Dependence of P/E tRNA hybrid formation on subunit rotation in the ribosome.

Abstract

The ribosome, a massive nucleoprotein assembly that executes protein synthesis in all living cells, undergoes several large-scale functional rearrangements during the protein elongation cycle. Here we explore two such rearrangements in the ribosome bound tRNA molecules during the translocation step in bacteria, namely, P/E tRNA hybrid formation and inter-subunit rotation in the ribosome. We utilize multi-basin all-atom structure-based models and Ribosome Angle Decomposition (RAD) method to study the dependence of P/E hybrid formation on rotation of small subunit body with respect to the large subunit. Structure-based models provide simplified energetics with experimental atomic structures defined to be the potential energy minima. We employ these models to simulate spontaneous transition of the P-tRNA from P to E tRNA binding site on the large subunit for different degrees of small subunit body rotation. RAD method provides a complete coordinate system that describes any orientation of the ribosomal small subunit body and head in terms of rotation, tilt, tilt direction and translation. We identify reference E. coli structures at different degrees of body rotation but with minimal body tilt, head rotation and head tilt from the Ribosome Analysis Database based on RAD. Utilizing these methods, we explore the influence of subunit rotation on the free-energy barrier associated with P/E tRNA hybrid formation and obtain the quantitative dependence of P/E hybrid formation on subunit rotation.