How subunit rotation controls tRNA dynamics in the ribosome

Abstract

In order to translate messenger RNA into proteins, the ribosome must coordinate a wide range of conformational rearrangements. Some steps involve individual molecules, whereas others require synchronization of multiple collective motions. For example, the ribosomal "small" subunit ([~]1 MDa) is known to undergo rotational motion ([~] 10{whitebullet}) that is correlated with large-scale displacements of tRNA molecules ([~]50[A]). While decades of biochemical, single-molecule and structural analysis have provided many insights into the timing of these motions, little is known about how these dynamical processes influence each other. To address this, we use molecular simulations to isolate specific interactions that allow tRNA kinetics to be controlled by subunit rotation. Specifically, we applied an all-atom structure-based model to perform molecular simulations of P/E hybrid formation, a process by which the tRNA molecules are displaced between ribosomal binding sites. By varying the extent of subunit rotation in each simulation, these calculations reveal a pronounced non-monotonic dependence of tRNA kinetics on subunit rotation. That is, tRNA kinetics increase and then decrease as the subunit is rotated. We further show that this behavior is due to the steric contributions of a single ribosomal protein. Together, these calculations provide insights into the physicochemical properties of the ribosome, while establishing a strategy for isolating causal relationships in biomolecular assemblies.