{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T14:54:56Z","timestamp":1772117696461,"version":"3.50.1"},"reference-count":66,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2024,3,4]],"date-time":"2024-03-04T00:00:00Z","timestamp":1709510400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["febs.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["FEBS Letters"],"published-print":{"date-parts":[[2024,4]]},"abstract":"<jats:p>\n                    The human Mediator complex subunit MED25 binds transactivation domains (TADs) present in various cellular and viral proteins using two binding interfaces, named H1 and H2, which are found on opposite sides of its ACID domain. Here, we use and compare deep learning methods to characterize human MED25\u2013TAD interfaces and assess the predicted models to published experimental data. For the H1 interface, AlphaFold produces predictions with high\u2010reliability scores that agree well with experimental data, while the H2 interface predictions appear inconsistent, preventing reliable binding modes. Despite these limitations, we experimentally assess the validity of MED25 interface predictions with the viral transcriptional activators Lana\u20101 and IE62. AlphaFold predictions also suggest the existence of a unique hydrophobic pocket for the\n                    <jats:italic>Arabidopsis<\/jats:italic>\n                    MED25 ACID domain.\n                  <\/jats:p>","DOI":"10.1002\/1873-3468.14837","type":"journal-article","created":{"date-parts":[[2024,3,4]],"date-time":"2024-03-04T05:37:00Z","timestamp":1709530620000},"page":"758-773","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Assessment of machine\u2010learning predictions for the Mediator complex subunit\n                    <scp>MED25 ACID<\/scp>\n                    domain interactions with transactivation domains"],"prefix":"10.1002","volume":"598","author":[{"given":"Didier","family":"Mont\u00e9","sequence":"first","affiliation":[{"name":"CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 \u2013 RID\u2010AGE, Univ. Lille, CHU Lille Institut Pasteur de Lille  France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zo\u00e9","family":"Lens","sequence":"additional","affiliation":[{"name":"CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 \u2013 RID\u2010AGE, Univ. Lille, CHU Lille Institut Pasteur de Lille  France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fr\u00e9d\u00e9rique","family":"Dewitte","sequence":"additional","affiliation":[{"name":"CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 \u2013 RID\u2010AGE, Univ. Lille, CHU Lille Institut Pasteur de Lille  France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Villeret","sequence":"additional","affiliation":[{"name":"CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 \u2013 RID\u2010AGE, Univ. Lille, CHU Lille Institut Pasteur de Lille  France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0299-2344","authenticated-orcid":false,"given":"Alexis","family":"Verger","sequence":"additional","affiliation":[{"name":"CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 \u2013 RID\u2010AGE, Univ. Lille, CHU Lille Institut Pasteur de Lille  France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2024,3,4]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrm.2017.115"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2010.10.011"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2013244117"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.emboj.7601797"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/cdg619"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0308676100"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.017715-0"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00054-09"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.109803"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2022.167763"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.01297-22"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt199"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv650"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2017.06.024"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01636"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.112.202697"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbi.2020.06.006"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks265"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0098575"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2021.101504"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1997"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1999"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10969-011-9115-1"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3943"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1806202115"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules23102726"},{"key":"e_1_2_9_28_1","first-page":"1205","article-title":"Multivalent and bidirectional binding of transcriptional transactivation domains to the MED25 coactivator","volume":"10","author":"Jeffery HM","year":"2020","journal-title":"Biomol Ther"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj8754"},{"key":"e_1_2_9_31_1","doi-asserted-by":"crossref","unstructured":"WuR DingF WangR ShenR ZhangX LuoS SuC WuZ XieQ BergerBet\u00a0al. (2022)High\u2010resolution de novo structure prediction from primary sequence.bioRxiv: the preprint server for biology10.1101\/2022.07.21.500999[PREPRINT]","DOI":"10.1101\/2022.07.21.500999"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.ade2574"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01488-1"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1052"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad350"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03828-1"},{"key":"e_1_2_9_37_1","unstructured":"EvansR O'NeillM PritzelA AntropovaN SeniorA GreenT \u017d\u00eddekA BatesR BlackwellS YimJet\u00a0al. (2021)Protein complex prediction with AlphaFold\u2010Multimer.bioRxiv: the preprint server for biology.10.1101\/2021.10.04.463034[PREPRINT]"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M113.496968"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/26.19.4487"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M112.369504"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01693-08"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2023.102645"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.75751"},{"key":"e_1_2_9_44_1","first-page":"1467","article-title":"Digging into the 3D structure predictions of AlphaFold2 with low confidence: disorder and beyond","volume":"12","author":"Bruley A","year":"2022","journal-title":"Biomol Ther"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1002981108"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2006.06.007"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-313X.2012.04935.x"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2018.03.013"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.1c04214"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2018.02.097"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrm1589"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2117338119"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80463-8"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2021.167208"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac187"},{"key":"e_1_2_9_56_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22441-4"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2011.11.008"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.2c01189"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06832-9"},{"key":"e_1_2_9_60_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44288-7"},{"key":"e_1_2_9_61_1","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202213362"},{"key":"e_1_2_9_62_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2018.01.015"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2022.01.002"},{"key":"e_1_2_9_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.04.020"},{"key":"e_1_2_9_65_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.68068"},{"key":"e_1_2_9_66_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-44859-2"},{"key":"e_1_2_9_67_1","doi-asserted-by":"publisher","DOI":"10.1038\/s44320-023-00005-6"}],"container-title":["FEBS Letters"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/febs.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/1873-3468.14837","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,20]],"date-time":"2024-05-20T23:01:46Z","timestamp":1716246106000},"score":1,"resource":{"primary":{"URL":"https:\/\/febs.onlinelibrary.wiley.com\/doi\/10.1002\/1873-3468.14837"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,4]]},"references-count":66,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2024,4]]}},"alternative-id":["10.1002\/1873-3468.14837"],"URL":"https:\/\/doi.org\/10.1002\/1873-3468.14837","archive":["Portico"],"relation":{"has-review":[{"id-type":"doi","id":"10.1002\/1873-3468.14837\/v2\/review2","asserted-by":"object"},{"id-type":"doi","id":"10.1002\/1873-3468.14837\/v2\/decision1","asserted-by":"object"},{"id-type":"doi","id":"10.1002\/1873-3468.14837\/v2\/review1","asserted-by":"object"},{"id-type":"doi","id":"10.1002\/1873-3468.14837\/v1\/review1","asserted-by":"object"},{"id-type":"doi","id":"10.1002\/1873-3468.14837\/v1\/review2","asserted-by":"object"},{"id-type":"doi","id":"10.1002\/1873-3468.14837\/v2\/response1","asserted-by":"object"},{"id-type":"doi","id":"10.1002\/1873-3468.14837\/v1\/decision1","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.11.30.569364","asserted-by":"object"}]},"ISSN":["0014-5793","1873-3468"],"issn-type":[{"value":"0014-5793","type":"print"},{"value":"1873-3468","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,4]]},"assertion":[{"value":"2023-11-30","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-02-10","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-03-04","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}