Modulation of Intersubunit Interactions during tRNA Translocation through the Ribosome

Abstract

During protein synthesis, the ribosome undergoes large-scale conformational changes. In particular, the process of tRNA translocation is accompanied by concerted rotations of the 30S ribosomal subunit of more than 20 degrees relative to the 50S. At each step of the translocation process, affinity between the two independent subunits must be finely tuned in order to allow such high conformational flexibility while still maintaining integrity of the ribosomal complex. How the ribosome achieves this is still not fully understood. We address this question by extensive all-atom, explicit solvent molecular dynamics simulations (total simulation time > 1.5 μs) of the 70S ribosome starting from 13 distinct translocation intermediates. The resulting structural ensemble provides a detailed picture of translocation dynamics. Analysis of the trajectories at the residue level reveals two classes of intersubunit contact interactions: i) persistent residue contacts which are independent of 30S rotation and located close to the axis of rotation. ii) state specific contacts, seen mostly on the periphery. The baseline of the interaction energy needed to maintain the ribosomal assembly is provided by class i) interactions, while the rupture and formation of class ii) contacts contributes low changes to the overall interaction energy and may serve as an affinity tuning mechanism in switching between different translocation states. Our simulations reveal decreased amplitude of the intersubunit rotations and weakening of stabilizing peripheral contacts upon removal of the tRNAs. This finding is confirmed by cryo-EM analysis of tRNA depleted ribosomes.