Masahiro Shirakawa

Masahiro Shirakawa

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Masahiro Shirakawa

Masahiro Shirakawa

Publications by authors named "Masahiro Shirakawa"

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

Biochem Biophys Res Commun 2020 Aug 1;529(2):418-424. Epub 2020 Jul 1.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2020.06.008DOI Listing
August 2020

Tracking the 3D Rotational Dynamics in Nanoscopic Biological Systems.

J Am Chem Soc 2020 Apr 14;142(16):7542-7554. Epub 2020 Apr 14.

Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan.

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http://dx.doi.org/10.1021/jacs.0c01191DOI Listing
April 2020

Nanodiamonds for bioapplications-specific targeting strategies.

Biochim Biophys Acta Gen Subj 2020 02 7;1864(2):129354. Epub 2019 May 7.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03044165193011
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http://dx.doi.org/10.1016/j.bbagen.2019.04.019DOI Listing
February 2020

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

Biochim Biophys Acta Gen Subj 2020 02 12;1864(2):129383. Epub 2019 Jun 12.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbagen.2019.06.006DOI Listing
February 2020

pH Nanosensor Using Electronic Spins in Diamond.

ACS Nano 2019 10 20;13(10):11726-11732. Epub 2019 Sep 20.

Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology , Anagawa 4-9-1 , Inage-ku, Chiba 263-8555 , Japan.

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http://dx.doi.org/10.1021/acsnano.9b05342DOI Listing
October 2019

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

ACS Nano 2019 06 29;13(6):6461-6468. Epub 2019 May 29.

Department of Molecular Engineering, Graduate School of Engineering , Kyoto University , Nishikyo-Ku , Kyoto 615-8510 , Japan.

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http://dx.doi.org/10.1021/acsnano.8b09383DOI Listing
June 2019

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

Angew Chem Int Ed Engl 2019 05 25;58(22):7284-7288. Epub 2019 Apr 25.

Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.

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http://dx.doi.org/10.1002/anie.201900840DOI Listing
May 2019

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

Biomol NMR Assign 2019 04 21;13(1):59-62. Epub 2018 Sep 21.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.

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http://dx.doi.org/10.1007/s12104-018-9851-2DOI Listing
April 2019

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

Biomol NMR Assign 2019 04 19;13(1):149-153. Epub 2018 Dec 19.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.

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http://dx.doi.org/10.1007/s12104-018-09868-5DOI Listing
April 2019

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

Bioconjug Chem 2018 08 18;29(8):2786-2792. Epub 2018 Jul 18.

Department of Molecular Engineering, Graduate School of Engineering , Kyoto University , Nishikyo-ku, Kyoto 615-8519 , Japan.

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http://dx.doi.org/10.1021/acs.bioconjchem.8b00412DOI Listing
August 2018

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

Sci Rep 2018 04 3;8(1):5463. Epub 2018 Apr 3.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto, 615-8510, Japan.

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http://dx.doi.org/10.1038/s41598-018-23635-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883028PMC
April 2018

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

Anal Sci 2016 ;32(11):1165-1170

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University.

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http://dx.doi.org/10.2116/analsci.32.1165DOI Listing
February 2018

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

Sci Rep 2018 02 9;8(1):2711. Epub 2018 Feb 9.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.

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http://dx.doi.org/10.1038/s41598-018-21144-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807323PMC
February 2018

Hydrogen-Deuterium Exchange Profiles of Polyubiquitin Fibrils.

Polymers (Basel) 2018 Feb 27;10(3). Epub 2018 Feb 27.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.

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http://www.mdpi.com/2073-4360/10/3/240
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http://dx.doi.org/10.3390/polym10030240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6414897PMC
February 2018

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

FEBS J 2017 10 11;284(20):3455-3469. Epub 2017 Sep 11.

Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Japan.

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http://dx.doi.org/10.1111/febs.14205DOI Listing
October 2017

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 2017 Oct;68(2):350-360.e7

Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.09.037DOI Listing
October 2017

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

Int J Mol Sci 2017 Oct 28;18(11). Epub 2017 Oct 28.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.3390/ijms18112271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5713241PMC
October 2017

High-Sensitivity Rheo-NMR Spectroscopy for Protein Studies.

Anal Chem 2017 07 5;89(14):7286-7290. Epub 2017 Jul 5.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura , Nishikyo-ku, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1021/acs.analchem.7b01816DOI Listing
July 2017

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

Chembiochem 2017 05 24;18(10):951-959. Epub 2017 Mar 24.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8510, Japan.

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http://dx.doi.org/10.1002/cbic.201700071DOI Listing
May 2017

F F -selective NMR spectroscopy.

J Biomol NMR 2017 May 4;68(1):41-52. Epub 2017 May 4.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku Kyoto-Daigaku Katsura, Kyoto, 615-8510, Japan.

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http://link.springer.com/10.1007/s10858-017-0113-x
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http://dx.doi.org/10.1007/s10858-017-0113-xDOI Listing
May 2017

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

Int J Mol Sci 2017 May 27;18(6). Epub 2017 May 27.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.3390/ijms18061145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5485969PMC
May 2017

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

Biomol NMR Assign 2017 04 26;11(1):81-84. Epub 2016 Dec 26.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.

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http://dx.doi.org/10.1007/s12104-016-9724-5DOI Listing
April 2017

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

J Biomol NMR 2017 03 28;67(3):201-209. Epub 2017 Feb 28.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, 615-8510, Kyoto, Japan.

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http://dx.doi.org/10.1007/s10858-017-0097-6DOI Listing
March 2017

[Structure basis of versatile base recognition of MBD4].

Yakugaku Zasshi 2015 ;135(1):3-9

Institute for Integrated Cells-Material Sciences, Kyoto University.

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http://dx.doi.org/10.1248/yakushi.14-00202-1DOI Listing
January 2017

Ubiquitylation Directly Induces Fold Destabilization of Proteins.

Sci Rep 2016 12 19;6:39453. Epub 2016 Dec 19.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1038/srep39453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172356PMC
December 2016

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

J Biomol NMR 2016 10 8;66(2):99-110. Epub 2016 Sep 8.

Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.

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http://dx.doi.org/10.1007/s10858-016-0059-4DOI Listing
October 2016

Efficient identification and analysis of chemical exchange in biomolecules by R1ρ relaxation dispersion with Amaterasu.

Bioinformatics 2016 08 8;32(16):2539-41. Epub 2016 Apr 8.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btw188DOI Listing
August 2016

Dual Function of Phosphoubiquitin in E3 Activation of Parkin.

J Biol Chem 2016 08 9;291(32):16879-91. Epub 2016 Jun 9.

the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan

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http://dx.doi.org/10.1074/jbc.M116.728600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4974400PMC
August 2016

[Non-invasive analysis of proteins in living cells using NMR spectroscopy].

Yakugaku Zasshi 2015 ;135(3):391-8

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University.

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https://www.jstage.jst.go.jp/article/yakushi/135/3/135_14-00
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http://dx.doi.org/10.1248/yakushi.14-00240-3DOI Listing
July 2016

The evolving world of ubiquitin: transformed polyubiquitin chains.

Biomol Concepts 2016 Jun;7(3):157-67

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http://dx.doi.org/10.1515/bmc-2016-0009DOI Listing
June 2016

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

Nanomaterials (Basel) 2016 Mar 25;6(4). Epub 2016 Mar 25.

Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo-ku, Kyoto 606-8502, Japan.

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http://dx.doi.org/10.3390/nano6040056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302567PMC
March 2016

Nucleosome compaction facilitates HP1γ binding to methylated H3K9.

Nucleic Acids Res 2015 Dec 28;43(21):10200-12. Epub 2015 Aug 28.

Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan

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http://dx.doi.org/10.1093/nar/gkv841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666388PMC
December 2015

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

J Am Chem Soc 2015 Jan 6;137(2):799-806. Epub 2015 Jan 6.

Advanced Biomedical Engineering Research Unit, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University , Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1021/ja510479vDOI Listing
January 2015

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

Nat Commun 2015 Jan 20;6:6116. Epub 2015 Jan 20.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1038/ncomms7116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309437PMC
January 2015

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

Proc Natl Acad Sci U S A 2014 Dec 17;111(48):17236-41. Epub 2014 Nov 17.

Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan; and Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1073/pnas.1414867111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260609PMC
December 2014

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

Nat Commun 2014 Dec 15;5:5340. Epub 2014 Dec 15.

1] Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan [2] Biomedical Informatics, Medical Information Sciences Division, The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1194, Japan.

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http://dx.doi.org/10.1038/ncomms6340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275594PMC
December 2014

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

Acta Crystallogr F Struct Biol Commun 2014 Oct 25;70(Pt 10):1351-6. Epub 2014 Sep 25.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188078PMC
http://dx.doi.org/10.1107/S2053230X14016926DOI Listing
October 2014

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

Plant J 2014 Jun 21;78(6):1014-21. Epub 2014 May 21.

Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.

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http://dx.doi.org/10.1111/tpj.12528DOI Listing
June 2014

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

J Biol Chem 2014 May 1;289(20):13890-902. Epub 2014 Apr 1.

From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and

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http://www.jbc.org/lookup/doi/10.1074/jbc.M114.555441
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http://dx.doi.org/10.1074/jbc.M114.555441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022861PMC
May 2014

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

Mol Immunol 2014 Mar 5;58(1):66-76. Epub 2013 Dec 5.

Department of Pediatrics, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan; Heisei College of Health Sciences, 180 Kurono, Gifu 501-1131, Japan.

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http://dx.doi.org/10.1016/j.molimm.2013.11.008DOI Listing
March 2014

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

Biochem Biophys Res Commun 2013 Sep 8;438(4):653-9. Epub 2013 Aug 8.

Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0373, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2013.07.127DOI Listing
September 2013

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

J Am Chem Soc 2013 Aug 8;135(33):12360-5. Epub 2013 Aug 8.

Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1021/ja405745vDOI Listing
August 2013

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

J Am Chem Soc 2013 Jul 8;135(28):10266-9. Epub 2013 Jul 8.

Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1021/ja404425rDOI Listing
July 2013

MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain.

J Biochem 2013 May 19;153(5):473-81. Epub 2013 Feb 19.

Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.

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http://dx.doi.org/10.1093/jb/mvt012DOI Listing
May 2013

Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR.

Chem Commun (Camb) 2013 Apr;49(27):2801-3

Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan.

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http://dx.doi.org/10.1039/c3cc39205hDOI Listing
April 2013

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

J Biol Chem 2013 Mar 9;288(9):6053-62. Epub 2013 Jan 9.

Division of Epigenetics, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M112.433284
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http://dx.doi.org/10.1074/jbc.M112.433284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585044PMC
March 2013

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

J Am Chem Soc 2013 Feb 27;135(5):1688-91. Epub 2013 Jan 27.

Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0373, Japan.

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http://dx.doi.org/10.1021/ja310928uDOI Listing
February 2013

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

Angew Chem Int Ed Engl 2013 Feb 30;52(9):2430-4. Epub 2013 Jan 30.

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Sendai, Japan.

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http://dx.doi.org/10.1002/anie.201206563DOI Listing
February 2013

Hinge and chromoshadow of HP1α participate in recognition of K9 methylated histone H3 in nucleosomes.

J Mol Biol 2013 Jan 6;425(1):54-70. Epub 2012 Nov 6.

Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1016/j.jmb.2012.10.018DOI Listing
January 2013

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

J Biomol NMR 2013 Jan 6;55(1):19-31. Epub 2012 Dec 6.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1007/s10858-012-9675-9DOI Listing
January 2013

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

Nano Lett 2012 Nov 22;12(11):5726-32. Epub 2012 Oct 22.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1021/nl302979dDOI Listing
November 2012

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

Mol Immunol 2012 Oct 4;52(3-4):108-16. Epub 2012 Jun 4.

Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan.

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http://dx.doi.org/10.1016/j.molimm.2012.05.003DOI Listing
October 2012

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

Proc Natl Acad Sci U S A 2012 Aug 25;109(32):12950-5. Epub 2012 Jul 25.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1073/pnas.1203701109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420164PMC
August 2012

[Structural analysis of proteins in living eukaryotic cells using magnetic resonance spectroscopy].

Yakugaku Zasshi 2012 ;132(2):185-93

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1248/yakushi.132.185DOI Listing
July 2012

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

FEBS J 2012 Apr 5;279(7):1339-52. Epub 2012 Mar 5.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1111/j.1742-4658.2012.08528.xDOI Listing
April 2012

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

J Biomol NMR 2012 Apr 18;52(4):339-50. Epub 2012 Feb 18.

Graduate School of Engineering, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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http://link.springer.com/content/pdf/10.1007/s10858-012-9614
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http://link.springer.com/10.1007/s10858-012-9614-9
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http://dx.doi.org/10.1007/s10858-012-9614-9DOI Listing
April 2012

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

ACS Chem Biol 2012 Mar 19;7(3):535-42. Epub 2012 Jan 19.

Advanced Biomedical Engineering Research Unit, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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http://pubs.acs.org/doi/10.1021/cb2003972
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http://dx.doi.org/10.1021/cb2003972DOI Listing
March 2012

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

J Biol Chem 2011 Sep 29;286(36):31864-74. Epub 2011 Jun 29.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1074/jbc.M111.259630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173063PMC
September 2011

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

J Biol Chem 2011 Jun 7;286(24):21732-41. Epub 2011 Apr 7.

Division of Structural Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan.

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http://dx.doi.org/10.1074/jbc.M110.174680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122229PMC
June 2011

Structural difference of vasoactive intestinal peptide in two distinct membrane-mimicking environments.

Biochim Biophys Acta 2011 May 23;1814(5):724-30. Epub 2011 Mar 23.

Graduate School of Medicine, Kobe University, Chuo-ku, Kobe, Hyogo, Japan.

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http://dx.doi.org/10.1016/j.bbapap.2011.03.009DOI Listing
May 2011

Application of NMR spectroscopy in medicinal chemistry and drug discovery.

Curr Top Med Chem 2011 ;11(1):68-73

Division of Nutritional physiology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-15 Kuramoto-cho, Tokushima, Japan.

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http://dx.doi.org/10.2174/156802611793611878DOI Listing
April 2011

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

Biomol NMR Assign 2010 Oct 31;4(2):123-5. Epub 2010 Mar 31.

Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1194, Japan.

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http://dx.doi.org/10.1007/s12104-010-9222-0DOI Listing
October 2010

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

Acta Crystallogr Sect F Struct Biol Cryst Commun 2010 Jul 24;66(Pt 7):834-7. Epub 2010 Jun 24.

Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8015, Japan.

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http://dx.doi.org/10.1107/S1744309110018804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898474PMC
July 2010

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

J Am Chem Soc 2010 Jun;132(24):8228-9

Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1021/ja906104eDOI Listing
June 2010

A common substrate recognition mode conserved between katanin p60 and VPS4 governs microtubule severing and membrane skeleton reorganization.

J Biol Chem 2010 May 25;285(22):16822-9. Epub 2010 Mar 25.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8530, Japan.

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http://dx.doi.org/10.1074/jbc.M110.108365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878028PMC
May 2010

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

Genes Cells 2010 Feb 19;15(2):101-10. Epub 2010 Jan 19.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1111/j.1365-2443.2009.01369.xDOI Listing
February 2010

Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain.

EMBO Rep 2009 Nov 16;10(11):1235-41. Epub 2009 Oct 16.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.

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http://embor.embopress.org/cgi/doi/10.1038/embor.2009.218
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http://dx.doi.org/10.1038/embor.2009.218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775176PMC
November 2009

Self-assembling nanoprobes that display off/on 19F nuclear magnetic resonance signals for protein detection and imaging.

Nat Chem 2009 Oct 23;1(7):557-61. Epub 2009 Sep 23.

Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Japan.

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http://www.nature.com/articles/nchem.365
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October 2009

Dual-function probe to detect protease activity for fluorescence measurement and 19F MRI.

Angew Chem Int Ed Engl 2009 ;48(20):3641-3

Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1002/anie.200806328DOI Listing
June 2009

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

Proc Natl Acad Sci U S A 2009 Jun 8;106(25):10260-5. Epub 2009 Jun 8.

Department of Pediatrics, Graduate School of Medicine, Center for Emerging Infectious Diseases, and Center for Advanced Drug Research, Gifu University, Gifu, Japan.

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http://dx.doi.org/10.1073/pnas.0812956106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2693180PMC
June 2009

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

Nature 2009 Mar;458(7234):106-9

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan.

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http://www.nature.com/articles/nature07839
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http://dx.doi.org/10.1038/nature07839DOI Listing
March 2009

Molecular basis for SUMOylation-dependent regulation of DNA binding activity of heat shock factor 2.

J Biol Chem 2009 Jan 18;284(4):2435-47. Epub 2008 Nov 18.

Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1074/jbc.M806392200DOI Listing
January 2009

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

Allergol Int 2008 Dec 1;57(4):367-76. Epub 2008 Dec 1.

Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan.

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http://dx.doi.org/10.2332/allergolint.O-08-546DOI Listing
December 2008

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

Protein Sci 2008 Nov 7;17(11):1915-24. Epub 2008 Aug 7.

Field of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.

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http://doi.wiley.com/10.1110/ps.034736.108
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http://dx.doi.org/10.1110/ps.034736.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2578811PMC
November 2008

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

Nature 2008 Oct 3;455(7214):818-21. Epub 2008 Sep 3.

Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1038/nature07249DOI Listing
October 2008

[Molecular mechanism for the ligand recognition by the extracellular domain of class B GPCR].

Seikagaku 2008 Oct;80(10):948-58

Division of Structural Biology, Graduate School of Medicine, Kobe University, 7-5-1 Suehiro-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan.

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October 2008

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

Exp Cell Res 2008 Aug 29;314(13):2352-61. Epub 2008 May 29.

Division of Biophysics, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1016/j.yexcr.2008.05.008DOI Listing
August 2008

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

Biochemistry 2008 Mar 12;47(10):3266-71. Epub 2008 Feb 12.

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1021/bi7019029DOI Listing
March 2008

Paramagnetic relaxation-based 19f MRI probe to detect protease activity.

J Am Chem Soc 2008 Jan 23;130(3):794-5. Epub 2007 Dec 23.

Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan.

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http://pubs.acs.org/doi/abs/10.1021/ja077058z
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January 2008

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

Anal Biochem 2007 Dec 10;371(2):247-9. Epub 2007 Aug 10.

Division of Biophysics, Graduate School of Integrated Sciences, Yokohama City University, Yokohama 230-0045, Japan.

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http://dx.doi.org/10.1016/j.ab.2007.08.006DOI Listing
December 2007

Structural analysis of pituitary adenylate cyclase-activating polypeptides bound to phospholipid membranes by magic angle spinning solid-state NMR.

Biochim Biophys Acta 2007 Dec 23;1768(12):3001-11. Epub 2007 Oct 23.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.

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http://linkinghub.elsevier.com/retrieve/pii/S000527360700400
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http://dx.doi.org/10.1016/j.bbamem.2007.10.015DOI Listing
December 2007

[Protein modification by SUMO].

Seikagaku 2007 Dec;79(12):1120-30

Biomolecular Function Chemistry, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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December 2007

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

Nucleic Acids Res 2007 30;35(12):3918-27. Epub 2007 May 30.

Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan.

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http://dx.doi.org/10.1093/nar/gkm397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919474PMC
August 2007

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

Biochim Biophys Acta 2007 Feb 6;1773(2):141-6. Epub 2006 Dec 6.

Division of Molecular Biophysics, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1016/j.bbamcr.2006.11.016DOI Listing
February 2007