CNRS, Centre de Nanosciences et Nanotechnologies, Université Paris-Saclay, Palaiseau, France.
PLoS One. 2020 Oct 5;15(10):e0239700. doi: 10.1371/journal.pone.0239700. eCollection 2020.
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.
在过去的二十年中，对核糖体的生化、生物物理和结构特性的研究揭示了蛋白质翻译的许多不同步骤。然而，要完全理解它们如何导致快速而准确的蛋白质合成仍然是一个挑战。在这里，我们考虑了在细菌核糖体中形成的粗网络分析，该网络由核糖体（r）蛋白和 RNA 在延伸循环的不同阶段之间的连接形成。发现核糖体网络是去关联的和小世界的，这意味着结构允许在远距离位置之间进行有效的信息交换。中心性分析表明，23S rRNA 的第二和第五结构域是所有网络中最重要的元素。核糖体蛋白枢纽连接到的节点要少得多，但被证明在网络内提供了重要的连接（高接近中心性）。模块化分析揭示了一些不同的功能社区，表明了一些已知的和一些新的可能的通信途径。我们的数学结果证实了之前研究中讨论的重要通信途径，从而验证了该技术在表示核糖体方面的应用，并且还揭示了核糖体元件的集体功能的新见解。
