Simulating mRNA-tRNA Translocation through the Ribosome

Abstract

The ribosome is a massive molecular complex that undergoes large-scale rotary motions during the translocation step of protein synthesis. During translocation, tRNA molecules move (along with the mRNA) by one binding site (∼20-50A displacement), in order to allow the next mRNA codon to be decoded. To illuminate the physical relationship between the movement of the tRNAs and the rotations in the ribosome, we applied molecular dynamics (MD) simulations with an all-atom structure-based model. By using a model that contains a simplified description of the potential energy, while explicitly representing all heavy atoms (∼150,000), we specifically probe the roles of steric interactions and molecular flexibility during this process. For the ribosome, we constructed a forcefield for which each “classical” ribosome configuration is a potential energy minimum. With this model, we simulated over 1000 spontaneous, unguided translocation events. Statistical analysis of the simulated trajectories shows that our model accurately captures known aspects of translocation, including the population of a so-called chimeric ap/P-pe/E intermediate ensemble. In addition, we find that the ribosome subsequently adopts a previously unreported conformation, which is characterized by a distinct tilt of the head of the small subunit. By introducing perturbations to the model, we have identified the specific steric interactions that lead to the observed head tilting motion. Our results provide a conceptual energy landscape framework for understanding translocation dynamics, and suggest strategies to obtain quantitative control of ribosome function.