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Thermodynamic basis of life: protein-carbohydrate interaction

Research Project

Project/Area Number 15K06962
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionKyushu University (2016-2017)
The University of Tokyo (2015)

Principal Investigator

CAAVEIRO Jose  九州大学, 薬学研究院, 准教授 (00536732)

Research Collaborator TSUMOTO Kouhei  東京大学, 大学院工学系研究科, 教授
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
KeywordsGlycan / Sugar / Antibody / Enzyme / Pore-forming protein / X-ray crystallography / Thermodynamics / Kinetics / glycan / sugar / antibody / enzyme / pore forming protein / kinetics / Antobody / Pore forming protein / Thernodynamics / X-ray Crystallography
Outline of Final Research Achievements

We clarified the thermodynamic and structural basis of the interaction between proteins and carbohydrates from a fundamental point of view in several biologically relevant systems. Atomic-level demonstration, for the first time, of the full and reversible refolding of a transmembrane protein into a water-soluble form by employing sugar-containing detergents. Atomic-level demonstration, for the first time, of the binding of a carbohydrate to a pore-forming toxin (FraC) using its lipid binding module. Elucidation of the recognition mechanism of the glycoprotein Env of HIV-1 by a broadly-neutralizing anti-HIV-1 antibody at the atomic level. Demonstration that the terminal galactose of the glycan attached to the Fc region of IgG modulate the effector function of IgG. And explanation of the thermodynamic role of the glycan attached to residue Asn297 of the Fc region of IgG was revealed.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (29 results)

All 2018 2017 2016 2015 Other

All Journal Article (15 results) (of which Int'l Joint Research: 15 results,  Peer Reviewed: 15 results,  Open Access: 7 results,  Acknowledgement Compliant: 9 results) Presentation (12 results) (of which Int'l Joint Research: 5 results,  Invited: 7 results) Remarks (2 results)

  • [Journal Article] Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column2018

    • Author(s)
      Kiyoshi M, Caaveiro JMM, Tada M, Tamura H, Tanaka T, Terao Y, Morante K, Harazono A, Hashii N, Shibata H, Kuroda D, Nagatoishi S, Oe S, Ide T, Tsumoto K, Ishii-Watabe A
    • Journal Title

      Scientific Reports

      Volume: 8:3955 Issue: 1 Pages: 1-11

    • DOI

      10.1038/s41598-018-22199-8

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.2018

    • Author(s)
      Miyanabe, K., Akiba, H., Kuroda, D., Nakakido, M., Kusano-Arai, O., Iwanari, H., Hamakubo, T., Caaveiro, J.M.M., and Tsumoto, K.
    • Journal Title

      J. Biochem.

      Volume: in press Issue: 1 Pages: 65-76

    • DOI

      10.1093/jb/mvy032

    • NAID

      40021625331

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin2018

    • Author(s)
      Takumi Tashima , Satoru Nagatoishi, Jose M.M. Caaveiro, Makoto Nakakido, Hiroshi Sagara, Osamu Kusano-Arai, Hiroko Iwanari, Hitomi Mimuro, Takao Hamakubo, Shin-ichi Ohnuma and Kouhei Tsumoto
    • Journal Title

      Communications Biology

      Volume: 1:33 Issue: 1 Pages: 1-10

    • DOI

      10.1038/s42003-018-0038-2

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Glycosylation of IgG-Fc: a molecular perspective2017

    • Author(s)
      Kiyoshi Masato、Tsumoto Kouhei、Ishii-Watabe Akiko、Caaveiro Jose M M
    • Journal Title

      International Immunology

      Volume: 29 Issue: 7 Pages: 311-317

    • DOI

      10.1093/intimm/dxx038

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Haemolytic actinoporins interact with carbohydrates using their lipid-binding module.2017

    • Author(s)
      Tanaka K, Caaveiro JMM, Morante K and Tsumoto K.
    • Journal Title

      Philos. Trans. R. Soc. B.

      Volume: 372 Issue: 1726 Pages: 20160216-20160216

    • DOI

      10.1098/rstb.2016.0216

    • NAID

      120006328969

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin2017

    • Author(s)
      S. Kudo, J. M. M. Caaveiro, S. Nagatoishi, T. Miyafusa, T. Matsuura, Y. Sudou, and K. Tsumoto
    • Journal Title

      Sci. Rep.

      Volume: 7 Issue: 1 Pages: 39518-39518

    • DOI

      10.1038/srep39518

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Peripheral membrane interactions boost the engagement by an anti HIV-1 broadly neutralizing antibody2017

    • Author(s)
      Rujas, E., Caaveiro, J.M.M., Insausti, S., Garcia-Porras, M., Tsumoto, K., and Nieva, J.L.
    • Journal Title

      J. Biol. Chem.

      Volume: 292 Issue: 13 Pages: 5571-5583

    • DOI

      10.1074/jbc.m117.775429

    • NAID

      120006328971

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Functional contacts between MPER and the anti-HIV-1 broadly neutralizing antibody 4E10 extend into the core of the membrane2017

    • Author(s)
      Rujas, E., Insausti, S., Garcia-Porras, M., Sanchez-Eugenia, R., Tsumoto, K., Nieva, J.L., and Caaveiro, J.M.M.
    • Journal Title

      J. Mol. Biol.

      Volume: 429 Issue: 8 Pages: 1213-1226

    • DOI

      10.1016/j.jmb.2017.03.008

    • NAID

      120006328970

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Identification of a membrane-bound prepore species clarifies the lytic mechanism of actinoporins2016

    • Author(s)
      Morante, K., Bellomio, A., Gil-Carton, D., Redondo-Morata, L., Sot, J., Scheuring, S., Valle, M., Gonzalez-Manas, J.M., Tsumoto, K., and Caaveiro, J.M.M.
    • Journal Title

      J. Biol. Chem.

      Volume: 291 Issue: 37 Pages: 19210-19219

    • DOI

      10.1074/jbc.m116.734053

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Adhesive dimerization of human P-cadherin catalyzed by a chaperone-like mechanism2016

    • Author(s)
      Kudo, S., Caaveiro, J.M.M., and Tsumoto, K.
    • Journal Title

      Structure

      Volume: 24 Issue: 9 Pages: 1523-1536

    • DOI

      10.1016/j.str.2016.07.002

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Differential effect of membrane composition on the pore forming ability of four different sea anemone actinoporins2016

    • Author(s)
      Garcia-Linares, S., Rivera-de-Torre, E., Morante, K., Tsumoto, K., Caaveiro, J.M.M., Gavilanes, J.G., Slotte, J.P., and Martinez-del-Pozo, A.
    • Journal Title

      Biochemistry

      Volume: 55 Issue: 48 Pages: 6630-6641

    • DOI

      10.1021/acs.biochem.6b01007

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface2016

    • Author(s)
      Rujas, E., Caaveiro, J.M.M., Partida-Hanon, A., Gulzar, N., Morante, K., Apellaniz, B., Garcia-Porras, M., Bruix, M., Tsumoto, K., Scott, J.K., Jimenez, M.A., and Nieva, J.L.
    • Journal Title

      Sci Rep.

      Volume: 6 Issue: 1 Pages: 38177-38177

    • DOI

      10.1038/srep38177

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Structural Analysis of Fc/FcγR Complexes: A Blueprint for Antibody Design.2015

    • Author(s)
      Caaveiro, J.M.M., Kiyoshi, M. and Tsumoto, K.
    • Journal Title

      Immunological Reviews

      Volume: 268 Issue: 1 Pages: 201-221

    • DOI

      10.1111/imr.12365

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Structural and thermodynamics basis of epitope binding to neutralizing and non-neutralizing forms of the anti-HIV-1 4E10 antibody2015

    • Author(s)
      Rujas, E., Gulzar, N., Morante, K., Tsumoto, K., Scott, J.K., Nieva, J.L. and Caaveiro, J.M.M.
    • Journal Title

      Journal of Virology

      Volume: 89 Issue: 23 Pages: 11975-11991

    • DOI

      10.1128/jvi.01793-15

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Bidirectional transformation of a protein between its Native Water-Soluble and Transmembrane Conformations.2015

    • Author(s)
      Tanaka, K., Caaveiro, J.M.M., and Tsumoto, K.
    • Journal Title

      Biochemistry

      Volume: 54 Issue: 46 Pages: 6863-6866

    • DOI

      10.1021/acs.biochem.5b01112

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Molecular recognition phenomena involving proteins of therapeutic interest.2017

    • Author(s)
      Caaveiro J.M.M.
    • Organizer
      3rd HU-TMU-KU Joint Symposium for Pharmaceutical Sciences
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Protein-lipid interactions in a pore-forming toxin.2017

    • Author(s)
      Tsumoto, K. and Caaveiro, J.M.M.
    • Organizer
      55th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Caaveiro, J.M.M., Kiyoshi, M., Ueda, T., and Tsumoto, K.2017

    • Author(s)
      Structural Biology of Fc receptors.
    • Organizer
      Antibody Engineering & Therapeutics (Annual meeting of the Antibody Society)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The Fascinating journey of a metamorphic protein to the cell membrane2017

    • Author(s)
      Caaveiro, J.M.M.
    • Organizer
      Bioforo 5th Alumni Research Meeting
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Thermodynamic properties of the transition state in biomolecular recognition phenomena2017

    • Author(s)
      Caaveiro, J.M.M.
    • Organizer
      23rd Forum of Pharmaceutical Sciences, The Biophysical Society of Japan
    • Place of Presentation
      Sapporo, Japan
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Biomolecular recognition: a structural and physicochemical perspective2016

    • Author(s)
      Caaveiro, J.M.M.
    • Organizer
      Chile-Japan Academic Forum 2016 at Patagonia
    • Place of Presentation
      Puerto Natales, Chile
    • Year and Date
      2016-11-07
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Principles of Biomolecular Recognition of IgG-Fc by its receptors2016

    • Author(s)
      Caaveiro, J.M.M., Kiyoshi, M. and Tsumoto, K.
    • Organizer
      Gordon Conference (Antibody Biology and Engineering)
    • Place of Presentation
      Galveston, TX, USA
    • Year and Date
      2016-03-20
    • Related Report
      2015 Research-status Report
  • [Presentation] Pore formation assisted by lipids2016

    • Author(s)
      Caaveiro, J.M.M.
    • Organizer
      Membrane pores: from structure and assembly, to medicine and technology, The Royal Society
    • Place of Presentation
      London, UK
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Thermodynamic tools in fragment-based drug discovery2016

    • Author(s)
      Caaveiro, J.M.M.
    • Organizer
      2016 UT-PUCC Joint Workshop for Frontiers in Bioengineering and Biomedical Engineering
    • Place of Presentation
      Santiago, Chile
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Structural and mechanistic basis of capsular polysaccharide-synthesizing enzymes CapE/F, and the route to discovery novel inhibitors with antibacterial properties.2015

    • Author(s)
      Caaveiro J.M.M., Miyafusa, T., Chigira, T., Nakano, K., Nagatoishi, S. and Tsumoto, K.
    • Organizer
      7th International Chemical Congress of Pacific Basin Societies PacificChem
    • Place of Presentation
      Honolulu, HI, USA
    • Year and Date
      2015-12-18
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Molecular basis of heme transfer between NEAT transporters in Staphylococcus aureus2015

    • Author(s)
      Caaveiro, J.M.M., Morante, K., Vu, N., Moriwaki, Y., and Tsumoto, K.
    • Organizer
      7th International Chemical Congress of Pacific Basin Societies PacificChem
    • Place of Presentation
      Honolulu, HI, USA
    • Year and Date
      2015-12-17
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Use of thermodynamic tools in the early stages of fragment-based drug discovery2015

    • Author(s)
      Caaveiro J.M.M., Kobe, A., Mitani, T. and Tsumoto, K
    • Organizer
      7th International Chemical Congress of Pacific Basin Societies PacificChem
    • Place of Presentation
      Honolulu, HI, USA
    • Year and Date
      2015-12-16
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Remarks] Issue cover and paper of the week in JBC

    • URL

      http://www.jbc.org/content/291/37.toc#PapersoftheWeek

    • Related Report
      2016 Research-status Report
  • [Remarks] Highligted by the Biophysical Society of Spain

    • URL

      http://biofisica.info/rujas-nieva-sci-rep-6-38177/

    • Related Report
      2016 Research-status Report

URL: 

Published: 2015-04-16   Modified: 2019-03-29  

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