Abstract
In the past two decades, research into the biochemical, biophysical and structural properties of the ribosome have revealed many different steps of protein translation. Nevertheless, a complete understanding of how they lead to a rapid and accurate protein synthesis still remains a challenge. Here we consider a coarse network analysis in the bacterial ribosome formed by the connectivity between ribosomal (r) proteins and RNAs at different stages in the elongation cycle. The ribosomal networks are found to be dis-assortative and small world, implying that the structure allows for an efficient exchange of information between distant locations. An analysis of centrality shows that the second and fifth domains of 23S rRNA are the most important elements in all of the networks. Ribosomal protein hubs connect to much fewer nodes but are shown to provide important connectivity within the network (high closeness centrality). A modularity analysis reveals some of the different functional communities, indicating some known and some new possible communication pathways Our mathematical results confirm important communication pathways that have been discussed in previous research, thus verifying the use of this technique for representing the ribosome, and also reveal new insights into the collective function of ribosomal elements.
Highlights
The wealth of high resolution images of the ribosome have revealed many of the steps involved in its function [1,2,3,4]
We have included the counts of different types of connections: rRNA-rRNA, rprotein-rprotein, rRNA-rprotein and the connections involving mRNA and tRNA
The rRNA-rprotein connections alone form more than 50% of the network, many of which are formed during ribosome biogenesis
Summary
The wealth of high resolution images of the ribosome have revealed many of the steps involved in its function [1,2,3,4]. Throughout this vast literature, the importance of connectivity has often been remarked and discussed, only a few papers have considered viewing the connections as a network. Some explorations considered using the nucleotides or amino acids as nodes and their interactions as edges [5, 6], and showed that a network analysis highlights important mutations that have deleterious effects on ribosome function or highlighted highly conserved residues, drug binding sites and/or allosteric pathways. The motivation for this research is to explore mathematically how ribosomal elements function together and determine important communication pathways
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