Kinetic isotope effects (KIEs) for a series of phosphate/phosphorothioate ester hydrolysis reactions and RNA transesterification model reactions have been studied with quantum chemical calculations. Good correlation between experimental and computational KIEs has been obtained for the former set of reactions, in which various KIE values are found to be crucial for examining transition state (TS) structures as well as probing mechanistic details. As for the later system, good and poor leaving groups lead to two distinct KIE signatures, which correspond to early and late rate-limiting TSs and agree well with our recently published linear free energy relationship (LFER) analysis. These model systems presented a strong coordinate-KIE correlation that was used to develop a model for predication. This model was applied to a small TS model of RNA phosphoryl transfer catalyzed by ribonuclease A (RNAse A) and was shown to be accurate with the exact result. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of small model systems that may aid in the interpretation of KIE measurements of more complex biological systems such as phosphoryl transfer enzymes and ribozymes.

Mechanistic implication on RNA transphosphorylation from model reaction kinetic isotope effects: A computational study

247th National Meeting (2014)

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