Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia.
Molecules. 2021 Sep 9;26(18):5479. doi: 10.3390/molecules26185479.
Despite several decades of research, the physics underlying translation-protein synthesis at the ribosome-remains poorly studied. For instance, the mechanism coordinating various events occurring in distant parts of the ribosome is unknown. Very recently, we suggested that this allosteric mechanism could be based on the transport of electric charges (electron holes) along RNA molecules and localization of these charges in the functionally important areas; this assumption was justified using tRNA as an example. In this study, we turn to the ribosome and show computationally that holes can also efficiently migrate within the whole ribosomal small subunit (SSU). The potential sites of charge localization in SSU are revealed, and it is shown that most of them are located in the functionally important areas of the ribosome-intersubunit bridges, FeS cluster, and the pivot linking the SSU head to its body. As a result, we suppose that hole localization within the SSU can affect intersubunit rotation (ratcheting) and SSU head swiveling, in agreement with the scenario of electronic coordination of ribosome operation. We anticipate that our findings will improve the understanding of the translation process and advance molecular biology and medicine.
尽管已经进行了几十年的研究，但核糖体翻译-蛋白质合成的基础物理学仍未得到充分研究。例如，协调核糖体中不同部位发生的各种事件的机制尚不清楚。最近，我们提出这种变构机制可能基于沿着 RNA 分子传输电荷（电子空穴）并将这些电荷定位在功能重要区域；这一假设使用 tRNA 作为示例得到了证明。在这项研究中，我们转向核糖体，并通过计算表明空穴也可以在核糖体小亚基（SSU）内高效迁移。揭示了 SSU 中电荷定位的潜在位点，并表明它们中的大多数位于核糖体亚基间桥、FeS 簇和连接 SSU 头部与其主体的枢轴的功能重要区域。因此，我们假设 SSU 内的空穴定位可以影响亚基间旋转（棘轮）和 SSU 头部旋转，这与核糖体操作的电子协调方案一致。我们预计我们的发现将提高对翻译过程的理解，并推动分子生物学和医学的发展。
