Publications

    2022

  1. Structural insights into methylated DNA recognition by the methyl-CpG binding domain of MBD6 from Arabidopsis thaliana.

    Mahana, Y., Ohki, I., Walinda, E., Morimoto, D., Sugase, K., and Shirakawa, M.

    ACS Omega, 2022, in press

    doi:10.1021/acsomega.1c04917

  2. 2021

  3. Rigorous analysis of the interaction between proteins and low water-solubility drugs by qNMR-aided NMR titration experiments.

    Hirakawa, T., Walinda, E., Morimoto, D., and Sugase, K.

    Phys. Chem. Chem. Phys, 2021, 23, 21484-21488

    doi.org/10.1039/D1CP03175A

  4. Expression, solubility monitoring, and purification of the co-folded LUBAC LTM domain by structure-guided tandem folding in autoinducing cultures.

    Walinda, E., Morimoto, D., Sorada, T., Iwai, K., and Sugase, K.

    Protein Expr. Purif., 2021, 187, 105953

    doi:10.1016/j.pep.2021.105953

  5. Effects of Weak Nonspecific Interactions with ATP on Proteins.

    Nishizawa, M., Walinda, E., Morimoto, D., Kohn, B., Scheler, U., Shirakawa, M., and Sugase, K.

    JACS, 2021, 143, 31, 11982-11993

    doi:10.1021/jacs.0c13118

  6. Fabrication of Detonation Nanodiamonds Containing Silicon-Vacancy Color Centers by High Temperature Annealing.

    Shimazaki, K., Kawaguchi, H., Takashima, H., Segawa, TF., So, FTK., Terada, D., Onoda, S., Ohshima, T., Shirakawa, M., and Takeuchi, S.

    Phys. Status Solidi A, 2021, 2100144

    doi:10.1002/pssa.202100144

  7. Backbone resonance assignments of the A2 domain of mouse von Willebrand factor.

    Morimoto, D., Osugi, M., Mahana, Y., Walinda, E., Shirakawa, M., and Sugase, K.

    Biomol. NMR Assign., 2021, 15(2), 427-431

    doi.org/10.1007/s12104-021-10041-8

  8. Multiple-State Monitoring of SOD1 Amyloid Formation at Single-Residue Resolution by Rheo-NMR Spectroscopy.

    Iwakawa, N., Morimoto, D., Walinda, E., Shirakawa, M., and Sugase, K.

    JACS, 2021, 143, 28, 10604-10613

    doi:10.1021/jacs.1c02974

  9. Label-free tomographic imaging of nanodiamonds in living cells.

    Ikliptikawati, DK., Hazawa, M., So, FTK., Terada, D., Kobayashi, A., Segawa, TF., Shirakawa, M., and Wong, RW.

    Diam. Relat. Mater., 2021, 118, 108517

    doi:10.1016/j.diamond.2021.108517

  10. Machine-Learning Optimization of Multiple Measurement Parameters Nonlinearly Affecting the Signal Quality.

    Fujisaku, T., So, FTK., Igarashi, R., and Shirakawa, M.

    ACS Meas. Au, 2021, 1, 1, 20–26

    doi:10.1021/acsmeasuresciau.1c00009

  11. Glycyrrhizin Derivatives Suppress Cancer Chemoresistance by Inhibiting Progesterone Receptor Membrane Component 1.

    Kabe, Y., Koike, I., Yamamoto, T., Hirai, M., Kanai, A., Furuhata, R., Tsugawa, H., Harada, E., Sugase, K., Hanadate, K., Yoshikawa, N., Hayashi, H., Noda, M., Uchiyama, S., Yamazaki, H., Tanaka, H., Kobayashi, T., Handa, H., and Suematsu, M.

    cancers, 2021, 13(13), 3265

    doi.org/10.3390/cancers13133265

  12. Molecular recognition and deubiquitination of cyclic K48-linked ubiquitin chains by OTUB1.

    Sorada, T., Morimoto, D., Walinda, E., and Sugase, K.

    BBRC, 2021, 562, 12, 94-99

    doi:10.1016/j.bbrc.2021.05.031

  13. Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel.

    Iwakawa, N., Morimoto, D., Walinda, E., Leeb, S., Shirakawa, M., Danielsson, J., and Sugase, K.

    J. Phys. Chem. B, 2021, 125, 10, 2521-2532

    doi:10.1021/acs.jpcb.0c11162

  14. Structural dynamic heterogeneity of polyubiquitin subunits affects phosphorylation susceptibility.

    Morimoto, D., Walinda, E., Takashima, S., Nishizawa, M., Iwai, K., Shirakawa, M., and Sugase, K.

    Biochemistry, 2021, 60, 573-583

    doi:10.1021/acs.biochem.0c00619

  15. Room-temperature hyperpolarization of polycrystalline samples with optically polarized triplet electrons: pentacene or nitrogen-vacancy center in diamond?

    Miyanishi, K., Segawa, TF., Takeda, K., Ohki, I., Onoda, S., Ohshima, T., Abe, H., Takashima, H., Takeuchi, S., Shames, AI., Morita, K., Wang, Y., So, FTK., Terada, D., Igarashi, R., Kagawa, A., Kitagawa, M., Mizuochi, N., Shirakawa, M., and Negoro, M.

    Mag. Res., 2021, 2, 33-48

    doi.org/10.5194/mr-2-33-2021

  16. Structural dynamics of double-stranded DNA with epigenome modification.

    Furukawa, A., Walinda, E., Arita, K., and Sugase, K.

    NAR, 2021, 49(2), 1152-1162

    doi:10.1093/nar/gkaa1210

  17. 2020

  18. Nanometre-scale visualization of chemical parameter changes by T1-weighted ODMR imaging using a fluorescent nanodiamond.

    Fujisaku, T., Igarashi, R.,and Shirakawa, M.

    Chemosensors, 2020, 8(3), 68

    doi:10.3390/chemosensors8030068

  19. Quantitative monitoring of ubiquitination/deubiquitination reaction cycles by 18O-incorporation.

    Tanaka, Y., Morimoto, D., Walinda, E., Sugase, K., and Shirakawa, M.

    Biochem. Biophys. Res. Commun. 2020, 529(2), 418-424

    doi:10.1016/j.bbrc.2020.06.008

  20. Nanodiamond mediated interfacial polymerization for high performance nanofiltration membrane.

    Qin, D., Huang, G., Terada, D., Jiang, H., Ito, M.M., Gibbons, A.H., Igarashi, R., Yamaguchi, D., Shirakawa, M., Sivaniah, E., and Ghalei, B.

    J. Mem. Sci., 2020, 603, 118003

    doi:10.1016/j.memsci.2020.118003

  21. Tracking the 3D rotational dynamics in nanoscopic biological systems.

    Igarashi, R., Sugi, T., Sotoma, S., Genjo, T., Kumiya, Y., Walinda, E., Ueno, H., Ikeda, K., Sumiya, H., Tochio, H., Yoshinari, Y., Harada, Y., and Shirakawa, M.

    JACS, 2020, 142, 16, 7542-7554

    doi:10.1021/jacs.0c01191

  22. Pinpoint analysis of a protein in slow exchange using F1F2-selective ZZ-exchange spectroscopy: assignment and kinetic analysis.

    Nishizawa, M., Walinda, E., Morimoto, D., and Sugase, K.

    J. Biomol. NMR, 2020, 74, 205-211

    doi:10.1007/s10858-020-00309-x

  23. Chain-length dependent physical properties and degradation of ubiquitin chains.

    Morimoto, D., Shirakawa, M.

    J. Jpn. Biochem. Soc. (Seikagaku) 2020, 92(1), 7-13

    doi:10.14952/SEIKAGAKU.2020.920007

  24. Visualizing protein motion in Couette flow by all-atom molecular dynamics.

    Walinda, E., Morimoto, D., Shirakawa, M., Scheler, U. and Sugase, K.

    Biochim. Biophys. Acta Gen. Subj., 2020, 1864, 2, 129383.

    doi:10.1016/j.bbagen.2019.06.006

  25. Nanodiamonds for bioapplications-specific targeting strategies.

    Terada, D., Genjo, T., Segawa, TF., Igarashi, R., and Shirakawa, M.

    Biochim. Biophys. Acta Gen. Subj., 2020, 1864, 2, 129354.

    doi:10.1016/j.bbagen.2019.04.019

  26. 2019

  27. Conformational exchange in the potassium channel blocker ShK.

    Iwakawa, N., Baxter, N.J., Wai, D.C.C., Fowler, N.J., Morales, R.A.V., Sugase, K., Norton, R.S., and Williamson, M.P.

    Sci. Rep., 2019, 9, 19307.

    doi:10.1038/s41598-019-55806-3

  28. 生体分子レオロジーNMRの開発と応用

    森本 大智、菅瀬 謙治

    日本核磁気共鳴学会機関誌 2019年度 第10巻

    日本核磁気共鳴学会のサイトへ: Link to the website of NMRJ

  29. Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody.

    Akiba, H., Tamura, H., Kiyoshi, M., Yanaka, S., Sugase, K., Caaveiro, M. M. J., and Kouhei Tsumoto, K.

    Sci. Rep., 2019, 9, 15481.

    doi:10.1038/s41598-019-50722-y

  30. 高感度Rheo-NMRによるアミロイド線維化過程のその場観察

    森本 大智、菅瀬 謙治

    月刊「細胞」2019年 10月臨時増刊号

    北隆館のサイトへ: Link to the website of HOKURYUKAN

  31. pH Nanosensor Using Electronic Spins in Diamond.

    Fujisaku T., Tanabe R., Onoda S., Kubota R., Segawa T.F., So F.T., Ohshima T., Hamachi I., Shirakawa M., and Igarashi R.

    ACS Nano 2019, 13, 11726-11732.

    doi:10.1021/acsnano.9b05342

  32. Contribution of Coiled-Coil Assembly to Ca2+/Calmodulin-Dependent Inactivation of TRPC6 Channel and its Impacts on FSGS-Associated Phenotypes.

    Polat, OK., Uno, M., Maruyama, T., Tran, HN., Imamura, K., Wong, CF., Sakaguchi, R., Ariyoshi, M., Itsuki, K., Ichikawa, J., Morii, T., Shirakawa, M., Inoue, R., Asanuma, K., Reiser, J., Tochio, H., Mori, Y., and Mori, MX.

    J. Am. Soc. Nephrol., 2019, 30(9), 1587-1603.

    doi:10.1681/ASN.2018070756

  33. Monodisperse Five-Nanometer-Sized Detonation Nanodiamonds Enriched in Nitrogen-Vacancy Centers.

    Terada, D., Segawa, TF., Shames, AI., Onoda, S., Ohshima, T., Osawa, E., Igarashi, R., and Shirakawa, M.

    ACS Nano 2019, 13, 6461-6468

    doi:10.1021/acsnano.8b09383

  34. An innate interaction between IL-18 and the propeptide that inactivates its precursor form.

    Tsutsumi, N., Yokota, A., Kimura, T., Kato, Z., Fukao, T., Shirakawa, M., Ohnishi, H., and Tochio, H.

    Sci. Rep., 2019, 9, 6160.

    doi:10.1038/s41598-019-42661-5

  35. High Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.

    Tanaka, T., Ikeya, T., Kamoshida, H., Suemoto, Y., Mishima, M., Shirakawa M., Güntert, P., and Ito, Y.

    Angew. Chem. Int. Ed., 2019, 58(22), 7284-7288.

    doi:10.1002/anie.201900840

  36. 2018

  37. NMR resonance assignments of the NZF domain of mouse HOIL-1L free and bound to linear di-ubiquitin.

    Ishii, N., Walinda, E., Iwakawa, N., Morimoto, D., Iwai, K., Sugase, K., and Shirakawa, M.

    Biomol. NMR Assign., 2018, 13(1), 149-153.

    doi:10.1007/s12104-018-09868-5

  38. Intramolecular interaction suggests an autosuppression mechanism for the innate immune adaptor protein MyD88.

    Uno, M., Watanabe-Nakayama, T., Konno, H., Akagi, KI., Tsutsumi, N., Fukao, T., Shirakawa, M., Ohnishi, H., and Tochio, H.

    Chem. Commun., 2018, 54, 12318-12321.

    doi:10.1039/C8CC06480F

  39. Backbone and side-chain resonance assignments of the methyl-CpG-binding domain of MBD6 from Arabidopsis thaliana.

    Iwakawa, N., Mahana, Y., Ono, A., Ohki, I., Walinda, E., Morimoto, D., Sugase, K., and Shirakawa, M.

    Biomol. NMR Assign., 2018, 13(1), 59-62.

    doi:10.1007/s12104-018-9851-2

  40. One-Pot Synthesis of Highly Dispersible Fluorescent Nanodiamonds for Bioconjugation.

    Terada, D., Sotoma, S., Harada, Y., Igarashi, R., and Shirakawa, M.

    Bioconj. Chem., 2018, 29(8), 2786–2792.

    doi:10.1021/acs.bioconjchem.8b00412

  41. Resolving biomolecular motion and interactions by R2 and R Relaxation Dispersion NMR.

    Walinda, E., Morimoto, D., and Sugase, K.

    Methods, 2018, 148, 28-38.

    doi:10.1016/j.ymeth.2018.04.026

  42. Cooperative Domain Formation by Homologous Motifs in HOIL-1L and SHARPIN Plays A Crucial Role in LUBAC Stabilization.

    Fujita, H., Tokunaga, A., Shimizu, S., Whiting, A.L., Aguilar-Alonso, F., Takagi, K., Walinda, E., Sasaki, Y., Shimokawa, T., Mizushima, T., Ohki, I., Ariyoshi, M., Tochio, H., Bernal, F., Shirakawa, M., and Iwai, K.

    Cell Rep., 2018, 23(4), 1192–1204.

    doi:10.1016/j.celrep.2018.03.112

  43. Overview of Relaxation Dispersion NMR Spectroscopy to Study Protein Dynamics and Protein-Ligand Interactions.

    Walinda, E., Morimoto, D., and Sugase, K.

    Curr. Protoc. Protein Sci., 2018, 92(1), e57.

    doi:10.1002/cpps.57

  44. Enrichment of ODMR-active nitrogen-vacancy centres in five-nanometre-sized detonation-synthesized nanodiamonds: Nanoprobes for temperature, angle and position.

    Sotoma, S., Terada, D., Segawa, TF., Igarashi, R., Harada, Y., and Shirakawa, M.

    Sci. Rep., 2018, 8, 5463.

    doi:10.1038/s41598-018-23635-5

  45. Hydrogen-Deuterium Exchange Profiles of Polyubiquitin Fibrils.

    Morimoto, D., Nishizawa, R., Walinda, E., Takashima, S., Sugase, K., and Shirakawa, M.

    Polymers, 2018, 10(3), 240.

    doi:10.3390/polym10030240

  46. Isolation and characterization of a minimal building block of polyubiquitin fibrils.

    Morimoto, D., Walinda, E., Shinke, M., Sugase, K., and Shirakawa, M.

    Sci. Rep., 2018, 8, 2711.

    doi:10.1038/s41598-018-21144-z

  47. 2017

  48. Elucidating Functional Dynamics by R and R2 Relaxation Dispersion NMR Spectroscopy.

    Walinda, E. and Sugase, K.

    Experimental Approaches of NMR Spectroscopy, Springer, 2017, 197-225.

    doi:10.1007/978-981-10-5966-7_7

  49. Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR.

    Iwakawa, N., Morimoto, D., Walinda, E., Kawata, Y., Shirakawa, M., and Sugase, K.

    Int. J. Mol. Sci., 2017, 18(11), 2271.

    doi:10.3390/ijms18112271

  50. Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance.

    Ishiyama, S., Nishiyama, A., Saeki, Y., Moritsugu, K., Morimoto, D., Yamaguchi, L., Arai, N., Matsumura, R., Kawakami, T., Mishima, Y., Hojo, H., Shimamura, S., Ishikawa, F., Tajima, S., Tanaka, K., Ariyoshi, M., Shirakawa, M., Ikeguchi, M., Kidera, A., Suetake, I., Arita, K., and Nakanishi, M.

    Mol. Cell, 2017, 68(2), 350–360.e7.

    doi:10.1016/j.molcel.2017.09.037

  51. RFTS-dependent negative regulation of Dnmt1 by nucleosome structure and histone tails.

    Mishima, Y., Brueckner, L., Takahashi S., Kawakami, T., Arita, K., Oka, S., Otani, J., Hojo, H., Shirakawa, M., Shinohara, A., Watanabe, M., and Suetake, I.

    FEBS J., 2017.

    doi:10.1111/febs.14205

  52. Elucidation of potential sites for antibody engineering by fluctuation editing.

    Yanaka, S., Moriwaki, Y., Tsumoto, K., and Sugase, K.

    Sci. Rep., 2017, 7, 9597.

    doi:10.1038/s41598-017-10246-9

  53. High-Sensitivity Rheo-NMR Spectroscopy for Protein Studies.

    Morimoto, D., Walinda, E., Iwakawa, N., Nishizawa, M., Kawata, Y., Yamamoto, A., Shirakawa, M., Scheler, U., and Sugase, K.

    Anal. Chem., 2017, 89(14), 7286-7290.

    doi:10.1021/acs.analchem.7b01816

  54. Biological and Physicochemical Functions of Ubiquitylation Revealed by Synthetic Chemistry Approaches.

    Morimoto, D., Walinda, E., Sugase, K., and Shirakawa, M.

    Int. J. Mol. Sci., 2017, 18(6), 1145.

    doi:10.3390/ijms18061145

  55. Exploration of the Conformational Dynamics of Major Histocompatibility Complex Molecules.

    Yanaka, S. and Sugase, K.

    Front. Immunol., 2017, 8, 632.

    doi:10.3389/fimmu.2017.00632

  56. F1F2-selective NMR spectroscopy.

    Walinda, E., Morimoto, D., Shirakawa, M., and Sugase, K.

    J. Biomol. NMR, 2017, 68(1), 41–52.

    doi:10.1007/s10858-017-0113-x

  57. Hexaphyrin as a Potential Theranostic Dye for Photothermal Therapy and 19F Magnetic Resonance Imaging.

    Higashino, T., Nakatsuji, H., Fukuda, R., Okamoto, H., Imai, H., Matsuda, T., Tochio, H., Shirakawa, M., Tkachenko, NV., Hashida, M., Murakami, T., and Imahori, H.

    Chembiochem, 2017, 18(10), 951-959.

    doi:10.1002/cbic.201700071

  58. Practical considerations for investigation of protein conformational dynamics by 15N R relaxation dispersion.

    Walinda, E., Morimoto, D., Shirakawa, M., and Sugase, K.

    J. Biomol. NMR, 2017, 67(3), 201–209.

    doi:10.1007/s10858-017-0097-6

  59. Backbone resonance assignments of monomeric SOD1 in dilute and crowded environments.

    Iwakawa, N., Morimoto, D., Walinda, E., Sugase, K., and Shirakawa, M.

    Biomol. NMR Assign., 2017, 11(1), 81–84.

    doi:10.1007/s12104-016-9724-5

  60. 2016

  61. Ubiquitylation Directly Induces Fold Destabilization of Proteins.

    Morimoto, D., Walinda, E., Fukada, H., Sugase, K., and Shirakawa, M.

    Sci. Rep., 2016, 6, 39453.

    doi:10.1038/srep39453

  62. A Nanodiamond-peptide Bioconjugate for Fluorescence and ODMR Microscopy of a Single Actin Filament.

    Genjo, T., Sotoma, S., Tanabe, R., Igarashi, R., and Shirakawa, M.

    Anal. Sci., 2016, 32, 1165-1170.

    doi:10.2116/analsci.32.1165

  63. Quantitative analysis of protein–ligand interactions by NMR.

    Furukawa, A., Konuma, T., Yanaka, S., and Sugase, K.

    Prog. Nucl. Magn. Reson. Spectrosc., 2016, 96, 47–57.

    doi:10.1016/j.pnmrs.2016.02.002

  64. A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells.

    Hikone, Y., Hirai, G., Mishima M., Inomata K., Ikeya, T., Arai, S., Shirakawa, M., Sodeoka, M., and Ito, Y.

    J. Biomol. NMR, 2016, 66, 99-110

    doi:10.1007/s10858-016-0059-4

  65. The evolving world of ubiquitin: transformed polyubiquitin chains.

    Morimoto, D. and Shirakawa, M.

    Biomol. Concepts, 2016, 7(3), 157-167.

    doi:10.1515/bmc-2016-0009

  66. Efficient identification and analysis of chemical exchange in biomolecules by R relaxation dispersion with Amaterasu.

    Walinda, E., Morimoto, D., Nishizawa, M., Shirakawa, M., and Sugase, K.

    Bioinformatics, 2016, 32, 2539-2541.

    doi:10.1093/bioinformatics/btw188

  67. Dual Function of Phosphoubiquitin in E3 Activation of Parkin.

    Walinda, E., Morimoto, D., Sugase, K., and Shirakawa, M.

    J. Biol. Chem., 2016, 291, 16879-16891.

    doi:10.1074/jbc.M116.728600

  68. Selective Labeling of Proteins on Living Cell Membranes Using Fluorescent Nanodiamond Probes.

    Sotoma, S., Iimura, J., Igarashi, R., Hirosawa, K., Ohnishi, H., Mizukami, S., Kikuchi, K., Fujiwara, T., Shirakawa, M., and Tochio, H.

    Nanomaterials, 2016, 6(4), 56.

    doi:10.3390/nano6040056

  69. Moderate plasma treatment enhances the quality of optically detected magnetic resonance signals of nitrogen-vacancy centres in nanodiamonds.

    Sotoma, S., Igarashi, R., and Shirakawa, M.

    Appl. Phys. A, 2016, 122, 522.

    doi:10.1007/s00339-016-0030-y

  70. Monodispersed Colloidal Solutions of Surface-modified Detonation-synthesized Nanodiamonds and Their Aggregation Resistance.

    Sotoma, S. and Shirakawa, M.

    Chem. Lett., 2016, 45(6), 697.

    doi:10.1246/cl.160250

  71. 2015

  72. Selective autophagic receptor p62 regulates the abundance of transcriptional coregulator ARIP4 during nutrient starvation.

    Tsuchiya, M., Isogai, S., Taniguchi, H., Tochio, H., Shirakawa, M., Morohashi, K., Hiraoka, Y., Haraguchi, T., and Ogawa, H.

    Sci. Rep., 2015, 5, 14498.

    doi:10.1038/srep14498

  73. Nucleosome compaction facilitates HP1γ binding to methylated H3K9.

    Mishima, Y., Jayasinghe, C.D., Lu, K., Otani, J., Shirakawa, M., Kawakami, T., Kimura, H., Hojo, H., Carlton, P., Tajima, S., and Suetake, I.

    Nucleic. Acids. Res., 2015, 43(21), 10200-12.

    doi:10.1093/nar/gkv841

  74. Suppression of Nonspecific Protein­Nanodiamond Adsorption Enabling Specific Targeting of Nanodiamonds to Biomolecules of Interest.

    Sotoma, S., Igarashi, R., Iimura, J., Kumiya, Y., Tochio, H., Harada, Y., and Shirakawa, M.

    Chem. Lett., 2015, 44(3), 354-356.

    doi:10.1246/cl.141036

  75. Comprehensive and quantitative analysis for controlling the physical/chemical states and particle properties of nanodiamonds for biological applications.

    Sotoma, S., Akagi, K., Hosokawa, S., Igarashi, R., Tochio, H., Harada, Y., and Shirakawa, M.

    RSC Adv., 2015, 5, 13818-13827.

    doi:10.1039/C4RA16482B

  76. The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates.

    Morimoto, D., Walinda, E., Fukada, H., Sou, YS., Kageyama, S., Hoshino, M., Fujii, T., Tsuchiya, H., Saeki, Y., Arita, K., Ariyoshi, M., Tochio, H., Iwai, K., Namba, K., Komatsu, M., Tanaka, K., and Shirakawa, M.

    Nat. Commun., 2015, 6, 6116.

    doi:10.1038/ncomms7116

  77. Magnetic resonance imaging of tumor with a self-traceable phosphorylcholine polymer.

    Yamada, H., Hasegawa, Y., Imai ,H., Takayama, Y., Sugihara, F., Matsuda, T., Tochio, H., Shirakawa, M., Sando, S., Kimura, Y., Toshimitsu, A., Aoyama, Y., and Kondo, T.

    J. Am. Chem. Soc., 2015, 137, 799-806.

    doi: 10.1021/ja510479v

  78. Optically Detected Magnetic Resonance of Nanodiamonds in Vivo; Implementation of Selective Imaging and Fast Sampling.

    Yoshinari, Y., Mori, S., Igarashi, R., Sugi, T., Yokota, H., Ikeda, K., Sumiya, H., Mori, I., Tochio, H., Harada, Y., and Shirakawa, M.

    J. Nanosci. Nanotechnol., 2015, 15(2), 1014-21.

    doi:10.1166/jnn.2015.9739

  79. 2014

  80. Effective Production of Fluorescent Nanodiamond Containing Negatively-Charged Nitro-gen-Vacancy Center by Ion Irradiation.

    Sotoma, S., Yoshinari, Y., Igarashi, R., Yamazaki, A., Yoshimura, S. H., Tochio, H., Shirakawa, M., and Harada, Y.

    Diam. Relat. Mater., 2014, 49, 33-38.

    doi:10.1016/j.diamond.2014.07.011

  81. The structural basis for receptor recognition of human interleukin-18.

    Tsutsumi, N., Kimura, T., Arita, K., Ariyoshi, M., Ohnishi, H., Yamamoto, T., Zuo ,X., Maenaka, K., Park, EY., Kondo, N., Shirakawa, M., Tochio, H., Kato, Z.

    Nat. Commun., 2014, 5, 5340.

    doi:10.1038/ncomms6340

  82. High-throughput optical quantification of mechanosensory habituation reveals neurons encoding memory in Caenorhabditis elegans.

    Sugi, T., Ohtani, Y., Kumiya, Y., Igarashi, R., Shirakawa, M.

    Proc. Natl. Acad. Sci. U S A., 2014, 111, 17236-41.

    doi:10.1073/pnas.1414867111

  83. Purification, crystallization and preliminary X-ray crystallographic analysis of human IL-18 and its extracellular complexes.

    Kimura, T., Tsutsumi, N., Arita, K., Ariyoshi, M., Ohnishi, H., Kondo, N., Shirakawa, M., Kato Z, Tochio, H.

    Acta. Crystallogr. F. Struct. Biol. Commun., 2014, 70(Pt 10), 1351-6.

    doi:10.1107/S2053230X14016926

  84. Solution structure of the ubiquitin-associated (UBA) domain of human autophagy receptor NBR1 and its interaction with ubiquitin and polyubiquitin.

    Walinda, E., Morimoto, D., Sugase ,K., Konuma ,T., Tochio, H., Shirakawa, M.

    J. Biol. Chem., 2014, 289, 13890-902.

    doi:10.1074/jbc.M114.555441

  85. Ubiquitin-proteasome-mediated degradation of S-RNase in a solanaceous cross-compatibility reaction.

    Entani, T., Kubo, K., Isogai, S., Fukao, Y., Shirakawa, M., Isogai, A., Takayama, S.

    Plant. J., 2014, 78, 1014-21.

    doi:10.1111/tpj.12528

  86. Functional assessment of the mutational effects of human IRAK4 and MyD88 genes.

    Yamamoto, T., Tsutsumi, N., Tochio, H., Ohnishi, H., Kubota, K., Kato, Z., Shirakawa, M., Kondo, N.

    Mol. Immunol., 2014, 58, 66-76.

    doi:10.1016/j.molimm.2013.11.008

  87. The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger-associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA.

    Berkyurek, AC., Suetake, I., Arita, K., Takeshita, K., Nakagawa, A., Shirakawa, M., Tajima, S.

    J. Biol. Chem., 2014, 289, 379-86.

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  89. Cell cycle –dependent turnover of 5-hydroxymethyl Cytosine in mouse embryonic stem cells.

    Otani, J., Kimura, H., Sharif, J., Endo, TA., Mishima, Y., Kawakami, T., Koseki, H., Shirakawa, M., Suetake, I., Tajima, S.

    PLos. One., 2013, 8(12), e82961.

    doi:10.1371/journal.pone.0082961

  90. An in-cell NMR study of monitoring stress-induced increase of cytosolic Ca2+ concentration in HeLa cells.

    Hembram, DS., Haremaki, T., Hamatsu, J., Inoue, J., Kamoshida, H., Ikeya, T., Mishima, M., Mikawa, T., Hayashi, N., Shirakawa, M., Ito, Y.

    Biochem. Biophys. Res. Commun., 2013, 438, 653-9.

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  91. Development of fluorogenic probes for quick no-wash live-cell imaging of intracellular proteins.

    Hori, Y., Norinobu, T., Sato, M., Arita, K., Shirakawa, M., Kikuchi, K.

    J. Am. Chem. Soc., 2013, 135, 12360-5.

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  92. Pruning the ALS-associated protein SOD1 for in-cell NMR.

    Danielsson, J., Inomata, K., Murayama, S., Tochio, H., Lang, L., Shirakawa, M., Oliveberg, M.

    J. Am. Chem. Soc., 2013, 135, 10266-9.

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  93. A structured monodisperse PEG for the effective suppression of protein aggregation.

    Muraoka, T., Adachi, K., Ui, M., Kawasaki, S., Sadhukhan, N., Obara, H., Tochio, H., Shirakawa, M., Kinbara, K.

    Angew. Chem. Int. Ed. Engl., 2013, 52, 2430-4.

    doi:10.1002/anie.201206563

  94. High-resolution heteronuclear multidimensional NMR of proteins in living insect cells using a baculovirus protein expression system.

    Hamatsu, J., O'Donovan, D., Tanaka, T., Shirai, T., Hourai, Y., Mikawa, T., Ikeya, T., Mishima, M., Boucher, W., Smith, BO., Laue, ED., Shirakawa, M., Ito, Y.

    J. Am. Chem. Soc., 2013, 135, 1688-91.

    doi:10.1021/ja310928u

  95. Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.

    Otani, J., Arita, K., Kato, T., Kinoshita, M., Kimura, H., Suetake, I., Tajima, S., Ariyoshi, M., Shirakawa, M.

    J. Biol. Chem., 2013, 288, 6351-62.

    doi:10.1074/jbc.M112.431098

  96. Lysyl 5-hydroxylation, a novel histone modification, by Jumonji domain containing 6 (JMJD6).

    Unoki, M., Masuda, A., Dohmae, N., Arita, K., Yoshimatsu, M., Iwai, Y., Fukui, Y., Ueda, K., Hamamoto, R., Shirakawa, M., Sasaki, H., Nakamura, Y.

    J. Biol. Chem., 2013, 288, 6053-62.

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  97. Utilization of lysine 13C-methylation NMR for protein- protein interaction studies.

    Hattori, Y., Furuita, K., Ohki, I., Ikegami, T., Fukada, H., Shirakawa, M., Fujiwara, T., Kojima, C.

    J. Biomol. NMR, 2013, 55(1), 19-31.

    doi:10.1007/s10858-012-9675-9

  98. Hinge and Chromoshadow of HP1α Participate in Recognition of K9 Methylated Histone H3 in Nucleosomes.

    Mishima, Y., Watanabe, M., Kawakami, T., Jayasinghe, CD., Otani, J., Kikugawa, Y., Shirakawa, M., Kimura, H., Nishimura, O., Aimoto, S., Tajima, S., Suetake, I.

    J. Mol. Biol., 2013, 425(1), 54-70.

    doi:10.1016/j.jmb.2012.10.018

  99. 2012

  100. Watching protein structure at work in living cells using NMR spectroscopy.

    Tochio, H.

    Curr. Opin. Chem. Biol., 2012, 16(5-6), 609-613.

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  101. Real-time background-free selective imaging of fluorescent nanodiamonds in vivo.

    Igarashi, R., Yoshinari, Y., Yokota, H., Sugi, T., Sugihara, F., Ikeda, K., Sumiya, H., Tsuji, S., Mori, I., Tochio, H., Harada, Y., Shirakawa, M.

    Nano Lett., 2012, 12(11), 5726-32.

    doi:10.1021/nl302979d

  102. Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1.

    Arita, K., Isogai, S., Oda, T., Unoki, M., Sugita, K., Sekiyama, N., Kuwata, K., Hamamoto, R., Tochio, H., Sato, M., Ariyoshi, M., Shirakawa, M.

    Proc. Natl. Acad. Sci. U S A., 2012, 109(32), 12950-5.

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  103. TRAM is involved in IL-18 signaling and functions as a sorting adaptor for MyD88.

    Ohnishi, H., Tochio, H., Kato, Z., Kawamoto, N., Kimura, T., Kubota, K., Yamamoto, T., Funasaka, T., Nakano, H., Wong, R. W., Shirakawa, M., Kondo, N.

    PLoS. One., 2012, 7(6), e38423.

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  104. Molecular analysis of the binding mode of Toll/interleukin-1 receptor (TIR) domain proteins during TLR2 signaling.

    Nada, M., Ohnishi, H., Tochio, H., Kato, Z., Kimura, T., Kubota, K., Yamamoto, T., Kamatari, Y. O., Tsutsumi, N., Shirakawa, M., Kondo, N.

    Mol Immunol., 2012, 52(3-4), 108-16.

    doi:10.1016/j.molimm.2012.05.003

  105. NMR analysis of Lys63-linked polyubiquitin recognition by the tandem ubiquitin-interacting motifs of Rap80.

    Sekiyama, N., Jee, J., Isogai, S., Akagi, K., Huang, T. H., Ariyoshi, M., Tochio, H., Shirakawa, M.

    J. Biomol. NMR, 2012, 52(4), 339-50.

    doi:10.1007/s10858-012-9614-9

  106. Effect of Ca2+ on the microtubule-severing enzyme p60-katanin. Insight into the substrate-dependent activation mechanism.

    Iwaya, N., Akiyama, K., Goda, N., Tenno, T., Fujiwara, Y., Hamada, D., Ikura, T., Shirakawa, M., Hiroaki, H.

    FEBS. J., 2012, 279(7), 1339–52.

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  107. Substrate/Product-targeted NMR monitoring of pyrimidine catabolism and its inhibition by a clinical drug.

    Yamada, H., Mizusawa, K., Igarashi, R., Tochio, H., Shirakawa, M., Tabata, Y., Kimura, Y., Kondo, T., Aoyama, Y., Sando, S.

    ACS Chem. Biol., 2012, 7(3), 535-42.

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  108. 2011

  109. Crystal structure of the ubiquitin-associated (UBA) domain of p62 and its interaction with ubiquitin.

    Isogai S., Morimoto D., Arita K., Unzai S., Tenno T., Hasegawa J., Sou YS., Komatsu M., Tanaka K., Shirakawa M., Tochio H.

    J. Biol. Chem., 2011, 286(36), 31864-74.

    doi:10.1074/jbc.M111.259630

  110. Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal.

    Fujiwara Y., Fujiwara K., Goda N., Iwaya N., Tenno T., Shirakawa M., Hiroaki H.

    J. Biol. Chem., 2011, 286(24), 21732-41.

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  111. 2010

  112. Purification, crystallization and preliminary crystallographic studies of Lys48-linked polyubiquitin chains.

    Morimoto D., Isogai S., Tenno T., Tochio H., Shirakawa M., Ariyoshi M.

    Acta Crystallogr Sect F Struct Biol Cryst Commun, 2010, 66(Pt 7), 834-7.

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  113. NMR protein structure determination in living E. coli cells using nonlinear sampling.

    Ikeya T., Sasaki A., Sakakibara D., Shigemitsu Y., Hamatsu J., Hanashima T., Mishima M., Yoshimasu M., Hayashi N., Mikawa T., Nietlispach D., Wälchli M., Smith BO., Shirakawa M., Güntert P., Ito Y.

    Nat. Protoc., 2010, 5(6), 1051-60.

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  114. Distance determination in proteins inside Xenopus laevis oocytes by double electron-electron resonance experiments.

    Igarashi R., Sakai T., Hara H., Tenno T., Tanaka T., Tochio H., Shirakawa M.

    J. Am. Chem. Soc., 2010, 132(24), 8228-9.

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  115. 1H, 13C, and 15N resonance assignment of the TIR domain of human MyD88.

    Ohnishi, H., Tochio, H., Kato, Z., Kimura T., Hiroaki, H., Kondo, N. and Shirakawa, M.

    Biomol. NMR Assign., 2010, 4(2), 123-5.

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  116. A common substrate recognition mode conserved between katanin P60 and VPS4 governs microtubule severing and membrane skeleton reorganization.

    Iwaya, N., Kuwahara, Y., Fujiwara, Y., Goda, N., Tenno, T., Akiyama, K., Mase, M., Tochio, H., Ikegami6, T., Shirakawa, M. and Hiroaki, H.

    J. Biol. Chem., 2010, 285(22), 16822-9.

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  117. Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins.

    Jee, J.-G.,Mizuno, T. Kamada, K., Tochio, T., Chiba, Y., Yanagi, K., Yasuda, G., Hiroaki, H., Hanaoka, F. and Shirakawa, M.

    J. Biol. Chem., 2010, 285(21), 15931-40.

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  118. Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45.

    Sekiyama, N., Arita, K., Ikeda, Y., Hashiguchi, K., Ariyoshi, M., Tochio, H., Saitoh, H. and Shirakawa, M.

    Proteins, 2010, 78(6), 1491-502.

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  119. Solution structure of a zinc-finger domain that binds to poly-ADP-ribose.

    Isogai, S., Kanno, S., Ariyoshi, M., Tochio, H., Ito, Y., Yasui, A. and Shirakawa, M.

    Genes Cells, 2010, 15(2), 101-10.

    doi:10.1111/j.1365-2443.2009.01369.x

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  121. Structural basis for recognition of H3K4 methylation status by the DNMT3A ADD domain.

    Otani, J., Nankumo, T., Arita, K., Inamoto, S., Ariyoshi, M. and Shirakawa, M.

    EMBO Rep. 2009, 10(11), 1235-41.

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  122. Self-assembling nano-probes displaying off/on 19F NMR signals for protein detection and imaging.

    Takaoka, Y., Sakamoto, T., Tsukiji, S., Narazaki, M., Matsuda, T., Tochio, H., Shirakawa, M. and Hamachi, I.

    Nat Chem. 2009, 1(7), 557-61.

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  123. Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling.

    Ohnishi, H., Tochio, H., Kato, Z., Orii,K., Li, A., Kimura, T., Hiroaki,H., Kondo, N., and Shirakawa, M.

    Proc Natl Acad Sci U S A. 2009, 106(25), 10260-5.

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  124. Dual-Function Probe to Detect Protease Activity for Fluorescence Measurement and 19F MRI.

    Mizukami, S., Takikawa, R., Sugihara, F., Shirakawa, M. and Kikuchi, K.

    Angew Chem Int Ed Engl. 2009, 48(20), 3641-3.

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  125. High-resolution multi-dimensional NMR spectroscopy of proteins in human cells.

    Inomata, K., Ohno, A., Tochio, H., Isogai, S., Tenno, T., Nakase, I., Takeuchi, T., Futaki, S., Ito, Y., Hiroaki, H, and Shirakawa, M.

    Nature. 2009, 458(7234), 106-9.

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  126. Protein structure determination in living cells by in-cell NMR spectroscopy.

    Sakakibara, D., Sasaki, A., Ikeya, T., Hamatsu, J., Hanashima, T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Walchli, M., Smith, B. O., Shirakawa, M., Guntert, P. and Ito, Y.

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  127. Molecular basis for SUMOylation-dependent regulation of DNA binding activity of Heat Shock Factor 2.

    Tateishi, Y., Ariyoshi, M., Igarashi, R., Hara, H., Mizuguchi, K., Seto, A., Nakai, A., Kokubo, T., Tochio, H. and Shirakawa, M.

    J Biol Chem. 2009, 284(4), 2435-47.

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  129. Structure of the SUMO-interacting motif of MBD1-containing chromatin associated factor 1 (MCAF1) bound to SUMO-3.

    Sekiyama, N., Ikegami, T., Yamane, T., Ikeguchi, M., Uchimura, Y., Baba, D., Ariyoshi, M., Tochio, H., Saitoh, H. and Shirakawa, M.

    J Biol Chem., 2008, 283(51), 35966-75.

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  130. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.

    Arita, K., Ariyoshi, M., Tochio, H., Nakamura, Y. and Shirakawa, M.

    Nature., 2008, 455(7214), 818-21.

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  131. The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold.

    Kuwahara, Y., Ohno, A., Morii, T., Yokoyama, H., Matsui, I., Tochio, H., Shirakawa, M., and Hiroaki, H.

    Protein Sci., 2008, 17(11), 1915-24.

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  132. Expression, purification, and structural analysis of human IL-18 binding protein: A potent therapeutic molecule for allergy.

    Kimura, T., Kato, Z., Ohnishi, H., Tochio, H., Shirakawa, M., Kondo, N.

    Allergol Int. 2008, 57(4), 367-76.

    doi:10.2332/allergolint.O-08-546

  133. Intracellular protein delivery activity of peptides derived from insulin-like growth factor binding proteins 3 and 5.

    Goda, N., Tenno, T., Inomata, K., Shirakawa, M., Tanaka, T., Hiroaki, H.

    Exp Cell Res., 2008, 314(13), 2352-61.

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  134. Kinetic and Thermodynamic evidence for flipping of a methyl-CpG binding domain on methylated DNA.

    Inomata, K., Ohki, I., Tochio, H., Fujiwara, K., Hiroaki, H., Shirakawa, M.

    Biochemistry. 2008, 47(10), 3266-71.

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  135. Paramagnetic Relaxation-Based 19F MRI Probe to Detect Protease.

    Mizukami, S., Takikawa, R., Sugihara, F., Hori, Y., Tochio, H., Waelchli, M., Shirakawa, M., Kikuchi, K.

    J Am Chem Soc., 2008, 130(3), 794-5.

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  137. Structural Analysis of Pituitary Adenylate Cyclase-Activating polypeptides Bound to Phospholipid embranes by Magic Angle Spinning Solid-State NMR.

    Komi, N., Okawa, K., Tateishi, Y., Shirakawa, M., Fujiwara, T., Akutsu, H.

    Biochim Biophys Acta. 2007, 1768(12), 3001-11.

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  138. Fluoroscopic assessment of protein leakage during Xenopus oocytes in-cell NMR experiment by co-injected EGFP.

    Sakai, T., Tochio, H., Inomata, K., Sasaki, Y., Tenno, T., Tanaka, T., Kokubo, T., Hiroaki, H., Shirakawa, M.

    Anal Biochem. 2007, 371(2), 247-9.

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  139. Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies.

    Maita, N., Aoyagi, H., Osanai, M., Shirakawa, M., Fujiwara, H.

    Nucleic Acids Res. 2007, 35(12), 3918-27.

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  140. Magnetic resonance-based visualization of gene expression in mammalian cells using a bacterial polyphosphate kinase reporter gene.

    Ki, S., Sugihara, F., Kasahara, K., Tochio, H., Shirakawa, M. and Kokubo, T.

    Biotechniques. 2007, 42(2), 209-15.

  141. LBT/PTD dual tagged vector for purification, cellular protein delivery and visualization in living cells.

    Goda, N., Tenno, T., Inomata, K., Iwaya, N., Sasaki, Y., Shirakawa, M., Hiroaki, H.

    Biochim Biophys Acta. 2007, 1773(2), 141-6.

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  142. Distance determination in human ubiquitin by pulsed double electron-electron resonance and double quantum coherence ESR methods.

    Hara, H., Tenno, T. and Shirakawa, M.

    J Magn Reson. 2007, 184(1), 78-84.

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  143. Fine-tuning of protein domain boundary by minimizing potential coiled coil regions.

    Iwaya, N., Goda, N., Unzai, S., Fujiwara, K., Tanaka, T., Tomii, K., Tochio, H., Shirakawa, M. and Hiroaki, H.

    J Biomol NMR. 2007, 37(1), 53-63.

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  145. In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes.

    Sakai, T., Tochio, H., Tenno, T., Ito, Y., Kokubo, T., Hiroaki, H. and Shirakawa, M.

    J Biomol NMR. 2006, 36(3), 179-88.

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  146. Crystal structure of SUMO-3-modified thymine-DNA glycosylase.

    Baba, D., Maita; N., Jee, J.-G., Uchimura, Y., Saitoh, H., Sugasawa, K., Hanaoka, F., Tochio, H., Hiroaki, H, Shirakawa, M.

    J Mol Biol. 2006, 359(1), 137-47.

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  147. A novel magnetic resonance-based method to measure gene expression in living cells.

    Ki, S., Sugihara, F., Kasahara, K., Tochio, H., Okada-Marubayashi, A., Tomita, S., Morita, M., Ikeguchi, M., Shirakawa, M. and Kokubo, T.

    Nucleic Acids Res. 2006, 34(6), e51.

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  148. The structure of the third intracellular loop of the muscarinic acetylcholine receptor M2 subtype.

    Ichiyama, S., Oka, Y., Haga, K., Kojima, S., Tateishi, Y., Shirakawa, M., and Haga, T.

    FEBS Lett. 2006, 580(1), 23-6.

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  150. Crystal Structure of thymine DNA glycosylase conjugated to SUMO-1.

    Baba, D., Maita, N., Jee, J.-G., Uchimura, Y., Saitoh, H., Sugasawa, K., Hanaoka, F., Tochio, H., Hiroaki, H., Shirakawa, M.

    Nature. 2005, 435(7044), 979-82.

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  151. Role of the UBL-UBA protein KPC2 in degradation of p27 at G1 phase of the cell cycle.

    Hara, T., Kamura, T., Kotoshiba, S., Fujiwara, K., Onoyama, I., Shirakawa, M. and Nakayama, K.-I.

    Mol Cell Biol. 2005, 25(21), 9292-303.

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  152. Molecular mechanism of a temperature-sensitive phenotype in peroxisomal biogenesis disorder.

    Hashimoto, K., Kato, Z., Nagase, T., Shimozawa, N., Kuwata, K., Omoya, K., Li, A., Matsukuma, E., Yamamoto, Y., Ohnishi, H., Tochio, H., Shirakawa, M., Suzuki, Y., Wanders, R. J. A., Kondo, N.

    Pediatr Res. 2005, 58(2), 263-9.

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  153. Structural characterization of the MIT domain from human Vps4b.

    Takasu, H., Jee, J. G., Ohno, A., Goda, N., Fujiwara, K., Tochio, H., Shirakawa, M., and Hiroaki, H.

    Biochem Biophys Res Commun. 2005, 334(2), 460-5.

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  154. Plc1p, Arg82p, and Kcs1p, enzymes involved in inositol pyrophosphate synthesis, are essential for phosphate regulation and polyphosphate accumulation in Saccharomyces cerevisiae.

    Auesukaree, C., Tochio, H., Shirakawa, M., Kaneko, Y., and Harashima, S.

    J Biol Chem. 2005, 280(26), 25127-33.

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  155. Structure of the UBA domain of Dsk2p in complex with Ubiquitin: Molecular Determinants for Ubiquitin Recognition.

    Ohno, A., Jee, J-G, Fujiwara, K., Tenno, T., Goda, N., Tochio, H., Kobayashi, H., Hiroaki, H., Shirakawa, M.

    Structure. 2005, 13(4), 521-32.

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  156. Backbone 1H, 13C, and 15N assignments of a 56 kDa E. coli nickel binding protein NikA

    Rajesh, S., Heddle, J. G., Kurashima-Ito, K., Nietlispach, D., Shirakawa, M., Tame, J. R., and Ito, Y.

    J Biomol NMR. 2005, 32(2), 177.

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  158. p53 suppresses c-Myb-induced trans-activation and transformation by recruiting the corepressor mSin3A.

    Tanikawa, J., Nomura, T., Macmillan, E. M., Shinagawa, T., Jin, W., Kokura, K., Baba, D., Shirakawa, M., Gonda, T. J., and Ishii, S.

    J Biol Chem. 2004, 279(53), 55393-400.

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  159. Two-Metal Ion, Ni(II) and Cu(II), Binding a-Helical Coiled-coil Peptide.

    Tanaka, T., Mizuno, T., Fukui, S., Hiroaki, H., Oku, J., Kanaori, K., Tajima, K. and Shirakawa, M.

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  160. Structure of the N-terminal domain of PEX1 AAA-ATPase: characterization of a putative adaptor-binding domain.

    Shiozawa, K. Maita, N., Tomii, K, Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H.

    J Biol Chem. 2004, 279(48), 50060-8.

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  161. Crystallographic characterization of the N-terminal domain of PEX1.

    Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., and Hiroaki, H.

    Acta Crystallogr D Biol Crystallogr. 2004, 60(Pt 11), 2098-9.

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  162. Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains.

    Tenno, T., Fujiwara, K., Tochio, H., Iwai, K., Morita, E. H., Hayashi, H., Murata, S., Hiroaki, H., Sato, M., Tanaka, K., and Shirakawa, M.

    Genes Cells. 2004, 9(10), 865-75.

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  163. Small ubiquitin-like modifier 1 (SUMO-1) modification of the synergy control motif of Ad4 binding protein/steroidogenic factor 1 (Ad4BP/SF-1) regulates synergistic transcription between Ad4BP/SF-1 and Sox9.

    Komatsu, T., Mizusaki, H., Mukai, T., Ogawa, H., Baba, D., Shirakawa, M., Hatakeyama, S., Nakayama, K. I., Yamamoto, H., Kikuchi, A., and Morohashi, K.

    Mol Endocrinol. 2004, 18(10), 2451-62.

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  164. MUTYH prevents OGG1 or APEX1 from inappropriately processing its substrate or reaction product with its C-terminal domain.

    Tominaga, Y., Ushijima, Y., Tsuchimoto, D., Mishima, M., Shirakawa, M., Hirano, Sakumi, K., Nakabeppu, Y.

    Nucleic Acids Res. 2004, 32(10), 3198-211.

    doi:10.1093/nar/gkh642

  165. Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates.

    Mishima, M., Sakai, Y., Itoh, N., Kamiya, H., Furuichi, M., Takahashi, M., Yamagata, Y., Iwai, S., Nakabeppu, Y., and Shirakawa, M.

    J Biol Chem. 2004, 279(32), 33806-15.

    doi:10.1074/jbc.M402393200

  166. High-throughput construction method for expression vector of peptides for NMR study suited for isotopic labeling.

    Tenno, T., Goda, N., Tateishi, Y., Tochio, H., Mishima, M., Shirakawa, M. and Hiroaki, H.

    Protein Eng Des Sel. 2004, 17(4), 305-14.

    doi:10.1093/protein/gzh044

  167. Paramagnetic NMR study of Cu(2+)-IDA complex localization on a protein surface and its application to elucidate long distance information.

    Nomura, M., Kobayashi, T., Kohno, T., fujiwara, K., Tenno, T., Shirakawa, M., Ishizaki, I., Yamamoto, K., Matsuyama, T., Mishima, M., Kojima, C.

    FEBS Lett. 2004, 566(1-3), 157-61.

    doi:10.1016/j.febslet.2004.04.023

  168. Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccharomyces cerevisiae.

    Auesukaree, C., Homma, T., Tochio, H., Shirakawa, M., Kaneko, Y., and Harashima, S.

    J Biol Chem. 2004, 279(17), 17289-94.

    doi:10.1074/jbc.M312202200

  169. Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B.

    Fujiwara, K., Tenno, T., Sugasawa, K., Jee, J.-G., Ohki, I., Kojima, C., Tochio, H., Hiroaki, H., Hanaoka, F., and Shirakawa, M.

    J Biol Chem. 2004, 279(6), 4760-7.

    doi:10.1074/jbc.M309448200

  170. The PRESAT-vector:Asymmetric T-vector for high-throughput screening of soluble protein domains for structural proteomics.

    Goda, N., Tenno, T., Takasu, H., Hiroaki, H., and Shirakawa, M.

    Protein Sci. 2004, 13(3), 652-8.

    doi:10.1110/ps.03439004

  171. 2003

  172. The structure and binding mode of interleukin-18.

    Kato, Z, Jee, J.-G., Shikano, H., Mishima, M., Ohki, I., Ohnishi, H., Li, A., Hashimoto, K., Matsukuma, E., Omoya, K., Yamamoto, Y., Yoneda, T., Hara, T., Kondo, N., and Shirakawa, M.

    Nat Struct Biol. 2003, 10(11), 966-71.

    doi:10.1038/nsb993

  173. Structure of the male determinant factor for Brassica self-incompatibility.

    Mishima, M., Takayama, S., Sasaki, K., Jee, J. G., Kojima, C., Isogai, A., and Shirakawa, M.

    J Biol Chem. 2003, 278(38), 36389-95.

    doi:10.1074/jbc.M305305200

  174. Methylated DNA-binding domain 1 and methylpurine-DNA glycosylase link transcriptional repression and DNA repair in chromatin.

    Watanabe, S., Ichimura, T., Fujita, N., Tsuruzoe, S., Ohki, I., Shirakawa, M., Kawasuji, M., and Nakao, M.

    Proc Natl Acad Sci U S A. 2003, 100(22), 12859-64.

    doi:10.1073/pnas.2131819100

  175. 2002

  176. Solution structure of the Fibronectin Type III Domain from Bacillus circulans WL-12 Chitinase A1.

    Jee, J.-G., Ikegami, T., Hashimoto, M., Kawabata, T., Ikeguchi, M., Watanabe, T., and Shirakawa, M.

    J Biol Chem. 2002, 277(2), 1388-97.

    doi:10.1074/jbc.M109726200

  177. Role of tryptophan residues in the recognition of mutagenic oxidized nucleotides by human antimutator MTH1 protein.

    Takahashi, M., Maraboeuf, F., Sakai, Y., Yakushiji, H., Mishima, M., Shirakawa, M., Iwai, S., Hayakawa, H., Sekiguchi, M., and Nakabeppu, Y. (2002).

    J Mol Biol. 2002, 319(1), 129-39.

  178. A molecular basis for the selective recognition of 2-hydroxy-dATP and 8-oxo-dGTP by human MTH1.

    Sakai, Y., Furuichi, M., Takahashi, M., Mishima, M., Iwai, S., Shirakawa, M., and Nakabeppu, Y.

    J Biol Chem. 2002, 277(10), 8579-87.

    doi:10.1074/jbc.M110566200

  179. 1H, 13C and 15N resonance assignments of GABARAP, GABAA receptor associated protein.

    Kouno, T., Miura, K., Kanematsu, T., Shirakawa, M., Hirata, M., and Kawano, K.

    J Biomol NMR. 2002, 22(1), 97-8.

  180. 2001

  181. Solution Structure of the Methyl-CpG-binding Domain of Human MBD1 in Complex with Methylated DNA.

    Ohki, I., Shimotake, N., Fujita, N., Jee, J.-G., Ikegami, T., Nakao, M., and Shirakawa, M.

    Cell. 2001, 105(4), 487-97.

    doi:10.1016/S0092-8674(01)00324-5

  182. Conformation of a peptide ligand bound to its G-protein coupled receptor.

    Inooka, H., Ohtaki, T., Kitahara, O., Ikegami, T., Endo, S., Kitada, C., Ogi, K., Onda, H., Fujino, M., and Shirakawa, M.

    Nat Struct Biol. 2001, 8(2), 161-5.

    doi:10.1038/84159

  183. 2000

  184. Intermolecular 31P-15N and 31P-1H scalar couplings across hydrogen bonds formed between a protein and a nucleotide.

    Mishima, M., Hatanaka, M., Yokoyama, S., Ikegami, T., Markus Waelchli, Y. I., and Shirakawa, M.

    J. Am. Chem. Soc., 2000, 122 (24), 5883–5884.

    doi:10.1021/ja000005w

  185. Solution structure and dynamic character of the histidine-containing phosphotransfer domain of anaerobic sensor kinase ArcB from Escherichia coli.

    Ikegami, T., Okada, T., Ohki, I., Hirayama, J., Mizuno, T., and Shirakawa, M.

    Biochemistry. 2001, 40(2), 375-86.

    doi:10.1021/bi001619g

  186. Expression and characterization of the chitin-binding domain of chitinase A1 from bacillus circulans WL-12

    Hashimoto, M., Ikegami, T., Seino, S., Ohuchi, N., Fukada, H., Sugiyama, J., Shirakawa, M., and Watanabe, T.

    J Bacteriol. 2000, 182(11), 3045-54.

    doi:10.1128/JB.182.11.3045-3054.2000

  187. Solution Structure of the Chitin-Binding Domain of Bacillus circulans WL-12 Chitinase A1.

    Ikegami, T., Okada, T., Hashimoto, M., Seino, S., Watanabe, T., and Shirakawa, M.

    J Biol Chem. 2000, 275(18), 13654-61.

    doi:10.1074/jbc.275.18.13654

  188. Mechanism of transcriptional regulation by methyl-CpG binding protein MBD1.

    Fujita, N., Shimotake, N., Ohki, I., Chiba, T., Saya, H., Shirakawa, M., and Nakao, M.

    Mol Cell Biol. 2000, 20(14), 5107-18.

    doi:10.1128/MCB.20.14.5107-5118.2000

  189. 1999

  190. Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1.

    Ohki, I., Shimotake, N., Fujita, N., Nakao, M., and Shirakawa, M.

    EMBO J. 1999, 18(23), 6653-61.

    doi:10.1093/emboj/18.23.6653

  191. The Role of Human MBF1 as a Transcriptional Coactivator.

    Kabe, Y., Goto, M., Shima, D., Imai, T., Wada, T., Morohashi, K., Shirakawa, M., Hirose, S., and Handa, H.

    J Biol Chem. 1999, 274(48), 34196-202.

    doi:10.1074/jbc.274.48.34196

  192. Resonance assignments, secondary structure and 15N relaxation data of the human transcriptional coactivator hMBF1 (57-148).

    Mishima, M., Ozaki, J., Ikegami, T., Kabe, Y., Goto, M., Ueda, H., Hirose, S., Handa, H. and Shirakawa, M.

    J Biomol NMR. 1999, 14(4), 373-6.

    doi:10.1023/A:1008347729176

  193. Identification of the core domain and the secondary structure of the transcriptional coactivator MBF1.

    Ozaki, J., Ikegami, T., Mishima, M., Takemaru, K.-i., Kabe, Y., Handa, H., Ueda, H., Hirose, S. and Shirakawa, M.

    Genes Cells. 1999, 4(7), 415-24.

    doi:10.1046/j.1365-2443.1999.00267.x

  194. Resonance assignments, solution structure, and backbone dynamics of the DNA- and RPA-binding domain of Human repair factor XPA.

    Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K. and Shirakawa, M.

    J Biochem. 1999, 125(3), 495-506.

    doi:10.1093/oxfordjournals.jbchem.a022313

  195. 1998

  196. In vitro selection of a DNA aptamer binding to thyroxine.

    Kawazoe, N., Ito, Y., Shirakawa, M. and Imanishi, Y.

     Bull. Chem. Soc. Jpn., 1998, 71(7):1699-1703

    doi:10.1246/bcsj.71.1699

  197. Solution structure of the IRF-2 DNA binding domain: a novel subgroup of the winged helix-turn-helix family.

    Furui, J., Uegaki, K., Yamazaki, T., Shirakawa, M., Swindells, M. B., Harada, H., Taniguchi, T. and Kyogoku, Y.

    Structure. 1998, 6(4),491-500.

    doi:10.1016/S0969-2126(98)00050-1

  198. Crystal Structure of Human RhoA in a Dominantly Active Form Complexed with a GTP Analogue.

    Ihara, K., Muraguchi, S., Kato, M., Shimizu, T., Shirakawa, M., Kuroda, K., Kaibuchi, K. and Hakoshima, T.

    J Biol Chem. 1998, 273(16), 9656-66.

    doi:10.1074/jbc.273.16.9656

  199. Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA.

    Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K. and Shirakawa, M.

    Nat Struct Biol. 1998, 5(8), 701-6.

    doi:10.1038/1400

  200. 1997

  201. An Efficient HN(CA)NH Pulse Scheme for Triple-Resonance 4D Correlation of Sequential Amide Protons and Nitrogens-15 in Deuterated Proteins

    Ikegami, T., Sato, S., Waelchli, M., Kyogoku, Y. and Shirakawa, M.

    J Magn Reson. 1997, 124(1), 214-7.

    doi:10.1006/jmre.1996.7497

  202. 1996

  203. Backbone dynamics of the λ-Cro repressor protein determined by 15N relaxation measurements. Application of an efficient method for calculation of dynamics parameters

    Matsuo, H., Sugeta, H., Shirakawa, M. and Kyogoku, Y.

    J Mol Struct., 1996, 379(1):143-150

    doi:10.1016/0022-2860(95)09160-2

  204. Identification of a damaged-DNA binding domain of the XPA protein.

    Kuraoka, I., Morita, E. H., Saijo, M., Matsuda, T., Morikawa, K., Shirakawa, M. and Tanaka, K.

    Mutat Res. 1996, 362(1), 87-95.

    doi:10.1016/0921-8777(95)00038-0

  205. Implications of the zinc-finger motif found in the DNA-binding domain of the human XPA protein.

    Morita, E. H., Ohkubo, T., Kuraoka, I., Shirakawa, M., Tanaka, K. and Morikawa, K.

    Genes Cells. 1996, 1(5), 437-42.

    doi:10.1046/j.1365-2443.1996.d01-252.x

  206. Linkage and Solvent Dependence of Photoinduced Electron Transfer in Zincporphyrin-C60 Dyads

    Imahori, H., Hagiwara, K., Aoki, M., Akiyama, T., Taniguchi, S., Okada, T., Shirakawa, M. and Sakata, Y.

    J. Am. Chem. Soc., 1996, 118 (47), pp 11771–11782

    doi:10.1021/ja9628415

  207. The Small Reorganization Energy of C60 in Electron Transfer.

    Imahori, H., Hagiwara, K., Akiyama, T., Aoki, M., Taniguchi, S., Okada, T., Shirakawa, M. and Sakata, Y.

    Chem Phys Lett., 1996, 263(3-4):545-550.

    doi:10.1016/S0009-2614(96)01244-4

  208. 1995

  209. Structure of the Oct-3 POU-homeodomain in Solution, as Determined by Triple Resonance Heteronuclear Multidimensional NMR Spectroscopy.

    Morita, E. H., Shirakawa, M., Hayashi, F., Imagawa, M. and Kyogoku, Y.

    Protein Sci. 1995, 4(4), 729-39.

    doi:10.1002/pro.5560040412

  210. Secondary structure and folding topology of the DNA binding domain of interferon regulatory factor 2, as revealed by NMR spectroscopy.

    Uegaki, K., Shirakawa, M., Harada, H., Taniguchi, T. and Kyogoku, Y.

    FEBS Lett. 1995, 359(2-3), 184-8.

    doi:10.1016/0014-5793(95)00040-G

  211. The use of heteronuclear cross-polarization for backbone assignment of 2H-, 15N- and 13C-labeled proteins: A pulse scheme for triple-resonance 4D correlation of sequential amide protons and 15N

    Shirakawa, M., Walechli, M., Shimizu, M. and Kyogoku, Y.

    J Biomol NMR., 1995, 5(3):323-326.

    doi:10.1007/BF00211761

  212. Three-dimensional Dimer Structure of the l-Cro Repressor in Solution as Determined by Heteronuclear Multidimensional NMR.

    Matsuo, H., Shirakawa, M. and Kyogoku, Y.

    J Mol Biol. 1995, 254(4), 668-80.

    doi:10.1006/jmbi.1995.0646

  213. Solution Structure of the Activator Contact Domain of the RNA Polymerase a Subunit.

    Jeon, Y. H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A. and Kyogoku, Y.

    Science. 1995, 270(5241), 1495-7.

    doi:10.1126/science.270.5241.1495

  214. 1994

  215. Unique structure of the DNA binding domain of Interferon Regulatory Factor 2 determined by NMR spectroscopy.

    Uegaki, K., Shirakawa, M., Harada, H., Taniguchi, T. and Kyogoku, Y.

    Structure. 1998, 6(4), 491-500.

    https://www.jstage.jst.go.jp/article/pjab1977/70/10/70_10_200/_articledoi:10.2183/pjab.70.200

  216. The XPA protein is a zinc metalloprotein with an ability to recognize various kinds of DNA damage.

    Asahina, H., Kuraoka, I., Shirakawa, M., Morita, E. H., Miura, N., Miyamoto, I., Ohtsuka, E., Okada, Y. and Tanaka, K.

    Mutat Res. 1994, 315(3), 229-37.

    doi:10.1016/0921-8777(94)90034-5

  217. 1993

  218. Characterization of the DNA binding domain of the mouse IRF-2 protein.

    Uegaki, K., Shirakawa, M., Fujita, T., Taniguchi, T. and Kyogoku, Y.

    Protein Eng. 1993, 6(2), 195-200.

    doi:10.1093/protein/6.2.195

  219. Assignment of 1H, 15N, and 13C resonances, identification of elements of secondary structure and determination of the global fold of the DNA-binding domain of GAL4.

    Shirakawa, M., Fairbrother, W. J., Serikawa, Y., Ohkubo, T., Kyogoku, Y. and Wright, P. E.

    Biochemistry. 1993, 32(9), 2144-53.

  220. Crystallographic characterization of a PHO4-DNA complex.

    Hakoshima, T., Teranishi, Y., Ohira, T., Suzuki, K., Shimizu, M., Shirakawa, M., Kyogoku, Y., Ogawa, N. and Oshima, Y.

    J Mol Biol. 1993, 229(2), 566-9.

    doi:10.1006/jmbi.1993.1059

  221. Structure of the Oct-3 POU-homeodomain in solution, as determined by triple resonance heteronuclear multidimensional NMR spectroscopy.

    Morita, E. H., Shirakawa, M., Hayashi, F., Imagawa, M. and Kyogoku, Y.

    Protein Sci. 1995, 4(4), 729-39.

    doi:10.1002/pro.5560040412

  222. 1992

  223. Fission yeast pap1-dependent transcription is negatively regulated by and essential nuclear protein, crm1.

    Toda, T., Shimanuki, M., Saka, Y., Yamano, H., Adachi, Y., Shirakawa, M., Kyogoku, Y. and Yanagida, M.

    Mol Cell Biol. 1992, 12(12), 5474-84.

    doi:10.1128/MCB.12.12.5474

  224. Determination of the DNA binding site of the GAL4 protein: A photo-CIDNP study.

    Serikawa, Y., Shirakawa, M. and Kyogoku, Y.

    FEBS Lett. 1992, 299(3), 205-8.

    doi:10.1016/0014-5793(92)80115-W

  225. Characterization of the bacterially expressed Drosophila engrailed homeodomain.

    Yamamoto, K., Yee, C. C., Shirakawa, M. and Kyogoku, Y.

    J Biochem. 1992, 111(6), 793-7.

    doi:10.1093/oxfordjournals.jbchem.a123838

  226. 1991

  227. Assignments of 1H-15N magnetic resonances and identification of secondary structure elements of the λ-cro repressor.

    Matsuo, H., Shirakawa, M., Ohkubo, T., Yamazaki, T. and Kyogoku, Y.

    J Biomol NMR. 1991, 1(2), 191-204.

    doi:10.1007/BF01877230

  228. Stringent integrity requirements for both trans-activation and DNA-binding in a trans-activator, Oct3.

    Imagawa, M., Miyamoto, A., Shirakawa, M., Hamada, H. and Muramatsu, M.

    Nucleic Acids Res. 1991, 19(16), 4503-8.

    doi:10.1093/nar/19.16.4503

  229. Interaction of the λ-cro repressor protein with operator DNA fragments monitored as to amide proton magnetic resonances

    Shirakawa, M., Lee, S. J., Takimoto, M., Matsuo, H., Akutsu, H. and Kyogoku, Y.

    J Mol Struct., 1991, 242, 355-366

    doi:10.1016/0022-2860(91)87147-A

  230. Intersubunit disulfide-bonded λ-Cro protein

    Shirakawa, M., Matsuo, H. and Kyogoku, Y.

    Protein Eng. 1991, 4(5), 545-52.

    doi:10.1093/protein/4.5.545

  231. 1990

  232. Efficient expression and Zn(II)-dependent structure of the DNA binding domain of the yeast GAL4 protein.

    Serikawa, Y., Shirakawa, M., Matsuo, H. and Kyogoku, Y.

    Protein Eng. 1990, 3(4), 267-72.

    doi:10.1093/protein/3.4.267

  233. 1987

  234. Base sequence-specific interactions of operator DNA fragments with the λ-Cro repressor coupled with changes in their conformations.

    Lee, S. J., Shirakawa, M., Akutsu, H., Kyogoku, Y., Shiraishi, M., Kitano, K., Shin, M., Otsuka, E. and Ikehara, M.

    EMBO J. 1987, 6(4), 1129-35.

  235. 1985

  236. Exposed tyrosine residues of lambda Cro repressor protein evidenced by nitration and photo CIDNP experiments.

    Shirakawa, M., Kawata, Y., Lee, S. J., Akutsu, H., Sakiyama, F. and Kyogoku, Y.

    J Biochem. 1985, 98(3), 799-805.

    doi:10.1093/oxfordjournals.jbchem.a135337

  237. Photo CIDNP study on the complex formation of λ- Cro protein with OR3.

    Shirakawa, M., Lee, S. J., Akutsu, H., Kyogoku, Y., Kitano, K., Shin, M., Otsuka, E. and Ikehara, M.

    FEBS Lett. 1985, 181(2), 286-90.

    doi:10.1016/0014-5793(85)80277-5

  238. 1984

  239. Plasmid vectors designed for high-efficiency expression controlled by portable recA promoter-operator of Eshrerichi coli.

    Shirakawa, M., Tsurimoto, T. and Matsubara, K.

    Gene. 1984, 28(1), 127-32.

    doi:10.1016/0378-1119(84)90096-9