Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density
| Autor: | Abir Ganguly, Sharon Hammes-Schiffer, Pallavi Thaplyal, Philip C. Bevilacqua |
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| Rok vydání: | 2015 |
| Předmět: |
Proton
Cations Divalent Inorganic chemistry Molecular Sequence Data Thio Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Biochemistry Article Divalent Ion Metal 03 medical and health sciences chemistry.chemical_compound Imidazole RNA Catalytic 030304 developmental biology chemistry.chemical_classification 0303 health sciences Base Sequence Substrate (chemistry) Charge density Cations Monovalent Hydrogen-Ion Concentration 0104 chemical sciences Crystallography Kinetics chemistry visual_art visual_art.visual_art_medium Quantum Theory RNA Viral Hepatitis Delta Virus Sulfur |
| Zdroj: | Biochemistry |
| ISSN: | 1520-4995 |
| Popis: | The hepatitis delta virus (HDV) ribozyme self-cleaves in the presence of a wide range of monovalent and divalent ions. Prior theoretical studies provided evidence that self-cleavage proceeds via a concerted or stepwise pathway, with the outcome dictated by the valency of the metal ion. In the present study, we measure stereospecific thio effects at the nonbridging oxygens of the scissile phosphate under a wide range of experimental conditions, including varying concentrations of diverse monovalent and divalent ions, and combine these with quantum mechanical/molecular mechanical (QM/MM) free energy simulations on the stereospecific thio substrates. The RP substrate gives large normal thio effects in the presence of all monovalent ions. The SP substrate also gives normal or no thio effects, but only for smaller monovalent and divalent cations, such as Li(+), Mg(2+), Ca(2+), and Sr(2+); in contrast, sizable inverse thio effects are found for larger monovalent and divalent cations, including Na(+), K(+), NH4(+), and Ba(2+). Proton inventories are found to be unity in the presence of the larger monovalent and divalent ions, but two in the presence of Mg(2+). Additionally, rate-pH profiles are inverted for the low charge density ions, and only imidazole plus ammonium ions rescue an inactive C75Δ variant in the absence of Mg(2+). Results from the thio effect experiments, rate-pH profiles, proton inventories, and ammonium/imidazole rescue experiments, combined with QM/MM free energy simulations, support a change in the mechanism of HDV ribozyme self-cleavage from concerted and metal ion-stabilized to stepwise and proton transfer-stabilized as the charge density of the metal ion decreases. |
| Databáze: | OpenAIRE |
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