Abstract
Vitamin K1 (VK1) plays an important role in the modulation of bleeding disorders. It has been reported that ω-hydroxylation on the VK1 aliphatic chain is catalyzed by cytochrome P450 4F2 (CYP4F2), an enzyme responsible for the metabolism of eicosanoids. However, the mechanism of VK1 ω-hydroxylation by CYP4F2 has not been disclosed. In this study, we employed a combination of quantum mechanism (QM) calculations, homology modeling, molecular docking, molecular dynamics (MD) simulations, and combined quantum mechanism/molecular mechanism (QM/MM) calculations to investigate the metabolism profile of VK1 ω-hydroxylation. QM calculations based on the truncated VK1 model show that the energy barrier for ω-hydroxylation is about 6-25 kJ/mol higher than those at other potential sites of metabolism. However, results from the MD simulations indicate that hydroxylation at the ω-site is more favorable than at the other potential sites, which is in accordance with the experimental observation. The evaluation of MD simulations was further endorsed by the QM/MM calculation results. Our studies thus suggest that the active site residues of CYP4F2 play a determinant role in the ω-hydroxylation. Our results provide structural insights into the mechanism of VK1 ω-hydroxylation by CYP4F2 at the atomistic level and are helpful not only for characterizing the CYP4F2 functions but also for looking into the ω-hydroxylation mediated by other CYP4 enzymes.
Highlights
The cytochrome P450 enzyme family 4 (CYP4) has 12 members and is the second largest human CYP family
The hydrogen atom transfer (HAT) is generally the first and ratelimiting step for the aliphatic hydroxylation, which is one of the most common types of metabolism mediated by CYP enzymes (Ogliaro et al, 2000)
The chemical reactivities of all potential HAT sites on the substrate are important for evaluating the selectivity of C–H hydroxylation (Cruciani et al, 2013; Kirchmair et al, 2015; Bonomo et al, 2017b)
Summary
The cytochrome P450 enzyme family 4 (CYP4) has 12 members and is the second largest human CYP family. The crystal structure of the P450 BM3 (CYP102A1) A264E mutant, which is located in the similar flanking position of helix I, reveals that the carboxyl group of Glu264 ligates to the iron rather than covalently bonds to the 5-methyl group of the heme as expected (Joyce et al, 2004) These studies suggested that the ester bond between a specific glutamic acid in helix I and heme is formed inherently and automatically in the CYP4 enzymes (LeBrun et al, 2002). The ratio of ω/ω-1 hydroxylation increases significantly in these mutants, indicating that the covalent bond between Glu310 and heme could reduce the conformational entropies in the active site (Hsu et al, 2017), the existence of this covalent bond is not necessary in the selective ω-hydroxylation of short chain alkanes. Based on the evaluation of MD simulations, combined quantum mechanism/molecular mechanism (QM/MM) calculations were carried out to justify the selectivity of VK1 hydroxylation by CYP4F2
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
