Co-translational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Abstract

Many large proteins suffer from slow or inefficient folding in vitro. Here, we provide evidence that this problem can be alleviated in vivo if proteins start folding co-translationally. Using an all-atom simulation-based algorithm, we compute the folding properties of various large protein domains as a function of nascent chain length, and find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by non-native interactions involving C-terminal residues. Thus, co-translational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins’ sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modelling, we show that under certain conditions, such a slowdown indeed improves co-translational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from co-translational folding due to a lack of significant non-native interactions, and indeed these proteins’ sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell, and how biomolecular self-assembly may be optimized evolutionarily.Significance StatementMany proteins must adopt a specific structure in order to perform their functions, and failure to do so has been linked to disease. Although small proteins often fold rapidly and spontaneously to their native conformations, larger proteins are less likely to fold correctly due to the myriad incorrect arrangements they can adopt. Here, we show that this problem can be alleviated if proteins start folding while they are being translated, namely, built one amino acid at a time on the ribosome. This process of co-translational folding biases certain proteins away from misfolded states that tend to hinder spontaneous refolding. Signatures of unusually slow translation suggest that some of these proteins have evolved to fold co-translationally.