Original Papers 2020

Y. Fujioka, J. M. Alam, D. Noshiro, K. Mouri, T. Ando, Y. Okada, A. I. May, R. L. Knorr, K. Suzuki, Y. Ohsumi, N. N. Noda, “Phase separation organizes the site of autophagosome formation”, Nature 578, 301-305 (2020).
S. Sakamoto, T. Komatsu, R. Watanabe, Y. Zhang, T. Inoue, M. Kawaguchi, H. Nakagawa, T. Ueno, T. Okusaka, K. Honda, H. Noji, and Y. Urano, “Multiplexed single-molecule enzyme activity analysis for counting disease-related proteins in biological samples”, Science Advances 6, eaay0888 (2020).
T. Hamaguchi and K. Yonekura, “Tidy up cryo-EM sample grids with 3D printed tools”, J. Struct. Biol. 209, 107414 (2020).
R. Umeda, Y. Satouh, M. Takemoto, Y. Nakada-Nakura, K. Liu, T. Yokoyama, M. Shirouzu, S. Iwata, N. Nomura, K. Sato, M. Ikawa, T. Nishizawa and O. Nureki, “Structural insights into tetraspanin CD9 function.”, Nat Commun 11(1), 1606 (2020) DOI: 10.1038/s41467-020-15459-7.
A. Marintchev and T. Ito, “eIF2B and the integrated stress response: a structural and mechanistic view”, Biochemistry 59, 1299-1308 (2020) DOI: 10.1021/acs.biochem.0c00132
T. Mori and S. Sekine “Overview of the “1SBA: integrative approaches towards understanding of gene expression” session at the 57th BSJ meeting”, Biophys Rev. (2020) DOI: 10.1007/s12551-020-00644-1.
K. Weiss, HP. Lazar, A. Kurolap, AF. Martinez, T. Paperna, L. Cohen, MF. Smeland, S. Wallen, H. Solveig, B. Keren, P. Terhal, M. Irving, M. Takaku, JD. Roberts, RM. Petrovich, SA. Schrier Vergano, A. Kenney, H. Hove, E. DeChene, SC. Quinonez, E. Colin, A. Ziegler, M. Rumple, M. Jain, D. Monteil, ER. Roeder, K. Nugent, A. van Haeringen, M. Gambello, A. Santani, L. Medne, B. Krock, CM. Skraban, EH. Zackai, HA. Dubbs, T. Smol, J. Ghoumid, MJ. Parker, M. Wright, P. Turnpenny, J. Clayton-Smith, K. Metcalfe, H. Kurumizaka, BD. Gelb, H. Baris Feldman, PM. Campeau, M. Muenke, PA. Wade, and K. Lachlan. “The CHD4-related syndrome: a comprehensive investigation of the clinical spectrum, genotype-phenotype correlations, and molecular basis”, Genet Med. 22, 389-397 (2020)
Y. Takizawa, CH. Ho, H. Tachiwana, H. Matsunami, W. Kobayashi, M. Suzuki, Y. Arimura, T. Hori, T. Fukagawa, MD. Ohi, M. Wolf, and H. Kurumizaka. “Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome” Structure, 28, 44-53 (2020)
T. Kujirai, and H. Kurumizaka, “Transcription through the nucleosome” Current Opinion in Structural Biology, 61, 42-49 (2020)
H. Yuzurihara, Y. Aizawa, M. Saotome, Y. Ichikawa, H. Yokoyama, Y. Chikashige, T. Haraguchi, Y. Hiraoka, H. Kurumizaka, and W. Kagawa, Improved Methods for Preparing the Telomere Tethering Complex Bqt1-Bqt2 for Structural Studies. Protein J., 39, 174-181 (2020)
R. Fujita, T. Yamamoto, Y. Arimura, S. Fujiwara, H. Tachiwana, Y. Ichikawa, Y. Sakata, L. Yang, R. Maruyama, M. Hamada, M. Nakao, N. Saitoh, and H. Kurumizaka, Nucleosome destabilization by nuclear non-coding RNAs. Commun. Biol., 3, 60. (2020)
K. Saikusa, D. Kato, A. Nagadoi, H. Kurumizaka, and Akashi, S. Native Mass Spectrometry of Protein and DNA Complexes Prepared in Nonvolatile Buffers. J. Am. Soc. Mass Spectrom., 31, 711-718 (2020)
T. Mori and Y. Sugita, “Implicit micelle model for membrane proteins using superellipsoid approximation”, J. Chem. Theory Comput., 16, 711-724 (2020).
D. Matsuoka, M. Kamiya, T. Sato, Y. Sugita, “Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3”, J. Comput. Chem., 41, 561-572 (2020).
Tiwari SP, Chhabra S, Tama F, Miyashita O. “Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps”, J Chem Inf Model. 60, 2570-2580 (2020).
Dasgupta B, Miyashita O, Tama F. “Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images”, Biochim Biophys Acta Gen Subj., 1864, 129420 (2020).
H. Kouno, K. Orihashi, K. Nishimura, Y. Kawashima, K. Tateishi, T. Uesaka, N. Kimizuka, N. Yanai, “Triplet dynamic nuclear polarization of crystalline ice using water-soluble polarizing agents”, Chem. Commum. 56, 3717-3720 (2020).
M. Inoue, T. Hayashi, S. Hikiri, M. Ikeguchi, and M. Kinoshita, “Hydration properties of a protein at low and high pressures: Physics of pressure denaturation”, J. Chem. Phys., 152, 065103 (2020).
T. Sunami, Y. Hirano, T. Tamada, and H. Kono, “Structural basis for an array of engrailed homeodomains”. Acta Crystallographica Section D (Accepted).

Original Papers 2019

H. Ehara, T. Kujirai, Y. Fujino, M. Shirouzu, H. Kurumizaka, S-I. Sekine, “Structural insight into nucleosome transcription by RNA polymerase II with elongation factors”, Science 363, 744-747 (2019).
B. G. David, H. Fujita, K. Yasuda, K. Okamoto, Y. Panina, J. Ichinose, O. Sato, M. Horie, T. Ichimura, Y. Okada, T. M. Watanabe, “Linking substrate and nucleus via actin cytoskeleton in pluripotency maintenance of mouse embryonic stem cells”, Stem Cell Research 41, 101614-101614 (2019).
J. Kaneshiro, Y. Okada, T. Shima, M. Tsuji, K. Imada, T. Ichimura, T. M. Watanabe, “Second harmonic generation polarization microscopy as a tool for protein structure analysis”, Biophys Physbiol. 16, 147-157 (2019).
C. Wang, M. Taki, Y. Sato, Y. Tamura, H. Yaginuma, Y. Okada, S. Yamaguchi, “A photostable fluorescent marker for the superresolution live imaging of the dynamic structure of the mitochondrial cristae”, Proc Natl Acad Sci U S A 116, 15817-15822 (2019).
H. Tanaka, T. Okazaki, S. Aoyama, M. Yokota, M. Koike, Y. Okada, Y. Fujiki, Y. Gotoh, “Peroxisomes control mitochondrial dynamics and the mitochondrion-dependent apoptosis pathway”, J Cell Sci 132, jcs224766 (2019).
K. Kono, S. Yoshiura, I. Fujita, Y. Okada, A. Shitamukai, T. Shibata, F. Matsuzaki, “Reconstruction of Par-dependent polarity in apolar cells reveals a dynamic process of cortical polarization”, eLife 8, e45559 (2019).
C. H. Lu, W. C. Tang, Y. T. Liu, S. W. Chang, F. C. M. Wu, C. Y. Chen, Y. C. Tsai, S. M. Yang, C. W. Kuo, Y. Okada, Y. K. Hwu, P. Chen, B. C. Chen, “Lightsheet localization microscopy enables fast, large-scale, and three-dimensional super-resolution imaging”, Commun Biol 2, 177 (2019).
J. Li, K. Suda, I. Ueoka, R. Tanaka, H. Yoshida, Y. Okada, Y. Okamoto, Y. Hiramatsu, H. Takashima, M. Yamaguchi, “Neuron-specific knockdown of Drosophila HADHB induces a shortened lifespan, deficient locomotive ability, abnormal motor neuron terminal morphology and learning disability”, Exp Cell Res 379, 150-158 (2019).
S. Hasegawa, T. Sagawa, K. Ikeda, Y. Okada, K. Hayashi, “Investigation of multiple-dynein transport of melanosomes by non-invasive force measurement using fluctuation unit χ”, Sci. Rep 9, 5099, (2019).
Suga, M., Akita, F., Yamashita, K., Nakajima, Y., Ueno, G., Li, H., Yamane, T., Hirata, K., Umena, Y., Yonekura, S., Yu, L.-J., Murakami, H., Nomura, T., Kimura, T., Kubo, M., Baba, S., Kumasaka, T., Tono, K., Yabashi, M., Isobe, H., Yamaguchi, K. Yamamoto, M., Ago, H., Shen, J.-R. “An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an X-ray free electron laser”, Science 366, 334-338 (2019).
T. Yokoyama, K. Machida, W. Iwasaki, T. Shigeta, M. Nishimoto, M. Takahashi, A. Sakamoto, M. Yonemochi, Y. Harada, H. Shigematsu, M. Shirouzu, H. Tadakuma, H. Imataka, and T. Ito, “HCV IRES Captures an Actively Translating 80S Ribosome”, Mol. Cell 74, 1205-1214 (2019). DOI: 10.1016/j.molcel.2019.04.022
K. Kashiwagi, T. Yokoyama, M. Nishimoto, M. Takahashi, A. Sakamoto, M. Yonemochi, M. Shirouzu, and T. Ito, “Structural basis for eIF2B inhibition in integrated stress response”, Science 364, 495-499 (2019). DOI: 10.1126/science.aaw4104.
S. Iwasaki, W. Iwasaki, M. Takahashi, A. Sakamoto, C. Watanabe, Y. Shichino, S. N. Floor, K. Fujiwara, M. Mito, K. Dodo, M. Sodeoka, H. Imataka, T. Honma, K. Fukuzawa, T. Ito and N. T. Ingolia, “The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA”, Mol. Cell 73, 738-748 (2019). DOI: 10.1016/j.molcel.2018.11.026.
R. Hirano, T. Kujirai, L. Negishi, and H. Kurumizaka. “Biochemical characterization of the placeholder nucleosome for DNA hypomethylation maintenance” Biochem Biophys Rep., 18, 100634, (2019)
Kobayashi W, Takizawa Y, Aihara M, Negishi L, Ishii H, and Kurumizaka H. “Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding” Commun Biol., 2, 163, (2019)
N. Horikoshi, T. Kujirai, K. Sato, H. Kimura, and H. Kurumizaka. “Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo”      Biochem Biophys Res Commun., 515, 719-724, (2019)
CI. Chung, Y. Sato, Y. Ohmuro-Matsuyama, S. Machida, H. Kurumizaka, H. Kimura, H. and Ueda. “Intrabody-based FRET probe to visualize endogenous histone acetylation” Sci Rep. 9, 10188 (2019)
S. Sato, Y. Arimura, T. Kujirai, A. Harada, K. Maehara, J. Nogami, Y. Ohkawa, and H. Kurumizaka. “Biochemical analysis of nucleosome targeting by Tn5 transposase” Open Biol. 9, 190116, (2019)
R. Sugiyama, K. Kasho, K. Miyoshi, S. Ozaki, W. Kagawa, and H. Kurumizaka, T. Katayama. “A novel mode of DnaA–DnaA interaction promotes ADP dissociation for reactivation of replication initiation activity” Nucleic Acids Res., 47, 11209-11224 (2019)
E. Oya, R. Nakagawa, Y. Yoshimura, M. Tanaka, G. Nishibuchi, S. Machida, A. Shirai, K. Ekwall, H. Kurumizaka, H. Tagami, and JI. Nakayama. “H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin assembly” EMBO Rep., 20, e48111 (2019)
W. Kobayashi, and H. Kurumizaka. “Structural transition of the nucleosome during chromatin remodeling and transcription” Curr Opin Struct Biol., 29, 107-114 (2019)
M. Saotome, N. Horikoshi, K. Urano, T. Kujirai, H. Yuzurihara, H. Kurumizaka, and W. Kagawa. “Structure determination of the nucleosome core particle by selenium SAD phasing” Acta Crystallogr D Struct Biol. 75, 930-936 (2019)
M. Dacher, H. Tachiwana, N. Horikoshi, T. Kujirai, H. Taguchi, H. Kimura, H. Kurumizaka. “Incorporation and influence of Leishmania histone H3 in chromatin” Nucleic Acids Res., 47, 11637-11648 (2019)
S. Matsumoto, S. Cavadini, RD. Bunker, RS. Grand, A. Potenza, J. Rabl, J. Yamamoto, AD. Schenk, D. Schübeler, S. Iwai, K. Sugasawa, H. Kurumizaka, and NH. Thomä. “DNA damage detection in nucleosomes involves DNA register shifting” Nature, 571, 79-84 (2019)
A. Kumar, K. Y. J. Zhang, “Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model”. J. Comput-Aided Mol. Des., 33, 1045-1055 (2019).
A. Kumar, K. Y. J. Zhang, “Shape similarity guided pose prediction: Lessons from D3R Grand Challenge 3”. J. Comput-Aided Mol. Des., 33, 47-59 (2019).
T. Mori, M. Kulik, O. Miyashita, J. Jung, F. Tama, and Y. Sugita, “Acceleration of cryo-EM flexible fitting for large biomolecular systems by efficient space partitioning”, Structure, 27, 161-174 (2019).
M. Sakakura, Y. Ohkubo, H. Oshima, S. Re, M. Ito, Y. Sugita, H. Takahashi “Structural mechanisms underlying activity changes in an AMPA-type glutamate receptor induced by substitutions in its ligand-binding domain”, Structure, 27, 1698–1709 (2019).
H. Oshima, S. Re, M. Sakakura, H. Takahashi, Y. Sugita, “Population Shift Mechanism for Partial Agonism of AMPA Receptor”, Biophys. J., 116, 57-68 (2019).
K. Tateishi, M. Negoro, H. Nonaka, A. Kagawa, S. Sando, S. Wada, M. Kitagawa, T. Uesaka, “Dynamic nuclear polarization with photo-excited triplet electrons using 6,13-diphenylpentacene”, Phys. Chem. Chem. Phys. 21, 19737-19741 (2019).
K. Nishimura, H. Kouno, K. Tateishi, T. Uesaka, K. Ideta, N. Kimizuka, N. Yanai, “Triplet dynamic nuclear polarization of nanocrystals dispersed in water at room temperature”, Phys. Chem. Chem. Phys. 21, 16408-16412 (2019).
H. Kouno, Y. Kawashima, K. Tateishi, T. Uesaka, N. Kimizuka, N. Yanai, “Non-Pentacene Polarizing Agents with Improved Air-Stability for Triplet Dynamic Nuclear Polarization at Room Temperature”, J. Phys. Chem. Lett. 10, 2208-2213 (2019).
W. Li, J. Wang, J. Zhang, S. Takada, W. Wang, “Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration”, Phys. Rev. Lett., 122, 238102 (2019).
R. Kanada, T. Terakawa, H. Kenzaki, S. Takada, “Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins”, Biophys. J., 116, 2285 (2019)
T. Yamada, T. Hayashi, S. Hikiri, N. Kobayashi, H. Yanagawa, M. Ikeguchi, M. Katahira, T. Nagata, and M. Kinoshita, “How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?”, J. Chem. Inf. Model., 59, 3533-3544 (2019).
T. Ekimoto, Y. Kokabu, T. Oroguchi, M. Ikeguchi, “Combination of coarse-grained molecular dynamics simulations and small-angle x-ray scattering experiments”, Biophys. Physicobiol., 16, 377-390 (2019).
S. Hikiri, T. Hayashi, M.Inoue, T. Ekimoto, M. Ikeguchi, and M. Kinoshita, “An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins”, J. Chem. Phys., 150, 175101-1-12 (2019).
A. Singharoy, C. Chipot, T. Ekimoto, K. Suzuki, M. Ikeguchi, I. Yamato, and T. Murata, “Rotational mechanism model of the bacterial V1 motor based on structural and computational analyses”, Front. Physiol., 10:46, 1-12 (2019).
T. Sunami and H. Kono, “Balance between DNA-binding affinity and specificity enables selective recognition of longer target sequences in vivo”. Protein Science, 28, 1630-1639 (2019).

Original Papers 2018

T. Kujirai, H. Ehara, Y. Fujino, M. Shirouzu, S. Sekine, and H. Kurumizaka, “Structural basis of the nucleosome transition during RNA polymerase II passage”, Science 362, 595-598 (2018).
T. Shima, M. Morikawa, J. Kaneshiro, T. Kambara, S. Kamimura, T. Yagi, H. Iwamoto, S. Uemura, H. Shigematsu, M. Shirouzu, T. Ichimura, TM. Watanabe, R. Nitta, Y. Okada, and N. Hirokawa, “Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport”, J. Cell Biol. jcb.201711178 (2018).
H. Ehara, and S. Sekine, “Architecture of the RNA polymerase II elongation complex new insights into Spt4/5 and Elf1”, Transcription 9, 286-291 (2018).
S. Inouye, Y. Tomabechi, T. Hosoya, S. Sekine, and M. Shirouzu, “Slow luminescence kinetics of semi-synthetic aequorin: expression, purification and structure determination of cf3-aequorin”, J. Biochem. 164, 247-255 (2018).
G. Kasuya, T. Nakane, T. Yokoyama, Y. Jia, M. Inoue, K. Watanabe, R. Nakamura, T. Nishizawa, T. Kusakizako, A. Tsutsumi, H. Yanagisawa, N. Dohmae, M. Hattori, H. Ichijo, Z. Yan, M. Kikkawa, M. Shirouzu, R. Ishitani, and O. Nureki, “Cryo-EM structures of the human volume-regulated anion channel LRRC8”, Nat. Struct. Mol. Biol. 25, 797-804 (2018).
K. Katsura, Y. Tomabechi, T. Matsuda, M. Yonemochi, J. Mikuni, N. Ohsawa, T. Terada, S. Yokoyama, M. Kukimoto-Niino, C. Takemoto, and M. Shirouzu, “Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression”, Protein Expr. Purif. 150, 92-99 (2018).
T. Matsuda, T. Ito, C. Takemoto, K. Katsura, M. Ikeda, M. Wakiyama, M. Kukimoto-Niino, S. Yokoyama, Y. Kurosawa, and M. Shirouzu, “Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction”, PLoS One. 13, e0193158 (2018).
N. Ohbayashi, K. Murayama, M. Kato-Murayama, M. Kukimoto-Niino, T. Uejima, T. Matsuda, N. Ohsawa, S. Yokoyoma, H. Nojima, and M. Shirouzu, “Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib”, ChemistryOpen. 7, 721-727 (2018).
W.-Y. Ooi, Y. Murayama, V. Mekler, L. Minakhin, K. Severinov, S. Yokoyama, and S. Sekine, “A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation”, Nucleic Acids Res. 46, 431-441 (2018).
H. Shigematsu, T. Imasaki, C. Doki, T. Sumi, M. Aoki, T. Uchikubo-Kamo, A. Sakamoto, K. Tokuraku, M. Shirouzu and R. Nitta, “Structural insight into microtubule stabilization and kinesin inhibition by Tau family MAPs”, J. Cell Biol. jcb.201711182 (2018).
T. Sumi, T. Imasaki, M. Aoki, N. Sakai, E. Nitta, M. Shirouzu, and R. Nitta, “Structural Insights into the Altering Function of CRMP2 by Phosphorylation”, Cell Struct. Funct. 43, 15-23 (2018).
J. Tamogami, T. Kikukawa, K. Ohkawa, N. Ohsawa, T. Nara, M. Demura, S. Miyauchi, T. Kimura-Someya, M. Shirouzu, S. Yokoyama, K. Shimono, and N. Kamo, “Interhelical interactions between D92 and C218 in the cytoplasmic domain regulate proton uptake upon N-decay in the proton transport of Acetabularia rhodopsin II”, J. Photochem. Photobiol. B 183, 35-45 (2018).
A. Yamagata, Y. Miyazaki, N. Yokoi, H. Shigematsu, Y. Sato, S. Goto-Ito, A. Maeda, T. Goto, M. Sanbo, M. Hirabayashi, M. Shirouzu, Y. Fukata, M. Fukata, S. Fukai, “Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22”, Nat. Commun. 9, 1546 (2018).
K. Hayashi, Y. Tsuchizawa, M. Iwaki, and Y. Okada, “Application of the fluctuation theorem for non-invasive force measurement in living neuronal axons”, Mol. Biol. Cell. 10.1091/mbc.E18-01-0022 (2018).
M. Gzrybowski, M. Taki, K. Senda, Y. Sato, T. Ariyoshi, Y. Okada, R. Kawakami, T. Imamura, and S. Yamaguchi, “A highly photostable near-infrared labeling agent based on a phospha-rhodamine for long-term and deep imaging”, Angew. Chem. 57,10137-10141 (2018).
H. Asada, S. Horita, K. Hirata, M. Shiroishi, Y. Shiimura, H. Iwanari, T. Hamakubo, T. Shimamura, N. Nomura, O. Kusano-Arai, T. Uemura, C. Suno, T. Kobayashi, and S. Iwata, “Crystal structure of the human angiotensin II type 2 receptor bound to an angiotensin II analog”, Nat. Struct. Mol. Biol. 25, 570-576 (2018).
K. Yamashita, K. Hirata, and M. Yamamoto, “KAMO: towards automated data processing for microcrystals”, Acta Cryst. D74, 441–449 (2018).
T. Hori, T. Okuno, K. Hirata, K. Yamashita, Y. Kawano, M. Yamamoto, M. Hato, M. Nakamura, T. Shimizu, T. Yokomizo, M. Miyano, and S. Yokoyama, “Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1”, Nat. Chem. Biol. 14, 262-269 (2018).
T. P. Halsted, K. Yamashita, K. Hirata, H. Ago, G. Ueno, T. Tosha, R. Eady, S. Antonyuk, M. Yamamoto, and S. S. Hasnain, “An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase”, IUCrJ 5, 22-31 (2018).
S. Machida, Y. Takizawa, M. Ishimaru, Y. Sugita, S. Sekine, J. Nakayama, M. Wolf, and H. Kurumizaka, “Structural Basis of Heterochromatin Formation by Human HP1”, Mol. Cell. 69, 385-397 (2018).
K. Shiraishi, A. Shindo, A. Harada, H. Kurumizaka, H. Kimura, Y. Ohkawa, and H. Matsuyama, “Roles of histone H3.5 in human spermatogenesis and spermatogenic disorders”, Andrology 6, 158-165 (2018).
A. Fukuto, M. Ikura, T. Ikura, J. Sun, Y. Horikoshi, H. Shima, K. Igarashi, M. Kusakabe, M. Harata, N. Horikoshi, H. Kurumizaka, Y. Kiuchi, and S. Tashiro, “SUMO modification system facilitates the exchange of histone variant H2A.Z-2 at DNA damage sites”, Nucleus 9, 87-94 (2018).
M. Saotome, K. Saito, T. Yasuda, H. Ohtomo, S. Sugiyama, Y. Nishimura, H. Kurumizaka, and W. Kagawa, “Structural Basis of Homology-based DNA Repair Mediated by RAD52”, iScience, 3, 50-62 (2018).
Y. Takizawa, H. Tanaka, S. Machida, M. Koyama, K. Maehara, Y. Ohkawa, P. A. Wade, M. Wolf, and H. Kurumizaka, “Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence”, Open Biology 8, 170255 (2018).
Y. Okamoto, M. W. Iwasaki, K. Kugou, K. K. Takahashi, A. Oda, K. Sato, W. Kobayashi, H. Kawai, R. Sakasai, A. Takaori-Kondo, T. Yamamoto, M. T. Kanemaki, M. Taoka, T. Isobe, H. Kurumizaka, H. Innan, K. Ohta, M. Ishiai, and M. Takata, “Replication stress induces accumulation of FANCD2 at central region of large fragile genes”, Nucleic Acids Res. 46, 2932-2944 (2018).
M. Koyama and H. Kurumizaka, “Structural diversity of the nucleosome”, J. Biochem.163, 85-95 (2018).
M. Ishiai, K. Sato, J. Tomida, H. Kitao, H. Kurumizaka, and M. Takata, “Activation of the FA pathway mediated by phosphorylation and ubiquitination”, Mutat Res. 803-805, 89-95 (2018).
A. Harada, K. Maehara, Y. Ono, H. Taguchi, K. Yoshioka, Y. Kitajima, Y. Xie, Y. Sato, T. Iwasaki, J. Nogami, S. Okada, T. Komatsu, Y. Semba, T. Takemoto, H. Kimura, H. Kurumizaka, and Y. Ohkawa, “Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration”, Nat. Commun. 9, 1400 (2018).
K. Saikusa, A. Osakabe, D. Kato, S. Fuchigami, A. Nagadoi, Y. Nishimura, H. Kurumizaka, and S. Akashi, “Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry”, Anal. Chem. 90, 8217-8226 (2018).
D. Luo, D. Kato, J. Nogami, Y. Ohkawa, H. Kurumizaka, and H. Kono, “MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast”, Nucleic Acids Res. 46, 7124-7137 (2018).
M. R. Higgs, K. Sato, J. J. Reynolds, S. Begum, R. Bayley, A. Goula, A. Vernet, K. L. Paquin, D. G. Skalnik, W. Kobayashi, M. Takata, N. G. Howlett, H. Kurumizaka, H. Kimura, and G. S. Stewart, “Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2”, Mol. Cell. 71, 25-41.e6 (2018).
A. Osakabe, Z. J. Lorkovic, W. Kobayashi, H. Tachiwana, R. Yelagandula, H. Kurumizaka, and F. Berger, “Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility”, Nucleic Acids Res. 46, 7675-7685 (2018).
Y. Arimura, T. Kono, K. Kino, and H. Kurumizaka, “Structural polymorphism of the Escherichia coli poly-α-L-glutamate synthetase RimK”, Acta Crystallogr. F Struct. Biol. Commun. 74, 385-390 (2018).
Y. Arimura, M. Ikura, R. Fujita, M. Noda, W. Kobayashi, N. Horikoshi, J. Sun, L. Shi, M. Kusakabe, M. Harata, Y. Ohkawa, S. Tashiro, H. Kimura, T. Ikura, and H. Kurumizaka, “Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome”, Nucleic Acids Res. 10.1093/nar/gky661 (2018).
J. Kijima, Y. Shibuya, K. Katayama, T. Itoh, H. Iwase, Y. Fukushima, M. Kubo, and A. Yamaguchi, “Structural characterization of myoglobin molecules adsorbed within mesoporous silicas”, J. Phys. Chem. C 122, 15567-15574 (2018).
R. Komiya, T. Kimura, T. Nomura, M. Kubo, and J. Yan, “Ultraprecision cutting of single-crystal calcium fluoride for fabricating micro flow cells”, J. Adv. Mech. Des. Syst. Manuf. 12, JAMDSM0021 (2018).
K. Tanabe, J. Liu, D. Kato, H. Kurumizaka, K. Yamatsugu, M. Kanai, and S.A. Kawashima, “LC–MS/MS-based quantitative study of the acyl group- and site-selectivity of human sirtuins to acylated nucleosomes”, Sci. Rep. 8, 2656 (2018).
K. Yonekura, R. Matsuoka, Y. Yamashita, T. Yamane, M. Ikeguchi, A, Kidera, and S. Maki-Yonekura, “Ionic scattering factors of atoms that compose biological molecules”, IUCrJ 5, 348-353 (2018).
S. Maki-Yonekura, R. Matsuoka, Y. Yamashita, H. Shimizu, M. Tanaka, F. Iwabuki, and K. Yonekura, “Hexameric and pentameric complexes of the ExbBD energizer in the Ton system”, eLife 7, e35419 (2018).
S. Fujiwara, M. Hosoyamada, K. Tateishi, T. Uesaka, K. Ideta, N. Kimizuka, and N. Yanai, “Dynamic Nuclear Polarization of Metal-Organic Frameworks Using Photoexcited Triplet Electrons”, J. Am. Soc. Chem. in press.
T. Xie, F. Shi, S. Chen, M. Guo, Y. Chen, Y. Zhang, Y. Yang, X. Gao, X. Kong, P. Wang, K. Tateishi, T. Uesaka, Y. Wang, B. Zhang, and J. Du, “Mesoscopic Magnetic Resonance Spectroscopy with a Remote Spin Sensor”, Phys. Rev. Applied 9, 064003 (2018).
S. Chebotaryov, S. Sakaguchi, T. Uesaka, T. Akieda, Y. Ando, M. Assie, D. Beaumel, N. Chiga, M. Dozono, A. Galindo-Uribarri, B. Heffron, A. Hirayama, T. Isobe, K. Kaki, S. Kawase, W. Kim, T. Kobayashi, H. Kon, Y. Kondo, Y. Kubota, S. Leblond, H. Lee, T. Lokotko, Y. Maeda, Y. Matsuda, K. Miki, E. Milman, T. Motobayashi, T. Mukai, S. Nakai, T. Nakamura, A. Ni, T. Noro, S. Ota, H. Otsu, T. Ozaki, V. Panin, S. Park, A. Saito, H. Sakai, M. Sasano, H. Sato, K. Sekiguchi, Y. Shimizu, I. Stefan, L. Stuhl, M. Takaki, K. Taniue, K. Tateishi, S. Terashima, Y. Togano, T. Tomai, Y. Wada, T. Wakasa, T. Wakui, A. Watanabe, H. Yamada, Z. Yang, M. Yasuda, J. Yasuda, K. Yoneda, and J. Zenihiro, “Proton elastic scattering at 200 A MeV and high momentum transfers of 1.7–2.7 fm−1 as a probe of the nuclear matter density of 6He”, Prog. Theor. Exp. Phys., 5, 053D01 (2018).
T. Kasai and T. Kigawa, “Selective isotope labeling strategy and computational interpretation of spectra for protein NMR analyses”, J. Phys.: Conf. Ser. 1036, 012007 (2018).
K. Kitamura, K. Asahina, Y. Nagai, H. Sugiyama, H. Uekusa, and T. Hamura, “Tetrakis(phenylethynyl)tetracene: a new p-extended rubrene derivatives”, Chem. Eur. J. 24, 14034-14038 (2018).
J. Morimoto, Y. Hosono, and S. Sando, “Isolation of a peptide containing D-amino acid residues that inhibits the α-helix-mediated p53–MDM2 interaction from a one-bead one-compound library”, Bioorg. Med. Chem. Lett. 28, 231-234 (2018).
T. Sugiki, D. Egawa, K. Kumagai, C. Kojima, T. Fujiwara, K. Takeuchi, I. Shimada, K. Hanada, and H. Takahashi, “Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif”, J. Biol. Chem., 293, 11206-11217 (2018).
R. Suzuki, M. Sakakura, M. Mori, M. Fujii, S. Akashi, and H. Takahashi, “Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system”, J. Biomol. NMR, 71, 213-223 (2018).
M. Sakakura, M. Tamura, N. Fujii, T. Takeuchi, T. Hatanaka, S. Kishimoto, Y. Arata, and H. Takahashi, “Structural mechanisms for the S-nitrosylation-derived protection of mouse galectin-2 from oxidation-induced inactivation revealed by NMR”, FEBS J., 285, 1129-1145 (2018).
Y. Matsunaga, T. Yamane, T. Terada, K. Moritsugu, H. Fujisaki, S. Murakami, M. Ikeguchi, and A. Kidera, “Energetics and Conformational Pathways of Functional Rotation in the Multidrug Transporter AcrB”, eLife 7, e31715 (2018).
K. Yonekura, R. Matsuoka, Y. Yamashita, T. Yamane, M. Ikeguchi, A. Kidera, and S. Maki-Yonekura, “Ionic Scattering Factors of Atoms Composing Biological Molecules”, IUCrJ 5, 348-353 (2018).
Y. Kajiwara, S. Yasuda, S. Hikiri, T. Hayashi, M. Ikeguchi, T. Murata, and M. Kinoshita, “Physical Origin of Thermostabilization by a Quadruple Mutation for the Adenosine A2a Receptor in the Active State”, J. Phys. Chem. B 122, 4418-4427 (2018).
S. Hikiri, T. Hayashi, M. Ikeguchi, and M. Kinoshita, “Statistical thermodynamics for the unexpectedly large difference between disaccharide stereoisomers in terms of solubility in water”, Phys. Chem. Chem. Phys. 20, 23684-23693 (2018).
D. Luo, D. Kato, J. Nogami, Y. Ohkawa, H. Kurumizaka, and H. Kono, “MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast”, Nucleic Acids Res. 46, 7124-7137 (2018).
M. Kulik, T. Mori, Y. Sugita and J. Trylska, “Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides”, Nucleic Acids Res. 46, 9960-9970 (2018).
M. Kamiya and Y. Sugita, “Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations”, J. Chem. Phys. 149, 072304 (2018).
Y. Matsunaga and Y. Sugita, “Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning”, eLife 7, e32668 (2018).
Y. Matsunaga and Y. Sugita, “Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories”, J. Chem. Phys. 148, 241731 (2018).
J. Jung, C. Kobayash, and Y. Sugita, “Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation”, J. Chem. Phys. 148, 164109 (2018).
S.P. Tiwari, F. Tama, and O. Miyashita, “Searching for 3D structural models from a library of biological shapes using a few 2D experimental images”, BMC Bioinformatics 19, 320 (2018).
G.B. Brandani, T. Niina, C. Tan, and S. Takada, “DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations”, Nucleic Acids Res. 46, 2788-2801 (2018).
M. Shimizu and S. Takada, “Reconstruction of atomistic structures from coarse-grained models for protein-DNA complexes”, J. Chem. Theory Comput. 14, 1682-1694 (2018).
C. Tan and S. Takada, “Dynamic and Structural Modeling of the Specificity in Protein–DNA Interactions Guided by Binding Assay and Structure Data”, J. Chem. Theory Comput. 14, 3877-3889 (2018).
G.B. Brandani and S. Takada, “Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA”, PLoS Comp. Biol., 14, e1006512 (2018).
A. Kumar and K.Y.J. Zhang, “A cross docking pipeline for improving pose prediction and virtual screening performance”, J. Comput-Aided Mol. Des., 32, 163-173 (2018).
T. Ekimoto, T.Yamane, and M. Ikeguchi,”Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method”, J. Chem. Theory Comput., 14, 6544-6559 (2018).
T. Ekimoto and M. Ikeguchi,”Multiscale Molecular Dynamics Simulations of Rotary Motor Proteins”, Biophys. Rev., 10, 605-615 (2018).

Original Papers 2017

T. Tosha, T. Nomura, T. Nishida, N. Saeki, K. Okubayashi, R. Yamagiwa, M. Sugahara, T. Nakane, K. Yamashita, K. Hirata, G. Ueno, T. Kimura, T. Hisano, K. Muramoto, H. Sawai, H. Takeda, E. Mizohata, A. Yamashita, Y. Kanematsu, Y. Takano, E. Nango, R. Tanaka, O. Nureki, O.Shoji, Y. Ikemoto, H. Murakami, S. Owada, K. Tono, M. Yabashi, M. Yamamoto, H. Ago, S. Iwata, H. Sugimoto, Y. Shiro, and M. Kubo, “Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate”, Nat. Commun. 8, 1585 (2017).
T. Asano, H. Ito, Y. Kariya, K. Hoshi, A. Yoshihara, Y. Ugawa, H. Sekine, S. Hirohata, Y.Yamaguchi, S. Sato, H. Kobayashi, K. Migita, H. Ohira, Y. Hashimoto, and H. Watanabe, “Evaluation of blood-brain barrier function by quotient alpha2 macroglobulin and its relationship with interleukin-6 and complement component 3 levels in neuropsychiatric systemic lupus erythematosus”, PLoS One. 12, e0186414 (2017).
T. Christian, R. Sakaguchi, AP. Perlinska, G. Lahoud, T. Ito, EA. Taylor, S. Yokoyama, JI. Sulkowska, and YM. Hou, “Methyl transfer by substrate signaling from a knotted protein fold”, Nat. Struct. Mol. Biol. 23, 941-948 (2017).
H. Ehara, T. Umehara, S. Sekine, and S. Yokoyama, “Crystal structure of RNA polymerase II from Komagataella pastoris”, Biochem. Biophys. Res. Commun. 487, 230-235 (2017).
H. Ehara, T. Yokoyama, H. Shigematsu, S. Yokoyama, M. Shirouzu, and S. Sekine, “Structure of the complete elongation complex of RNA polymerase II with basal factors”, Science 357, 921-924 (2017).
K. Hasegawa, Y. Someya, H. Shigematsu, T. Kimura-Someya, N. Nuemket, and T. Kumasaka, “Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain”, Acta Crystallogr. F Struct. Biol. Commun. 73, 568-573 (2017).
T. Hosaka, M. Okazaki, T. Kimura-Someya, Y. Ishizuka-Katsura, K. Ito, S. Yokoyama, K. Dodo, M. Sodeoka, and M. Shirouzu, “Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1”, Protein Sci. 26, 1749-1758 (2017).
N. Iwakura, T. Yokoyama, F. Quaglia, K. Mitsuoka, K. Mio, H. Shigematsu, M. Shirouzu, A. Kaji, and H. Kaji, “Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G”, PLoS One 12, e0177972 (2017).
K. Katsura, T. Matsuda, Y. Tomabechi, M. Yonemochi, K. Hanada, N. Ohsawa, K. Sakamoto, C. Takemoto, and M. Shirouzu, “A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis”, J. Biochem. 162, 357-369 (2017).
A.R. Chase, E. Laudermilch, J. Wang, H. Shigematsu, T. Yokoyama, and C. Schlieker, “Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1”, Mol. Biol. Cell 28, 2765-2772 (2017).
J.P. López-Alonso, T. Kaminishi, T. Kikuchi, Y. Hirata, I. Iturrioz, N. Dhimole, A. Schedlbauer, Y. Hase, S. Goto, D. Kurita, A. Muto, S. Zhou, C. Naoe, D.J. Mills, D. Gil-Carton, C. Takemoto, H. Himeno, P. Fucini, and S.R. Connell, “RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket”, Nucleic Acids Res. 45, 6945-6959 (2017).
S. Niwa, F. Nakamura, Y. Tomabechi, M. Aoki, H. Shigematsu, T. Matsumoto, A. Yamagata, S. Fukai, N. Hirokawa, Y. Goshima, M. Shirouzu, and R. Nitta, “Structural basis for CRMP2-induced axonal microtubule formation”, Sci. Rep. 7, 10681 (2017).
H. Shimizu, A. Tosaki, N. Ohsawa, Y. Ishizuka-Katsura, S. Shoji, H. Miyazaki, F. Oyama, T. Terada, M. Shirouzu, SI. Sekine, N. Nukina, and S. Yokoyama, “Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel β4 subunit explain its role in cell-cell adhesion”, J. Biol. Chem. 292, 13428-13440 (2017).
A. Sotokawauchi, M. Kato-Murayama, K. Murayama, T. Hosaka, I. Maeda, M. Onjo, N. Ohsawa, D.I. Kato, K. Arima, and M. Shirouzu, “Structural basis of cucumisin protease activity regulation by its propeptide”, J. Biochem. 161, 45-53 (2017).
J. Tamogami, T. Kikukawa, T. Nara, M. Demura, T. Kimura-Someya, M. Shirouzu, S. Yokoyama, S. Miyauchi, K. Shimono, and N. Kamo, “Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga”, Biophys. Physicobiol. 14, 49-55 (2017).
K. Chiba, K. Chien, Y. Sobu, S. Hata, S. Kato, T. Nakaya, Y. Okada, A.C. Nairn, M. Kinjo, H. Taru, R. Wang, and T. Suzuki, “Phosphorylation of KLC1 modifies interaction with JIP1 and abolishes the enhanced fast velocity of APP transport by kinesin-1”, Mol. Biol. Cell 28, 3857-3869 (2017).
T. Nozaki, R. Imai, M. Tanbo, R. Nagashima, S. Tamura, T. Tani, Y. Joti, M. Tomita, K. Hibino, MT. Kanemaki, KS. Wendt, Y. Okada, T. Nagai, and K. Maeshima, “Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging”, Mol. Cell 67, 282-293 (2017).
A. Shimada, M. Kubo, S. Baba, K. Yamashita, K. Hirata, G. Ueno, T. Nomura, T. Kimura, K. Shinzawa-Itoh, J. Baba, K. Hatano, Y. Eto, A. Miyamoto, H. Murakami, T. Kumasaka, S. Owada, K. Tono, M. Yabashi, Y. Yamaguchi, S. Yanagisawa, M. Sakaguchi, T. Ogura, R. Komiya, J. Yan, E. Yamashita, M. Yamamoto, H. Ago, S. Yoshikawa, and T. Tsukihara, “A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase”, Sci. Adv. 3, e1603042 (2017).
W. Shihoya, T. Nishizawa, K. Yamashita, A. Inoue, K. Hirata, F. M. N. Kadji, A. Okuta, K. Tani, J. Aoki, Y. Fujiyoshi, T. Doi, and O. Nureki, “X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog”, Nat. Struct. Mol. Biol. 24, 758-764 (2017).
R. Taniguchi, A. Inoue, M. Sayama, A. Uwamizu, K. Yamashita, K. Hirata, M. Yoshida, Y. Tanaka, H.E. Kato, Y. Nakada-Nakura, Y. Otani, T. Nishizawa, T. Doi, T. Ohwada, R. Ishitani, J. Aoki, and O. Nureki, “Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA6”, Nature 548, 356-360 (2017).
S. Abe, H. Tabe, H. Ijiri, K. Yamashita, K. Hirata, K. Atsumi, T. Shimoi, M. Akai, H. Mori, S. Kitagawa, and T. Ueno, “Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells”, ACS Nano 11, 2410-2419 (2017).
M. Suga, F. Akita, M. Sugahara, M. Kubo, Y. Nakajima, T. Nakane, K. Yamashita, Y. Umena, M. Nakabayashi, T. Yamane, T. Nakano, M. Suzuki, T. Masuda, S. Inoue, T. Kimura, T. Nomura, S. Yonekura, L. J. Yu, T. Sakamoto, T. Motomura, J. H. Chen, Y. Kato, T. Noguchi, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, E. Nango, R. Tanaka, H. Naitow, Y. Matsuura, A. Yamashita, M. Yamamoto, O. Nureki, M. Yabashi, T. Ishikawa, S. Iwata, and J.-R. Shen, “Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL”, Nature 543, 131-135 (2017).
M. Yamamoto, K. Hirata, K. Yamashita, K. Hasegawa, G. Ueno, H. Ago, H., and T. Kumasaka, “Protein microcrystallography using synchrotron radiation”, IUCrJ 4, 529-539 (2017).
K. Hasegawa, K. Yamashita, T. Murai, N. Nuemket, K. Hirata, G. Ueno, H. Ago, T. Nakatsu, T. Kumasaka, and M. Yamamoto, “Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography”, J. Synchrotron Rad. 24, 29-41 (2017).
R.A. Chase, E. Laudermilch, J. Wang, H. Shigematsu, T. Yokoyama, and C. Schlieker, “Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1”, Mol. Biol. Cell 28, 2765-2772 (2017).
E. Kakumu, S. Nakanishi, H.M. Shiratori, A. Kato, W. Kobayashi, S. Machida, T. Yasuda, N. Adachi, N. Saito, T. Ikura, H. Kurumizaka, H. Kimura, M. Yokoi, W. Sakai, K. Sugasawa, “Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3”, Genes Cells 22, 310-327 (2017).
A, Osakabe, Y. Arimura, S. Matsumoto, N. Horikoshi, K. Sugasawa, and H. Kurumizaka, “Polymorphism of apyrimidinic DNA structures in the nucleosome”, Sci. Rep. 7, 41783 (2017).
T. Kujirai, N. Horikoshi, Y. Xie, H. Taguchi, H. Kurumizaka, “Identification of the amino acid residues responsible for stable nucleosome formation by histone H3. Y”, Nucleus 24, 1-10 (2017).
J. Ueda, A. Harada, T. Urahama, S. Machida, K. Maehara, M. Hada, Y. Makino, J. Nogami, N. Horikoshi, A. Osakabe, H. Taguchi, H. Tanaka, H. Tachiwana, T. Yao, M. Yamada, T. Iwamoto, A. Isotani, M. Ikawa, T. Tachibana, Y. Okada, H. Kimura, Y. Ohkawa, H. Kurumizaka, and K. Yamagata, “Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis”, Cell Rep. 18, 593-600 (2017).
M. Koyama, W. Nagakura, H. Tanaka, T. Kujirai, Y. Chikashige, T. Haraguchi, Y. Hiraoka, and H. Kurumizaka, “In vitro reconstitution and biochemical analyses of the Schizosaccharomyces pombe nucleosome”, Biochem. Biophys. Res. Commun. 482, 896-901 (2017).
T. Kujirai, S. Machida, A. Osakabe, and H. Kurumizaka, “Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin”, J. Biochem. 161, 381-388 (2017).
T. Hori, N. Kagawa, A. Toyoda, A. Fujiyama, S. Misu, N. Monma, F. Makino, K. Ikeo, and T. Fukagawa, “Constitutive centromere-associated network controls centromere drift in vertebrate cell”, J. Cell. Biol. 216, 101-113 (2017).
W. Kobayashi, M. Takaku, S. Machida, H. Tachiwana, K. Maehara, Y. Ohkawa, and H. Kurumizaka, “Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing”, Sci. Rep. 6, 24228 (2017).
T. Fuse, K. Katsumata, K. Morohoshi, Y. Mukai, Y. Ichikawa, H. Kurumizaka, A. Yanagida, T. Urano, H. Kato, and M. Shimizu, “Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo”, PLoS One 12, e0186974 (2017).
T. Kawaguchi, S. Machida, H. Kurumizaka, H. Tagami, and J.I. Nakayama, “Phosphorylation of CBX2 controls its nucleosome-binding specificity”, J. Biochem. 162, 343-355 (2017).
Y. Hatanaka, T. Tsusaka, N. Shimizu, K. Morita, T. Suzuki, S. Machida, M. Satoh, A. Honda, M. Hirose, S. Kamimura, N. Ogonuki, T. Nakamura, K. Inoue, Y. Hosoi, N. Dohmae, T. Nakano, H. Kurumizaka, K. Matsumoto, Y. Shinkai, and A. Ogura, “Histone H3 methylated at arginine 17 is essential for reprogramming the paternal genome in zygotes”, Cell Rep. 20, 2756-2765 (2017).
W. Kobayashi, N. Hosoya, S. Machida, K. Miyagawa, and H. Kurumizaka, “SYCP3 regulates strand invasion activities of RAD51 and DMC1”, Genes Cells 22, 181-189 (2017).
T. Hori, W.H. Shang, M. Hara, M. Ariyoshi, Y. Arimura, R. Fujita, H. Kurumizaka, and T. Fukagawa, “Association of M18BP1/KLN2 with CENP-A nucleosome is essential for centromere formation in non-mammalian vertebrates”, Dev. Cell 42, 181-189 (2017).
Y. Amamoto, Y. Aoi, N. Nagashima, H. Suto, D. Yoshidome, Y. Arimura, A. Osakabe, D. Kato, H. Kurumizaka, S. Kawashima, K. Yamatsugu, and M. Kanai, “Synthetic posttranslational modifications: chemical catalyst-driven regioselective histone acylation of native chromatin”, J. Am. Chem. Soc. 139, 7568-7576 (2017).
T. Ishiguro, Y. Amamoto, K. Tanabe, J. Liu, H. Kajino, A. Fujimura, Y. Aoi, A. Osakabe, N. Horikoshi, H. Kurumizaka, K. Yamatsugu, S.A. Kawashima, and M. Kanai, “Synthetic chromatin acylation by an artificial catalyst system”, Chem 2, 840-859 (2017).
S. Inano, K. Sato, Y. Katsuki, W. Kobayashi, H. Tanaka, K. Nakajima, S. Nakada, H. Miyoshi, K. Knies, A. Takaori-Kondo, D. Schindler, M. Ishiai, H. Kurumizaka, and M. Takata, “RFWD3-mediated ubiquitination promotes timely removal of both RPA and RAD51 from DNA damage sites to facilitate homologous recombination”, Mol. Cell 66, 622-634 (2017).
J. Bednar, I. Garcia-Saez, R. Boopathi, A.R. Cutter, G. Papai, A. Reymer, S.H. Syed, I.N. Lone, O. Tonchev, C. Crucifix, H. Menoni, C. Papin, D.A. Skoufias, H. Kurumizaka, R. Lavery, A. Hamiche, J.J. Hayes, P. Schultz, D. Angelov, C. Petosa, and A. Dimitrov, “Structure and dynamics of a 197 base-pair nucleosome in complex with linker histone H1”, Mol. Cell 66, 384-397 (2017).
H. Taguchi, Y. Xie, N. Horikoshi, K. Maehara, A. Harada, J. Nogami, K. Sato, Y. Arimura, A. Osakabe, T. Kujirai, T. Iwasaki, Y. Semba, T. Tachibana, H. Kimura, Y. Ohkawa, and H. Kurumizaka, “Crystal structure and characterization of novel human histone H3 variants, H3.6, H3.7, and H3.8”, Biochemistry 56, 2184-2196 (2017).
D. Kato, A. Osakabe, Y. Arimura, Y. Mizukami, N. Horikoshi, K. Saikusa, S. Akashi, Y. Nishimura, S. Y. Park, J. Nogami, K. Maehara, Y. Ohkawa, A. Matsumoto, H. Kono, R. Inoue, M. Sugiyama, and H. Kurumizaka, “Crystal structure of the overlapping dinucleosome composed of hexasome and octasome”, Science 356, 205-208 (2017).
S. Barral, Y. Morozumi, H. Tanaka, E. Montellier, J. Govin, M. de Dieuleveult, G. Charbonnier, Y. Couté, D. Puthier, T. Buchou, F. Boussouar, T. Urahama, F. Fenaille, S. Curtet, P. Héry, N. Fernandez-Nunez, H. Shiota, M. Gérard, S. Rousseaux, H. Kurumizaka, and S. Khochbin, “Histone variant H2A.L.2 guides transition protein-dependent protamine assembly in male germ cells”, Mol. Cell 66, 89-101 (2017).
M. Kubo, E. Nango, K. Tono, T. Kimura, S. Owada, C. Song, F. Mafuné, K. Miyajima, Y. Takeda, J. Kohno, N. Miyauchi, T. Nakane, T. Tanaka, T. Nomura, J. Davidsson, R. Tanaka, M. Murata, T. Kameshima, T. Hatsui, Y. Joti, R. Neutze, M. Yabashi, and S. Iwata, “Nanosecond pump-probe system for time-resolved serial femtosecond crystallography developed at SACLA”, J. Synchrotron Rad. 24, 1086-1091 (2017).
T. Kigawa, “Advances in stable isotope assisted labeling strategies with information science”, Arch. Biochem. Biophys. 628, 17-23, (2017).
K. Inomata, H. Kamoshida, M. Ikari, Y. Ito, and T. Kigawa, “Impact of cellular health conditions on the protein folding state in mammalian cells”, Chem. Commun. 53, 11245-11248 (2017).
H. Tozawa, T. Kakuda, K. Adachi, and T. Hamura, “Star-Shaped Polycyclic Aromatic Ketones via 3-Fold Cycloadditions of Isobenzofuran Trimer Equivalent”, Org. Lett. 19, 4118-4121 (2017).
R. Kudo, K. Kitamura, and T. Hamura, “1,3-Dialkyny- and 1,3-dialkenyl-isobenzofurans: new π-extended congeners prepared by double nucleophilic addition of alkynyllithiums to o-phthalaldehyde”, Chem. Lett. 46, 25-28 (2017).
H. Nonaka, M. Hirano, Y. Imakura, Y. Takakusagi, K. Ichikawa, and S. Sando, “Design of a 15N Molecular Unit to Achieve Long Retention of Hyperpolarized Spin State”, Sci. Rep. 12, 40104 (2017).
T. Nishihara, Y. Kameyama, H. Nonaka, Y. Takakusagi, F. Hyodo, K. Ichikawa, and S. Sando, “A Strategy to Design Hyperpolarized ¹³C Magnetic Resonance Probes Using [1-¹³C]α-Amino Acid as a Scaffold Structure”, Chem. Asian. J. 12, 949-953 (2017).
Y. Isaka, T. Ekimoto, Y. Kokabu, I. Yamato, T. Murata, and M. Ikeguchi, “Rotation mechanism of molecular motor V1-ATPase studied by multiscale molecular dynamics simulation”, Biophys. J. 112, 911-920 (2017).
S. Fujimura, Y. Ito, M. Ikeguchi, K. Adachi, J. Yajima, and T. Nishizaka, “Dissection of the angle of single fluorophore attached to the nucleotide in corkscrewing microtubules”, Biochem. Biophys. Res. Comm. 485, 614-620 (2017).
S. Ishiyama, A. Nishiyama, Y. Saeki, K. Moritsugu, D. Morimoto, L. Yamaguchi, N. Arai, R. Matsumura, T. Kawakami, Y. Mishima, H. Hojo, S. Shimamura, F. Ishikawa, S. Tajima, K. Tanaka, M. Ariyoshi, M. Shirakawa, M. Ikeguchi, A. Kidera, I. Suetake, K. Arita, and M. Nakanishi, “Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance”, Mol. Cell. 68, 350-360 (2017).
G. Nawrocki, P.-H. Wang, I. Yu, Y. Sugita, and M. Feig, “Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation”, J. Phys. Chem. B, 121, 11072-11084 (2017).
B. Thomsen, T. Kawakami, I. Shigemoto, Y. Sugita, and K. Yagi, “Weight-Averaged Anharmonic Vibrational Analysis of Hydration Structures of Polyamide 6”, J. Phys. Chem. B 121, 6050-6063 (2017).
R. Galvelis, and Y. Sugita, “Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics”, J. Chem. Theory Comput. 13, 2489-2500 (2017).
R. Galvelis, S. Re, and Y. Sugita, “Enhanced Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics”, J. Chem. Theory Comput. 13, 1934-1942 (2017).
P.-H. Wang, I. Yu, M. Feig, and Y. Sugita, “Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding”, Chem. Phys. Lett. 671, 63-70 (2017).
T. Niina, G. B. Brandani, C. Tan, and S. Takada, “Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations”, PLoS Comp. Biol. 13, e1005880 (2017).
O. Miyashita, C. Kobayashi, T. Mori, Y. Sugita, and F. Tama, “Flexible Fitting to Cryo-EM Density Map using Ensemble Molecular Dynamics Simulations”, J. Comp. Chem. 38, 1447-1461 (2017).

Original Papers 2016

T. Hosaka, S. Yoshizawa, Y. Nakajima, N. Ohsawa, M. Hato, E.F. DeLong, K. Kogure, S. Yokoyama, T. Kimura-Someya, W. Iwasaki, and M. Shirouzu, “Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3”, J. Biol. Chem. 291, 17488-17495 (2016).
A. Fabbretti, A. Schedlbauer, L. Brandi, T. Kaminishi, AM. Giuliodori, R. Garofalo, R. Ochoa-Lizarralde, C. Takemoto, S. Yokoyama, S.R. Connell, C.O. Gualerzi, and P. Fucini, “Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding”, Proc. Natl. Acad. Sci. USA 113, E2286-E2295 (2016).
H. Jeong, J.S. Kim, S. Song, H. Shigematsu, T. Yokoyama, J. Hyun, and N.C. Ha, “Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC”, Structure 24, 272-276 (2016).
K. Kashiwagi, T. Shigeta, H. Imataka, T. Ito, and S. Yokoyama, “Expression, purification, and crystallization of Schizosaccharomyces pombe eIF2B”, J. Struct. Funct. Genomics. 17, 33-38 (2016).
K. Kashiwagi, M. Takahashi, M. Nishimoto, T.B. Hiyama, T. Higo, T. Umehara, K. Sakamoto, T. Ito, and S. Yokoyama, “Crystal structure of eukaryotic translation initiation factor 2B”, Nature 531, 122-125 (2016).
M. Masuda, Y. Uno, N. Ohbayashi, H. Ohata, A. Mimata, M. Kukimoto-Niino, H. Moriyama, S. Kashimoto, T. Inoue, N. Goto, K. Okamoto, M. Shirouzu, M. Sawa, and T. Yamada, “TNIK inhibition abrogates colorectal cancer stemness”, Nat. Commun. 7, 12586 (2016).
T. Nakane, S. Hanashima, M. Suzuki, H. Saiki, T. Hayashi, K. Kakinouchi, S. Sugiyama, S. Kawatake, S. Matsuoka, N. Matsumori, E. Nango, J. Kobayashi, T. Shimamura, K. Kimura, C. Mori, N. Kunishima, M. Sugahara, Y. Takakyu, S. Inoue, T. Masuda, T. Hosaka, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, M. Yabashi, T. Inoue, O. Nureki, S. Iwata, M. Murata, and E. Mizohata, “Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent”, Proc. Natl. Acad. Sci. USA 113, 13039-13044 (2016).
E. Nango, A. Royant, M. Kubo, T. Nakane, C. Wickstrand, T. Kimura, T. Tanaka, K. Tono, C. Song, R. Tanaka, T. Arima, A. Yamashita, J. Kobayashi, T. Hosaka, E. Mizohata, P. Nogly, M. Sugahara, D. Nam, T. Nomura, T. Shimamura, D. Im, T. Fujiwara, Y. Yamanaka, B. Jeon, T. Nishizawa, K. Oda, M. Fukuda, R. Andersson, P. Båth, R. Dods, J. Davidsson, S. Matsuoka, S. Kawatake, M. Murata, O. Nureki, S. Owada, T. Kameshima, T. Hatsui, Y. Joti, G. Schertler, M. Yabashi, AN. Bondar, J. Standfuss, J. Neutzex, and S. Iwata, “A three-dimensional movie of structural changes in bacteriorhodopsin”, Science 354, 1552-1557 (2016).
S. Rahman, I. Yamato, S. Saijo, K. Mizutani, Y. Takamuku, Y. Ishizuka-Katsura, N. Ohsawa, T. Terada, M. Shirouzu, S. Yokoyama, and T. Murata, “Binding interactions of the peripheral stalk subunit isoforms from human V-ATPase”, Biosci. Biotechnol. Biochem. 80, 878-890 (2016).
H. Shimizu, H. Miyazaki, N. Ohsawa, S. Shoj, Y. Ishizuka-Katsura, A. Tosaki, F. Oyama, T. Terada, K. Sakamoto, M. Shirouzu, SI. Sekine, N. Nukina, and S. Yokoyama, “Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits”, Sci. Rep. 6, 1-12 (2016).
T. Shinoda, N. Shinya, K. Ito, Y. Ishizuka-Katsura, N. Ohsawa, T. Terada, K. Hirata, Y. Kawano, M. Yamamoto, T. Tomita, Y. Ishibashi, Y. Hirabayashi, T. Kimura-Someya, M. Shirouzu, and S. Yokoyama, “Cell-free methods to produce structurally intact mammalian membrane proteins”, Sci. Rep. 6, 30442 (2016).
T. Shinoda, N. Shinya, K. Ito, N. Ohsawa, T. Terada, K. Hirata, Y. Kawano, M. Yamamoto, T. Kimura-Someya, S. Yokoyama, and M. Shirouzu, “Structural basis for disruption of claudin assembly in tight junctions by an enterotoxin”, Sci. Rep. 6, 33632 (2016).
T. Suenaga, M. Watanabe-Matsui, T. Uejima, H. Shima, T. Matsui, M. Ikeda-Saito, M. Shirouzu, K. Igarashi, and K. Murayama, “Charge-state-distribution analysis of Bach2 intrinsically disordered heme binding region”, J. Biochem. 160, 291-298 (2016).
K. Suzuki, K. Mizutani, S. Maruyama, K. Shimono, FL. Imai, E. Muneyuki, Y. Kakinuma, Y. Ishizuka-Katsura, M. Shirouzu, S. Yokoyama, I. Yamato, and T. Murata, “Crystal structures of the ATP-binding and ADP-release dwells of the V(1) rotary motor”, Nat. Commun. 7, 13235 (2016).
K. Terasawa, Y. Tomabechi, M. Ikeda, H. Ehara, M. Kukimoto-Niino, M. Wakiyama, KA. Podyma-Inoue, AR. Rajapakshe, T. Watabe, M. Shirouzu, and M. Hara-Yokoyama, “Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes”, Biochem. Biophys. Res. Commun. 479, 489-495 (2016).
Y. Tomabechi, T. Hosoya, H. Ehara, S. Sekine, S.I. Shirouzux, and S. Inouye, “Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine”, Biochem. Biophys. Res. Commun. 470, 88-93 (2016).
K.A. Verba, R.Y. Wang, A. Arakawa, Y. Liu, M. Shirouzu S. Yokoyama, and D.A. Agard, “Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase”, Science 352, 1542-1547 (2016).
M. Yamagishi, H. Shigematsu, T. Yokoyama, M. Kikkawa, M. Sugawa, M. Aoki, M. Shirouzu, J. Yajima, and R. Nitta, “Structural basis of backwards motion in kinesin-1–kinesin-14 chimera: implication for kinesin-14 motility”, Structure 24, 1322-1334 (2016).
D. Wang, R. Nitta, M. Morikawa, H. Yajima, S. Inoue, H. Shigematsu, M. Kikkawa, and N. Hirokawa, “Structural basis of Motile and MT depolymerizing functions in kinesin-8 KIF19A”, eLife, 5, 2728 (2016).
W.S.V. Yip, H. Shigematsu, D.W. Taylor, and S.J. Baserga, “Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs”, Nucleic Acids Res. 44, 8976-8989 (2016).
G. Qu, P.S. Kaushal, J. Wang, H. Shigematsu, C.L. Piazza, R.K. Agrawal, M. Belfort, H.-W. Wang, “Structure of a group II intron in complex with its reverse transcriptase”, Nat. Struct. Mol. Boil. 23, 549-557 (2016).
Y. Yang, J. Wang, H. Shigematsu, W. Xu, W.M. Shih, J.E. Rothman, and L. Chenxiang, “Self-assembly of size-controlled liposomes on DNA nanotemplates”, Nat. Chem. 8, 476-483 (2016).
K.H. Jensen, S.S. Brandt, H. Shigematsu, and F.J. Sigworth, “Statistical modeling and removal of lipid membrane projections for cryo-EM structure determination of reconstituted membrane proteins”, J. Struct. Biol. 194, 49-60 (2016).
H. Jeong, J.-S. Kim, S. Song, H. Shigematsu, T. Yokoyama, J. Hyun, and N.-C. Ha, “Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC”, Structure 24, 272-276 (2016).
Y. Ichikawa, N. Morohashi, N. Tomita, A.P. Mitchell, H. Kurumizaka, and M. Shimizu, “Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo”, Biochem. Biophys. Res. Commun. 476, 57-62 (2016).
K. Sato, M. Shimomuki, Y. Katsuki, D. Takahashi, W. Kobayashi, M. Ishiai, H. Miyoshi, M. Takata, and H. Kurumizaka, “FANCI-FANCD2 stabilizes the RAD51-DNA complex by binding RAD51 and protects the 5′-DNA end”, Nucleic Acids Res. 44, 10758-10771 (2016).
Y. Sato, T. Kujirai, R. Arai, H. Asakawa, C. Ohtsuki, N. Horikoshi, K. Yamagata, J. Ueda, T. Nagase, T. Haraguchi, Y. Hiraoka, A. Kimura, H. Kurumizaka, and H. Kimura, “Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation”, J. Mol. Biol. 428, 3885-3902 (2016).
M. Saotome, K. Saito, K. Onodera, H. Kurumizaka, and W. Kagawa, “Structure of the human DNA-repair protein RAD52 containing surface mutations”, Acta Crystallogr. F Struct. Biol. Commun. 72, 598-603 (2016).
Y. Roulland, K. Ouararhni, M. Naidenov, L. Ramos, M. Shuaib, S.H. Syed, I.N. Lone, R. Boopathi, E. Fontaine, G. Papai, H. Tachiwana, T. Gautier, D. Skoufias, K. Padmanabhan, J. Bednar, H. Kurumizaka, P. Schultz, D. Angelov, A. Hamiche, and S. Dimitrov, “The Flexible Ends of CENP-A Nucleosome Are Required for Mitotic Fidelity”, Mol. Cell. 63, 674-685 (2016).
T. Kujirai, N. Horikoshi, K. Sato, K. Maehara, S. Machida, A. Osakabe, H. Kimura, Y. Ohkawa, and H. Kurumizaka. “Structure and function of human histone H3. Y nucleosome”, Nucleic Acids Res. 44, 6127-6141 (2016).
S. Machida, S. Sekine, Y. Nishiyama, N. Horikoshi, and H. Kurumizaka, “Structural and biochemical analyses of monoubiquitinated human histones H2B and H4”, Open Biol. 6, 160090 (2016).
N. Horikoshi, Y. Arimura, H. Taguchi, and H. Kurumizaka, “Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A”, Open Biol. 6, 160127 (2016).
P. Nogly, V. Panneels, G. Nelson, C. Gati, T. Kimura, C. Milne, D. Milathianaki, M. Kubo, W. Wu, C. Conrad, J. Coe, R. Bean, Y. Zhao, P. Båth, R. Dods, R. Harimoorthy, K. R. Beyerlein, J. Rheinberger, D. James, D. DePonte, C. Li, L. Sala, G. Williams, M. Hunter, J. E. Koglin, P. Berntsen, E. Nango, S. Iwata H. N., Chapman, P. Fromme, M. Frank, R. Abela, S. Boutet, A. Barty, T. A. White, U. Weierstall, J. Spence, R. Neutze, G. Schertler, and J. Standfuss, “Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography”, Nat. Commun. 7, 12314 (2016).
A. Otomo, H. Ishikawa, M. Mizuno, T. Kimura, M. Kubo, Y. Shiro, S. Aono, and Y. Mizutani, “A study of the dynamics of the heme pocket and C-helix in CooA upon CO dissociation using time-resolved visible and UV resonance Raman spectroscopy”, J. Phys. Chem. B 120, 7836-7843 (2016).
K. Yonekura, and S. Maki-Yonekura, “Refinement of cryo-EM structures using scattering factors of charged atoms”, J. Appl. Cryst. 49, 1517-1523 (2016).
Y. Takayama, and K. Yonekura, “Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy”, Acta Crystallogr. A Found. Adv. 72, 179-189 (2016).
E. Nango, S. Akiyama, S. Maki-Yonekura, Y. Ashikawa, Y. Kusakabe, E. Krayukhina., T. Maruno, S. Uchiyama, N. Nuemket, K. Yonekura, M. Shimizu, N. Atsumi, N. Yasui, T. Hikima, M. Yamamoto, Y. Kobayashi, and A. Yamashita, “Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains”, Sci. Rep. 6, 25745 (2016).
T. Uesaka, “Spins in exotic nuclei: RI beam experiments with polarized Targets”, Eur. Phys. J. Plus. 131, 403 (2016).
T. Kasai, K. Nagata, M. Okada, and T. Kigawa, “NMR spectral analysis using prior knowledge”, J. Phys.: Conf. Ser. 699, 012003 (2016).
T. Ikeya, S. Ikeda, T. Kigawa, Y. Ito, and P. Güntert, “Protein NMR Structure Refinement based on Bayesian Inference”, J. Phys.: Conf. Ser. 699, 012005 (2016).
H. Okamura, H. Nishimura, T. Nagata, T. Kigawa, T. Watanabe, and M. Katahira, “Accurate and molecular-size-tolerant NMR quantitation of diverse components in solution”, Sci. Rep. 6, 21742 (2016).
S. Kiyonaka, R. Kubota, Y. Michibata, M. Sakakura, H. Takahashi, T. Numata, R. Inoue, M. Yuzaki, and I. Hamachi, “Allosteric activation of membrane-bound glutamate receptors using coordination chemistry within living cells”, Nat. Chem., 8, 958-967 (2016).
Y. Moriwaki, T. Yamane, H. Ohtomo, M. Ikeguchi, J. Kurita, M. Sato, A. Nagadoi, H. Shimojo, and Y. Nishimura, “Solution structure of the isolated histone H2A-H2B heterodimer”, Sci. Rep. 6, 24999 (2016).
N. Kuwabara, H. Manya, T. Yamada, H. Tateno, M. Kanagawa, K. Kobayashi, K. Akasaka-Manya, Y. Hirose, M. Mizuno, M. Ikeguchi, T. Toda, J. Hirabayashi, T. Senda, T. Endo, and R. Kato, “Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan”, Proc. Natl. Acad. Sci. USA, 113, 9280-9285 (2016).
Y. Anami, N. Shimizu, T. Ekimoto, D. Egawa, T. Itoh, M. Ikeguchi, and K. Yamamoto, “Apo- and antagonist-binding structures of vitamin D receptor ligand-binding domain revealed by hybrid approach combining small-angle x-ray scattering and molecular dynamics”, J. Med. Chem. 59, 7888-7900 (2016).
S. Hikiri, T. Yoshidome, and M. Ikeguchi, “Computational methods for configurational entropy using internal and Cartesian coordinates”, J. Chem. Theory Comput. 12, 5990-6000 (2016).
M. Ota, M. Ikeguchi, and A. Kidera, “Itinerary profiling to analyze a large number of protein-folding trajectories”, Biophys. Physicobiol. 13, 295-304 (2016).
A. Kumar and K.Y.J. Zhang, “Prospective Evaluation of Shape Similarity Based Pose Prediction Method in D3R Grand Challenge 2015”, J. Comput-Aided Mol. Des., 30, 685-693 (2016).