Počet záznamů: 1  

Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis

  1. 1.
    0486054 - BFÚ 2018 RIV US eng J - Článek v odborném periodiku
    Mlýnský, V. - Kührová, P. - Jurečka, P. - Šponer, Jiří - Otyepka, M. - Banáš, Pavel
    Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis.
    Journal of Physical Chemistry B. Roč. 121, č. 48 (2017), s. 10828-10840. ISSN 1520-6106. E-ISSN 1520-5207
    Grant CEP: GA ČR GAP208/12/1878
    Institucionální podpora: RVO:68081707
    Klíčová slova: delta-virus ribozyme * self-cleaving ribozymes
    Obor OECD: Physical chemistry
    Impakt faktor: 3.146, rok: 2017

    Ribozymes utilize diverse catalytic strategies. We report systematic quantum chemical calculations mapping the catalytic space of RNA cleavage by comparing all chemically feasible reaction mechanisms of RNA self-cleavage, using appropriate model systems including those chemical groups that may directly participate in ribozyme catalysis. We calculated the kinetics of uncatalyzed cleavage reactions proceeding via both monoanionic and dianionic pathways, and explicitly probed effects of various groups acting as general bases (GBs) and/or general acids (GAs), or electrostatic transition state stabilizers. In total, we explored 115 different mechanisms. The dianionic scenarios are generally preferred to monoanionic scenarios, although they may compete with one-another under some conditions. Direct GA catalysis seems to exert the dominant catalytic effect, while GB catalysis electrostatic stabilization are less efficient. Our results indirectly suggest that the dominant part of the catalytic effect might be explained by the shift of the reaction mechanism from the mechanism of uncatalyzed cleavage to the mechanism occurring in ribozymes. This would contrast typical protein enzymes, primarily achieving catalysis by overall electrostatic effects in their catalytic center.
    Trvalý link: http://hdl.handle.net/11104/0280942

     
     
Počet záznamů: 1  

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