Translational tuning optimizes nascent protein folding in cells

Abstract

In cells, biosynthetic machinery coordinates protein synthesis and folding to optimize efficiency and minimize off-pathway outcomes. However, it has been difficult to delineate experimentally the mechanisms responsible. Using fluorescence resonance energy transfer, we studied cotranslational folding of the first nucleotide-binding domain from the cystic fibrosis transmembrane conductance regulator. During synthesis, folding occurred discretely via sequential compaction of N-terminal, α-helical, and α/β-core subdomains. Moreover, the timing of these events was critical; premature α-subdomain folding prevented subsequent core formation. This process was facilitated by modulating intrinsic folding propensity in three distinct ways: delaying α-subdomain compaction, facilitating β-strand intercalation, and optimizing translation kinetics via codon usage. Thus, de novo folding is translationally tuned by an integrated cellular response that shapes the cotranslational folding landscape at critical stages of synthesis.

Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD

“…Thus, codon usage affects the amount of time available for cotranslational folding. This is consistent with previous studies showing that translation rate and synonymous codon usage can affect protein folding and functions (Komar et al 1999;Zhang et al 2009;Siller et al 2010;Spencer et al 2012;Kim et al 2015;Presnyak et al 2015). We previously observed genome-wide correlations showing that optimal codons are preferentially used in regions that are predicted to be well folded, while relatively more unpreferred codons are used in protein regions predicted to be unstructured.…”

Protein folding and tRNA biology

“…Furthermore, in semipermeabilized cells, it was shown using limited proteolysis, that CFTR (cystic fibrosis transmembrane conductance regulator) folds mostly co-translationally, domain by domain (Kleizen et al 2005). Recently, the use of FRET (fluorescence resonance energy transfer) opened the way to study structural transitions of ribosome-bound folding intermediates, generated through in vitro translation of truncated RNA transcripts (Kim et al 2015). Finally, co-translational protein folding has been studied by NMR spectroscopy providing atomic-resolution information on ribosome-nascent chain complexes isolated from E. coli .…”

Accurate Prediction of Cellular Co-Translational Folding Indicates Proteins can Switch from Post- to Co-Translational Folding

“…Thus, multiplying the unscaled codon translation rates by w yields the set of scaled rates that maintain the desired 3.9 AA per second average. This process is summarized in equations (5) and (6). …”