Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
Int J Biol Macromol. 2019 Nov 1;140:323-329. doi: 10.1016/j.ijbiomac.2019.08.127. Epub 2019 Aug 15.
Ribosomes are the translational machineries having two unequal subunits, small subunit (SSU) and large subunit (LSU) across all the domains of life. Origin and evolution of ribosome are encoded in its structure, and the core of the ribosome is highly conserved. Here, we have used Shannon entropy to analyze the evolution of ribosomal proteins (r-proteins) across the three domains of life. Moreover, we have analyzed the residue conservation at protein-protein (PP) and protein-RNA (PR) interfaces in SSU and LSU. Furthermore, we have studied the evolution of early, intermediate and late binding r-proteins. We show that the r-proteins of Thermus thermophilus are better conserved during the evolution. Furthermore, we find the late binders are better conserved than the early and the intermediate binders. The residues at the interior of the r-proteins are the most conserved followed by those at the interface and the solvent accessible surface. Additionally, we show that the residues at the PP interfaces are better conserved than those at the PR interfaces. However, between PR and PP interfaces, the multi-interface residues at the former are better conserved than those at the latter ones. Our findings may provide insights into the evolution of r-proteins in ribosomal assembly and function.
核糖体是具有两个不等亚基的翻译机器，小亚基（SSU）和大亚基（LSU）存在于所有生命领域。核糖体的起源和进化都编码在其结构中，核糖体的核心高度保守。在这里，我们使用香农熵来分析核糖体蛋白（r-蛋白）在三个生命领域的进化。此外，我们还分析了 SSU 和 LSU 中蛋白质-蛋白质（PP）和蛋白质-RNA（PR）界面处残基的保守性。此外，我们研究了早期、中期和晚期结合 r-蛋白的进化。结果表明，嗜热栖热菌的 r-蛋白在进化过程中保存得更好。此外，我们发现晚期结合物比早期和中期结合物更保守。r-蛋白内部的残基最保守，其次是界面处和溶剂可及表面的残基。此外，我们发现 PP 界面处的残基比 PR 界面处的残基更保守。然而，在 PR 和 PP 界面之间，前者的多界面残基比后者的残基更保守。我们的研究结果可能为核糖体组装和功能中 r-蛋白的进化提供新的见解。
