A newly identified class of protein misfolding is observed in all-atom folding simulations and supported by experimental structural ensembles

Several mechanisms intrinsic to a protein’s primary structure are known to cause monomeric protein misfolding. Coarse-grained simulations, in which multiple atoms are represented by a single interaction site, have predicted that a novel mechanism of misfolding exists involving off-pathway, non-covalent lasso entanglements, which are distinct from protein knots and slip knots. These misfolded states can act as long-lived kinetic traps and, intriguingly, may resemble the native state structurally according to those simulations. Here, we examine whether such misfolded states occur in long-timescale, physics-based all-atom simulations of protein folding, focusing on ubiquitin and λ-repressor. Our findings confirm the formation of these entangled misfolded states in this higher-resolution model, some of which share structural similarities with the native state. However, due to the small size of ubiquitin and λ-repressor, these misfolded states are short-lived. In contrast, coarse-grained simulations of a larger, typical size protein, ispE, reveal several long-lived misfolded clusters with non-native entanglements. These misfolded clusters are consistent with digestion patterns observed in Limited Proteolysis and Cross-linking Mass Spectrometry experiments. Using an Arrhenius extrapolation from all-atom simulations we estimate these ispE misfolded clusters can persist for extended periods, potentially months, while remaining soluble. Our results suggest that monomeric proteins can exhibit subpopulations of misfolded, self-entangled states that may explain long-timescale changes in protein structure and function in vivo.