Publications

Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane.
J Mol Biol 2017 Apr 11;429(8):1213-1226. Epub 2017 Mar 11.
Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan; Laboratory of Global Healthcare, School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan. Electronic address:

Peripheral Membrane Interactions Boost the Engagement by an Anti-HIV-1 Broadly Neutralizing Antibody.
J Biol Chem 2017 Mar 17;292(13):5571-5583. Epub 2017 Feb 17.
From the Biofisika Institute (Consejo Superior de Investigaciones Científicas, UPV/EHU), and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain and

Production and characterization of genetically modified human IL-11 variants.
Biochim Biophys Acta 2017 Feb 22;1861(2):205-217. Epub 2016 Nov 22.
Department of Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. Electronic address:

Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface.
Sci Rep 2016 Dec 1;6:38177. Epub 2016 Dec 1.
Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain.

Identification of a Membrane-bound Prepore Species Clarifies the Lytic Mechanism of Actinoporins.
J Biol Chem 2016 Sep 21;291(37):19210-9. Epub 2016 Jul 21.
From the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan,

Integrative Network Analysis Combined with Quantitative Phosphoproteomics Reveals Transforming Growth Factor-beta Receptor type-2 (TGFBR2) as a Novel Regulator of Glioblastoma Stem Cell Properties.
Mol Cell Proteomics 2016 Mar 15;15(3):1017-31. Epub 2015 Dec 15.
From the ‡Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan;


Differential binding of prohibitin-2 to estrogen receptor α and to drug-resistant ERα mutants.
Biochem Biophys Res Commun 2015 Aug 4;463(4):726-31. Epub 2015 Jun 4.
Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Bioengineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan. Electronic address:

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.
J Biochem 2015 Jul 7;158(1):1-13. Epub 2015 May 7.
Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656 and Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo 108-8639 Japan Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656 and Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo 108-8639 Japan

Osteomodulin regulates diameter and alters shape of collagen fibrils.
Biochem Biophys Res Commun 2015 Jul 20;463(3):292-6. Epub 2015 May 20.
Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Bioengineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan; Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. Electronic address:

pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides.
Protein Sci 2015 May 2;24(5):883-94. Epub 2015 Apr 2.
Department of Medical Genome Sciences, Graduate School of Frontier, The university of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan; Institute for Biomolecular Science, Gakushuin University, Toshima-ku, Tokyo, Japan.

The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region.
J Biol Chem 2015 May 18;290(21):12999-3015. Epub 2015 Mar 18.
From the Biophysics Unit (Consejo Superior de Investigaciones Científicas, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain,

A pore-forming toxin requires a specific residue for its activity in membranes with particular physicochemical properties.
J Biol Chem 2015 Apr 10;290(17):10850-61. Epub 2015 Mar 10.
From the Department of Bioengineering, Graduate School of Engineering and Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan, the Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Minato-ku, 108-8639 Tokyo, Japan

Structural basis for binding of human IgG1 to its high-affinity human receptor FcγRI.
Nat Commun 2015 Apr 30;6:6866. Epub 2015 Apr 30.
1] Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan [2] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan [3] Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.


Structural basis for self-assembly of a cytolytic pore lined by protein and lipid.
Nat Commun 2015 Feb 26;6:6337. Epub 2015 Feb 26.
1] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan [2] Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan [3] Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

Preparation and characterization of anti-tissue factor single-chain variable fragment antibody for cancer diagnosis.
Cancer Sci 2014 Dec 20;105(12):1631-7. Epub 2014 Nov 20.
Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Chiba, Japan; Laboratory of Cancer Biology, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

The staphylococcal elastin-binding protein regulates zinc-dependent growth/biofilm formation.
J Biochem 2014 Sep 29;156(3):155-62. Epub 2014 Apr 29.
Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-

Protective effect of the long pentraxin PTX3 against histone-mediated endothelial cell cytotoxicity in sepsis.
Sci Signal 2014 Sep 16;7(343):ra88. Epub 2014 Sep 16.
Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.

Role of positions e and g in the fibrous assembly formation of an amphipathic α-helix-forming polypeptide.
Biopolymers 2014 May;102(3):260-72
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan; Institute for Biomolecular Science, Gakushuin University, Tokyo, Japan.

Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex.
PLoS One 2014 27;9(1):e87099. Epub 2014 Jan 27.
Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan ; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan ; Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan ; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme.
Biochemistry 2013 Dec 25;52(49):8866-77. Epub 2013 Nov 25.
Department of Biotechnology and ‡Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Effects of subclass change on the structural stability of chimeric, humanized, and human antibodies under thermal stress.
Protein Sci 2013 Nov 30;22(11):1542-51. Epub 2013 Sep 30.
Bio Process Research and Development Laboratories, Production Division, Kyowa Hakko Kirin Company Limited, 100-1 Hagiwara-machi, Takasaki, Gunma, 370-0013, Japan; Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, , The University of Tokyo, Kashiwa, 277-8562, Japan.

Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus.
FEBS Lett 2013 Nov 21;587(23):3824-30. Epub 2013 Oct 21.
Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.

Secretory production of single-chain antibody (scFv) in Brevibacillus choshinensis using novel fusion partner.
Appl Microbiol Biotechnol 2013 Oct 20;97(19):8569-80. Epub 2013 Jan 20.
Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065, Japan,

Bidirectional binding property of high glycine-tyrosine keratin-associated protein contributes to the mechanical strength and shape of hair.
J Struct Biol 2013 Sep 19;183(3):484-494. Epub 2013 Jun 19.
Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. Electronic address:

Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation.
Biochemistry 2013 Apr 15;52(16):2810-20. Epub 2013 Apr 15.
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.

Interleukin-11 links oxidative stress and compensatory proliferation.
Sci Signal 2012 Jan 17;5(207):ra5. Epub 2012 Jan 17.
Department of Immunology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.

Gene expression profiles predicting the response to IFN-β and a combination of temozolomide and IFN-β in malignant gliomas.
Int J Oncol 2011 Sep 6;39(3):529-42. Epub 2011 Jun 6.
Department of Neurological Surgery, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan.

The structural mechanism of the inhibition of archaeal RelE toxin by its cognate RelB antitoxin.
Biochem Biophys Res Commun 2010 Sep 20;400(3):346-51. Epub 2010 Aug 20.
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Graduate School, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.

Structural basis for amino acid export by DMT superfamily transporter YddG.
Nature 2016 06 30;534(7607):417-20. Epub 2016 May 30.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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