tRNA kinetics on the ribosome depends non-monotonically on intersubunit rotation.

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°) that is correlated with large-scale displacements of tRNA molecules (∼50Å). 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 simulate movement of tRNA between ribosomal binding sites (P/E hybrid formation). These calculations reveal a pronounced non-monotonic dependence of tRNA kinetics on subunit rotation, where the rate of P/E formation initially increases and then decreases as the subunit rotates. In addition, there a sharp increase in rate for low degrees of rotation, suggesting that adoption of P/E tRNA conformations may occur early in the rotation process. Together, these calculations demonstrate how molecular structure gives rise to an intricate relationship between these complex rearrangements.