{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T01:03:10Z","timestamp":1782867790726,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011321","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,8,3]],"date-time":"2023-08-03T00:00:00Z","timestamp":1691020800000}}],"reference-count":58,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2023,7,24]],"date-time":"2023-07-24T00:00:00Z","timestamp":1690156800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology","doi-asserted-by":"publisher","award":["JPMXP1020200101"],"award-info":[{"award-number":["JPMXP1020200101"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology","doi-asserted-by":"publisher","award":["JPMXP1020200101"],"award-info":[{"award-number":["JPMXP1020200101"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["KAKENHI20H05934"],"award-info":[{"award-number":["KAKENHI20H05934"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["KAKENHI21H02441"],"award-info":[{"award-number":["KAKENHI21H02441"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002241","name":"Japan Science and Technology Agency","doi-asserted-by":"publisher","award":["JPMJCR1762"],"award-info":[{"award-number":["JPMJCR1762"]}],"id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The phase separation model for transcription suggests that transcription factors (TFs), coactivators, and RNA polymerases form biomolecular condensates around active gene loci and regulate transcription. However, the structural details of condensates remain elusive. In this study, for Nanog, a master TF in mammalian embryonic stem cells known to form protein condensates\n                    <jats:italic>in vitro<\/jats:italic>\n                    , we examined protein structures in the condensates using residue-level coarse-grained molecular simulations. Human Nanog formed micelle-like clusters in the condensate. In the micelle-like cluster, the C-terminal disordered domains, including the tryptophan repeat (WR) regions, interacted with each other near the cluster center primarily via hydrophobic interaction. In contrast, hydrophilic disordered N-terminal and DNA-binding domains were exposed on the surface of the clusters. Electrostatic attractions of these surface residues were responsible for bridging multiple micelle-like structures in the condensate. The micelle-like structure and condensate were dynamic and liquid-like. Mutation of tryptophan residues in the WR region which was implicated to be important for a Nanog function resulted in dissolution of the Nanog condensate. Finally, to examine the impact of Nanog cluster to DNA, we added DNA fragments to the Nanog condensate. Nanog DNA-binding domains exposed to the surface of the micelle-like cluster could recruit more than one DNA fragments, making DNA-DNA distance shorter.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1011321","type":"journal-article","created":{"date-parts":[[2023,7,24]],"date-time":"2023-07-24T13:28:41Z","timestamp":1690205321000},"page":"e1011321","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study"],"prefix":"10.1371","volume":"19","author":[{"given":"Azuki","family":"Mizutani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8957-4267","authenticated-orcid":true,"given":"Cheng","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuji","family":"Sugita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5385-7217","authenticated-orcid":true,"given":"Shoji","family":"Takada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,7,24]]},"reference":[{"key":"pcbi.1011321.ref001","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1016\/j.cell.2011.01.032","article-title":"Control of the embryonic stem cell state","volume":"144","author":"RA Young","year":"2011","journal-title":"Cell"},{"key":"pcbi.1011321.ref002","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/ncb0511-490","article-title":"The transcriptional and signalling networks of pluripotency","volume":"13","author":"HH Ng","year":"2011","journal-title":"Nat Cell Biol"},{"key":"pcbi.1011321.ref003","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/j.cell.2011.05.019","article-title":"Chromatin connections to pluripotency and cellular reprogramming","volume":"145","author":"SH Orkin","year":"2011","journal-title":"Cell"},{"key":"pcbi.1011321.ref004","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/nature09380","article-title":"Mediator and cohesin connect gene expression and chromatin architecture","volume":"467","author":"MH Kagey","year":"2010","journal-title":"Nature"},{"key":"pcbi.1011321.ref005","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.cell.2013.03.035","article-title":"Master transcription factors and mediator establish super-enhancers at key cell identity genes","volume":"153","author":"WA Whyte","year":"2013","journal-title":"Cell"},{"key":"pcbi.1011321.ref006","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.cell.2019.05.029","article-title":"Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells","volume":"178","author":"J Li","year":"2019","journal-title":"Cell"},{"key":"pcbi.1011321.ref007","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1038\/s41594-020-0493-6","article-title":"Single-gene imaging links genome topology, promoter\u2013enhancer communication and transcription control","volume":"27","author":"J Li","year":"2020","journal-title":"Nat Struct Mol Biol"},{"key":"pcbi.1011321.ref008","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.cell.2017.02.007","article-title":"A Phase Separation Model for Transcriptional Control","volume":"169","author":"D Hnisz","year":"2017","journal-title":"Cell"},{"key":"pcbi.1011321.ref009","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.1016\/j.cell.2018.10.042","article-title":"Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains","volume":"175","author":"A Boija","year":"2018","journal-title":"Cell"},{"key":"pcbi.1011321.ref010","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.sbi.2012.01.010","article-title":"Coarse-grained molecular simulations of large biomolecules","volume":"22","author":"S. 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