Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism
Abstract Ribozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries along independent MD simulations with different protonation states of the active site basic species reveals that only the canonical system, with no additional protonation changes, renders reactive conformations. A change in the coordination sphere of the $ Mg^{2+} $ ion has been observed during the simulations, which allows proposing a mechanism to explain the unique mode of action of the pistol ribozyme by comparison with other ribozymes. The present results are at the center of the debate originated from recent experimental and theoretical studies on pistol ribozyme..
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:65 |
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| Enthalten in: |
Topics in catalysis - 65(2021), 1-4 vom: 25. Aug., Seite 505-516 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Serrano-Aparicio, Natalia [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| BKL: | |
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| Themen: |
Molecular dynamics |
| Anmerkungen: |
© The Author(s) 2021 |
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| doi: |
10.1007/s11244-021-01494-1 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 245 | 1 | 0 | |a Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism |
| 264 | 1 | |c 2021 | |
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| 520 | |a Abstract Ribozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries along independent MD simulations with different protonation states of the active site basic species reveals that only the canonical system, with no additional protonation changes, renders reactive conformations. A change in the coordination sphere of the $ Mg^{2+} $ ion has been observed during the simulations, which allows proposing a mechanism to explain the unique mode of action of the pistol ribozyme by comparison with other ribozymes. The present results are at the center of the debate originated from recent experimental and theoretical studies on pistol ribozyme. | ||
| 650 | 4 | |a Pistol ribozyme | |
| 650 | 4 | |a Self-cleavage ribozymes | |
| 650 | 4 | |a Molecular dynamics | |
| 650 | 4 | |a QM/MM | |
| 650 | 4 | |a Reaction mechanisms | |
| 700 | 1 | |a Świderek, Katarzyna |0 (orcid)0000-0002-7528-1551 |4 aut | |
| 700 | 1 | |a Tuñón, Iñaki |0 (orcid)0000-0002-6995-1838 |4 aut | |
| 700 | 1 | |a Moliner, Vicent |0 (orcid)0000-0002-3665-3391 |4 aut | |
| 700 | 1 | |a Bertran, Joan |0 (orcid)0000-0002-2868-2571 |4 aut | |
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