The Molecular Origins of the Influence of Translation-Elongation Kinetics on the Specific Activity of Enzymes

Abstract

Synonymous codon substitutions, which change the mRNA sequence but not the protein sequence, have been found to affect co-translational folding and post-translational structure of some proteins due to their impact on translation elongation speed. For example, the specific activities of chloramphenicol acetyltransferase III (CAT-III) and Firefly luciferase (LUC) have been found to change due to synonymous codon substitutions. In this study, we use multi-scale modeling to investigate how synonymous mutations lead to changes in the kinetics and structural ensemble of enzymes that alter their specific activities for relatively long time scales. We simulated the synthesis of the enzymes CAT-III, DDLB and DHFR on the ribosome under fast and slow translation schedules, arising from synonymous mRNA variants, followed by post-translational simulations off the ribosome. The specific activity of each protein mutant was then estimated in silico. Our simulation model recapitulates the experimental trends of CAT-III specific activity changes and identifies a reduced activity of the slow-synthesizing DDLB mutant. For the misfolding-prone proteins CAT-III and DDLB, we identified diverse near-native-like, soluble misfolded kinetic traps with topological entanglements formed near the active site, which could establish a memory of the co-translational structural divergence arising from the different translation speeds that persists in the post-translational folding process and causes the altered enzymatic activity. The fast-folding protein DHFR without kinetic traps has no memory of co-translational structural divergence persisting in the post-translation and hence no altered function could be observed in synonymous mutants. We conclude that synonymous mutations lead to populations shifts that can promote the formation of entangled, near-native like structures that are kinetic traps with reduced functionality, but are native enough to bypass the proteostasis quality control systems of the cell.