biostudies-literatureVu QVNIGMS NIH HHSeadt8974https://www.ebi.ac.uk/biostudies/studies/S-EPMC12333692biostudies-literatureUnknown11(32)Several mechanisms are known to cause monomeric protein misfolding. Coarse-grained simulations have predicted an additional mechanism exists involving off-pathway, noncovalent lasso entanglements, which are long-lived kinetic traps and structurally resemble the native state. Here, we examine whether such misfolded states occur in long-timescale, all-atom folding simulations of ubiquitin and λ-repressor. We find that these entangled misfolded states are populated in higher-resolution models. However, because of the small size of ubiquitin and λ-repressor, these states are short-lived. In contrast, coarse-grained simulations of a larger protein, IspE, predict that it populates long-lived misfolded states. Using an Arrhenius extrapolation applied to all-atom simulations, we estimate that thesScience advancesNon-native entanglement protein misfolding observed in all-atom simulations and supported by experimental structural ensembles.PMC12333692DP2 GM140926R35 GM124818Jiang YXia YSharma PSitarik ILi MSVu QVFried SDO'Brien EPYadav DSong HfalseNon-native entanglement protein misfolding observed in all-atom simulations and supported by experimental structural ensembles.Several mechanisms are known to cause monomeric protein misfolding. Coarse-grained simulations have predicted an additional mechanism exists involving off-pathway, noncovalent lasso entanglements, which are long-lived kinetic traps and structurally resemble the native state. Here, we examine whether such misfolded states occur in long-timescale, all-atom folding simulations of ubiquitin and λ-repressor. We find that these entangled misfolded states are populated in higher-resolution models. However, because of the small size of ubiquitin and λ-repressor, these states are short-lived. In contrast, coarse-grained simulations of a larger protein, IspE, predict that it populates long-lived misfolded states. Using an Arrhenius extrapolation applied to all-atom simulations, we estimate that thes2025-01-01T00:00:00Z2025 Aug2026-06-03T07:01:26.602Z2026-04-25T03:21:39.587ZS-EPMC123336924077962210.1126/sciadv.adt8974