Publications

    2023

  1. An integrated approach of NMR experiments and MD simulations visualizes structural dynamics of a cyclic multi‐domain protein.

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

    Protein Sci., 2023, 32(10), e4768

    doi:10.1002/pro.4768

  2. Solution structure of the HOIL-1L NZF domain reveals a conformational switch regulating linear ubiquitin affinity.

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

    J. Biol. Chem., 2023, 299, 9, 105165

    doi:10.1016/j.jbc.2023.105165

  3. Conformational fluctuations and induced orientation of a protein, its solvation shell, and bulk water in weak non-unfolding external electric fields.

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

    J. Phys. Chem. B, 2023, 127, 34, 7417-7430

    doi:10.1021/acs.jpcb.3c01683

  4. NMRによるアミロイド形成の原子レベル機構解明

    森本 大智

    日本核磁気共鳴学会、Vol.13

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

  5. タンパク質の構造解析手法とIn silicoスクリーニングへの応用事例

    森本 大智、菅瀬 謙治

    技術情報協会、第3節 タンパク質を多角的に捉えるNMR測定法

    技術情報協会のサイトへ: Link to the website of Technical information institute

  6. 混雑環境がタンパク質の構造揺らぎと異常凝集体形成に影響を与える

    森本 大智、Erik Walinda、菅瀬 謙治

    月刊「細胞」2023年 3月号

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

  7. Distance measurements between 5 nanometer diamonds – single particle magnetic resonance or optical super-resolution imaging?

    Pinotsi, D., Tian, R., Anand, P., Miyanishi, K., Boss, JM., Chang, KK., Welter, P., So, FTK., Terada, D., Igarashi, R., Shirakawa, M., Degenb, CL., and Segawa, TF.

    Nanoscale Adv., 2023, 5, 1345-1355

    doi:10.1039/D2NA00815G

  8. Distance measurements between 5 nanometer diamonds – single particle magnetic resonance or optical super-resolution imaging?

    Pinotsi, D., Tian, R., Anand, P., Miyanishi, K., Boss, JM., Chang, KK., Welter, P., So, FTK., Terada, D., Igarashi, R., Shirakawa, M., Degenb, CL., and Segawa, TF.

    Nanoscale Adv., 2023, 5, 1345-1355

    doi:10.1039/D2NA00815G

    9. 2022

  9. Rheo-NMR spectroscopy for cryogenic-probe-equipped NMR instruments to monitor protein aggregation.

    Morimoto, D., Walinda, E., Yamamoto, A., Scheler, U., and Sugase, K.

    Curr. Protoc., 2022, 2, e617

    doi:10.1002/cpz1.617

  10. Counter-flow phenomena studied by nuclear magnetic resonance (NMR) velocimetry and flow simulations.

    Kohn, BD., Walinda, E., Sugase, K., Morimoto, D., and Scheler, U.

    Phys. Fluids, 2022, 34, 073608

    doi:10.1063/5.0097543

  11. Anomalous Formation of Irradiation-Induced Nitrogen-Vacancy Centers in 5 nm-Sized Detonation Nanodiamonds.

    So, FTK., Shames, AI., Terada, D., Genjo, T., Morishita, H., Ohki, I., Ohshima, T., Onoda, S., Takashima, H., Takeuchi, S., Mizuochi, N., Igarashi, R., Shirakawa, M., and Segawa, TF.

    J. Phys. Chem. C, 2022, 126, 11, 5206-5217.

    doi:10.1021/acs.jpcc.1c10466

  12. A simple and soft chemical deaggregation method producing single-digit detonation nanodiamonds.

    Terada, D., So, FTK., Hattendorf, D., Yanagi, T., Ōsawa, E., Mizuochi, N., Shirakawa, M., Igarashi, R., and Segawa, TF.

    Nanoscale Adv., 2022, 4, 2268-2277.

    doi:10.1039/D1NA00556A

  13. 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, 7, 4, 3212-3221.

    doi:10.1021/acsomega.1c04917

    14. 2021

  14. Overcoming humidity-induced swelling of graphene oxide-based hydrogen membranes using charge-compensating nanodiamonds.

    Huang, G., Ghalei, B., Isfahani, AP, Karahan, HE, Terada, D., Qin, D., Li, C., Tsujimoto, M., Yamaguchi, D., Sugimoto, K., Igarashi, R., Chang, BK, Li, T., Shirakawa, M., and Sivaniah, E.

    Nat. Energy, 2021, 6, 1176-1187.

    doi:10.1038/s41560-021-00946-y

  15. 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:10.1039/D1CP03175A

  16. 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

  17. Non-contact measurement of internal body temperature using subcutaneously implanted diamond microparticles.

    Kaminaga, K., Yanagihara, H., Genjo, T., Morioka, T., Abe, H., Shirakawa, M., Ohshima, T., Kakinuma, S., and Igarashi, R.

    Biomater. Sci., 2021, 9(21), 7049-7053.

    doi:10.1039/d1bm01187a

  18. 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

  19. 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

  20. 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:10.1007/s12104-021-10041-8

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

    30. 2020

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

    38. 2019

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

    47. 2018

  47. 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

  48. 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

  49. 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

  50. 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

  51. Resolving biomolecular motion and interactions by R2 and R1ρ Relaxation Dispersion NMR.

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

    Methods, 2018, 148, 28-38.

    doi:10.1016/j.ymeth.2018.04.026

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

    57. 2017

  57. Elucidating Functional Dynamics by R1ρ 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. Practical considerations for investigation of protein conformational dynamics by 15N R1ρ 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

  68. 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

    69. 2016

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. Efficient identification and analysis of chemical exchange in biomolecules by R1ρ 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

  75. 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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  159. 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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  160. 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.

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  161. 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.

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

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

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  163. 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.

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  164. 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.

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

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

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  168. 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.

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

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  170. 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.

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  171. 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).

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

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  173. 1H, 13C and 15N resonance assignments of GABARAP, GABAA receptor associated protein.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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  209. Characterization of the bacterially expressed Drosophila engrailed homeodomain.

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

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

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

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