{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T15:26:41Z","timestamp":1787153201987,"version":"build-2736575974"},"reference-count":48,"publisher":"American Chemical Society (ACS)","issue":"32","license":[{"start":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T00:00:00Z","timestamp":1785974400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T00:00:00Z","timestamp":1785974400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T00:00:00Z","timestamp":1785974400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Antagonistic epistasis often limits enzyme engineering by causing activity loss when beneficial mutations are combined. Here, we present a mechanism-guided multidimensional feature analysis (MDFA) strategy integrating rational design, structural partitioning, machine learning, and computational simulations to optimize D-amino acid oxidase (DAAO) for D-phosphinothricin (D-PPT). Channel geometry and electrostatics defined preferred screening ranges, while a CNN ensemble with a Random Forest surrogate enabled multisite classification. Computational and experimental analyses suggested that excessive local positive charge and imbalanced flexibility contribute to A. epistasis, whereas spatial partitioning reduces local conflict. OAEMT (N53R-V57R-S233 K-Q339R) increased catalytic efficiency 80.94-fold and converted 85.5% of D-PPT within 5 h in a 2 L reactor. MDFA thus improves combinatorial design within a defined mutational space.<\/jats:p>","DOI":"10.1021\/acs.jafc.6c03008","type":"journal-article","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T14:21:01Z","timestamp":1786026061000},"page":"25392-25406","source":"Crossref","is-referenced-by-count":0,"title":["Overcoming\n                    <i>Antagonistic epistasis<\/i>\n                    in DAAO Engineering via Mechanism-Guided\nMultidimensional Feature\nAnalysis"],"prefix":"10.1021","volume":"74","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0513-9816","authenticated-orcid":true,"given":"Heng","family":"Tang","sequence":"first","affiliation":[{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin-Qiao","family":"Zhao","sequence":"additional","affiliation":[{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Ling","family":"Ding","sequence":"additional","affiliation":[{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Ze","family":"Sun","sequence":"additional","affiliation":[{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mei","family":"Chen","sequence":"additional","affiliation":[{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0370-2502","authenticated-orcid":true,"given":"Ya-Ping","family":"Xue","sequence":"additional","affiliation":[{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6358-6243","authenticated-orcid":true,"given":"Yu-Guo","family":"Zheng","sequence":"additional","affiliation":[{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]},{"name":"Zhejiang University of Technology , , ,","place":["Hangzhou, China, 310014"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,6]]},"reference":[{"issue":"15","key":"2026081910143214100_cit1","doi-asserted-by":"publisher","first-page":"8303","DOI":"10.1021\/acscatal.0c01579","article-title":"Tandem Catalysis for\nHydrogenation of CO and CO2 to Lower Olefins with Bifunctional Catalysts\nComposed of Spinel Oxide and SAPO-34","volume":"10","author":"Liu","year":"2020","journal-title":"ACS Catal."},{"key":"2026081910143214100_cit2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biotechadv.2024.108376","article-title":"Unlocking\nthe potential of enzyme engineering via rational computational design\nstrategies","volume":"73","author":"Zhou","year":"2024","journal-title":"Biotechnol. Adv."},{"issue":"8","key":"2026081910143214100_cit3","doi-asserted-by":"publisher","first-page":"1779","DOI":"10.1093\/molbev\/mst096","article-title":"Patterns\nof Epistasis between Beneficial Mutations in an Antibiotic Resistance\nGene","volume":"30","author":"Schenk","year":"2013","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"2026081910143214100_cit4","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44333-5","article-title":"Pervasive\nepistasis exposes intramolecular\nnetworks in adaptive enzyme evolution","volume":"14","author":"Buda","year":"2023","journal-title":"Nat.\nCommun."},{"issue":"5","key":"2026081910143214100_cit5","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41929-024-01117-4","article-title":"Epistasis\narises from shifting the rate-limiting step during enzyme evolution\nof a \u03b2-lactamase","volume":"7","author":"Fro\u0308hlich","year":"2024","journal-title":"Nat. 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Genet."},{"issue":"22","key":"2026081910143214100_cit13","doi-asserted-by":"publisher","first-page":"14243","DOI":"10.1021\/acscatal.2c01426","article-title":"Learning\nEpistasis and Residue Coevolution\nPatterns: Current Trends and Future Perspectives for Advancing Enzyme\nEngineering","volume":"12","author":"Wittmund","year":"2022","journal-title":"ACS Catal."},{"issue":"10","key":"2026081910143214100_cit14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1001162","article-title":"Pervasive\nCryptic Epistasis in Molecular\nEvolution","volume":"6","author":"Lunzer","year":"2010","journal-title":"PLoS Genet."},{"key":"2026081910143214100_cit15","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-48480-y","article-title":"A novel thermostable\nd-amino acid oxidase of the thermophilic fungus Rasamsonia emersonii\nstrain YA","volume":"9","author":"Shimekake","year":"2019","journal-title":"Sci. Rep."},{"key":"2026081910143214100_cit16","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1107\/S2053230X20013333","article-title":"X-ray structure\nanalysis of a unique d-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA","volume":"76","author":"Shimekake","year":"2020","journal-title":"Acta Crystallogr., Sect. F:Struct. Biol. Commun."},{"issue":"6673","key":"2026081910143214100_cit17","doi-asserted-by":"publisher","DOI":"10.1126\/science.adh8615","article-title":"From nature\nto industry: Harnessing\nenzymes for biocatalysis","volume":"382","author":"Buller","year":"2023","journal-title":"Science"},{"issue":"1","key":"2026081910143214100_cit18","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04543-8","article-title":"The role of dynamic\nenzyme assemblies and substrate\nchannelling in metabolic regulation","volume":"9","author":"Sweetlove","year":"2018","journal-title":"Nat. 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Model."},{"issue":"45","key":"2026081910143214100_cit24","doi-asserted-by":"publisher","first-page":"28662","DOI":"10.1021\/acs.jafc.5c05535","article-title":"Discovery\nof Cycloheptanone-Pyrrole Derivatives with \u03b1-Hydroxycarboxylate\nFragments as Novel Dihydroxy Acid Dehydratase-Targeting Herbicides","volume":"73","author":"Xu","year":"2025","journal-title":"J. Agric. Food Chem."},{"issue":"9","key":"2026081910143214100_cit25","doi-asserted-by":"publisher","first-page":"1329","DOI":"10.1007\/s00439-021-02307-x","article-title":"Compensatory epistasis\nexplored by molecular dynamics\nsimulations","volume":"140","author":"Serrano","year":"2021","journal-title":"Hum. 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Biol."}],"container-title":["Journal of Agricultural\nand Food Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jafc.6c03008","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/32\/25392\/66445354\/acs.jafc.6c03008.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/32\/25392\/66445354\/acs.jafc.6c03008.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T14:47:31Z","timestamp":1787150851000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jafcau\/article\/74\/32\/25392\/5249541\/Overcoming-Antagonistic-epistasis-in-DAAO"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,6]]},"references-count":48,"journal-issue":{"issue":"32","published-online":{"date-parts":[[2026,8,6]]},"published-print":{"date-parts":[[2026,8,19]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jafc.6c03008","relation":{},"ISSN":["0021-8561","1520-5118"],"issn-type":[{"value":"0021-8561","type":"print"},{"value":"1520-5118","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,6]]}}}