General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility
| Authors | |
|---|---|
| Year of publication | 2008 |
| Type | Article in Periodical |
| Magazine / Source | Journal of Physical Chemistry B |
| MU Faculty or unit | |
| Citation | |
| Field | Biophysics |
| Keywords | quantum chemistry; molecular mechanical calculation; HDVr |
| Description | Investigation of active-site nucleotide C75 role in self-cleavage of HDVr. For this purpose quantum chemical/molecular mechanical calculations were carried out. Calculations show that C75 is readily capable of acting as the general base, in concert with the hydrated magnesium ion as the general acid. The calculated energy barrier of the proposed mechanism, minus 20 kcal/mol, would lower the reaction barrier by minus15 kcal/mol compared with the uncatalyzed reaction and is in good agreement with experimental data. |
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