In Vivo Translation Rates Can Substantially Delay the Co-Translational Folding of the E. Coli Cytosolic Proteome

Abstract

A question of fundamental importance concerning protein folding in vivo is whether the kinetics of translation or the thermodynamics of the ribosome nascent chain (RNC) complex is the major determinant of co-translational folding behavior. This is because the rate of translation can reduce the probability of co-translational folding below that associated with arrested ribosomes, whose behavior is determined by the equilibrium thermodynamics of the RNC complex. Here, we combine a chemical kinetic equation with genomic and proteomic data to predict domain folding probabilities as a function of nascent chain length for cytosolic proteins of E. coli synthesized on both arrested and continuously translating ribosomes. Our results indicate that, at the translation rates found in vivo, about one-third of the cytosolic proteins of E. coli exhibit co-translational folding, with at least one domain in each of these proteins folding into its stable native structure before the full-length protein is released from the ribosome. The majority of these co-translational folding domains are influenced by translation kinetics which reduces their probability of co-translational folding and consequently increases the nascent chain length at which they fold into their native structures. For about 20% of all cytosolic proteins this delay in folding can exceed the length of the completely synthesized protein, causing one or more of their domains to switch from co- to post-translational folding solely as a result of the in vivo translation rates. Large, β-strand rich domains are more likely to be affected by translation kinetics during co-translational folding than small, α-helical domains that generally fold much faster. These kinetic effects arise from the difference in time scales of folding and amino-acid addition, and they represent a source of metastability for the E. coli proteome.