Network theory of the bacterial ribosome

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.

Modeling the ribosome as a bipartite graph

“…As we have observed in previous research, [4] the modular groups change as a function of the different states. Typically, 23S-D2 and D5 are found together in the same module but 23S-D0 is found in a second LSU domain.…”

“…A more careful analysis might explore the specific connectivity of the different hypothesized oldest regions and whether they include conserved residues. Nevertheless, the analysis, along with that of previous work [4] does allow some relatively broad observations. First, the evolution from the universal ribosome appears to be constrained in the development of new interactions.…”

“…In a previous study, a network model of the ribosome considered a representation as a unipartite graph [4], and explored changes in the ribosome at different stages in translation. The graphs were constructed by separating the ribosome into its molecular elements (proteins, rRNAs and rRNA domains for the largest molecules, mRNA, tRNAs) and determining the interactions by seeing whether a solvent molecule of 1.4 Å could be rolled between each two elements.…”

Stabilization Mechanism of Initiator Transfer RNA in the Small Ribosomal Subunit from Coarse-Grained Molecular Simulations

“…Ribosomal proteins form a network structure within the ribosome. 8,47,48 The terminal region of several ribosomal proteins lacks secondary structure. However, structural analyses suggest that their terminal regions interact with tRNA.…”