Electrostatic Interactions Between Nascent Chains and the Ribosome Exit Tunnel Generate Forces That Modify Translation Rates

Several co-translational processes have been shown to generate tensile forces that are transmitted to the catalytic core of the ribosome. These forces have the ability to modify translation rates, which can in turn affect the structure and function of the protein being synthesized, which can then modify the cellular phenotype. These processes all occur as the nascent chain emerges from the exit tunnel. It has also been shown that positively charged residues can stall translation while still in the exit tunnel, although the mechanism by which stalling occurs is still unknown. Here, we use three levels of simulations to demonstrate that charged residues in the exit tunnel generate tensile forces that act on the P-site residue, which in turn changes the transition state barrier heights to peptide bond formation. We find that the forces generated by positive and negatively charged residues act in opposite directions, causing only the positively charged residues to stall, and that these forces increase as the length of the charged segment increases. Furthermore, we use ribosome profiling to show that the changes in translation speeds occur in vivo and that the largest slowdowns that occur when strings of positively charged residues are translated occur at the same locations as the largest forces measured in silico.