The Dynamics of Subunit Rotation in a Eukaryotic Ribosome

Abstract

Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ∼1 MDa) undergoes spontaneous and reversible rotation events (∼8∘). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.

Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome

“…This perspective is consistent with theoretical approaches for characterizing biomolecular folding, 39,40 and it has served as a motivation for applying simplified models to simulate subunit rotation in the ribosome. 22,41 In addition, this implied character of the landscape is consistent with studies of the ribosome using coarse-grained models 42–44 and explicit-solvent simulations, 45 which have predicted that rotational motions correspond to low-energy deformations. Finally, this general framework has also been applied to quantify dynamics along rotation-like coordinates in explicit-solvent simulations, 18 though that effort did not probe energetics.…”

“…While these are not the highest resolution structures available (3.0 and 3.5 Å), they were used for continuity with previous analyses. 14,18,22 However, as described in the result, there are many alternate structures that exhibit nearly identical domain orientations. Accordingly, other structures could have been used as reference models, while introducing minimal changes in the calculated angles.…”

“…As computing capabilities continue to expand and novel theoretical models allow for subunit rotation in the ribosome to be simulated, 14,22,41 there is a growing need for quantitative approaches that allow for comparison of simulated dynamics and experimental data. To this end, RADtool also supports the analysis of simulated trajectories.…”

“…non-targeted) tRNA translocation events 14 and rotation in a eukaryotic ribosome. 22 Methods for categorizing subunit/domain rotation states have yielded insights into bacterial (and some eukaryotic) ribosome structures, though significant challenges remain. Most notably, previous efforts have not provided a complete coordinate system that can distinguish between arbitrary orientations of the head and body.…”

“…10 To expand to a more general approach, Euler angles have been applied to separately describe rotation and tilt of the SSU head 14 and body. 22 While Euler angles provide a natural coordinate system for quantifying rotations, the orientation of an arbitrary rigid body (e.g. the body or head of the SSU) is associated with three rotational degrees of freedom (rotation, tilt and tilt direction), as well as three translational degrees of freedom (Δ x , Δ y , Δ z ).…”