{"id":196,"date":"2024-04-28T14:19:46","date_gmt":"2024-04-28T05:19:46","guid":{"rendered":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/?page_id=196"},"modified":"2026-01-22T13:34:53","modified_gmt":"2026-01-22T04:34:53","slug":"publications-en","status":"publish","type":"page","link":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/publications-en\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Publications<\/h2>\n\n\n\n<ul class=\"wp-block-list icon\">\n<li><a href=\"#1\">Original articles<\/a><\/li>\n\n\n\n<li><a href=\"#2\">Reviews<\/a><\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"1\">Original articles<\/h3>\n\n\n\n<h4 class=\"wp-block-heading\">2026<\/h4>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Design, synthesis, and structural analysis of an inhibitor of the gastric proton pump with a diaza-tricyclic skeleton<br>Umekubo, N., Hashizume, A., Saito, H., Kato, S., Kanai, C., Gopalasingam, C. C., Gerle, C., Shigematsu, H., *Yoshimori, A.,<strong> *<strong><u>Abe, K.<\/u><\/strong>,<\/strong> *Yokoshima, S.<br><strong><em>Org. Biomol. Chem.,<\/em><\/strong> In press (2026) <a href=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2026\/ob\/d5ob01828e\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1039\/d5ob01828e<\/a><\/li>\n<\/ol>\n\n\n\n<h4 class=\"wp-block-heading\">2025<\/h4>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Cryo-EM Structure of the ATP11C Q79E Mutant Reveals the Structural Basis for Altered Phospholipid Recognition<br>Qian, Y., Gopalasingam, C. C., Gerle, C., Shigematsu, H., *<strong><u>Abe, K.<\/u><\/strong>, Oshima, A.<br><strong><em>J. Biol. Chem.<\/em><\/strong>, Volume 302, Issue 1, 110935 (2025)&nbsp;<a href=\"https:\/\/doi.org\/10.1016\/j.jbc.2025.110935\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1016\/j.jbc.2025.110935<\/a><\/li>\n\n\n\n<li>A unique gating mechanism revealed by the cryo-EM structure of monomeric ATP9A flippase<br>*<strong><u>Abe, K.<\/u><\/strong>, Marimuthu, P., Qian, Y., Gopalasingam, C. C., Gerle, C., Shigematsu, H., Tanaka, K., Khandelia, H.<br><strong><em>J. Biol. Chem.<\/em><\/strong>, Volume 301, Issue 10, 110631 (2025)&nbsp;<a href=\"https:\/\/doi.org\/10.1016\/j.jbc.2025.110631\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1016\/j.jbc.2025.110631<\/a><\/li>\n<\/ol>\n\n\n\n<h4 class=\"wp-block-heading\">2024<\/h4>\n\n\n\n<ol reversed class=\"wp-block-list\">\n<li>Molecular Structure of the Na+,K+-ATPase \u03b14\u03b21 Isoform in Its Ouabain-Bound Conformation<br>*<strong><u>Abe, K.<\/u><\/strong>, McDermott, J., Madapally, H.V., Marimuthu, P., Gopalasingam, C.C., Gerle, C., Shigematsu, H., Khandelia, H. &amp; *Blanco, G.,<strong><em> <\/em><\/strong><br><strong><em>Int. J. Mol. Sci.<\/em><\/strong>, 25(22), 12397 (2024)<a href=\" DOI:10.3390\/ijms252212397\"> <\/a><a href=\"https:\/\/doi.org\/10.3390\/ijms252212397\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.3390\/ijms252212397<\/a><\/li>\n\n\n\n<li>Human F-ATP synthase as a drug target. <br>*Gerle, C., Jiko, C., Nakano, A., Yokoyama, K., Gopalasingam, C.C., Shigematsu, H., <strong><u>Abe, K.<\/u><\/strong>, <br><strong><em>Pharmacol. Res.<\/em><\/strong>, 209, 107423 (2024) <a href=\"https:\/\/doi.org\/10.1016\/j.phrs.2024.107423\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1016\/j.phrs.2024.107423<\/a><\/li>\n\n\n\n<li>Specific protonation of acidic residues confers K<sup>+<\/sup> selectivity to the gastric proton pump<br>Madapally, H.V., <strong><u>Abe, K.<\/u><\/strong>, Dubey, V. &amp; *Khandelia, H.<br><strong><em>J. Biol. Chem.<\/em><\/strong>, 300, 105542 (2024) <a href=\"https:\/\/doi.org\/10.1016\/j.jbc.2023.105542\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1016\/j.jbc.2023.105542<\/a><\/li>\n<\/ol>\n\n\n\n<h4 class=\"wp-block-heading\">-2023 (selected)<\/h4>\n\n\n\n<ol reversed class=\"wp-block-list\">\n<li>A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities<br>*Artigas, P., Meyer, D.J., Young, V.C., Spontarelli, K., Eastman, J., Strandquist, E., Rui, H., Roux, B., Brik, M., Nakanishi, H., *<strong><u>Abe, K.<\/u><\/strong> &amp; *Gatto, C.<br><strong><em>Proc. Natl. Acad. Sci. USA.<\/em><\/strong>, 120, e2313999120 (2023) <a href=\"https:\/\/doi.org\/10.1073\/pnas.2313999120\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1073\/pnas.2313999120<\/a><\/li>\n\n\n\n<li>Deep learning driven de novo drug design based on gastric proton pump structures.<br>*<strong><u>Abe K.<\/u><\/strong>, Ozako, M., Inukai, M., Matsuyuki, Y., Kitayama, S., Kanai, C., Nagai, C., Gopalasingam, C.C., Gerle, C., Shigematsu, H., Umekubo, N., *Yokoshima, S. &amp; *Yoshimori, A.<br><strong><em>Commun. Biol.<\/em><\/strong>, 6, 956 (2023) <a href=\"https:\/\/doi.org\/10.1038\/s42003-023-05334-8\">DOI: 10.1038\/s42003-023-05334-8<\/a><\/li>\n\n\n\n<li>Structure and function of H<sup>+<\/sup>\/K<sup>+<\/sup> pump mutants reveal Na<sup>+<\/sup>\/K<sup>+<\/sup> pump mechanism.<br><sup>\u2020<\/sup>Young, V.C., <sup>\u2020<\/sup>Nakanishi, H., Meyer, D.J., Nishizawa, T., Artigas, P. &amp; <strong>*<u>Abe, K.<\/u><\/strong><br><strong><em>Nat. Commun.<\/em><\/strong>, 13, 5270 (2022) <a href=\"https:\/\/doi.org\/10.1038\/s41467-022-32793-0\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1038\/s41467-022-32793-0<\/a><\/li>\n\n\n\n<li>Structural basis for binding of potassium-competitive acid blockers to the gastric proton pump.<br>Tanaka, S., Morita, M., Yamagishi, T., Hridya, V.M., Hayashida, K., Khandelia, H., Gerle, C., Shigematsu, H., Oshima, A. &amp; <strong>*<u>Abe K.<\/u><\/strong><br><strong><em>J. Med. Chem.<\/em><\/strong>, 65, 7843-7853 (2022) <a href=\"https:\/\/doi.org\/10.1021\/acs.jmedchem.2c00338\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1021\/acs.jmedchem.2c00338<\/a><\/li>\n\n\n\n<li>Gastric proton pump with two occluded K<sup>+<\/sup> engineered with sodium pump-mimetic mutations.<br><strong>*<u>Abe, K.<\/u><\/strong>, Yamamoto, K., Irie, K., Nishizawa, T. &amp; Oshima, A.<br><strong><em>Nat. Commun.<\/em><\/strong>, 12, 5709 (2021) <a href=\"https:\/\/doi.org\/10.1038\/s41467-021-26024-1\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1038\/s41467-021-26024-1<\/a><\/li>\n\n\n\n<li>Transport cycle of plasma membrane flippase ATP11C by cryo-EM.<br>Nakanishi, H., Nishizawa, T., Irie, K., Segawa, K., Nureki, O., Fujiyoshi, Y., Nagata, S. &amp;<strong> *<u>Abe, K.<\/u><\/strong><br><strong><em>Cell Rep.<\/em><\/strong>, 32, 108208 (2020) <a href=\"https:\/\/doi.org\/10.1016\/j.celrep.2020.108208\" target=\"_blank\" rel=\"noreferrer noopener\">DOI:&nbsp; 10.1016\/j.celrep.2020.108208<\/a>&nbsp;<\/li>\n\n\n\n<li>A single K<sup>+<\/sup>-binding in the crystal structure of the gastric proton pump.<br>Yamamoto, K., Dubey, V., Irie, K., Nakanishi, H., Khandelia, H., Fujiyoshi, Y. &amp;<strong>*<u>Abe, K.<\/u><\/strong><br><strong><em>eLife<\/em><\/strong>., 8, e47701 (2019) <a href=\"https:\/\/doi.org\/10.7554\/eLife.47701\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.7554\/eLife.47701<\/a><\/li>\n\n\n\n<li>Crystal structures of the gastric proton pump.<br><strong>*<u>Abe, K.<\/u><\/strong>, Irie, K., Nakanishi, H., Suzuki, H. &amp; Fujiyoshi, Y.<br><strong><em>Nature<\/em><\/strong>, 556, 214-218 (2018) <a href=\"https:\/\/doi.org\/10.1038\/s41586-018-0003-8\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1038\/s41586-018-0003-8<\/a><\/li>\n\n\n\n<li>Cryo-EM structure of gastric H<sup>+<\/sup>,K<sup>+<\/sup>-ATPase with a single occupied cation-binding site.<br><strong>*<u>Abe, K.<\/u><\/strong>, Tani, K., Friedrich, T. &amp; Fujiyoshi, Y.<br><strong><em>Proc. Natl. Acad. Sci. USA<\/em><\/strong><em>.<\/em>, 109 (45), 18401-18406 (2012) <a href=\"https:\/\/doi.org\/10.1073\/pnas.1212294109\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1073\/pnas.1212294109<\/a><\/li>\n\n\n\n<li>Inter-subunit interaction of gastric H<sup>+<\/sup>,K<sup>+<\/sup>-ATPase prevents reverse reaction of the transport cycle.<br><strong><u>Abe, K.<\/u><\/strong>, Tani, K., Nishizawa, T. &amp; *Fujiyoshi, Y.<br><strong><em>EMBO J.<\/em><\/strong>, 28, 1637-1643 (2009) <a href=\"https:\/\/doi.org\/10.1038\/emboj.2009.102\" target=\"_blank\" rel=\"noreferrer noopener\">DOI:&nbsp; 10.1038\/emboj.2009.102<\/a><\/li>\n<\/ol>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"2\">Reviews<\/h3>\n\n\n\n<ol reversed class=\"wp-block-list\">\n<li>AI\u304c\u63cf\u304f\u80c3\u85ac\u306e\u672a\u6765\u56f3 cryo-EM\u3068Deep Quartet\u304c\u62d3\u304f\u65b0\u305f\u306a\u963b\u5bb3\u5264\u306e\u30c7\u30b6\u30a4\u30f3<br>*\u963f\u90e8\u4e00\u5553\uff0c\u6a2a\u5cf6\u3000\u8061\uff0c\u5409\u68ee\u7be4\u53f2<br>\u5b9f\u9a13\u533b\u5b66\u5897\u520a\uff1a\u69cb\u9020\u751f\u547d\u79d1\u5b66\u3000AlphaFold\u6642\u4ee3\u306b\u3069\u3046\u6d3b\u304b\u3059\uff1f\u301c\u751f\u547d\u6a5f\u80fd\u3092\u89e3\u304f\u3001\u5909\u3048\u308b\u3001\u5275\u308b\u305f\u3081\u306e\u6280\u8853\u3068\u7814\u7a76\u6226\u7565\uff08\u52a0\u85e4\u82f1\u660e\uff0c\u897f\u5897\u5f18\u5fd7\uff0f\u7de8\uff09, Vol.43 No.15, ISBN 978-4-7581-0429-6<\/li>\n\n\n\n<li>Human F-ATP synthase as a drug target<br>Gerle, C., Jiko, C., Nakano, A., Yokoyama, K., Gopalasingam, C.C., Shigematsu, H., *Abe, K.,<br>Pharm Res (2024) DOI:10.1016\/j.phrs.2024.107423<\/li>\n\n\n\n<li>\u7d30\u80de\u819c\u30ea\u30f3\u8102\u8cea\u30d5\u30ea\u30c3\u30d1\u30fc\u30bcATP11C\u306e\u7acb\u4f53\u69cb\u9020\u3068\u8f38\u9001\u6a5f\u69cb.<br>\u4e2d\u897f\u83ef\u4ee3, *\u963f\u90e8\u4e00\u5553<br>\u751f\u5316\u5b66 (2022) DOI: 10.14952\/SEIKAGAKU.2021.930824<\/li>\n\n\n\n<li>\u80c3\u306e\u9178\u6027\u5316\u306e\u5206\u5b50\u30e1\u30ab\u30cb\u30ba\u30e0.<br>*\u963f\u90e8\u4e00\u5553<br>\u751f\u4f53\u306e\u79d1\u5b66, 71, 310-314 (2020) DOI: 10.11477\/mf.2425201181<\/li>\n\n\n\n<li>\u80c3\u306e\u4e2d\u304c\u5f37\u3044\u9178\u6027\u306b\u306a\u308b\u4ed5\u7d44\u307f.<br>*\u963f\u90e8\u4e00\u5553<br>\u751f\u7269\u7269\u7406, 59, 73-78 (2019) DOI: 10.2142\/biophys.59.073<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Publications Original articles 2026 2025 2024 -2023 (selected) Reviews<\/p>\n","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-196","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/pages\/196","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/comments?post=196"}],"version-history":[{"count":40,"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/pages\/196\/revisions"}],"predecessor-version":[{"id":1255,"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/pages\/196\/revisions\/1255"}],"wp:attachment":[{"href":"https:\/\/wwwchem.sci.hokudai.ac.jp\/~molbio\/wp-json\/wp\/v2\/media?parent=196"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}