batatus tuber lectin 1 to confer resistance against brown plant hopper. Plant Biotechnol., 29, 501-504 (2012)
Nakamura O., Watanabe M., Ogawa T., Muramoto K., Ogawa K., Tsutsui S., Kamiya H., Galectins in the abdominal cavity of conger eel, Conger myriaster, participate in the cellular encapsulation of parasitic nematode by host cells. FIsh & Shellfish Immun., 33, 780-787 (2012)
Watanabe M., Nakamura O., Muramoto K., Ogawa T., Allosteric regulation of the carbohydrate-binding ability of a novel conger Eel galectin by D-mannoside. J. Biol. Chem., 287, 31061-31072 (2012)
Matsui T., Yamane J., Mogi N., Yamaguchi H., Takemoto H., Yao M., Tanaka I., Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus. Acta Crystallogr. D., D68, 1175-1188 (2012)
Yu, F., Tanaka, Y., Yamashita, K., Suzuki, T., Nakamura, A., Hirano, N., Suzuki, T., Yao, M., and Tanaka, I.,
Molecular basis of dihydrouridine formation on tRNA. Proc. Natl. Acad. Sci. USA, 108, 19593-19598 (2011)
Yamashita, K., Kawai, Y., Tanaka, Y., Hirano, N., Kaneko, J., Tomita, N., Ohta, M., Kamio, Y., Yao, M., and Tanaka, I.,
Crystal Structure of the Octameric Pore of Staphylococcal γ-hemolysin Reveals the β-barrel Pore Formation Mechanism by Two Components. Proc. Natl. Acad. Sci. USA, 108, 17314-17319 (2011)
Moriwaki, Y., Caaveiro, JM., Tanaka, Y., Tsutsumi, H., Hamachi, I., Tsumoto K.
Molecular Basis of Recognition of Antibacterial Porphyrins by Heme-Transporter IsdH-NEAT3 of Staphylococcus aureus.Biochemistry., 50, 7311-7320 (2011)
Nuemket, N., Tanaka, Y., Tsukamoto, K., Tsuji, T., Nakamura, K., Kozaki, S., Yao, M., Tanaka, I., Structural and Mutational Analyses of the Receptor Binding Domain of Botulinum D/C Mosaic Neurotoxin: Insight into the Ganglioside Binding Mechanism. Biochem. Biophys. Res. Commun. , 411, 433-439 (2011)
Yu, F., Tanaka, Y., Yamamoto, S., Nakamura, A., Kita, S., Hirano, N., Tanaka, I., and Yao, M., Crystallization and preliminary X-ray crystallographic analysis of dihydrouridine synthase from Thermus thermophilus and its complex with tRNA. Acta Cryst. F., F67, 685-688 (2011)
Tanaka, Y., Hirano, N., Kaneko, J., Kamio, Y., Yao, M., and Tanaka, I., 2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal alpha-hemolysin into heptameric pore structure. Protein Science , 20, 448-456 (2011)
Matsuoka, E., Tanaka, Y., Kuroda, M., Shouji, Y., Ohta, T., Tanaka, I., and Yao, M., Crystal structure of the functional region of Uro-adherence factor A (UafA) from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding. Protein Science , 20, 406-416 (2011)
Ui, M., Tanaka, Y., Tsumuraya, T., Fujii, I., Inoue, M., Hirama, M., and Tsumoto, K., Structural and Energetic Hot-Spots for the Interaction between a Ladder-like Polycyclic Ether and the Anti-Ciguatoxin Antibody 10C9Fab. Molecular BioSystems, 7, 793-798 (2011)
Konno A., Kitagawa A., Watanabe M., Ogawa T., Shirai T., Tracing Protein Evolution through Ancestral Structures of Fish Galectin. Structure, 19, 711-721 (2011)
Krause J., Tshidino SC., Ogawa T., Watanabe Y., Oosthuizen V., Somai B., Muramoto K., Naudea RJ., Purification and partial characterization of ostrich skeletal muscle cathepsin D and its activity during meat maturation. Meat Sci., 87, 196-201 (2011)
Morikawa, K., Ohniwa, R. L., Ohta, T., Tanaka, Y., Takeyasu, K., and Msadek, T., Adaptation beyond the Stress Response: Cell Structure Dynamics and Population Heterogeneity in Staphylococcus aureus. Microbes and Environments , 25, 75-82 (2010)
Nuemket, N., Tanaka, Y., Tsukamoto, K., Tsuji, T., Nakamura, K., Kozaki, S., Yao, M., and Tanaka, I., Preliminary X-ray crystallographic study of the receptor binding domain of the D/C mosaic neurotoxin from Clostridium botulinum. Acta Cryst. F., F66, 608-610 (2010)
Nagatoishi, S., Tanaka, Y., Kudou, M., and Tsumoto, K., Temperature and salt concentration alter base-sequence selectivity of a duplex DNA-binding protein, Mol. Biosyst., 6, 98-101 (2010)
Yanaka, S., Kudou, M., Tanaka, Y., Sasaki, T., Takemoto, S., Sakata, A., Hattori, Y., Koshi, T., Futaki, S., Tsumoto, K., and Nakashima, T., Contribution of the flexible loop region to the function of Staphylococcal enterotoxin B (SEB), Protein Eng. Des. Select., 23, 415-421 (2010)
Kato T., Hori M., Ogawa T., Muramoto K., Toriyama K., Expression of gene for Dioscorea batatas tuber lectin 1 in transgenic tobacco confers resistance to green-peach aphid, Plant Biotechnol., 27, 141-145 (2010)
Kanno A., Yonemaru S., Kitagawa A., Muramoto K., Shirai T., Ogawa T., Protein engineering of conger eel galectins by tracing of molecular evolution using probable ancestral mutants, BMC Evol. Biol., 10, (2010)
Tanaka, Y., Yamagata, S., Kitago, Y., Yamada, Y., Chimnaronk, S., Yao, M., and Tanaka, I., Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand, RNA, 15, 1498-1506 (2009)
Nagatoishi, S., Tanaka, Y., Kudou, M., and Tsumoto, K., The interaction of hyperthermophilic TATA-box binding protein with single-stranded DNA is entropically favorable and exhibits a large negative heat capacity change at high salt concentration, Mol. BioSyst., 5, 957-961 (2009)
Sakamoto, S., Caaveiro, J. M., Sano, E., Tanaka, Y., Kudou, M., and Tsumoto, K., Contributions of interfacial residues of human Interleukin15 to the specificity and affinity for its private alpha-receptor, J. Mol. Biol., 389, 880-894 (2009)
Abe, R., Kudou, M., Tanaka, Y., Arakawa, T., and Tsumoto, K., Immobilized metal affinity chromatography in the presence of arginine, Biochem. Biophys. Res. Commun., 381, 306-310 (2009)
Konno A., Suzuki Y., Ogawa T., Taniuchi T., Irradiation Promotes the Accumulation of Triglyceride in Lipomyces lipofer, Biosci. Biotechnol. Biochem., 73, 2474-2477 (2009)
Watanabe Y., Abolhassani M., Tojo Y, Sudab Y., Miyazawa K., Igarashi Y., Sakuma K., Ogawa T.,, Muramoto K., Evaluation of silica gel-immobilized phosphorylcholine columns for size exclusion chromatography and their application in the analysis of the subunit structures of fish-egg lectins, J. Chromatogr. A., 1216, 8563-8566 (2009)
Shirai T., Watanabe Y., Lee MS., Ogawa T., Muramoto K., Structure of Rhamnose-binding Lectin CSL3: Unique Pseudo-tetrameric Architecture of a Pattern Recognition Protein, J. Mol. Biol., 391, 390-403 (2009)
Ohizumi Y., Gaidamashvili M., Ohwada S., Matsuda K., Kominami J., Nakamura-Tsuruta S., Hirabayashi J., Naganuma T., Ogawa T., Muramoto K., Mannose-binding lectin from yam (Dioscorea batatas) tubers with insecticidal properties against Helicoverpa armigera (Lepidoptera: Noctuidae), J. Agr. Food Chem., 57, 2896-2902 (2009)
Watanabe Y., Nakamura O., Watanabe T., Kamiya H., Naganuma T., Ogawa T., Naude RJ., Muramoto K., The function of rhamnose-binding lectin in innate immunity by restricted binding to Gb3, Dev. Comp. Immunol., 33, 187-197 (2009)
Yamamoto S., Naganuma T., Ogawa T., Muramoto K., Proteomic analysis of Caco-2 cells treated with food lectins, J. Clin. Biochem. Nutr., , (2009)
Matsui T., Tanaka T., Endoh H., Sato K., Tanaka H., Miyauchi E., Kawashima Y., Nagai-Makabe M., Komatsu H., Kohno T., Maeda T., Kodera Y., The RNA recognition mechanism of human immunodeficiency virus (HIV) type 2 NCp8 is different from that of HIV-1 NCp7, Biochemistry, 48, 4314-4323 (2009)
Kawashima Y., Fukuno T., Satoh M., Takahashi H., Matsui T., Maeda T., Kodera Y., A simple and highly reproducible method for discovering potential disease markers in low abundance serum proteins, J. Electrophor., 53, 13-18 (2009)
Gao, Y.-G., Suzuki, H., Itou, H., Zhou, Y., Tanaka, Y., Wachi, M., Watanabe, N., Tanaka, I., and Yao, M., Structural and Functional Characterization of the LidR from Corynebacterium glutamicum: a Transcriptional Repressor Involved in L-Lactate and Sugar Utilization, Nucleic Acids Res., 36, 7110-7123 (2008)
Kuroda, M., Ito, R., Tanaka, Y., Yao, M., Matoba, K., Saito, S., Tanaka, I., and Ohta, T., Staphylococcus aureus Surface Protein SasG Contributes to Intercellular Autoaggregation of Staphylococcus aureus, Biochem. Biophys. Res. Commun., 377, 1102-1106 (2008)
Sakamoto, S., Tanaka, Y., Tanaka, I., Takei, T., Yu, J., Kuroda, M., Yao, M., Ohta, T., and Tsumoto, K., Electron Microscopy and Computational Studies of Ebh, a Giant Cell-wall-associated Protein from Staphylococcus aureus, Biochem. Biophys. Res. Commun., 376, 261-266 (2008)
Watanabe, M., Tanaka, Y., Suenaga, A., Kuroda, M., Yao, M., Watanabe, N., Arisaka, F., Ohta, T., Tanaka, I., and Tsumoto, K., Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third NEAT domain of IsdH from Staphylococcus aureus, J. Biol. Chem.,283, 28649-28659 (2008)
Nakakido, M., Tanaka, Y., Mitsuhori, M., Kudou, M., Ejima, D., Arakawa, T., and Tsumoto, K., Structure-based analysis reveals hydration changes induced by arginine hydrochloride, Biophys. Chem., 137, 105-109 (2008)
Kuroda, M., Tanaka, Y., Aoki, R., Shu, D., Tsumoto, K., and Ohta, T., Staphylococcus aureus Giant Protein Ebh is Involved in Tolerance to Transient Hyperosmotic Pressure Biochem. Biophys. Res. Comm., 374, 237-241 (2008)
Ui, M., Tanaka, Y., Tsumuraya, T., Fujii, I., Inoue, M., Hirama, M., and Tsumoto, K., How Protein Recognizes Ladder-Like Polycyclic Ethers: Interactions
Between Ciguatoxin (CTX3C) Fragments and Its Specific Antibody 10C9 J. Biol. Chem., 283, 19440-19447 (2008)
Nakakido, M., Tanaka, Y., Sokabe, M., and Tsumoto, K., Thermodynamic Analysis Reveals that GTP Binding Affects the Interaction between the alpha- and gamma-subunits of Translation Initiation Factor 2. Biochem. Biophys. Res. Comm., 371, 596-599 (2008)
Miyafusa, T., Tanaka, Y., Kuroda, M., Ohta, T., and Tsumoto, K., Expression, Purification, Crystallization, and Primary Diffraction Analysis of CapF, a Capsular Polysaccharide Synthesis Enzyme from Staphylococcus aureus. Acta Cryst. F., F64, 512-515 (2008)
Tsumoto, K., Yokota, A., Tanaka, Y., Ui, M., Tsumuraya, T., Fujii, I., Kumagai, I., Nagumo, Y., Oguri, H., Inoue, M., and Hirama, M., Critical contribution of aromatic rings to specific recognition of polyether rings: the case of ciguatoxin CTX3C and its specific antibody 1C49. J. Biol. Chem., 283, 512259-12266 (2008)
Tanaka, Y., Sakamoto, S., Kuroda, M., Goda, S., Gao, Y.-G., Tsumoto, K., Hiragi, Y., Yao, M., Watanabe, N., Ohta, T., and Tanaka, I., A helical string of alternately connected two three-helix bundles for the 1.1-Megadalton cell wall-associated adhesion protein Ebh from Staphylococcus aureus. Structure, 16, 488-496, (2008)
Makabe, K., Nakanishi, T., Tsumoto, K., Tanaka, Y., Kondo, H., Umetsu, M., Sone, Y., Asano, R., and Kumagai, I., Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528. J. Biol. Chem., 283, 1156-1166 (2008)
Adebiyi AP., Adebiyi AO., Yamashita J., Ogawa T., Muramoto K., Purification and characterization of antioxidative peptides derived from rice bran protein hydrolysates. Eur. Food. Res. Technol., 228, 553-563 (2008)
Adebiyi AP., Adebiyi AO., Hasegawa Y., Ogawa T., Muramoto K., Isolation and characterization of protein fractions from deoiled rice bran. Eur. Food. Res. Technol., 228, 391-401 (2008)
Seto M., Ogawa T., Kodama K., Muramoto K., Kanayama Y., Sakai Y., Chijiwa T., Ohno M., A novel recombinant system for functional expression of myonecrotic snake phospholipase A2 in Escherichia coli using a new fusion affinity tag. Protein Expr. Purif., 58, 194-202 (2008)
Watanabe Y., Shiina N., Shinozaki F., Yokoyama H., Kominami J., Nakamura-Tsuruta S., Hirabayashi J., Sugahara K., Kamiya H., Matsubara H., Ogawa T., Muramoto K., Isolation and characterization of l-rhamnose-binding lectin, which binds to microsporidian Glugea plecoglossi, from ayu (Plecoglossus altivelis) egg. Dev. Comp. Immun., 32, 487-499 (2008)
Oshi Y., Nakata E., Miyagawa M., Tsukiji S., Ogawa T., Hamachi I., Target-Specific Chemical Acylation of Lectins by Ligand-Tethered DMAP Catalysts. J. Am. Chem. Soc., 130, 245-251 (2008)
Tanaka, Y., Morikawa, K., Ohki, Y., Yao, M., Tsumoto, K., Watanabe, N., Ohta, T., and Tanaka, I., Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity. J. Biol. Chem., 282, 5770-5780 (2007)
Shiroishi, M., Tsumoto, K., Tanaka, Y., Yokota, A., Nakanishi, T., Kondo, H., and Kumagai, I., Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex: the case of HyHEL-10-HEL. J. Biol. Chem., 282, 6783-6791 (2007)
Nagatoishi, S., Tanaka, Y., and Tsumoto, K., Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions. Biochem. Biophys. Res. Comm., 352, 812-817 (2007)
Arakawa, T., Ejima, D., Tsumoto, K., Obeyama, N., Tanaka, Y., Kita, Y., and Timasheff, S. N., Suppression of protein interactions by arginine: A proposed mechanism of arginine effects. Biophys. Chem., 127, 1-8 (2007)
Tanaka, Y., Sasaki, T., Kumagai, I., Yasutake, Y., Yao, M., Tanaka, I., and Tsumoto, K., Molecular properties of two proteins homologous to PduO-type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii, Proteins: Structure, Function, and Bioinformatics, 68, 446-457 (2007)
Tanaka, Y., Kuroda, M., Yasutake, Y., Yao, M., Tsumoto, K., Watanabe, N., Ohta, T., and Tanaka, I., Crystal structure analysis reveals a novel forkhead-associated (FHA) domain of ESAT-6 secretion system C (EssC) protein in Staphylococcus aureus. Proteins: Structure, Function, and Bioinformatics, 69, 659-664 (2007)
Nakakido, M., Tanaka, Y., and Tsumoto, K., The N-terminal domain of elastin-binding protein of Staphylococcus aureus changes its secondary structure in a membrane-mimetic environment. J. Biochem. (Tokyo), 142, 131-134 (2007)
Konno A., Ogawa T., Shirai T., Muramoto K., Reconstruction of a Probable Ancestral Form of Conger Eel Galectins Revealed. Mol. Biol. Evol., 24, 2504-2514 (2007)
Terada T., Watanabe Y., Tateno H., Naganuma T., Ogawa T., Muramoto K., Kamiya H., Structural characterization of a rhamnose-binding glycoprotein (lectin) from Spanish mackerel (Scomberomorous niphonius) eggs. Biochim. Biophys. Acta., 1770, 617-629 (2007)
Matsubara H., Nakamura-Tsuruta S., Hirabayashi J., Jimbo M., Kamiya H., Ogawa T., Muramoto K., Diverse Sugar-Binding Specificities of Marine Invertebrate C-Type Lectins. Biosci. Biotechol. Biochem., 71, 513-519 (2007)
Matsui T., Kodera Y., Miyauchi E., Tanaka H., Endoh H., Komatsu H., Tanaka T., Kohno T., Maeda T., Structural role of the secondary active domain of HIV-2 NCp8 in multi-functionality. Biochem. Biophys. Res. Commun., 358, 673-678 (2007)
Matsui T., Kodera Y., Endoh H., Miyauchi E., Komatsu H., Sato K., Tanaka T., Kohno T., Maeda T., RNA recognition mechanism of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. J. Biochem. (Tokyo), 141, 269-277 (2007)
Matsubara H., Ogawa T., Muramoto K., Structures and Functions of C-type Lectins in marine Invertebrates. Tohoku J. Agr. Res., 57, 71-86 (2006)
Shirai T., Shionyu-Mitsuyama C., Ogawa T., Muramoto K., Structure based studies of the adaptive diversification process of congerins. Mol. Divers., 10, 567-573 (2006)
Naganuma T., Ogawa T., Hirabayashi J., Kasai K., Hamiya H., Muramoto K., Isolation, characterization and molecular evolution of a novel pearl shell lectin from a marine bivalve, Pteria penguin. Mol. Divers., 10, 607-618 (2006)
Chijiwa T., Tokunaga E., Ikeda R., Terada K., Ogawa T., Oda-Ueda N., Hattori S., Nozaki M., Ohno M, Discovery of novel [Arg(49)]phospholipase A(2) isozymes from Protobothrops elegans venom and regional evolution of Crotalinae snake venom phospholipase A(2) isozymes in the southwestern islands of Japan and Taiwan. Toxicon, 48, 672-682 (2006)
Konno A., Ogawa T., Muramoto K., Shirai T., Reconstraction of Ancestral Conger Eel Galectins Have Revealed Their Molecular Diversification Process by Accelerated Evolution. Pep. Sci., 2006, 138-139 (2006)
Nakamura O., Matsuoka H., Ogawa T., Muramoto K., Kamiya H., Watanabe H., Opsonic effect of congerin, a mucosal galectin of the Japanese conger, Conger myriaster (Brevoort). Fish Shellfish Immunol., 20, 433-435 (2006)
Ohno Y., Naganuma T., Ogawa T., Muramoto K., Watanabe H., Effect of lectins on the transport of food factors in Caco-2 cell monolayers. J. Agr. Food Chem., 54, 548-553 (2006)
Umetsu, M., Kadota, T., Wang, Z.-Y., Tanaka, Y., Adschiri, T., and Nozawa, T., Selective detection of the dolid-state NMR signals from the bacteriochlorophyll a dimers in a reconstituted light-harvesting 1 complex, Chemistry Letters, 34, 940-941, (2005).
Tanaka, Y., Tsumoto, K., Tanabe, E., Yasutake, Y., Sakai, N., Yao, M., Tanaka, I., and Kumagai, I., Crystal structure of the hypothetical protein ST2072 from Sulfolobus tokodaii. Proteins: Structure, Function, and Bioinformatics, 61, 1127-1131 (2005).
Matsubara H., Kabuto S., Nakahara N., Ogawa T., Muramoto K., Jimbo M., Kamiya H., Structure and possible function of N-glycans of an invertebrate C-type lectin from the acorn barnacle Megabalanus rosa. Fisheries Sci., 71, 931-940 (2005).
Chijiwa T., Abe K., Ogawa T., Nikandrov N.N., Hattori S., Oda-Ueda N., Ohno M., Amino acid sequence of a basic aspartate-49-phospholipase A2 from Trimeresurus flavoviridis venom and phylogenetic analysis of Crotalinae venom phospholipases A2. Toxicon, 46, 185-195 (2005).
Shionyu-Mitsuyama C., Ito Y., Konno A., Miwa Y., Ogawa T., Muramoto K., Shirai T., In vitro evolutionary thermostabilization of congerin II: A limited reproduction of natural protein evolution by artificial selection pressure. J. Mol. Biol., 347, 385-397 (2005).
Adebiyi AP., Jin DH., Ogawa T., Muramoto K., Acid hydrolysis of protein in a microcapillary tube for the recovery of tryptophan. Biosci. Biotechnol. Biochem., 69, 255-257 (2005).
Ogawa T., Chijiwa T., Oda-Ueda N., Ohno M., Molecular diversity and accelerated evolution of C-type lectin-like proteins from snake venom. Toxicon, 45, 1-14 (2005).
Tanaka, Y., Tsumoto, K., Yasutake, Y., Umetsu, M., Yao, M., Fukada, H., Tanaka, I., and Kumagai, I., How oligomerization contributes to the thermostability of an archaeon protein: Protein L-Isoaspartyl-O-methyltransferase from Sulfolobus tokodaii. J. Biol. Chem., 279, 32957-32967 (2004).
Tanaka, Y., Tsumoto, K., Nakanishi, T., Yasutake, Y., Sakai, N., Yao, M., Tanaka, I., and Kumagai, I., Structural implications for heavy metal-induced reversible assembly and aggregation of a protein: the case of Pyrococcus horikoshii CutA. FEBS Letters, 556, 167-174 (2004).
Tanaka, Y., Tsumoto, K., Umetsu, M., Nakanishi, T., Yasutake, Y., Sakai, N., Yao, M., Tanaka, I., Arakawa, T., and Kumagai, I., Structural evidence for guanidine- protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3M guanidine hydrochloride. Biochem. Biophys. Res. Commun., 323, 185-191 (2004).
Tajika, Y., Sakai, N., Tanaka, Y., Yao, M., Watanabe, N., and Tanaka, I., Crystal structure of conserved protein PH1136 from Pyrococcus horikoshii. Proteins: Structure, Function, and Bioinformatics, 55, 210-213 (2004).
Umetsu, M., Tsumoto, K., Ashish, K., Nitta, S., Tanaka, Y., Adschiri, T., and Kumagai, I., Structural characteristics and refolding of in vivo aggregated hyperthermophilic archaeon proteins. FEBS Letters, 557, 49-56 (2004).
Ohno Y., Naganuma T., Ogawa T., Muramoto K., Effect of lectins on the transport of food ingredients in Caco-2 cell cultures. Biofactors, 21, 399-401 (2004).
Kimura T., Nakano T., Yamaguchi T., Sato M., Ogawa T., Muramoto K., Yokoyama T., Kan-no N., Nagahisa E., Janssen F., Grieshaber MK., Complementary DNA cloning and molecular evolution of opine dehydrogenases in some marine invertebrates. Marine Biotechnol., 6, 493-502 (2004).
Hayashi MAF., Ligny-Lemaire C., Wollberg Z., Wery M., Galat A., Ogawa T., Muller BH., Lamthanh H., Doljansky Y., Bdolah A., Stocklin R., Ducancel F., Long-sarafotoxins: characterization of a new family of endothelin-like peptides. Peptides, 25, 1243-1251 (2004).
Gaidamashvili M., Ohizumi Y., Iijima S., Takayama T., Ogawa T., Muramoto K., Characterization of the yam tuber storage proteins from Dioscorea batatas exhibiting unique lectin activities. J. Biol. Chem., 279, 26028-26035 (2004).
Yoshimi K., Shoji M., Ogawa T., Yamauchi A., Naganuma T., Muramoto K., Hanada S., Microstructure and orientation distribution of aragonite crystals in nacreous layer of pearl shells. Materials Transactions, 45, 999-1004 (2004).
Ogawa T., Shirai T., Shionyu-Mitsuyama C., Yamane T., Kamiya H., Muramoto K., The speciation of conger eel galectins by rapid adaptive evolution. Glycoconjugate J., 19, 451-458 (2004).
Ogawa T., Shirai T., Lectin Methods and Protocols Part4, Method in Molecular Biology: Tracing Ancestral Specificity of Lectins: Ancestral Sequence Reconstruction Method as a New Approach in Protein Engineering. Humana Press., (2014)
Ogawa T., Shirai T., Protein Engineering -Technology and Application: Experimental molecular archeology: reconstruction of ancestral mutants and evolutionary history of proteins as a new approach in protein engineering. InTech., (2013)
Watanabe Y., Chang YH., Nakamura O., Naganuma T., Ogawa T., Muramoto K., Antitumor potential and other emerging medicinal properties of natural compounds: Lectins of marine origin and their clinical applications. InTech., (2013)