Thermodynamic basis of life: protein-carbohydrate interaction

• Project/Area Number: 15K06962
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Kyushu 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: ¥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)
• Keywords: Glycan / 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.

Research Products

• [Journal Article] Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column (2018)
  • 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
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin (2018)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Glycosylation of IgG-Fc: a molecular perspective (2017)
  • 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
  • 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
  • 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-cadherin (2017)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Peripheral membrane interactions boost the engagement by an anti HIV-1 broadly neutralizing antibody (2017)
  • 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
  • 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 membrane (2017)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Identification of a membrane-bound prepore species clarifies the lytic mechanism of actinoporins (2016)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Adhesive dimerization of human P-cadherin catalyzed by a chaperone-like mechanism (2016)
  • 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
  • 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 actinoporins (2016)
  • 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
  • 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 interface (2016)
  • 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
  • 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
  • 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 antibody (2015)
  • 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
  • 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
  • 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
  • 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
  • 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)
  • Int'l Joint Research
• [Presentation] The Fascinating journey of a metamorphic protein to the cell membrane (2017)
  • Author(s): Caaveiro, J.M.M.
  • Organizer: Bioforo 5th Alumni Research Meeting
  • Invited
• [Presentation] Thermodynamic properties of the transition state in biomolecular recognition phenomena (2017)
  • Author(s): Caaveiro, J.M.M.
  • Organizer: 23rd Forum of Pharmaceutical Sciences, The Biophysical Society of Japan
  • Place of Presentation: Sapporo, Japan
  • Invited
• [Presentation] Biomolecular recognition: a structural and physicochemical perspective (2016)
  • 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
  • Invited
• [Presentation] Principles of Biomolecular Recognition of IgG-Fc by its receptors (2016)
  • 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
• [Presentation] Pore formation assisted by lipids (2016)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Thermodynamic tools in fragment-based drug discovery (2016)
  • Author(s): Caaveiro, J.M.M.
  • Organizer: 2016 UT-PUCC Joint Workshop for Frontiers in Bioengineering and Biomedical Engineering
  • Place of Presentation: Santiago, Chile
  • 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
  • Int'l Joint Research
• [Presentation] Molecular basis of heme transfer between NEAT transporters in Staphylococcus aureus (2015)
  • 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
  • Int'l Joint Research
• [Presentation] Use of thermodynamic tools in the early stages of fragment-based drug discovery (2015)
  • 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
  • Int'l Joint Research
• [Remarks] Issue cover and paper of the week in JBC
  • URL: http://www.jbc.org/content/291/37.toc#PapersoftheWeek
• [Remarks] Highligted by the Biophysical Society of Spain
  • URL: http://biofisica.info/rujas-nieva-sci-rep-6-38177/