Across the E. Coli Proteome it is Common for Proteins to Become Kinetically Trapped in Soluble, Near-Native, Non-Functional Conformations that Bypass the Proteostasis Network

Abstract

In the proteostasis model of in vivo protein structure and function, proteins attain one of three states: (1) folded and functional, (2) misfolded and aggregated, or (3) degraded. Various molecules help maintain functional proteins at correct concentrations by converting proteins between these three states. Contradictory to this model, it has been observed that changes to translation speed like those introduced by synonymous mutations can alter protein conformations and reduce functionality of soluble proteins for days. This suggests that some non-functional, misfolded protein conformations bypass the proteostasis machinery and remain soluble for long timescales. Here, we use coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative subset of globular, cytoplasmic E. coli proteins to determine the temporal and structural properties of these misfolded states and how they bypass cellular quality controls. We estimate that a majority of cytosolic proteins misfold for seconds to days. Approximately a third of proteins exhibit misfolded conformations that are likely to bypass molecular chaperones, fail to aggregate, or fail to be targeted for degradation. Characterizing the structures of these misfolded states, we find they are highly native, with localized misfolding arising from entanglements. These two properties allow these states to remain soluble but misfolded, as disentanglement is energetically unfavorable. Finally, through a comparison with the native ensemble, we estimate nearly one-tenth of proteins misfold into non-functional states. These results indicate that misfolding into soluble, entangled conformations that bypass quality controls is an underappreciated phenomenon that can lead to reduced protein function across the cytosolic proteome. These near-native-like entangled structures provide a potential explanation how synonymous mutations can modulate downstream protein structure and function.