{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T10:09:26Z","timestamp":1773655766622,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T00:00:00Z","timestamp":1772496000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"JSPS KAKENHI","award":["24\u00a0K03041"],"award-info":[{"award-number":["24\u00a0K03041"]}]},{"name":"JSPS KAKENHI","award":["19H03362"],"award-info":[{"award-number":["19H03362"]}]},{"DOI":"10.13039\/501100004906","name":"Fugaku Trust for Medicinal Research Tohoku Medical and Pharmaceutical University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004906","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Anti-glycan antibodies have become essential tools in biochemical assays, tissue staining, and diagnostic applications; however, the structural basis of glycan\u2013antibody interactions is poorly understood, limiting rational design of antibodies with enhanced affinity and specificity. Key challenges include the crystallization of glycan\u2013antibody complexes and the acquisition of complete electron density maps of bound glycans. To gain insight into the mechanisms of interaction between antibodies and glycans, here we constructed three-dimensional models of glycan\u2013antibody complexes by integrating NMR spectroscopy with computational simulations. As a representative system, we selected lacto-N-fucopentaose I (LNFP I), which is expressed on undifferentiated induced pluripotent stem cells, and two anti-glycan monoclonal antibodies, R-17F and R-13E. Saturation transfer difference NMR of antibody\u2013glycan solutions indicated that the fucose and N-acetylglucosamine moieties of LNFP I lie in close spatial proximity to the antibody and likely form the interaction surface, with R-17F exhibiting broader contact and more stable binding than R-13E. These data were used as experimental constraints for constructing antibody\u2013glycan complex models through molecular docking and molecular dynamics simulations based on an LNFP I crystal structure and AlphaFold models of the antibody Fv fragment. The resulting models revealed that the non-reducing end of LNFP I is specifically recognized by both R-17F and R-13E, while the reducing end is exposed to the solvent, suggesting compatibility with its native glycolipid anchor. This study provides new structural insights into glycan\u2013antibody recognition and highlights the utility of combining NMR and molecular simulations for the rational design of glycan-targeting antibodies.<\/jats:p>","DOI":"10.1093\/glycob\/cwag016","type":"journal-article","created":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T12:41:48Z","timestamp":1772714508000},"source":"Crossref","is-referenced-by-count":0,"title":["Integrative structural analysis of lacto-\n                    <i>N<\/i>\n                    -fucopentaose I recognition by antibodies R-17F and R-13E using NMR, docking, and molecular dynamics simulations"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4069-8744","authenticated-orcid":false,"given":"Shiho","family":"Ohno","sequence":"first","affiliation":[{"name":"Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akito","family":"Ohuchi","sequence":"additional","affiliation":[{"name":"Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuki","family":"Saitoh","sequence":"additional","affiliation":[{"name":"Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8866-0526","authenticated-orcid":false,"given":"Noriyoshi","family":"Manabe","sequence":"additional","affiliation":[{"name":"Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tsutomu","family":"Fujimura","sequence":"additional","affiliation":[{"name":"Division of Bioanalytical Chemistry, Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Noriyuki","family":"Yuasa","sequence":"additional","affiliation":[{"name":"Tokyo Chemical Industry Co., Ltd. , 4-10-2, Nihonbashi-honcho, Chuo-Ku, Tokyo 103-0023 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuji","family":"Matsuzaki","sequence":"additional","affiliation":[{"name":"Tokyo Chemical Industry Co., Ltd. , 4-10-2, Nihonbashi-honcho, Chuo-Ku, Tokyo 103-0023 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5607-4880","authenticated-orcid":false,"given":"Makoto","family":"Tsuiji","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences , 2-4-41 Ebara, Shinagawa-Ku, Tokyo 142-8501 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0993-0274","authenticated-orcid":false,"given":"Toshisuke","family":"Kawasaki","sequence":"additional","affiliation":[{"name":"Research Center for Glycobiotechnology, Ritsumeikan University , Noji-Higashi, 1-1-1, Kusatsu, Shiga 525-8577 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0100-5439","authenticated-orcid":false,"given":"Yoshiki","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,3,9]]},"reference":[{"key":"2026031605312817100_ref1","doi-asserted-by":"publisher","first-page":"5853","DOI":"10.1021\/bi0354886","article-title":"Oligosaccharides implicated in recognition are predicted to have relatively ordered structures","volume":"43","author":"Almond","year":"2004","journal-title":"Biochemistry"},{"key":"2026031605312817100_ref2","doi-asserted-by":"publisher","first-page":"2353","DOI":"10.1021\/ct900242e","article-title":"CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses","volume":"5","author":"Guvench","year":"2009","journal-title":"J Chem Theory 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