Critical Decoding Step in the Ribosome Revealed by Dynamical Network Analysis

Abstract

The ribosome needs to select the correct (cognate) aminoacyl-tRNA (aa-tRNA) among all the available aa-tRNAs to carry out protein synthesis. During the selection of the cognate aa-tRNA, also known as the decoding step, a ternary complex consisting of an aa-tRNA along with the elongation factor Tu (EF-Tu) and a GTP molecule approaches the ribosomal A-site. If the codon-anticodon pair matches in the decoding center, GTP hydrolysis occurs more than 75 A away, which gives rise to conformational change in EF-Tu and its detachment from the ribosome. The molecular mechanism of the decoding process, which occurs very rapidly (about 20 amino acids per second), and very accurately, is unknown despite decades of intense study. According to experimental data, helices h8 and h14 in 16S rRNA play a crucial role in the activity and fidelity of the decoding process. These two helices together interact with two protein helices of the large subunit, L14 and L19, to form bridge 8 (B8), which connects the two ribosomal subunits. All-atom molecular dynamics simulations were performed on the complete ribosome for 150 ns. Using the Dynamical Network Analysis plugin in VMD, a network was assigned to the system based on cross-correlations of the residues' displacements along the trajectory. Inter-correlated communities in the network and the strongest pathways between the decoding center and the GTP binding site were calculated to shed light on how codon-anticodon pairings regulate the GTP hydrolysis. Finally the results for the wild-type ribosome were compared with the results for ribosomes carrying mutated/deleted/inserted base pairs in their h8 and h16 helices in order to reveal the functional importance of these helices in the decoding process at the molecular level.