Ab initio dynamics of the cytochrome P450 hydroxylation reaction

Abstract

The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. C 2015 AIP Publishing LLC. [http://dx

Direct Dynamics Trajectories Demonstrate Dynamic Matching and Nonstatistical Radical Pair Intermediates during Fe-Oxo-Mediated C–H Functionalization Reactions

“…This observation of extremely fast rebound trajectories and slightly slower rebound trajectories is in good agreement with Goldberg’s kinetic measurements of a corrole-ligated Fe­(OH) complex where both concerted and stepwise rebound pathways were observed . These life-time measurements are also in the range of previous ab initio dynamic simulations of cytochrome P450 enzyme models , and Houk’s dynamics simulations of radical oxygen rebound during the oxidation of isobutane by dimethyldioxirane . Moreover, similar to the ideas proposed by Goldberg and co-workers, Newcomb et al, and Sarkar et al, our trajectory results support the viewpoint that rebound is perhaps better considered a dynamically concerted process rather than a full stepwise process.…”

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“…The imaginary frequencies, therefore, are not dramatically different between the model A II and model A III structures and would implicate similar kinetic isotope effects for replacing hydrogen by deuterium due to a similar shape of the potential energy profile around the transition state. These values are typical for hydrogen atom abstraction transition state and seen before for P450 model reactions. − The large imaginary frequency in the hydrogen atom abstraction transition states will result in a large kinetic isotope effect and a significant amount of quantum chemical tunneling for the reaction. , After the radical intermediate, a small rebound barrier via TS2 leads to the hydroxylated methoxy group products 4,2 P Hy,A with large exothermicity. From the hydroxylated methoxy group, a subsequent proton relay from the alcohol group to the methoxy oxygen atom leads to deformylation.…”

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