updated February 5, 2026
Original research.
2026
Sato J.‡, Kasahara K.‡, Nagatoishi S., Murakami K., Kuroda D., Caaveiro J.M.M., Nagai H., Tsumoto K. (2026) Hybrid Supercharged Antibodies: A Rational Approach to Boost Immunoassay Sensitivity via Controlled Nanoparticle Adsorption. Langmuir 42(15), 10303-10313. DOI: 10.1021/acs.langmuir.5c06029
Tagawa J., Yanaka S., Kato Y., Masuda A., Lee J.M., Senoo A., Oyama K., Uchihashi T., Nishida M., Kusakabe T., Caaveiro J.M.M. (2026) Characterization of high affinity IgM and IgG monoclonal antibodies against norovirus variants GII.4 and GII.17. Protein Sci. 35:e70522. DOI: 10.1002/pro.70522
Fernandez-Perez J., de Vega S., Caaveiro J.M.M., Nakakido M., Nagatoishi S., Senoo A., Tanai K., Nozawa T., Nakagawa I., Tsumoto K. (2026) Development of an inhibitory monoclonal nanobody targeting Streptococcus pyogenes siderophore binding protein FtsB. J. Biol. Chem. 302:111224, DOI: 10.1016/j.jbc.2026.111224
Koseki Y., Yamaguchi Y., Aoyama M., Hiraka K., Tada M., Kodama A., Senoo A., Ishii-Watabe A., Uchihashi T., Murata K., Uchiyama U., Kato K., Yanaka S., Caaveiro J.M.M. (2026) Key Role of Pro230 in the Hinge Region on the Architecture and Function of IgG1. J. Med. Chem. 69, 3902-3914, DOI: 10.1021/acs.jmedchem.5c02419
2025
Nishimuta H., Senoo A., Kasahara K., Kubo T., Yanaka S., Nagatoishi S., So T., Ueda T., Tsumoto K., Caaveiro J.M.M., Molecular mechanistic insights into the OX40-OX40L complex from biophysical and computational analyses. Protein Sci. 35:e70404, DOI: 10.1002/pro.70404
Seki K., Senoo A., Nagatoishi S., Yanaka S., Nakakido M., Tsumoto K., Caaveiro J.M.M. (2025) Structural basis for heme binding by the Shr protein from Streptococcus pyogenes. J. Biol. Chem. 302:111012, DOI: 10.1016/j.jbc.2025.111012
Yokoo T., Nakakido M., Matsuda K., Caaveiro J.M.M., Fernandez-Perez J., Yuzaki M., Tsumoto K. (2025) Development of a VHH that inhibits the binding of neuronal pentraxin 2 to a post-synaptic glutamate receptor, AMPAR. J. Biol. Chem. 302:110975, DOI: 10.1016/j.jbc.2025.110975
Uto Y., Nakakido M., Yokoo T., Fernandez-Perez J., Entzminger K., Maruyama T., Okumura C.J., Kuroda D., Caaveiro J.M.M., Tsumoto K. (2025) Improving the solubility of single domain antibodies using VH-like hallmark residues. Protein Sci. 34:e70189, DOI: 10.1002/pro.70189
Yamawaki T., Nakakido M., Nagatoishi S., Caaveiro J.M.M., Kuroda D., Aikawa C., Nakagawa I., Tsumoto K. (2025) Development of a small compound that regulates the function of a maltodextrin-binding protein of Streptococcus pyogenes by multifaceted screenings. Sci. Rep. 15, 19341, DOI: 10.1038/s41598-025-02175-9
Kasahara K., Nakakido M., Kuroda D., Nagatoishi S., Tsumoto K. (2025) Supercharging design of an anti-lysozyme Fab antibody to regulate ligand-dependent reversible aggregation. Polym. J. 57, 923-930, DOI: 10.1038/s41428-025-01046-4
Ujiie K., Nakakido M., Kinoshita S., Caaveiro J.M.M., Entzminger C.K., Okumura C.J., Maruyama T., Miyauchi K., Matano T., Tsumoto K. (2025) Specific recognition mechanism of an antibody to sulfated tyrosine and its potential use in biological research. J. Biol. Chem. 301, 108176, DOI: 10.1016/j.jbc.2025.108176
2024
Blackwell A.M., Jami-Alahmadi Y., Nasamu A.S., Kudo S., Senoo A., Slam C., Tsumoto K., Wohlschlegel J.A., Caaveiro J.M.M., Goldberg D.E., Sigala P.A. (2024) Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis. eLife 13, RP100256, DOI: 10.7554/eLife.100256.3
Kasahara K., Kawade R., Nakakido M., Matsunaga R., Akiba H., Entzminger K.C., Maruyama T., Okumura S.C.J., Caaveiro J.M.M., Kuroda D., Tsumoto K. (2024) Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies. J. Biol. Chem. 300, 107989, DOI: 10.1016/j.jbc.2024.107989
Fernandez-Perez J., Senoo A., Caaveiro J.M.M., Nakakido M., de Vega S., Nakagawa I., Tsumoto K. (2024) Structural basis for the ligand promiscuity of the hydroxymate siderophore binding protein FtsB from Streptococcus pyogenes. Structure 32, 2410-2421, DOI: 10.1016/j.str.2024.09.018
Insausti, S., Ramos-Caballero, A., Wiley, B., González-Resines, S., Torralba, J., Elizaga-Lara, A., Shamblin. C., Ojida, A., Caaveiro, J.M.M., Zwick, M.B., Rujas, E., Domene, C., Nieva, J.L. (2024) Generation of a nonbilayer lipid nanoenvironment after epitope binding potentiates neutralizing HIV-1 MPER antibody. ACS Appl. Mater. Interfaces DOI: 10.1021/acsami.4c13353
Nuntawong, P., Senoo, A., Tayama, Y., Caaveiro, J.M.M., Morimoto, S., Sakamoto, S. (2024) An aptamer-based fluorometric method for the rapid berberine detection in Kampo medicines. Anal. Chim. Acta 1318:342930, DOI: 10.1016/j.aca.2024.342930
Asano, R., Nakakido, M., Fernández Pérez, J., Ise, T., Caaveiro, J.M.M., Nagata, S., and Tsumoto, K. (2024) Crystal structures of human CD40 in complex with monoclonal antibodiesdacetuzumab and bleselumab. Biophys. Biochem. Res. Commun. 714:149969, DOI: 10.1016/j.bbrc.2024.149969
Senoo, A., Hoshino, M., Shiomi, T., Nakakido, M., Nagatoishi, S., Kuroda, D., Nakagawa, I., Tame, J.R.T., Caaveiro, J.M.M., and Tsumoto, K. (2024) Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes. Sci. Rep. 14:5374, DOI: 10.1038/s41598-024-55734-x
Rujas, E., Apellaniz, B., Torralba, J., Andreu, D., Caaveiro, J.M.M., Wang, S., Lu, S. and Nieva, J.L. (2024) Liposome-based peptide vaccines to elicit immune responses against the membrane active domains of the HIV-1 Env glycoprotein. Biochem. Biophys. Acta 1866:184235, DOI: 10.1016/j.bbamem.2023.184235
2023
Yamazaki, T., Nagatoishi, S., Yamawaki, T., Nozawa, T., Matsunaga, R., Nakakido, M., Caaveiro, J.M.M., Nakagawa, I. and Tsumoto, K. (2023) Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. J. Biol. Chem., 299: 105254, DOI: 10.1016/j.jbc.2023.105254.
Senoo, A., Nagatoishi, S., Kuroda, D., Ito, S., Ueno, G., Caaveiro, J.M.M., and Tsumoto, K. (2023) Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion. Protein Sci. 32:e4744, DOI: 10.1002/pro.4744.
Valenciano-Bellido, S., Caaveiro, J.M.M.*, Nakakido, M., Kuroda, D., Aikawa, C., Nakagawa, I. and Tsumoto, K. (2023) Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth. J. Biol. Chem. 299:104927, DOI: 10.1016/j.jbc.2023.104927.
Yanaka, S., Yogo, R., Yagi, H., Onitsuka, M., Wakaizumi, N., Yamaguchi, Y., Uchiyama, S., and Kato, K. (2023) Negative interference with antibody-dependent cellular cytotoxicity mediated by rituximab from its interactions with human serum proteins. Front. Immunol. 14:1090898, DOI: 10.3389/fimmu.2023.1090898.
2022
Torralba, J., de la Arada, I., Partida-Hanon, A., Rujas, E., Arribas, M., Insausti, S., Valotteau, C., Valle, J., Andreu, D., Caaveiro, J.M.M., Jiménez, M.A., Apellániz, B., Redondo-Morata, L. and Nieva, J.L. (2022) Molecular recognition of a membrane-anchored HIV-1 pan-neutralizing epitope. Commun. Biol. 5:1265, DOI: 10.1038/s42003-022-04219-6.
Hirose, Y., Shindo, N., Mori, M., Onitsuka, S., Isogai, H., Hamada, R., Hiramoto, T., Ochi, J., Takahashi, D., Ueda, T., Caaveiro, J.M.M., Yoshida, Y., Ohdo, S., Matsunaga, N., Toba, S., Sasaki, M., Orba, Y., Sawa, H., Sato, A., Kawanishi, E. and Ojida, A (2022) Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease. J. Med. Chem. 65:13852-13865, DOI: 10.1021/acs.jmedchem.2c01081.
Kinoshita, S., Nakakido, M., Mori, C., Kuroda, D., Caaveiro, J.M.M. and Tsumoto, K. (2022) Molecular basis for thermal stability and affinity in a VHH:Contribution of the framework region and its influence in the conformation of the CDR3. Prot. Sci. 31:e4450, DOI: 10.1002/pro.4450.
Insausti, S., Garcia-Porras, M., Torralba, J., Morillo, I., Ramos-Caballero, A., de la Arada, I., Apellaniz, B., Caaveiro, J.M.M., Carravilla, P. Eggeling, C., Rujas, E. and Nieva, J.L. (2022) Functional Delineation of a Protein–Membrane Interaction Hotspot Site on the HIV-1 Neutralizing Antibody 10E8. Int. J. Mol. Sci. 23:10767, DOI: 10.3390/ijms231810767.
Takahashi, D.,Yonezawa, K., Okizaki, Y., Caaveiro, J.M.M., Ueda, T., Shimada, A., Sakane, F., and Shimizu, N. (2022) Ca2+-induced structural changes and intramolecular interactions in N-terminal region of diacylglycerol kinase alpha. Protein Sci. 31:e4365, DOI: 10.1002/pro.4365.
Valenciano-Bellido, S., Caaveiro, J.M.M., Morante, K., Sushko, T., Nakakido, M., Nagatoishi, S., and Tsumoto, K. (2022) Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus.J. Biol. Chem. 298:101995, DOI: 10.1016/j.jbc.2022.101995 (JBC recommended read).
Yokoo, T., Tanabe, A., Yoshida, Y., Caaveiro, J.M.M., Nakakido, M., Ikeda, Y., Fujimura, Y., Matsumoto, M., Entzminger, K., Maruyama, T., Okumura, C.J., Nangaku, M., Tsumoto, K. (2022) Antibody recognition of complement Factor H reveals a flexible loop involved in Atypical Hemolytic Uremic Syndrome pathogenesis. J. Biol. Chem., 298:101962, DOI: 10.1016/j.jbc.2022.101962.
Takahashi, D., Matsunaga, E., Yamashita, T., Caaveiro, J.M.M., Abe, Y., and Ueda, T. (2022) Compound screening identified gossypetin and isoquercitrin as novel inhibitors for amyloid fibril formations of Vλ6 proteins associated with AL amyloidosis. Biochem. Biophys. Res. Commun. 596:22-28, DOI: 10.1016/j.bbrc.2022.01.066.
2021
Queliconi, B.B., Kojima, W., Kimura, M., Imai, I., Motono, C., Hirokawa, T., Tashiro, S., Caaveiro, J.M.M., Tsumoto, K., Yamano, K., Tanaka, K., and Matsuda, N. (2021) Destabilization-triggered mitochondrial import and degradation of cytosolic protein DJ-1. J. Cell Sci. 134:jcs258653 (15 pages), DOI: 10.1242/jcs.258653.
Rujas, E., Leaman, D.P., Insausti, S., Carravilla, P., García-Porras, M., Largo, E., Morillo, I., Sanchez-Eugenia, R., Zhang, L., Cui, H., Iloro, I., Elortza, F., Julien, J.-P., Eggeling, C., Zwick, M.B., Caaveiro, J.M.M., and Nieva, J.L. (2021) Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile. iScience 24:102987, DOI: 10.1016/j.isci.2021.102987.
Akiba, H., Tamura, H., Caaveiro, J.M.M., and Tsumoto, K. (2021) Epitope-dependent thermodynamic signature of single-domain antibodies against hen egg lysozyme. J. Biochem. 170:623-629, DOI: 10.1093/jb/mvab082.
Yui, A., Caaveiro, J.M.M., Kuroda, D., Nakakido, M., Nagatoishi, S., Goda, S., Maruno, T., Uchiyama, S., and Tsumoto, K. (2021) Mechanism of dimerization and structural features of human LI-cadherin. J. Biol. Chem., 297:101054, DOI: 10.1016/j.jbc.2021.101054.
Oyama, K., Ohkuri, T., Ochi, J., Caaveiro, J.M.M., and Ueda, T. (2021) Abolition of aggregation of CH2 domain of human IgG1 when combining glycosylation and protein stabilization. Biochem. Biophys. Res. Commun. 558:114-119, DOI: 10.1016/j.bbrc.2021.04.070
Oyama, K., Ohkuri, T., Inoue, M., Caaveiro, J.M.M., Ueda, T. (2021) High-level expression of human CH2 domain from the Fc region in Pichia pastoris and preparation of anti-CH2 antibodies. J. Biochem., in press, DOI: 10.1093/jb/mvab039.
Yamashita, T., Kamikaseda, S., Tanaka, A., Tozaki-Saitoh, H., Caaveiro, J.M.M., Inoue, K., Tsuda, M., (2021) New Inhibitory Effects of Cilnidipine on Microglial P2X7 Receptors and IL-1. Cells, 10:434, DOI: 10.3390/cells10020434.
2020
Ishii, M., Nakakido, M., Caaveiro, J.M.M., Kuroda, D., Okumura, C.J., Maruyama, T., Entzminger, K., Tsumoto, K. (2020) Structural Basis for Antigen Recognition by Methylated Lysine Specific Antibodies. J. Biol. Chem., 296:100176, DOI: 10.1074/jbc.RA120.015996.
Rujas, E., Insausti, S., Leaman, D.P., Carravilla, P., Gonzalez-Resines, S., Monceaux, V., Sánchez-Eugenia, R., García-Porras, M., Iloro, I., Zhang, L., Elortza, F., Julien, J.P., Saéz-Cirión, A., Zwick, M.B., Eggeling, C., Ojida, A., Domene, C., Caaveiro, J.M.M., and Nieva, J.L. (2020) Affinity for the Interface Underpins Potency of Antibodies Operating In Membrane Environments. Cell Rep., 32:108037, DOI: 10.1016/j.celrep.2020.108037.
Akiba, H., Tamura, H., Caaveiro, J.M.M., and Tsumoto, K (2020) Computer-guided library generation applied to the optimization of single-domain antibodies. Prot. Eng. Des. Select., 32:423-31, DOI: 10.1093/protein/gzaa006.
2019
Akiba, H., Tamura, H., Kiyoshi, M., Yanaka, S., Sugase, K., Caaveiro, J.M.M., and Tsumoto, K. (2019) Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci. Rep., 9:15481, DOI: 10.1038/s41598-019-50722-y.
Morante, K., Bellomio, A., Viguera, A.R., González-Mañas, J.M., Tsumoto, K., and Caaveiro, J.M.M. (2019) The isolation of new pore-forming toxins from the sea anemone Actinia fragacea provides insights into the mechanisms of actinoporin evolution. Toxins, 11:E401, DOI: 10.3390/toxins11070401.
Yamamoto, S., Yamashita, T., Ito, M., Caaveiro, J.M.M., Egashira, N., and Tsuda, M. (2019) New pharmacological effect of fulvestrant to prevent oxaliplatin-induced peripheral neuropathy in rats. Int. J. Cancer, 145: 2107–2113, DOI: 10.1002/ijc.32043.
Shindo, N., Fuchida, H., Sato, M., Watari, K., Shibata, T., Kuwata, K., Miura, C., Okamoto, K., Hatsuyama, Y., Tokunaga, K., Sakamoto, S., Morimoto, S., Abe, Y., Shiroishi, M., Caaveiro, J.M.M., Ueda, T., Tamura, T., Matsunaga, N., Nakao, T., Odo, S., Yamaguchi, Y., Hamachi, I., Ono, M., and Ojida A. (2019) Selective and reversible covalent modification of non-catalytic cysteines with weakly reactive α-chlorofluoroacetamides. Nat. Chem. Biol., 15:250-258, DOI: 10.1038/s41589-018-0204-3.
2018
Tashiro, S., Caaveiro, J.M.M., Nakakido, M., Tanabe, A., Nagatoishi, S., Tamura, Y., Matsuda, N., Liu, D., Hoang, Q.Q., and Tsumoto, K. (2018) Discovery and optimization of potent inhibitors of the Parkinson’s disease associated protein DJ-1. ACS Chem. Biol. 13:2783–2789, DOI: 10.1021/acschembio.8b00701.
Miyanabe, K., Yamashita, T., Akiba, H., Takamatsu, Y., Nakakido, M., Hamakubo, T., Caaveiro, J.M.M., and Tsumoto, K. (2018) Tyrosine sulfation restricts the conformational ensemble of a flexible peptide, strengthening the binding affinity for an antibody. Biochemistry 57:4177–4185, DOI: 10.1021/acs.biochem.8b00592
Tashima, T., Nagatoishi, S., Caaveiro, J.M.M., Nakakido, M., Sagara, H., Mimuro, H., Ohnuma, S-I., and Tsumoto, K. (2018) Weak electrostatic interactions between collagen and monomeric SLRP osteomodulin govern the shape of type I collagen fibrils. Commun. Biol. 1:33, DOI: 10.1038/s42003-018-0038-2.
Miyanabe, K., Akiba, H., Kuroda, D., Nakakido, M., Kusano-Arai, O., Iwanari, H., Hamakubo, T., Caaveiro, J.M.M., and Tsumoto, K. (2018) Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody. J. Biochem. 164:65–76, DOI: 10.1093/jb/mvy032 (Front Cover; 2019 JB paper award).
Kiyoshi, M., Caaveiro, J.M.M., 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., and Ishii-Watabe, A. (2018) Assessing the heterogeneity of the Fc-glycan of a therapeutic antibody using an engineered FcγReceptor IIIa-immobilized column. Sci. Rep. 8:3955, DOI: 10.1038/s41598-018-22199-8.
2017
Tanaka, K., Caaveiro, J.M.M., Morante, K., and Tsumoto, K. (2017) Hemolytic actinoporins interact with carbohydrates using their lipid-binding module. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372:20160216, DOI: 10.1098/rstb.2016.0216.
Rujas, E., Insausti, S., García-Porras, M., Sanchez-Eugenia, R., Tsumoto, K., Nieva, J.L., and Caaveiro, J.M.M. (2017) Functional contacts between MPER and the anti-HIV-1 broadly neutralizing antibody 4E10 extend into the core of the membrane. J. Mol. Biol. 429:1213–1226, DOI: 10.1016/j.jmb.2017.03.008.
Rujas, E., Caaveiro, J.M.M., Insausti, S., García-Porras, M., Tsumoto, K., and Nieva, J.L. (2017) Peripheral membrane interactions boost the engagement by an anti HIV-1 broadly neutralizing antibody. J. Biol. Chem. 292:5571–5583, DOI: 10.1074/jbc.M117.775429.
Kudo, S., Caaveiro, J.M.M., Nagatoishi, S., Miyafusa, T., Matsuura, T., Sudou, Y., and Tsumoto, K. (2017) Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin. Sci. Rep. 7:39518, DOI: 10.1038/srep39518.
Before 2017
Rujas, E., Caaveiro, J.M.M., Partida-Hanon, A., Gulzar, N., Morante, K., Apellániz, B., García-Porras, M., Bruix, M., Tsumoto, K., Scott, J.K., Jiménez, M.A., and Nieva, J.L. (2016) Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface. Sci. Rep. 6:38177, DOI: 10.1038/srep38177 (Selected as “Paper of the month” at SBE).
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. (2016) Differential effect of membrane composition on the pore–forming ability of four different sea anemone actinoporins. Biochemistry 55:6630-6641 DOI: 10.1021/acs.biochem.6b01007.
Kudo, S., Caaveiro, J.M.M., and Tsumoto, K. (2016) Adhesive dimerization of human P-cadherin catalyzed by a chaperone-like mechanism. Structure, 24:1523-1536, DOI: 10.1016/j.str.2016.07.002.
Sigala, P., Morante, K., Tsumoto, K., Caaveiro, J.M.M., and Goldberg, D.E. (2016) In-cell enzymology to probe the role of His-heme ligation in heme oxygenase catalysis. Biochemistry 55: 4836-4849, DOI: 10.1021/acs.biochem.6b00562.
Morante, K., Bellomio, A., Gil-Carton, D., Redondo-Morata, L., Sot, J., Scheuring, S., Valle, M., González-Mañas, J.M., Tsumoto, K., and Caaveiro, J.M.M. (2016) Identification of a membrane-bound prepore species clarifies the lytic mechanism of actinoporins. J. Biol. Chem. 291:19210-19219, DOI: 10.1074/jbc.M116.734053 (Paper of the week, Front Cover, and selected for the special virtual issue on structural biology).
Tanaka, K., Caaveiro, J.M.M., and Tsumoto, K. (2015) Bidirectional transformation of a protein between its native water-soluble and transmembrane conformations. Biochemistry 54:6863-6866, DOI: 10.1021/acs.biochem.5b01112.
Rujas, E., Gulzar, N., Morante, K., Tsumoto, K., Scott, J.K., Nieva, J.L., and Caaveiro, J.M.M. (2015) Structural and thermodynamic basis of epitope binding to neutralizing and non-neutralizing forms of the anti-HIV-1 4E10 antibody. J. Virol. 89:11975-11991, DOI: 10.1128/JVI.01793-15.
Nakano, K., Chigira, T., Miyafusa, T., Nagatoishi, S., Caaveiro, J.M.M., and Tsumoto, K (2015) Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus. Sci. Rep. 5:15337, DOI: 10.1038/srep15337.
Morante, K., Caaveiro, J.M.M., Viguera, A.R., Tsumoto, K., and González-Mañas, J.M. (2015) Functional characterization of Val60, a key residue involved in the membrane-oligomerization of fragaceatoxin C, an actinoporin from Actinia fragacea. FEBS Lett. 290:1840-1846, DOI: 10.1016/j.febslet.2015.06.012.
Kiyoshi, M., Caaveiro, J.M.M., Kawai, T., Tashiro, S., Ide, T., Asaoka, Y., Hatayama, K., and Tsumoto K. (2015) Structural basis for binding of human IgG1 to its high-affinity human receptor FcγRI. Nat. Commun. 6:6866, DOI: 10.1038/ncomms7866 (Hot paper and Highly-cited paper one term).
Apellaniz, B., Rujas, E., Serrano, S., Morante, K., Tsumoto, K., Caaveiro, J.M.M., Jimenez, M.A., and Nieva, J.L. (2015) The atomic structure of the HIV-1 gp41 transmembrane domain and its connection to the immunogenic membrane-proximal external region. J. Biol. Chem. 290:12999-13015, DOI: 10.1074/jbc.M115.644351 (Paper of the week).
Morante, K., Caaveiro, J.M.M., Tanaka, K., González-Mañas, J.M., and Tsumoto K. (2015) A pore forming toxin requires a specific residue for its activity in membranes with particular physicochemical properties. J. Biol. Chem. 290:10850-10861, DOI: 10.1074/jbc.M114.615211.
Tanaka, K., Caaveiro, J.M.M., Morante, K., González-Mañas, J.M., and Tsumoto K. (2015) Structural basis of self-assembly of a cytolytic pore lined by protein and lipid. Nat. Commun. 6:6337, DOI: 10.1038/ncomms7337 (Highly cited paper four terms).
Tashiro, S., Caaveiro, J.M.M., Wu, C-H., Hoang, Q.Q., and Tsumoto K. (2014) Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1. Biochemistry 53:2218-2220, DOI: 10.1021/bi500294h. (Rapid report)
Kudo, S., Caaveiro, J.M.M., Goda, S., Nagatoishi, S., Ishii, K., Matsuura, T., Sudou, Y., Kodama, K., Hamakubo, T., and Tsumoto, K. (2014) Identification and characterization of the X-dimer of human P-cadherin: Implications for homophilic cell adhesion. Biochemistry 53:1742-1752, DOI: 10.1021/bi401341g.
Kiyoshi, M., Caaveiro, J.M.M., Miura, E., Nagatoishi, S., Nakakido, M., Soga, S., Shirai, H., Kawabata, S., and Tsumoto, K. (2014) 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 9:e87099, DOI: 10.1371/journal.pone.0087099.
Moriwaki, Y., Terada, T., Caaveiro, J.M.M., Takaoka, Y., Hamachi, I., Tsumoto, K., and Shimizu K. (2013) Heme-binding mechanism of structurally similar Isd NEAT domains of Staphylococcus aureus exhibiting different affinities for heme. Biochemistry 52:8866−8877, DOI: 10.1021/bi4008325.
Miyafusa, T., Caaveiro, J.M.M., Tanaka, Y., and Tsumoto, K. (2013) Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus. FEBS Lett. 587:3824-3830, DOI: 10.1016/j.febslet.2013.10.009.
Sigala P.A., Fafarman A.T., Schwans J.P., Fried S.D., Fenn T.D., Caaveiro J.M.M., Pybus B., Ringe D., Petsko G.A., Boxer S.G., and Herschlag D. (2013) Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proc. Natl. Acad. Sci. 110:E2552–E2561, DOI: 10.1073/pnas.1302191110.
Vu, N.T., Moriwaki, Y., Caaveiro, J.M.M., Terada, T., Tsutsumi, H., Hamachi, I., Shimizu, K., and Tsumoto, K. (2013) Selective binding of antimicrobial porphyrins to the heme-receptor IsdH-NEAT3 of Staphylococcus aureus. Protein Sci. 22:942-953, DOI: 10.1002/pro.2276 (Front cover).
Miyafusa, T, Caaveiro, J.M.M., Tanaka, Y., Tanner, M.E., and Tsumoto, K. (2013) Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus. Biosci. Rep. 33:463-474, DOI: 10.1042/BSR20130017.
Kobe, A., Caaveiro, J.M.M., Tashiro, T., Kajihara, D., Kikkawa, M., Mitani, T., and Tsumoto, K. (2013) Incorporation of rapid thermodynamic data in fragment-based drug discovery. J. Med. Chem. 56:2155-2159, DOI: 10.1021/jm301603n.
Kudo, S., Caaveiro, J.M.M., Miyafusa, T., Goda, S., Ishii, K., Matsuura, T., Sudou, Y., Kodama, T., Hamakubo, T., and Tsumoto, K. (2012) Structural and thermodynamic characterization of the self-adhesive properties of human P-cadherin. Mol. Biosyst. 8:2050-2053, DOI: 10.1039/c2mb25161b.
Abe, R., Caaveiro, J.M.M., Kozuka-Hata H., Oyama, M., and Tsumoto. K. (2012) Mapping ultra-weak protein-protein interactions between heme transporters of Staphylococcus aureus. J. Biol. Chem. 287:16477-16487, DOI: 10.1074/jbc.M112.346700.
Miyafusa, T., Caaveiro, J.M.M., Tanaka, Y., and Tsumoto, K. (2012) Crystal structure of the enzyme CapF of Staphyloccus aureus reveals a unique architecture composed of two functional domains. Biochem. J. 443:671-670, DOI: 10.1042/BJ20112049.
Kawai, T., Caaveiro, J.M.M., Abe, R., Katagiri, T., and Tsumoto, K. (2011) Catalytic activity of MsbA reconstituted in nanodisc particles is modulated by remote interactions with the bilayer, FEBS Lett. 585:3533-3537. DOI: 10.1016/j.febslet.2011.10.015.
Moriwaki, Y.,Caaveiro, J.M.M., Tanaka, Y., Tsutsumi, H., Hamachi, I., and Tsumoto, K. (2011) Molecular basis of recognition of antibacterial porphyrins by heme-transporter IsdH-NEAT3 of Staphylococcus aureus. Biochemistry 50:7311-7320, DOI: 10.1021/bi200493h (Accelerated publication).
Yanaka, S., Sano, E., Naruse, N., Miura, K-I., Futatsumori-Sugai, M., Caaveiro, J.M.M., and Tsumoto, K. (2011) Non-core region modulates interleukin-11 signaling activity: generation of agonist and antagonist variants, J. Biol. Chem. 286:8085-8093, DOI: 10.1074/jbc.M110.152561.
Abe, R., Caaveiro, J.M.M., Kudou, M., and Tsumoto, K. (2010) Solubilization of membrane proteins with novel N-acylamino acid detergents, Mol. Biosyst. 6:677-679, DOI: 10.1039/b925791h (Journal cover).
Sakamoto, S.,# Caaveiro, J.M.M.,# Sano, E., Tanaka, Y., Kudou, M., and Tsumoto, K. (2009) Contributions of interfacial residues of human interleukin15 to the specificity and affinity for its private α-receptor. J. Mol. Biol. 389:880-894, DOI: 10.1016/j.jmb.2009.04.050 (#Equal Contribution).
Sigala, P.A., Caaveiro, J.M.M., Ringe, D., Petsko, G.A., and Herschlag, D. (2009) Hydrogen Bond coupling in the ketosteroid active site. Biochemistry 48:6932-6939, DOI: 10.1021/bi900713j.
Landon M.R., Lieberman, R.L., Hoang, Q.Q., Ju, S., Caaveiro, J.M.M., Orwig, S.D., Kozakov, D., Brenke, R., Beglov, D., Vajda, S., Petsko, G.A., and Ringe, D. (2009) Detection of ligand binding hot spots on protein surfaces via fragment-based methods: Application to DJ-1 and glucocerebrosidase. J. Comput. Aid. Mol. Des. 130:491-500, DOI: 10.1007/s10822-009-9283-2.
Sigala, P., Kraut, D. A., Caaveiro, J.M.M., Pybus, B., Ringe, D., Petsko, G.A., and Herschlag, D. (2008) Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J. Am. Chem. Soc. 130:13696-13708, DOI: 10.1021/ja803928m (Highlighted in Nature (2008), 456, 45-46; Recommended by Nobel laureate Arieh Warshel in F1000).
Barlic, A., Gutiérrez-Aguirre, I., Caaveiro, J.M.M., Cruz, A., Ruiz-Argüello, M.B., Pérez-Gil, J., and González-Mañas, J.M. (2004) Lipid phase coexistence favors membrane insertion of equinatoxin-II, a pore-forming toxin from Actinia equina. J. Biol. Chem. 279:34209-34216, DOI: 10.1074/jbc.M313817200.
Xie, Y., Das, P.K., Caaveiro, J.M.M., and Klibanov, A.M. (2002) Unexpectedly enhanced stereoselectivity of peroxidase-catalyzed sulfoxidation in branched alcohols. Biotechnol. Bioeng. 79:105-111, DOI: 10.1002/bit.10308.
Das, P.K., Caaveiro, J.M.M., Luque, S., and Klibanov, A.M. (2002) Asymmetric sulfoxidations mediated by α-chymotrypsin. Biotechnol. Bioeng. 78:104-109, DOI: 10.1002/bit.10187.
Das, P.K., Caaveiro, J.M.M., Luque, S., and Klibanov, A.M. (2002) Binding of hydrophobic hydroxamic acids enhances peroxidase’s stereoselectivity in nonaqueous sulfoxidations. J. Am. Chem. Soc. 124:782-787, DOI: 10.1021/ja012075o.
Caaveiro, J.M.M., Echabe, I., Gutierrez-Aguirre, I., Nieva, J.L., Arrondo, J.L.R., and González-Mañas, J.M. (2001) Differential interaction of equinatoxin II with model membranes in response to lipid composition. Biophys. J. 80:1343-1352, DOI: 10.1016/S0006-3495(01)76107-3.
Caaveiro, J.M.M., Gutierrez-Aguirre, I., Tribout, M., Paredes, S., and González-Mañas, J.M. (2000) An evaluation of some model systems commonly used in the study of the sea anemone toxin equinatoxin II with membranes. Acta Biol. Sloven. 43:93-97.
Caaveiro, J.M.M., Molina, A., Rodriguez-Palenzuela, P., Goñi, F.M., and Gonzalez-Mañas, J.M. (1998) Interaction of wheat α-thionin with large unilamellar vesicles. Protein Sci. 7:2567-2577, DOI: 10.1002/pro.5560071210.
Caaveiro, J.M.M., Molina, A., González-Mañas, J.M., Rodriguez-Palenzuela, P., Garcia-Olmedo, F., and Goñi, F.M. (1997) Differential effects of five types of antipathogenic plant peptides on model membranes. FEBS Lett. 410:338-342, DOI: 10.1016/S0014-5793(97)00613-3.
Taneva, S.G., Caaveiro, J.M.M., Muga, A., and Goñi, F.M. (1995) A pathway for the thermal denaturation of bacteriorhodopsin. FEBS Lett. 367:297-300, DOI: 10.1016/0014-5793(95)00570-Y.
Taneva, S.G., Caaveiro, J.M.M., Petkanchin, I. B., and Goñi, F.M. (1995) Electrokinetic charge of the anesthetic induced bR480 and bR380 spectral forms of bacteriorhodopsin. Biochim. Biophys. Acta. 1236:331-337, DOI: 10.1016/0005-2736(95)00074-D.
Reviews.
Senoo A., Tsumoto K., Caaveiro J.M.M. (2025) 病原性細菌の鉄取り込み戦略の分子構造基盤. 生物物理 65:206-209, DOI: 10.2142/biophys.65.206
Maenaka, K., Fukuhara, H., Hashiguchi, T., Caaveiro, J.M.M., Nagatoishi, S., Kuroda, D., and Tsumoto, K. (2021) ウイルス生物物理学:創薬モダリティへの貢献 (Viral Biophysics: Contributions to Drug Discovery Modalities). Seibutsu butsuri, 61:2, DOI: 10.2142/biophys.61.082 (Review written in Japanese).
Caaveiro, J.M.M. and Tsumoto, K (2021) Molecular basis for the activation of actinoporins by lipids. Methods Enzymol., 469:277, DOI: 10.1016/bs.mie.2021.01.008.
Nagatoishi, S., Caaveiro, J.M.M., and Tsumoto, K (2018) 次世代の低分子創薬を拓くタンパク質-低分子間相互作用の物理化学的解析 (Biophysical analysis of the protein-small molecule interactions to develop small molecule drug discovery). Yakugaku Zasshi 138:1033-1041 DOI: 10.1248/yakushi.17-00211-2 (Review written in Japanese).
Caaveiro, J.M.M. and Tsumoto, K. (2018) 黄色ブドウ球菌の鉄取り込み機構:Isd システム(Heme-acquisition in Staphylococcus aureus by the iron-regulated surface determinant (Isd) system). Seikagaku 90:279-289, DOI: 10.14952/SEIKAGAKU.2018.900279 (Review written in Japanese).
Kiyoshi, M., Tsumoto, K., Ishii-Watabe, A., and Caaveiro, J.M.M. (2017) Glycosylation of IgG-Fc: A molecular perspective. Int. Immunol. 29:311-317, DOI: 10.1093/intimm/dxx038.
Tsumoto, K. and Caaveiro, J.M.M. (2016) Antigen-Antibody Binding. In: Encyclopedia of Life Sciences (eLS). John Wiley & Sons, Ltd: Chichester, DOI: 10.1002/9780470015902.a0001117.pub3.
Caaveiro, J.M.M., Kiyoshi, M., and Tsumoto, K. (2015) Structural Analysis of Fc/FcγR Complexes: A Blueprint for Antibody Design. Immunol. Rev. 268:201-221, DOI: 10.1111/imr.12365.