biostudies-literatureJiang YNIGMS NIH HHSeads7379https://www.ebi.ac.uk/biostudies/studies/S-EPMC11908495biostudies-literatureUnknown11(11)Stretched-exponential protein refolding kinetics, first observed decades ago, were attributed to a nonnative ensemble of structures with parallel, non-interconverting folding pathways. However, the structural origin of the large energy barriers preventing interconversion between these folding pathways is unknown. Here, we combine simulations with limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS) to study the protein phosphoglycerate kinase (PGK). 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 extensiScience advancesProtein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics.PMC11908495R35 GM124818Jiang YXia YSharma PSitarik IFried SDO'Brien EPSong HfalseProtein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics.Stretched-exponential protein refolding kinetics, first observed decades ago, were attributed to a nonnative ensemble of structures with parallel, non-interconverting folding pathways. However, the structural origin of the large energy barriers preventing interconversion between these folding pathways is unknown. Here, we combine simulations with limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS) to study the protein phosphoglycerate kinase (PGK). 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 extensi2025-01-01T00:00:00Z2025 Mar2026-06-01T05:45:19.028Z2025-04-04T14:48:13.631ZS-EPMC119084954008570010.1126/sciadv.ads7379