Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-09-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/18/5479 |
| _version_ | 1797518045222010880 |
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| author | Andrey Yu. Sosorev |
| author_facet | Andrey Yu. Sosorev |
| author_sort | Andrey Yu. Sosorev |
| collection | DOAJ |
| description | 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, Fe<sub>4</sub>S<sub>4</sub> 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. |
| first_indexed | 2024-03-10T07:24:40Z |
| format | Article |
| id | doaj.art-f1291ac245404cea8ff04d7414ddeb98 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T07:24:40Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-f1291ac245404cea8ff04d7414ddeb982023-11-22T14:23:42ZengMDPI AGMolecules1420-30492021-09-012618547910.3390/molecules26185479Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron HolesAndrey Yu. Sosorev0Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, RussiaDespite 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, Fe<sub>4</sub>S<sub>4</sub> 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.https://www.mdpi.com/1420-3049/26/18/5479RNAribosomeallosteryDFTcharge transport |
| spellingShingle | Andrey Yu. Sosorev Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes Molecules RNA ribosome allostery DFT charge transport |
| title | Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes |
| title_full | Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes |
| title_fullStr | Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes |
| title_full_unstemmed | Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes |
| title_short | Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes |
| title_sort | walking around ribosomal small subunit a possible tourist map for electron holes |
| topic | RNA ribosome allostery DFT charge transport |
| url | https://www.mdpi.com/1420-3049/26/18/5479 |
| work_keys_str_mv | AT andreyyusosorev walkingaroundribosomalsmallsubunitapossibletouristmapforelectronholes |