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Computation of kinetic isotope effects for enzymatic reactions.

ABSTRACT: We describe a computational approach, incorporating quantum mechanics into enzyme kinetics modeling with a special emphasis on computation of kinetic isotope effects. Two aspects are highlighted: (1) the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) potential in which the bond forming and breaking processes are modeled by electronic structure theory, and (2) a free energy perturbation method in path integral simulation is used to determine both kinetic isotope effects (KIEs). In this approach, which is called the PI-FEP/UM method, a light (heavy) isotope is mutated into a heavy (light) counterpart in centroid path integral simulations. The method is illustrated in the study of primary and secondary KIEs in two enzyme systems. In the case of nitroalkane oxidase, the enzymatic reaction exhibits enhanced quantum tunneling over that of the uncatalyzed process in water. In the dopa delarboxylase reaction, there appears to be distinguishable primary carbon-13 and secondary deuterium KIEs when the internal proton tautomerism is in the N-protonated or in the O-protonated positions. These examples show that the incorporation of quantum mechanical effects in enzyme kinetics modeling offers an opportunity to accurately and reliably model the mechanisms and free energies of enzymatic reactions.

SUBMITTER: Gao J

PROVIDER: S-EPMC3749886 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Computation of kinetic isotope effects for enzymatic reactions.

Gao Jiali J

Science China. Chemistry 20121201 12

We describe a computational approach, incorporating quantum mechanics into enzyme kinetics modeling with a special emphasis on computation of kinetic isotope effects. Two aspects are highlighted: (1) the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) potential in which the bond forming and breaking processes are modeled by electronic structure theory, and (2) a free energy perturbation method in path integral simulation is used to determ ...[more]

PMID: 23976893

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Project description:Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate-controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition-state structure and bonding optimally requires the use of theoretical models. In this work, we apply density-functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2'-O-transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well-studied series of phosphate and phosphorothioate mono-, di- and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non-enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease?A, and demonstrate the reaction coordinate-KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.

Dataset Information

Computation of kinetic isotope effects for enzymatic reactions.

Publications

Computation of kinetic isotope effects for enzymatic reactions.

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