Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.
PLoS One. 2013 Aug 5;8(8):e69898. doi: 10.1371/journal.pone.0069898. Print 2013.
Here we compare the structural and evolutionary attributes of Thermus thermophilus and Escherichia coli small ribosomal subunits (SSU). Our results indicate that with few exceptions, thermophilic 16S ribosomal RNA (16S rRNA) is densely packed compared to that of mesophilic at most of the analogous spatial regions. In addition, we have located species-specific cavity clusters (SSCCs) in both species. E. coli SSCCs are numerous and larger compared to T. thermophilus SSCCs, which again indicates densely packed thermophilic 16S rRNA. Thermophilic ribosomal proteins (r-proteins) have longer disordered regions than their mesophilic homologs and they experience larger disorder-to-order transitions during SSU-assembly. This is reflected in the predicted higher conformational changes of thermophilic r-proteins compared to their mesophilic homologs during SSU-assembly. This high conformational change of thermophilic r-proteins may help them to associate with the 16S ribosomal RNA with high complementary interfaces, larger interface areas, and denser molecular contacts, compared to those of mesophilic. Thus, thermophilic protein-rRNA interfaces are tightly associated with 16S rRNA than their mesophilic homologs. Densely packed 16S rRNA interior and tight protein-rRNA binding of T. thermophilus (compared to those of E. coli) are likely the signatures of its thermal adaptation. We have found a linear correlation between the free energy of protein-RNA interface formation, interface size, and square of conformational changes, which is followed in both prokaryotic and eukaryotic SSU. Disorder is associated with high protein-RNA interface polarity. We have found an evolutionary tendency to maintain high polarity (thereby disorder) at protein-rRNA interfaces, than that at rest of the protein structures. However, some proteins exhibit exceptions to this general trend.
在这里，我们比较了嗜热栖热菌和大肠杆菌小核糖体亚基（SSU）的结构和进化属性。我们的结果表明，除了少数例外，与大多数类似的空间区域相比，嗜热 16S 核糖体 RNA（16S rRNA）的密度更高。此外，我们在这两个物种中都定位了物种特异性腔簇（SSCC）。与 T. thermophilus SSCC 相比，E. coli SSCC 数量更多且更大，这再次表明嗜热 16S rRNA 的密度更高。嗜热核糖体蛋白（r 蛋白）的无规则区域比它们的中温同源物更长，并且在 SSU 组装过程中经历更大的无序到有序的转变。这反映在预测的嗜热 r 蛋白在 SSU 组装过程中比它们的中温同源物经历更高的构象变化。与中温相比，这种嗜热 r 蛋白的高构象变化可能有助于它们与具有高互补界面、更大界面面积和更密集分子接触的 16S 核糖体 RNA 结合。因此，与中温相比，嗜热蛋白-rRNA 界面与 16S rRNA 的结合更为紧密。与 E. coli 相比，T. thermophilus 16S rRNA 内部的紧密包装和紧密的蛋白质-rRNA 结合（与 E. coli 相比）可能是其热适应的特征。我们发现蛋白质-RNA 界面形成的自由能、界面大小和构象变化的平方之间存在线性相关性，这种相关性在原核和真核 SSU 中都存在。无序与高蛋白质-RNA 界面极性相关。我们发现了一种进化趋势，即在蛋白质-rRNA 界面上保持高极性（因此是无序），而在蛋白质结构的其余部分则保持低极性。然而，一些蛋白质表现出对这种一般趋势的例外。
