Publications

2024

• Abe K., McDermott J., Madapally H. V., Marimuthu P., Gopalasingam C. C., Gerle C., Shigematsu H., Khandelia H., Blanco G.
  Molecular Structure of the Na⁺,K⁺-ATPase α4β1 Isoform in Its Ouabain-Bound Conformation
  Int. J. Mol. Sci., 25: 12397 (2024) .
• Chimari J., Li J., Moon Y., Tanaka Y., Gopalasingam C. G., Shigematsu H., Chae P. S., Kurisu G., Gerle C.
  NDT-C11 as a viable novel detergent for single particle cryo-EM
  ChemPlusChem, : e202400242 (2024) .
• Ishimaru H., Nishimura M., Shigematsu H., Marini M. I., Hasegawa N., Takamiya R, Iwata S., Mori Y.
  Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein
  J. Virol., 98: 00416-24 (2024) .
• Bokhove M., Kawamura T., Okumura H., Goto S., Kawano Y., Werner S., Jarczowski F., Klimyuk V., Saito A., Kumasaka T.
  The structure of the rat vitamin B₁₂ transporter TC and its complex with glutathionylcobalamin
  J Biol Chem, 5: 107289 (2024) .
• Liao Z., Gopalasingam C. C., Kameya M., Gerle C., Shigematsu H., Ishii M., Arakawa T., Fushinobu S.
  Structural insights into thermophilic chaperonin complexes
  Structure, 32: 679-689 (2024) .
• Nishio S., Emori C., Wiseman B., Fahrenkamp D., Dioguardi E., Zamora-Caballero S., Bokhove M., Han L., Stsiapanava A., Algarra B., Lu Y., Kodani M., Bainbridge R. E., Komondor K. M., Carlson A. E. Landreh M., de Sanctis D., Yasumasu S., Ikawa M., Jovine L.
  ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat
  Cell, 187: 1440-1459 (2024) .
• Yano N., Kondo T., Kusaka K., Arakawa T., Sakamoto T., Fushinobu S.
  Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography
  J Biol Chem, 300: 105774 (2024) .
• Fukuda Y., Lintuluoto M., Kurihara K., Hasegawa K., Inoue T., Tamada T.
  Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography
  Biochemistry, 63: 339-347 (2024) .

2023

• Aoki M., Aoki-Ogata H., Bulut H., Hayashi H., Takamune N., Kishimoto N., Tanaka H., Higashi-Kuwata N., Hattpri S., Das D. Rao K. V., Iwama K., Davis D. A., Hasegawa K., Murayama K., Yarchoan R., Ghosh A., Pau A. K., Machida S., Misumi S., Mitsuya H.
  GRL-142 binds to and impairs HIV-1 integrase nuclear localization signal and potently suppresses highly INSTI-resistant HIV-1 variants
  Science Advances, 9: eadg2955 (2023) .
• Fukui K., Yamamoto T., Murakawa T., Baba S., Kumasaka T., Yano T.
  Catalytic mechanism of the zinc-dependent MutL endonuclease reaction
  Life Science Alliance., 6: e202302001 (2023) .
• Ishimaru H., Nishimura M., Tjan L. H., Sutandhio S., Marini M. I., Effendi G. B., Shigematsu H., Kato K., Hasegawa N., Aoki K., Kurahashi Y., Furukawa K., Shinohara M., Nakamura T.Arii J., Nagano T., Nakamura S., Sano S., Iwata S., Okamura S., Mori Y.
  Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants
  J. Virol., 97: 00286-23 (2023) .
• Higashi-Kuwata N., Tsuji K., Hayashi H., Bulut H., Kiso M., Imai M., Ogata-Aoki H., Ishii T., Kobayakawa T., Nakano K., Takamune N., Kishimoto N., Hattori S., Das D., Uemura Y., Shimizu Y., Aoki M., Hasegawa K., Suzuki S., Nishiyama A., Saruwatari J., Shimizu Y., Sukenaga Y., Takamatsu Y., Tsuchiya K., Maeda K., Yoshimura K., Iida S., Ozono S., Suzuki T., Okamura T., Misumi S., Kawaoka Y., Tamamura H., Mitsuya H.
  Identification of SARS-CoV-2 M^pro inhibitors containing P1’ 4-fluorobenzothiazole moiety highly active against SARS-CoV-2
  Nat. Commun., 14: 1076 (2023) .
• Taguchi S., Niwa S., Dao H.-A., Tanaka Y., Takeda R., Fukai S., Hasegawa K., Takeda K.
  Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin
  Commun. Biol., 6: 190 (2023) .
• Sakaniwa, K, Fujimura A., Shibata T., Shigematsu H., Ekimoto T., Yamamoto M., Ikeguchi M., Miyake K., Ohto U., Shimizu T.
  TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction
  Nat. Commun., 14: 164 (2023) .

2022

• 長谷川 和也, 熊坂 崇
  放射光を用いた室温シリアル結晶構造解析
  日本結晶学会誌, 64(4): 294-299 (2022) .
• 馬場 清喜, 村川 武志
  Humid Air and Glue-coating method（HAG法）を用いた生理学的環境での銅含有アミン酸化酵素の構造解析
  日本結晶学会誌, 64(4): 285-289 (2022) .
• Nishida Y., Yanagisawa S., Morita R., Shigemastu H., Shinzawa-Itoh K., Yuki H., Ogasawara S., Shimuta K., Iwamoto T., Nakabayashi C., Matsumura W., Kato H., Gopalasingam C., Nagao T., Qaqorh T., Takahashi Y., Yamazaki S., Kamiya K., Harada R., Mizuno N., Takahashi H., Akeda Y., Ohnishi M., Ishi Y., Kumasaka T., Muramoto K., Toshia T., Shiro Y., Honma T., Shigeta Y., Kubo M., Takashima S. and Y. Shintani
  Identifying Antibiotics Based on Structural Differences in the Conserved Allostery from Mitochondrial Heme-copper Oxidases
  Nat. Commun., 13: 7591 (2022) .
• Boos J. R., Jandrain H. N., Hagiuda E., Taguchi A. T., Hasegawa K., Fedun B. L., Taylor S. J., Elad S. M., Faber S. E., Kumasaka T., Iwasaki T. and Geldenhuys W. J.
  Structure and biological evaluation of Caenorhabditis elegans CISD-1/mitoNEET, a KLP-17 tail domain homologue, supports attenuation of paraquat-induced oxidative stress through a p38 MAPK-mediated antioxidant defense response
  Adv. Redox Res., 6: 100048 (2022) .
• Taguchi S., Nakano J., Imasaki T., Kita T., Saijo-Hamano Y., Sakai N., Shigematsu H., Okuma H., Shimizu T., Nitta E., Kikkawa S., Mizobuchi S., Niwa S. and Nitta R.
  Structural model of microtubule dynamics inhibition by kinesin-4 from the crystal structure of KLP-12 –tubulin complex
  eLife, 11: e77877 (2022) .
• Inaba S., Saeki Y., Ichikawa M., Kabir A. Md. R., Iwasaki T., Shigematsu H., Kakugo A., Sada K., Tsukazaki T. and Matsuura K.
  Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside
  Science Advances, 8(36): abq3817 (2022) .
• Rose S. L., Baba S., Okumura H.,, Antonyuk S. V., Sasaki D., Hedison T. M., Shanmugam M., Heyes D. J., Scrutton N. S., Kumasaka T., Tosha T., Eady R. R., Yamamoto M. and Hasnain S. S.
  Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases
  Proc Natl Acad Sci USA, 119(30): e2205664119 (2022) .
• Imasaki T., Kikkawa S., Niwa S., Saijo-Hamano Y., Shigematsu H., Aoyama K., Mitsuoka K., Shimizu T., Aoki M., Sakamoto A., Tomabechi Y., Sakai N., Shirouzu M., Taguchi S., Yamagishi Y., Setsu T., Sakihama Y., Nitta E., Takeichi M. and Nitta R.
  SCAMSAP2 organizes a γ-tubulin-independent microtubule nucleation centre through phase separation
  eLife, 11: e77365 (2022) .
• Makino Y., Oe C., Iwama K., Suzuki S., Nishiyama A, Hasegawa K., Okuda H., Hirata K., Ueno M., Kawaji K., Sasano M., Usui E., Hosaka T., Yabuki Y., Shirouzu M., Katsumi M., Murayama K. and Kodama E. N.
  Serine hydroxymethyltransferase as a potential target of antibacterial agents acting synergistically with one-carbon metabolism-related inhibitors
  Commun. Biol., 5: 619 (2022) .
• Okumura H., Sakai N., Murakami H., Mizuno N., Nakamura Y., Ueno G., Masunaga T., Kawamura T., Baba S., Hasegawa K., Yamamoto M. and Kumasaka T.
  In situ crystal data-collection and ligand-screening system at SPring-8
  Acta Cryst., F78(6): 241-251 (2022) .
• Tanaka S., Morita M., Yamagishi T., Madapally H., Hayashida K., Khandelia H., Gerle C., Shigematsu H., Oshima A., and Abe K.
  Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump
  J. Med. Chem., 65(11): 7843-7853 (2022) .
• Asami J., Terakado Kimura K., Fujita-Fujiharu Y., Ishida H., Zhang Z., Nomura Y., Liu K., Uemura T., Sato Y., Ono M., Yamamoto M., Noda T., Shigematsu H., Drew D., Iwata S., Shimizu T., Nomura N. and Ohto U.
  Structure of bile acid transporter NTCP crucial for hepatitis B virus entry
  Nature, 606: 1021-1026 (2022) .
• Fukui K., Inoue M., Murakawa T., Baba S., Kumasaka T. and Yano T.
  Structural and functional insights into the mechanism by which MutS2 recognizes a DNA junction
  Structure, 30(7): 973-982 (2022) .
• Takeda M., Baba S., Okuma J., Hirose Y., Nishimura A., Takata M., Oda K., Shibata D., Kumasaka T. and Kondo Y.
  Metagenomic mining and structure-function studies of a hyper-thermostable cellobiohydrolase from hot spring sediment
  Commun. Biol, 5:247 (2022) .
• 山本 雅貴, 平田 邦生, 長谷川 和也
  SPring-8のタンパク質結晶構造解析
  日本結晶学会誌, 64(1):2-9 (2022) .
• Amano M., Yedidi R. S., Salced-Gómez P. M., Hayashi H., Hasegawa K., Martyr C. D., Ghosh A. K. and Mitsuya H.,
  Fluorine Modifications Contribute to Potent Antiviral Activity against Highly Drug-Resistant HIV-1 and Favorable Blood-Brain Barrier Penetration Property of Novel Central Nervous System-Targeting HIV-1 Protease Inhibitors In Vitro
  Antimicrob Agents Chemother., 66(2):e0171521 (2022) .
• Suzuki R., Baba S., Mizuno N., Hasegawa K., Koizumi H., Kojima K., Kumasaka T. and Tachibana M.
  Radiation-induced defects in protein crystals observed by X-ray topography
  Acta Cryst, D78(2):196-203 (2022) .

2021

• Numoto N., Kawano Y., Okumura H., Baba S., Fukumori Y., Miki. K. and Kondo Y.
  Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state
  IUCrJ, 8(6):954-962 (2021) .
• Baba S., Matsuura H., Kawamura T., Sakai N., Nakamura Y., Kawano Y., Mizuno N., Kumasaka T., Yamamoto M. and Hirata K.
  Guidelines for de novo phasing using multiple small-wedge data collection
  J Synchrotron Radiat,, 28(3):1284-1295 (2021) .
• 馬場 清喜, 水野 伸宏
  SPring-8構造生物学ビームラインにおける最新の自動測定／遠隔測定環境
  日本結晶学会誌,, 63(3):216-218 (2021) .
• Matsumoto S., Taniguchi-Tamura H., Araki M, Kawamura T, Miyamoto R, Tsuda C, Shima F, Kumasaka T, Okuno Y and Kataoka T.
  Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein
  Biochem Biophys Res Commun, 565:85-90 (2021) .
• Nomura T, Kimura T, Kanematsu Y, Yamada D, Yamashita K, Hirata K, Ueno G, Murakami H, Hisano T, Yamagiwa R, Takeda H, Gopalasingam C, Kousaka R, Yanagisawa S, Shoji O, Kumasaka T, Yamamoto M, Takano Y, Sugimoto H, Tosha T, Kubo M and Shiro Y.
  Short-lived intermediate in N₂O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography
  Proc Natl Acad Sci USA, 118(21):e2101481118 (2021).
• Hattori S, Higashi-Kuwata N, Hayashi H, Allu S, Raghavaiah J, Bulut H, Das D, Anson B, Lendy E, Takamatsu Y, Takamune N, Kishimoto N, Murayama K, Hasegawa K, Li M, Davis D, Kodama E, Yarchoan R, Wlodawer A, Misumi S, Mesecar A, Ghosh A and Mitsuya H
  A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication
  Nat Commun, 12:668 (2021).
• Hasegawa K, Baba S, Kawamura T, Yamamoto M and Kumasaka T
  Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method
  Acta Cryst, D77(3):300-312 (2021).

2020

• Nakamura Y, Baba S, Mizuno N, Irie T, Ueno G, Hirata K, Ito S, Hasegawa K, Yamamoto M and Kumasaka T
  Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals
  Acta Cryst, F76(12):616-622 (2020).
• 高場 圭章, 長谷川 和也, 竹田 一旗
  生命科学の飛躍のために一層深まるタンパク質結晶学の役割～タンパク質の超高分解能電荷密度解析
  日本結晶学会誌, 62(2):106-111 (2020).
• Masuda T, Baba S, Matsuo K, Ito S and Mikami B.
  The high-resolution crystal structure of lobster hemocyanin shows its enzymatic capability as a phenoloxidase
  Arch Biochem Biophys, 688:108370 (2020).
• Nakanishi K, Irie K, Segawa K, Hasegawa K, Fujiyoshi Y, Nagata S and Abe K.
  Crystal structure of a human plasma membrane phospholipid flippase
  J Biol Chem, 295(30):10180-10194 (2020).
• Izuhara K, Fukai K, Murakawa T, Baba S, Kumasaka T, Uchiyama K and Yano T
  A Lynch syndrome-associated mutation at a Bergerat ATP-binding fold destabilizes the structure of the DNA mismatch repair endonuclease MutL
  J Biol Chem, 295(33):11643-11655(2020).
• Ohnishi Y, Muraki N, Kiyota D, Okumura H, Baba S, Kawano Y, Kumasaka T, Tanaka H and Kurisu G.
  X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas einhardtii.
  J Biochem, 167(6):549-555 (2020).
• Murakami H, Hasegawa K, Ueno G, Yagi N, Yamamoto M and Kumasaka T.
  Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines.
  Acta Cryst, D76(2):155-165 (2020).

2019

• Suga M, Akita F, Yamashita K, Nakajima Y, Ueno G, Li H, Yamane T, Umena Y, Yonekura S, Yu LJ, Murakami H, Nomura T, Kimura T, Kubo M, Baba S, Kumasaka T, Tono K, Yabashi M, Isobe H, Yamaguchi K, Yamamoto M, Ago H and, Shen JR.
  An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.
  Science, 366(6463):334-338 (2019).
• Baba S, Shimada A, Mizuno N, Baba J, Ago H, Yamamoto M and Kumasaka T.
  A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method.
  J Appl Cryst, 52(4):699-705 (2019).
• Ueno G, Shimada A, Yamashita E, Hasegawa K, Kumasaka T, Shinzawa-Itoh K, Yoshikawa S, Tsukihara T and Yamamoto M.
  Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays.
  J Synchrotron Radiat, 26(4):912-921 (2019).
• Takaba K, Tai Y, Eki H, Dao HA, Hanazono Y, Hasegawa K, Miki K and, Takeda K.
  Subatomic resolution X-ray structures of green fluorescent protein.
  IUCrJ, 6(3):387-400 (2019).
• Amano M, Salcedo-Gómez PM, Yedidi RS, Zhao R, Hayashi H, Hasegawa K, Nakamura T, Martyr CD, Ghosh AK and Mitsuya H.
  Novel Central Nervous System (CNS)-Targeting Protease Inhibitors for Drug-Resistant HIV Infection and HIV-Associated CNS Complications.
  Antimicrob Agents Chemother., 63(7):e00466-19 (2019).
• Hattori SI, Hayashi H, Bulut H, Rao KV, Nyalapatla PR, Hasegawa K, Aoki M, Ghosh AK and, Mitsuya H.
  Halogen Bond Interactions of Novel HIV-1 Protease Inhibitors (PI) (GRL-001-15 and GRL-003-15) with the Flap of Protease Are Critical for Their Potent Activity against Wild-Type HIV-1 and Multi-PI-Resistant Variants.
  Antimicrob Agents Chemother., 63(6):e02635-18 (2019).
• Hirata K, Yamashita K, Ueno G, Kawano Y, Hasegawa K, Kumasaka T and Yamamoto M.
  ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography.
  Acta Cryst, D75(2):138-150 (2019).
• Baba S, Mizuno N, Okumura H, Nuemket N, Hasegawa K, Nakamura Y, Murakami H, Ueno G, Fukui T, Irie T, Tanaka M, Yamazaki H, Ohashi H, Yamamoto M, and Kumasaka T.
  Upgrade of bending magnet MX beamline BL38B1 at SPring-8.
  AIP Conf Proc, 2054, 060008 (2019).
• Murakawa T, Baba S, Kawano Y, Hayashi H, Yano T, Kumasaka T, Yamamoto M, Tanizawa K and, Okajima T.
  In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase.
  Proc Natl Acad Sci USA, 116(1):135-140 (2019).

2018

• 熊坂 崇, 馬場 清喜, 河村 高志
  結晶調湿Ｘ線回折法と 室温測定の再評価.
  日本結晶成長学会誌, 45(4):3-45-4-02 (2018).
• Makino M, Matsubayashi K, Kodama-Oda Y, Imawaka N, Mizuno N, Kumasaka T and Yoshino K.
  Construction of a supra­molecule comprising [2,3,9,10,16,17,23,24-octa­kis­(2,6-di­methyl­phen­oxy)phthalocyaninato]zinc(II) and (5,10,15,20-tetra­phenyl­porphyrinato)zinc(II)
  IUCrData, 3, x181741 (2018).
• Qiu B, Xia B, Zhou Q, Lu Y, He M, Hasegawa K, Ma Z, Zhang F, Gu L, Mao Q, Wang F, Zhao S, Gao Z, Liao J.
  Succinate-acetate permease from Citrobacter koseri is an anion channel that unidirectionally translocates acetate.
  Cell Res, 28(6):644–654 (2018).
• Fukui K, Baba S, Kumasaka T, Yano T.
  Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus.
  FEBS Lett, 592(9):1611-1619 (2018).
• Suzuki R, Koizumi H, Hirano K, Kumasaka T, Kojima K and Tachibana M
  Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals.
  PNAS, 115(14):3634-3639 (2018).
• Taguchi AT, Miyajima-Nakano Y, Fukazawa R, Lin MT, Baldansuren A, Gennis RB, Hasegawa K, Kumasaka T, Dikanov SA, Iwasaki T.
  Unpaired Electron Spin Density Distribution across Reduced [2Fe-2S] Cluster Ligands by 13Cβ-Cysteine Labeling.
  Inorg Chem, 57(2):741-746 (2018).

2017

• Yu X, Yang G, Yan C, Baylon JL, Jiang J, Fan H, Lu G, Hasegawa K, Okumura H, Wang T, Tajkhorshid E, Li S, Yan N.
  Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters.
  Cell Res, 27(8):1020-1033. (2017).
• Aoki M, Hayashi H, Rao KV, Das D, Higashi-Kuwata N, Bulut H, Aoki-Ogata H, Takamatsu Y, Yedidi RS, Davis DA, Hattori SI, Nishida N, Hasegawa K, Takamune N, Nyalapatla PR, Osswald HL, Jono H, Saito H, Yarchoan R, Misumi S, Ghosh AK, Mitsuya H
  A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency.
  eLife, 6:e28020 (2017).
• Hasegawa K, Someya Y, Shigematsu H, Kimura-Someya T, Nuemket N and Kumasaka T.
  Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain
  Acta Cryst, F73:568-573 (2017).
• Hashimoto T, Hanajiri R, Yasuda N, Nakamura Y, Mizuno N, Honda S, Hayakawa S, Nishiwaki Y and Kimura S.
  Single-crystal structure analysis of designer drugs circulating in the Japanese drug market by the synchrotron radiation X-ray diffraction
  Powder Diffr, 32:112-117 (2017).
• Yamamoto M, Hirata K, Yamashita K, Hasegawa K, Ueno G, Ago H and Kumasaka T.
  Protein microcrystallography using synchrotron radiation
  IUCrJ, 4:529-539 (2017).
• Kaneko A, Uenishi K, Maruyama Y, Mizuno N, Baba S, Kumasaka T, Mikami B, Murata K, Hashimoto W.
  A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate.
  J Biol Chem, 292:15681-15690 (2017).
• Matsunaga S, Hano Y, Saito Y, Fujimoto JK, Kumasaka T, Matsumoto S, Kataoka T, Shima F, Tanaka S.
  Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy
  J Mol Graph Model, 77:51-63 (2017).
• Ke H, Matsumoto S, Murashima Y, Taniguchi-Tamura H, Miyamoto R, Yoshikawa Y, Tsuda C, Kumasaka T, Mizohata E, Edamatsu H, Kataoka T.
  Structural basis for intramolecular interaction of posttranslationally modified H-Ras•GTP prepared by protein ligation.
  FEBS Lett,591:2470-2481 (2017).
• Shimada A, Kubo M, Baba S, Yamashita K, Hirata K, Ueno G, Nomura T, Kimura T, Shinzawa-Itoh K, Baba J, Hatano K, Eto Y, Miyamoto A, Murakami H, Kumasaka T, Owada S, Tono K, Yabashi M, Yamaguchi Y, Yanagisawa S, Sakaguchi M, Ogura T, Komiya R, Yan J, Yamashita E, Yamamoto M, Ago H, Yoshikawa S, Tsukihara T.
  A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
  Sci Adv, 3:e1603042 (2017).
• Fukui K, Iino H, Baba S, Kumasaka T, Kuramitsu S, Yano T.
  Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus.
  Biochim Biophys Acta, 1865:1178-1187 (2017).
• Nuemket N, Yasui N, Kusakabe Y, Nomura Y, Atsumi N, Akiyama S, Nango E, Kato Y, Kaneko MK, Takagi J, Hosotani M, Yamashita A.
  Structural basis for perception of diverse chemical substances by T1r taste receptors.
  Nat Commun, 8:15530 (2017).
• Norimatsu Y, Hasegawa K, Shimizu N, Toyoshima C.
  Protein-phospholipid interplay revealed with crystals of a calcium pump.
  Nature, 545:193-198 (2017).
• Inoguchi N, Mizuno N, Baba S, Kumasaka T, Natarajan C, Storz JF, Moriyama H.
  Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice.
  PLoS One, 12(3):e0174921 (2017).
• Yorinaga Y, Kumasaka T, Yamamoto M, Hamada K, Kawamukai M.
  Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.
  FEBS Lett, 591(3):540-547 (2017).
• Hasegawa K, Yamashita K, Murai T, Nuemket N, Hirata K, Ueno G, Ago H, Nakatsu T, Kumasaka T, Yamamoto M.
  Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography.
  J Synchrotron Radiat, 24(Pt 1):29-41 (2017).
• Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T.
  Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b.
  Biophys Chem, 221:41-48 (2017).

2016

• Tsuboi C, Tsukui S, Kimura F, Kimura T, Hasegawa K, Baba S and Mizuno N.
  X-ray diffraction from magnetically oriented microcrystal suspensions detected by a shutterless continuous rotation method
  J Appl Cryst, 49:2100-2105 (2016).
• Fujita D, Yoshihiro U, Sato S, Mizuno N, Kumasaka T and Fujita M.
  Self-assembly of tetravalent Goldberg polyhedra from 144 small components.
  Nature, 540:563-566 (2016).
• Watanabe Y, Yanai H, Kanagawa M, Suzuki S, Tamura S, Okada K, Baba S, Kumasaka T, Agari Y, Chen L, Fu Z Q, Chrzas J, Wang B C, Nakagawa N, Ebihara A, Masui R, Kuramitsu S, Yokoyama S, Sampei G and Kawai G.
  Crystal structures of a subunit of the formyl­glycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii
  Acta Cryst, F72:627-635 (2016).
• Tsukui S, Kimura F, Garman E F, Baba S, Mizuno N, Mikami B and Kimura T.
  X-ray crystal structure analysis of magnetically oriented microcrystals of lysozyme at 1.8 Å resolution
  J Appl Cryst, 49:457-461 (2016).
• Tsukui S, Kimura F, Kusaka K, Baba S, Mizuno N, Kimura T.
  Neutron and X-ray single-crystal diffraction from protein microcrystals via magnetically oriented microcrystal arrays in gels.
  Acta Cryst, D72:823-829 (2016).
• Fujita D, Ueda Y, Sato S, Yokoyama H, Mizuno N, Kumasaka T, Fujita M.
  Self-Assembly of M30L60 Icosidodecahedron.
  Chem, 1:91-101 (2016).
• Fukui K, Baba S, Kumasaka T, Yano T.
  Structural features and functional dependency on β-clamp define distinct sub-families of bacterial mismatch repair endonuclease MutL.
  J Biol Chem, 291:16990-17000 (2016).
• Nango E, Akiyama S, Maki-Yonekura S, Ashikawa Y, Kusakabe Y, Krayukhina E, Maruno T, Uchiyama S, Nuemket N, Yonekura K, Shimizu M, Atsumi N, Yasui N, Hikima T, Yamamoto M, Kobayashi Y, Yamashita A.
  Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains.
  Sci Rep, 6:25745 (2016).
• Matsumoto S, Miyano N, Baba S, Liao J, Kawamura T, Tsuda C, Takeda A, Yamamoto M, Kumasaka T, Kataoka T, Shima F.
  Molecular Mechanism for Conformational Dynamics of Ras•GTP Elucidated from In-Situ Structural Transition in Crystal.
  Sci Rep, 6:25931 (2016).
• Kanagawa M, Baba S, Watanabe Y, Nakagawa N, Ebihara A, Kuramitsu S, Yokoyama S, Sampei G, Kawai G.
  Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus.
  J Biochem, 159:313-21 (2016).

2015

• Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T.
  Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming.
  Biochem Biophys Res Commun, 464:929-935 (2015).
• Mizuno N, Nishibori E, Oka M, Jomori T, Takata M, Kumasaka T.
  Structural basis for polymer packing and solvation properties of the organogermanium crystalline polymers, propagermanium and its derivatives.
  J Pharm Sci, 104:2482-2488 (2015).
• Teh A-H, Makino M, Hoshino T, Baba S, Shimizu N, Yamamoto M, Kumasaka T.
  Structure of RsbX Phosphatase in General Stress Response of Bacillus subtilis.
  Acta Cryst, D71:1392-1399 (2015).

2014

• Kobayashi J, Yoshikane Y, Yagi T, Baba S, Mizutani K, Takahashi N, Mikami B.
  Structure of 4-pyridoxolactonase from Mesorhizobium loti.
  Acta Cryst, F70:424-432 (2014).
• 島 扶美, 熊坂 崇, 松本 篤幸, 吉川 陽子, 山本 雅貴, 片岡 徹
  rasがん遺伝子産物の新規立体構造情報を利用した分子標的がん治療薬の開発
  放射光, 27(1):3-9 (2014)
• 馬場 清喜, 熊坂 崇
  湿度調節と水溶性ポリマーのコーティングを用いたタンパク質結晶マウント法
  日本結晶学会誌, 56:194-200 (2014)

2013

• Sampei G, Kanagawa M, Baba S, Shimasaki T, Taka H, Mitsui S, Fujiwara S, Yanagida Y, Kusano M, Suzuki S, Terao K, Kawai H, Fukai Y, Nakagawa N, Ebihara A, Kuramitsu S, Yokoyama S, Kawai G.
  Structures and reaction mechanisms of the two related enzymes, PurN and PurU.
  J Biochem, 154:569-579 (2013).
• Shimizu N, Shimizu T, Baba S, Hasegawa K, Yamamoto M, Kumasaka T.
  Development of an online UV-visible microspectrophotometer for the macromolecular crystallography beamline.
  J Sync Rad, 20:948-952 (2013).
• Hasegawa K, Shimizu N, Okumura H, Mizuno N, Baba S, Hirata K, Takeuchi T, Yamazaki H, Senba Y, Ohashi H, Yamamoto M, Kumasaka T.
  SPring-8 BL41XU, a high-flux macromolecular crystallography beamline.
  J Sync Rad, 20:910-913 (2013).
• Mizuno N, Makino M, Kumasaka T.
  A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals.
  J Sync Rad, 20:999-1002 (2013).
• Baba S, Hoshino T, Ito L, Kumasaka T.
  Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments.
  Acta Cryst, D69:1839-1849 (2013).
• Shima F, Yoshikawa Y, Ye M, Araki M, Matsumoto S, Liao J, Hu L, Sugimoto T, Ijiri Y, Takeda A, Nishiyama Y, Sato C, Muraoka S, Tamura A, Osoda T, Tsuda KI, Miyakawa T, Fukunishi H, Shimada J, Kumasaka T, Yamamoto M, Kataoka T.
  In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction.
  Proc Natl Acad Sci USA, 110:8182-8187 (2013).
• Takei T, Hasegawa K, Imada K, Namba K, Tsumoto K, Kuriki Y, Yoshino M, Yazaki K, Kojima S, Takei T, Ueda T, Miura K.
  Effects of Chain Length of an Amphipathic Polypeptide Carrying the Repeated Amino Acid Sequence (LETLAKA)n on α-Helix and Fibrous Assembly Formation.
  Biochemistry, 52:2810-2820 (2013).
• Kato N, Suzuki H, Okumura H, Takahashi S, Osada H.
  A point mutation in ftmD blocks the fumitremorgin biosynthetic pathway in Aspergillus fumigatus strain Af293.
  Biosci Biotechnol Biochem, 77:1061-1067 (2013).
• 水野 伸宏, 藤田 大士, 佐藤 宗太, 熊坂 崇, 藤田 誠, 高田 昌樹
  MEMによるターゲット構造可視化法の開発: タンパク質を封じ込めた人工カプセルの合成と構造決定
  日本結晶学会誌, 55(3):211-217 (2013).

2012

• Iwasaki T, Fukazawa R, Miyajima-Nakano Y, Baldansuren A, Matsushita S, Lin MT, Gennis RB, Hasegawa K, Kumasaka T, Dikanov SA.
  Dissection of hydrogen bond interaction network around an iron-sulfur cluster by site-specific isotope labeling of hyperthermophilic archaeal Rieske-type ferredoxin.
  J Am Chem Soc, 134:19731-19738 (2012).
• Fujita D, Suzuki K, Sato S, Yagi-Utsumi M, Yamaguchi Y, Mizuno N, Kumasaka T, Takata M, Noda M, Uchiyama S, Kato K, Fujita M.
  Protein encapsulation within synthetic molecular hosts.
  Nat Commun, 3:1093 (2012).
• Fukakusa S, Kawahara K, Nakamura S, Iwashita T, Baba S, Nishimura M, Kobayashi Y, Honda T, Iida T, Taniguchi T, Ohkubo T.
  Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 A resolution by sulfur-SAD phasing.
  Acta Cryst, D68:1418-1429 (2012).
• Ito L, Okumura M, Tao K, Kasai Y, Tomita S, Oosuka A, Yamada H, Shibano T, Shiraki K, Kumasaka T, Yamaguchi H.
  Glutathione Ethylester, a Novel Protein Refolding Reagent, Enhances both the Efficiency of Refolding and Correct Disulfide Formation.
  Protein J, 31:499-503 (2012).
• Makino M, Wada I, Mizuno N, Hirata K, Shimizu N, Hikima T, Yamamoto M, Kumasaka T.
  Fine-needle capillary mounting for microcrystals.
  J Appl Cryst, 45:785-788 (2012).
• Zhang X, Ren W, DeCaen P, Yan C, Tao X, Tang L, Wang J, Hasegawa K, Kumasaka T, He J, Wang J, Clapham DE, Yan N.
  Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel.
  Nature, 486:130-134 (2012).
• Muraoka S, Shima F, Araki M, Inoue T, Yoshimoto A, Ijiri Y, Seki N, Tamura A, Kumasaka T, Yamamoto M, Kataoka T.
  Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants.
  FEBS Lett, 586:1715-1718 (2012).
• Murakami H, Ueno, G, Shimizu N, Kumasaka T, Yamamoto M.
  Upgrade of automated sample exchanger SPACE.
  J Appl Cryst, 45:234-238 (2012).
• Hashimoto S, Ito L, Okumura M, Shibano T, Nawata M, Kumasaka T, Yamaguchi H, Imaoka S.
  Crystallization and preliminary crystallographic analysis of the complex between triiodothyronine and the bb' fragment of rat protein disulfide isomerase.
  Acta Cryst, F68:476-8 (2012).
• Suzuki S, Yanai H, Kanagawa W, Tamura S, Watanabe Y, Fuse K, Baba S, Sampei G, Kawai G.
  Structure of N-formylglycinamide ribonucleotide aminotransferase II (PurL) from Thermus thermophilus HB8.
  Acta Cryst, F68:14-9 (2012).
• Someya T, Baba S, Fujimoto M, Kawai G, Kumasaka T, Nakamura K.
  Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq.
  Nucleic Acids Res, 40:1856-67 (2012).

2011

• Lin MT, Sperling LJ, Frericks Schmidt HL, Tang M, Samoilova RI. Kumasaka, T., Iwasaki, T., Dikanov, SA., Rienstra, CM., Gennis, RB.
  A rapid and robust method for selective isotope labeling of proteins.
  Methods, 55:370-8 (2011).
• Nango E, Yamamoto T, Kumasaka T, Eguchi T.
  Structure of Thermus thermophilus Homoisocitrate Dehydrogenase in Complex with a Designed Inhibitor.
  J Biochem, 150:607-14 (2011).
• Someya Y, Shirato H, Hasegawa K, Kumasaka T, Takeda N.
  Assembly of Homogeneous Norovirus-like Particles Accomplished by Amino Acid Substitution.
  J Gen Virol, 92:2320-3 (2011).
• Iwasaki T, Kappl R, Bracic G, Shimizu N, Ohmori D, Kumasaka T.
  ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization.
  J Biol Inorg Chem, 16(6):923-35 (2011).
• Ohnuma M, Ganbe T, Terui Y, Niitsu M, Sato T, Tanaka N, Tamakoshi M, Samejima K, Kumasaka T, Oshima T.
  Crystal structures and enzymatic properties of triamine/agmatine aminopropyltransferase from Thermus thermophilus.
  J Mol Biol, 408(5):971-86 (2011).
• Matsumoto K, Shima F, Muraoka S, Araki M, Hu L, Ijiri Y, Hirai R, Liao J, Yoshioka T, Kumasaka T, Yamamoto M, Tamura A, Kataoka T.
  Critical roles of interactions among switch I-preceding residues and between switch II and its neighboring {alpha}-helix on conformational dynamics of the GTP-bound Ras family small GTPases.
  J Biol Chem, 286(17):15403-12 (2011).
• Yazawa R, Takakura J, Sakata T, Ihsanawati, Yatsunami R, Fukui T, Kumasaka T, Tanaka N, Nakamura S.
  A Calcium-Dependent Xylan-Binding Domain of Alkaline Xylanase from Alkaliphilic Bacillus sp. Strain 41M-1.
  Biosci Biotechnol Biochem, 75(2):379-81 (2011).
• Ito L, Shiraki K, Makino M, Hasegawa K, Kumasaka T.
  Glycine amide shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation
  FEBS Letter, 585(3):555-60 (2011).
• Makino M, Sawai H, Shiro Y, Sugimoto H.
  Crystal structure of the carbon monoxide complex of human cytoglobin
  Proteins: Structure, Function, and Bioinformatics, 79(4):1143-53 (2011).
• Ito L, Shiraki K, Matsuura T, Okumura M, Hasegawa K, Baba S, Yamaguchi H, Kumasaka T.
  High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine.
  Protein Eng Des Sel, 24(3):269-74 (2011).
• Hoshino T, Nango E, Baba S, Eguchi T, Kumasaka T.
  Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii
  Acta Cryst, F67:101-103 (2011).

2010

• Tomita S, Ito L, Yamaguchi H, Konishi G, Nagasaki Y, Shiraki K.
  Mechanism of on-off switch for enzyme by complementary polymer pair system (CPPS)
  Soft Matter, 6:5320-5326 (2010).
• Ito L, Shiraki K, Uchida T, Okumura M, Yamaguchi H.
  Crystallization and preliminary crystallographic analysis of Achromobacter protease I mutants.
  Acta Cryst, F66:1531-1532 (2010).
• Sampei GI, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G.
  Crystal Structures of Glycinamide Ribonucleotide Synthetase, PurD, from Thermophilic Eubacteria.
  J Biochem, 148(4):429-38 (2010).
• Kanagawa M, Baba S, Ebihara A, Shinkai A, Hirotsu K, Mega R, Kim K, Kuramitsu S, Sampei G, Kawai G.
  Structures of hypoxanthine-guanine phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8.
  Acta Cryst, F66:893-898 (2010).
• Kounosu A, Hasegawa K, Iwasaki T, Kumasaka T.
  Crystallization and preliminary X-ray diffraction studies of hyperthermophilic archaeal Rieske-type ferredoxin (ARF) from Sulfolobus solfataricus P1.
  Acta Cryst, F66:842-845 (2010).
• Nishida Y, Ishikawa H, Baba S, Nakagawa N, Kuramitsu S, Masui R.
  Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii.
  Proteins, 78(10):2395-8 (2010).
• Ito L, Shiraki K, Yamaguchi H.
  Amino acids and glycine ethyl ester as new crystallization reagents for lysozyme.
  Acta Cryst, F66:750-4 (2010).
• Ito L, Shiraki K, Yamaguchi H.
  Comparative analysis of amino acids and amino-acid derivatives in protein crystallization.
  Acta Cryst, F66:744-9 (2010).
• Shima F, Ijiri Y, Muraoka S, Liao J, Ye M, Araki M, Matsumoto K, Yamamoto N, Sugimoto T, Yoshikawa Y, Kumasaka T, Yamamoto M, Tamura A, Kataoka T.
  Structural basis for conformational dynamics of GTP-bound Ras protein.
  J Biol Chem, 285(29):22696-705 (2010).
• Kumasaka T, Shimizu N, Baba S, Hasegawa K, Ueno G, Yamamoto M.
  SPring-8 structural biology beamline
  Yakugaku Zasshi, 130(5):649-55. (2010).
• Baba S, Someya T, Kawai G, Nakamura K, Kumasaka T.
  Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.
  Acta Cryst, F66:563-6 (2010).
• 清水 伸隆, 上野 剛, 長谷川 和也, 河本 正秀
  タンパク質X線結晶構造解析の測定戦略
  生物物理, 50:306-307 (2010).
• 熊坂 崇, 清水 伸隆, 馬場 清喜, 長谷川 和也, 上野 剛, 山本 雅貴
  SPring-8構造生物ビームライン
  薬学雑誌, 130:649-655 (2010).

2009

• Suganuma M, Teh A H, Makino M, Shimizu N, Kaneko T, Hirata K, Yamamoto M, Kumasaka T.
  Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis.
  Acta Cryst, F65:1128-30 (2009).
• Hasegawa K, Hirata K, Shimizu T, Shimizu N, Hikima T, Baba S, Kumasaka T Yamamoto M.
  Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography.
  J Appl Cryst, 42:1165-1175 (2009).
• Nango E, Yamamoto T, Kumasaka T, Eguchi T.
  Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor.
  Bioorg. Med Chem, 17:7789-94 (2009).
• Matsuda S, Yokochi N, Yoshikane Y, Kobayashi J, Huy C N, Baba S, Kuramitsu S, Mikami B, Yagi T.
  Crystallization and preliminary X-ray analysis of 4-pyridoxolactonase from Mesorhizobium loti.
  Acta Cryst, F65:886-889 (2009).
• Kumasaka T, Aritake K, Ago H, Irikura D, Tsurumura T, Yamamoto M, Miyano M, Urade Y, Hayaishi O.
  Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin-type prostaglandin D synthase.
  J Biol Chem, 284:22344-22352 (2009).
• Abe S, Hirata K, Ueno T, Morino K, Shimizu N, Yamamoto M, Takata M, Yashima E, Watanabe Y.
  Polymerization of Phenylacetylene by Rhodium Complexes within a Discrete Space of apo-Ferritin.
  J Am Chem Soc, 131:6958-60 (2009).
• Wang Y, Chen H, Makino M, Shiro Y, Nagano S, Asamizu S, Onaka H, Shaik S.
  Theoretical and Experimental Studies of the Conversion of Chromopyrrolic Acid to an Antitumor Derivative by Cytochrome P450 StaP: The Catalytic Role of Water Molecules.
  J Am Chem Soc, 131:6748-62 (2009).
• Makino M, Kondo S, Keneko T, Baba S, Hirata K, Kumasaka T.
  Expression, crystallization and preliminary crystallographic analysis of the PAS domain of RsbP, a stress-response phosphatase from Bacillus subtilis.
  Acta Cryst, F65:559-561 (2009).
• Yamaguchi S, Kamikubo H, Kurihara K, Kuroki R, Niimura N, Shimizu N, Yamazaki Y, Kataoka M.
  Low-barrier hydrogen bond in photoactive yellow protein.
  Proc Natl Acad Sci USA, 106:440-4 (2009).
• Tsuchiya D, Shimizu N, Tomita M.
  Cooperativity of two active sites in bacterial homodimeric aconitases.
  Biochem Biophys Res Commun, 379:485-488 (2009).
• Ueno T, Abe M, Hirata K, Abe S, Suzuki M, Shimizu N, Yamamoto M, Takata M, Watanabe Y.
  Process of accumulation of metal ions on the interior surface of apo-ferritin: crystal structures of a series of apo-ferritins containing variable quantities of Pd(II) ions.
  J Am Chem Soc, 131:5094-5100 (2009).
• 平田 邦生, 清水 伸隆, 上野 剛, 熊坂 崇, 山本 雅貴
  蛋白質微小結晶構造解析：その極限でめざすもの
  蛋白質核酸酵素, 54:1477-1483 (2009).

2008

• Nakasako M, Hirata M, Shimizu N, Hosokawa S, Matsuoka D, Oka T, Yamamoto M and Tokutomi S.
  Crystallization and preliminary X-ray diffraction anaylsis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana.
  Acta Cryst, F64:617-621(2008).
• Tsuchiya D, Shimizu N, Tomita M.
  Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase.
  Biochim Biophys Acta, 1784:1847-56 (2008).
• Kounosu A, Iwasaki T, Baba S, Hayashi-Iwasaki Y, Oshima T, Kumasaka T.
  Crystallization and preliminary X-ray diffraction studies of the prototypal homologue of mitoNEET (Tth-NEET0026) from the extreme thermophile Thermus thermophilus HB8.
  Acta Cryst, F64:1146-1148 (2008).
• Teh A-H, Kanamasa S, Kajiwara S, Kumasaka T.
  Structure of Cu/Zn superoxide dismutase from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6.
  Biochem Biophys Res Commun, 374:475-478 (2008).
• Nango E, Minami A, Kumasaka T, Eguchi T.
  Crystallization and preliminary X-ray analysis of vicenisaminyltransferase VinC.
  Acta Cryst, F64:558-560 (2008).
• Okazaki N, Hasegawa K, Ueno G, Murakami H, Kumasaka T, Yamamoto M.
  Mail-in data collection at SPring-8 protein crystallography beamlines.
  J Synchrotron Rad, 15:288-291 (2008).
• Nango E, Kumasaka T, Hirayama T, Tanaka N, Eguchi T.
  Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptaimine-containing aminoglycoside antibiotics, in complexed with a mechanism-based inhibitor and NAD+.
  Proteins, 70:517-527 (2008).
• 河本 正秀, 清水 伸隆, 馬場 清喜, 平田 邦生, 石地 耕太朗, 隅谷 和嗣, 本島 浩之, 岡島 敏浩, 熊坂 崇, 渡邉 啓一, 山本 雅貴
  SAGA-LSにおけるタンパク質結晶の長波長X線回折実験の試み
  放射光, 21:194-203 (2008).

2007

• Kumasaka T, Yamamoto M, Furuichi M, Nakasako M, Teh A-H, Kimura M, Yamaguchi I, Ueki T.
  Crystal structures of Blasticidin S Deaminase (BSD): Implications for dynamic properties of catalytic zinc.
  J Biol Chem, 282:37103-37111 (2007).
• Iwasaki T, Ohmori D, Shimizu N, Kumasaka T.
  Crystallization and preliminary X-ray diffraction studies of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004.
  Acta Cryst, F63:1014-1016 (2007).
• Ten-i T, Kumasaka T, Higuchi W, Tanaka S, Yoshimatsu K, Fujiwara T, Sato T.
  Expression, purification, crystallization and preliminary X-ray analysis of Met244Ala variant of catalase-peroxidase (KatG) from the haloarchaeon, Haloarcula marismortui.
  Acta Cryst, F63:940-943 (2007).
• Kanaujia S P, Ranjani C V, Jeyakanthan J, Nishida M, Kitamura Y, Baba S, Ebihara A, Shimizu N, Nakagawa N, Shinkai A, Yamamoto M, Kuramitsu S, Shiro Y, Sekar K, Yokoyama S.
  Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8.
  Acta Cryst, F63:446-8 (2007).
• Fibriansah G, Masuda S, Koizumi N, Nakamura S, Kumasaka T.
  The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.
  Proteins, 69:683-690 (2007).
• Shimizu N, Hirata K, Hasegawa K, Ueno G, Yamamoto M.
  Dose dependence of radiation damage for protein crystals studied at various X-ray energies.
  J Synchrotron Rad, 14:4-10 (2007).
• Kamikubo H, Shimizu N, Harigai M, Yamazaki Y, Imamoto Y, Kataoka M.
  Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering.
  Biophys J, 92:3633-42 (2007).
• Yamaguchi S, Kamikubo H, Shimizu N, Yamazaki Y, Imamoto Y, Kataoka M.
  Preparation of large crystals of photoactive yellow protein for neutron diffraction and high resolution crystal structure analysis.
  Photochem Photobiol, 83:336-8 (2007).
• Kanamasa S, Sumi K, Yamuki N, Kumasaka T, Miura T, Abe F, Kajiwara S.
  Cloning and functional characterization of the copper/zinc superoxide dismutase gene from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6.
  Mol Genet Genomics, 277:403-12 (2007).

-2006

• Shimizu N, Kamikubo H, Yamazaki Y, Imamoto Y, Kataoka M.
  The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein.
  Biochemistry, 45:3542-7 (2006).
• Ye M, Shima F, Muraoka S, Liao J, Okamoto H, Yamamoto M, Tamura A, Yagi N, Ueki T, Kataoka T.
  Crystal Structure of M-Ras Reveals a GTP-bound "Off" State Conformation of Ras Family Small GTPases.
  J Biol Chem, 280:31267-31275 (2005).
• Ueno G, Kanda H, Kumasaka T, Yamamoto M.
  Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8.
  J Synchrotron Rad, 12:380-384 (2005).
• Yagi N, Yamamoto M, Uesugi K, Inoue K.
  CMOS Imaging Detectors as X-ray Detectors for Synchrotron Radiation Experiments.
  AIP Conference Proc, 705:885-888 (2004).
• Kishimoto A, Hasegawa K, Suzuki H, Taguchi H, Namba K, Yoshida M.
  beta-Helix is a likely core structure of yeast prion Sup35 amyloid fibers..
  Biochem Biophys Res Commun, 315:739-45 (2004).
• Ueno G, Hirose R, Ida K, Kumasaka T, Yamamoto M.
  Sample management system for a vast amount of frozen crystals at SPring-8.
  J Appl Cryst, 37:867-873 (2004).
• Takeda K, Miyatake H, Park S-Y, Kawamoto M, Kamiya N, Miki K.
  Multi-wavelength Anomalous Diffraction Method for I and Xe Atoms Using Ultra-high-energy X-rays from SPring-8.
  J Appl Cryst, 37:925-933 (2004).
• Yagi N, Yamamoto M, Uesugi K, Inoue K.
  A large-area CMOS imager as an X-ray detector for synchrotron radiation experiments.
  J Synchrotron Rad, 11:347-352 (2004).
• Kumasaka T, Yamamoto M, Yamashita E, Moriyama H, Ueki T.
  Trichromatic concept optimizes MAD experiments in synchrotron X-ray crystallography.
  Structure, 10:1205-1210 (2002).
• Nakasako M, Sawano M, Kawamoto M.
  Development of an Open-Flow Cryostat Utilizing Helium Gas for Cryogenic X-Ray Diffraction Experiments.
  The Rigaku-Denki Journal, 32(2):8-15 (2001).
• Kawamoto M, Kawano Y, Kamiya N.
  The Bio-Crystallography beamline (BL41XU) at SPring-8.
  Nucl Instrum Meth, A467-468:1375-1379 (2001).
• Yamamoto M, Kumasaka T, Yamazaki H, Sasaki K, Yokozawa Y, Ishikawa T.
  Development of high-speed Imaging Plate detector.
  Nucl Instrum Meth, A467-468:1160-1162 (2001).