A widespread protein misfolding mechanism is differentially rescued by chaperones based on gene essentiality

The existence of a previously unrecognized class of monomeric protein misfolding – involving changes in self-entanglement status – has been suggested by simulations, biochemical assays, and mass spectrometry data. Those studies experimentally probed only a small number of proteins. Here, we employ a high-throughput, low-resolution approach, integrating E. coli proteome-wide limited-proteolysis mass spectrometry data covering 348 proteins with structural datasets of protein native structures. We address four questions: (1) Are proteins containing native, non-covalent lasso entanglements more likely to misfold than those that do not? (2) How does such misfolding occur at the molecular level? (3) Do chaperones rescue this class of misfolding? And (4) how do some of these misfolded proteins bypass chaperones? We demonstrate that proteins containing native entanglements, representing 70% of the globular E. coli proteome, exhibit a 300% increase in their propensity to misfold relative to proteins that do not. That the misfolding of these proteins is 44% more likely to occur in the natively entangled regions compared to their non-entangled regions. And that the chaperones DnaK and GroEL do not rescue, on average, proteins misfolding in this manner. However, these chaperones do correct entanglement misfolding in essential proteins but not non-essential ones. A statistical analysis finds differential rescue activity is related to weaker loop-closing contacts in the entanglements of essential proteins, suggesting misfolding involving these loops is easier to rectify by chaperones than in non-essential proteins. Through simulations, we identify a failure-to-form mechanism, wherein premature loop closure, prior to proper placement of the threading segment, results in long-lived misfolded states, explaining the misfolding signals observed in the mass spec data. Thus, this misfolding mechanism is prevalent across the proteome; for some proteins, such misfolded states cannot be rescued by chaperones, and there may be evolutionary selection pressure on loop sequence and stability in essential proteins to facilitate rescue.