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Simulations recapitulate its stretched-exponential folding kinetics and reveal that misfolded states involving changes of entanglement underlie this behavior: either formation of a nonnative, noncovalent lasso entanglement or failure to form a native entanglement. These misfolded states act as kinetic traps, requiring extensive unfolding to escape, which results in a distribution of free energy barriers and pathway partitioning. Using LiP-MS and XL-MS, we propose heterogeneous structural ensembles consistent with these data that represent the potential long-lived misfolded states PGK populates. This structural and energetic heterogeneity creates a hierarchy of refolding timescales, explaining stretched-exponential kinetics.<\/jats:p>","DOI":"10.1126\/sciadv.ads7379","type":"journal-article","created":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T17:58:26Z","timestamp":1741975106000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":15,"title":["Protein misfolding involving entanglements provides a structural explanation for the origin of stretched-exponential refolding kinetics"],"prefix":"10.1126","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1100-9177","authenticated-orcid":true,"given":"Yang","family":"Jiang","sequence":"first","affiliation":[{"name":"Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-0885-6959","authenticated-orcid":true,"given":"Yingzi","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8553-923X","authenticated-orcid":true,"given":"Ian","family":"Sitarik","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1102-8602","authenticated-orcid":true,"given":"Piyoosh","family":"Sharma","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1875-5009","authenticated-orcid":true,"given":"Hyebin","family":"Song","sequence":"additional","affiliation":[{"name":"Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA."},{"name":"Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2494-2193","authenticated-orcid":true,"given":"Stephen D.","family":"Fried","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA."},{"name":"Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9809-3273","authenticated-orcid":true,"given":"Edward P.","family":"O\u2019Brien","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA."},{"name":"Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA."},{"name":"Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.1.148"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja5049434"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.97.4.1525"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0901-765"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.105.075689"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2006.10.082"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.107.109868"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.3485286"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(02)75352-6"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.092686399"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1002\/iub.223"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1201811109"},{"key":"e_1_3_2_14_2","doi-asserted-by":"crossref","unstructured":"V. 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