Abstract
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, Fe4S4 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.
Highlights
Translation—protein synthesis at the ribosome—is necessary for life of all organisms and proceeds in similar way in all domains of life
We suggested that this allosteric mechanism could be based on the transport of electric charges along RNA molecules and localization of these charges in the functionally important areas; this assumption was justified using transfer RNA (tRNA) as an example
We have shown that electron holes can efficiently migrate within the ribosomal small subunit (SSU) and localize at certain sites
Summary
Translation—protein synthesis at the ribosome—is necessary for life of all organisms and proceeds in similar way in all domains of life. The ribosome structure has been recently resolved in detail [1], the physical mechanisms underlying ribosome operation are far from being well understood. It is not clear how the motions of the participants of the translation process—ribosome, transfer RNA (tRNA), and matrix RNA (mRNA) molecules—are precisely coordinated. Synchronized action of distant parts of the ribosome and tRNAs implies the existence of some mechanism orchestrating them [11,12,13]. This allosteric mechanism remains unknown, despite several decades of intensive studies of ribosome operation. We recently suggested that this mechanism is of electronic character and involves charge (electron hole) transport along and between the RNA molecules, charge localization at certain sites (areas), and subsequent conformational changes of the latter [14]
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