What Is the Catalytic Mechanism of Enzymatic Histone N‐Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?

• Published in: Chemistry : a European journal 2021-08, Vol.27 (46), p.11827-11836
• Main Authors: Ramanan, Rajeev, Waheed, Sodiq O., Schofield, Christopher J., Christov, Christo Z.
• Format: Article
• Language: English
• Subjects: Arginine; Arginine - metabolism; Binding; Catalysis; Chemistry; Demethylation; Electric fields; Electron transfer; Energy of dissociation; Epigenesis, Genetic; Epigenetics; Free energy; Heat of formation; histone demethylation; Histones; Histones - metabolism; Humans; Hydrogen bonds; Hydroxylation; Intermediates; Iron; JmjC demethylases (KDMs); Jumonji Domain-Containing Histone Demethylases - metabolism; Lysine; Methylation; Molecular dynamics; non-heme iron enzymes; QM/MM calculations; Quantum mechanics; Substrates
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.202101174

Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2‐oxoglutarate dependent Jumonji‐C (JmjC) Nϵ‐methyl lysine histone demethylases also have N‐methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N‐methyl arginine demethylation by human KDM4E and compare the results with those reported for N‐methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen‐bond between the substrate Ser1 and Tyr178. The calculations imply that in either C−H or N−H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N‐methyl arginine demethylation, electron transfer occurs via a σ‐channel; the transition state for the N−H pathway is ∼10 kcal/mol higher than for the C−H pathway due to the higher bond dissociation energy of the N−H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier‐lowering effect on the C−H pathway, by contrast, such EEFs inhibit the N−H activation rate. The overall results imply that KDM4 catalyzed N‐methyl arginine demethylation and N‐methyl lysine demethylation occur via similar C−H ion and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates. The QM/MM calculations of the demethylation of symmetrical dimethylated arginine (R3me2 s) substrate by KDM4E via C−H and N−H pathways show the preference for the former and application of external electric fields (EEFs) increases the rate of C−H activation, while inhibiting the rate of N−H activation.