Abstract
Ribosomes play a critical role in maintaining cellular proteostasis. The binding of messenger RNA (mRNA) to the ribosome regulates kinetics of protein synthesis. To generate an understanding of the structural, mechanistic, and dynamical features of mRNA recognition in the ribosome, we have analysed mRNA-protein interactions through a structural comparison of the ribosomal complex in the presence and absence of mRNA. To do so, we compared the 3-Dimensional (3D) structures of components of the two assembly structures and analysed their structural differences because of mRNA binding, using elastic network models and structural network-based analysis. We observe that the head region of 30S ribosomal subunit undergoes structural displacement and subunit rearrangement to accommodate incoming mRNA. We find that these changes are observed in proteins that lie far from the mRNA-protein interface, implying allostery. Further, through perturbation response scanning, we show that the proteins S13, S19, and S20 act as universal sensors that are sensitive to changes in the inter protein network, upon binding of 30S complex with mRNA and other initiation factors. Our study highlights the significance of mRNA binding in the ribosome complex and identifies putative allosteric sites corresponding to alterations in structure and/or dynamics, in regions away from mRNA binding sites in the complex. Overall, our work provides fresh insights into mRNA association with the ribosome, highlighting changes in the interactions and dynamics of the ribosome assembly because of the binding.
Highlights
Ribosomes are ubiquitous macromolecular complexes which help in translating genetic information from messenger RNA (mRNA) to proteins
The Global RMSD value among the three complexes was observed to be in the range of 2 to 2.4 Å implying that the binding of mRNA along with IFs or 50S does not significantly alter the global backbone conformation of the complexes
We find that all these proteins lie in the head region of the 30S complex and are involved in the positioning of tRNA at its binding site
Summary
Ribosomes are ubiquitous macromolecular complexes which help in translating genetic information from mRNA to proteins. Based on the analysis of several structures, it is appreciated that in the small 30S subunit, 16S rRNA can be divided into. The 30S ribosome complex has been divided into a head, neck, and body where the neck consists of a single helix (h44) of 16S rRNA. Translation initiation begins with the assembly of components of the 30S complex. This is followed by the formation of 30S initiation complex where 30S is bound to mRNA, initiation factors 1, 2, 3 (IF 1, 2, 3) and an initiator tRNA (Figure 1). Initiation factors play a role in the binding of tRNA at the P-site of the ribosome and help in improving the efficiency of translation initiation. The 50S subunit along with other tRNA associates with the 30S initiation complex resulting in a 70S initiation complex, where IFs dissociate to accommodate incoming tRNAs
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