Native Fold Delay and its implications for co-translational chaperone binding and protein aggregation

Abstract

ABSTRACT Because of vectorial protein production, residues that interact in the native protein structure but are distantly separated in the primary sequence are unavailable simultaneously. Instead, there is a temporal delay during which the N-terminal interaction partner is vulnerable to off-pathway, non-native interactions. In this analysis, we introduce “FoldDelay” (FD), a metric that integrates the topological pattern of atomic interactions of the native structure with translation kinetics to quantify such time delays. The FD metric reveals that many proteins, particularly at eukaryotic translation rates, exhibit residues with FDs in the range of tens of seconds. These residues, predominantly in well-structured, buried regions, often coincide with predicted aggregation-prone regions. We show a correlation between FD and co-translational engagement by the yeast Hsp70 chaperone Ssb, suggesting that fold-delayed regions have a propensity to misfold. In support of this, we show that proteins with high FDs are more frequently co-translationally ubiquitinated and prone to aggregate upon Ssb deletion. Finally, we find that FD cannot be adequately reduced through codon optimization, highlighting the importance of co-translational chaperones to shield these vulnerable regions. This work offers insights into co-translational proteostasis and the delicate balance between efficient folding and potential misfolding and aggregation during translation.