Codon Positions that Strongly Influence Cotranslational Folding are Far from Equilibrium: A Framework for Controlling Nascent-Protein Folding

Abstract

An emerging paradigm in the field of in vivo protein biophysics is that nascent protein behavior is type of non-equilibrium phenomenon, where the kinetics of translation elongation and cotranslational processes can be more important in determining protein behavior than the thermodynamic properties of the protein. Indeed, synonymous codon substitutions, which change the translation rate at select codon positions along a transcript, have been shown to alter the likelihood of cotranslational protein folding and proper functioning, suggesting that evolution likely shaped codon usage in the genomes of organisms in part to influence nascent protein behavior. Here, we develop a Monte-Carlo-master-equation method that allows for the control of nascent chain folding during translation through the rational design of mRNA sequences using synonymous codons. The method allows us to encode particular translation-rate profiles into an mRNA molecule to guide the cotranslational folding process. We test this framework using coarse-grained molecular dynamics simulations and find it provides optimal mRNA sequences to control the simulated, cotranslational folding of a protein in a user-prescribed manner. With this approach we discover the physical rules governing why synonymous mutations at some codon positions can have a much greater impact on nascent protein folding than others. We find that the impact of a synonymous mutation at a particular codon position is proportional to how far the populations of different nascent-chain conformational states are from equilibrium. As a consequence, different cotranslational profiles of a protein can have different critical codon positions. These findings explain a fundamental connection between the non-equilibrium nature of cotranslational processes, nascent protein behavior and codon usage.