Local Charge Distributions, Electric Dipole Moments, and Local Electric Fields Influence Reactivity Patterns and Guide Regioselectivities in α-Ketoglutarate-Dependent Non-heme Iron Dioxygenases

Abstract

Metrics & MoreArticle Recommendations CONSPECTUS: Non-heme iron dioxygenases catalyze vital processes for human health related to the biosynthesis of essential products and the biodegradation of toxic metabolites. Often the natural product biosyntheses by these non-heme iron dioxygenases is highly regio-and chemoselective, which are commonly assigned to tight substratebinding and positioning. However, recent high-level computational modeling has shown that substrate-binding and positioning is only part of the story and long-range electrostatic interactions can play a major additional role.In this Account, we review and summarize computational viewpoints on the high regioand chemoselectivity of α-ketoglutarate-dependent non-heme iron dioxygenases and how external perturbations affect the catalysis. In particular, studies from our groups have shown that often a regioselectivity in enzymes can be accomplished by stabilization of the rate-determining transition state for the reaction through external charges, electric dipole moments, or local electric field effects. Furthermore, bond dissociation energies in molecules are shown to be influenced by an electric field effect, and through targeting a specific bond in an electric field, this can lead to an unusually specific reaction. For instance, in the carbon-induced starvation protein, we studied two substrate-bound conformations and showed that regardless of what C−H bond of the substrate is closest to the iron(IV)-oxo oxidant, the lowest hydrogen atom abstraction barrier is always for the pro-S C 2 −H abstraction due to an induced dipole moment of the protein that weakens this bond. In another example of the hygromycin biosynthesis enzyme, an oxidative ring-closure reaction in the substrate forms an ortho-δ-ester ring. Calculations on this enzyme show that the selectivity is guided by a protonated lysine residue in the active site that, through its positive charge, triggers a low energy hydrogen atom abstraction barrier. A final set of examples in this Account discuss the viomycin biosynthesis enzyme and the 2-(trimethylammonio)ethylphosphonate dioxygenase (TmpA) enzyme.Both of these enzymes are shown to possess a significant local dipole moment and local electric field effect due to charged residues surrounding the substrate and oxidant binding pockets. The protein dipole moment and local electric field strength changes the C− H bond strengths of the substrate as compared to the gas-phase triggers the regioselectivity of substrate activation. In particular, we show that in the gas phase and in a protein environment C−H bond strengths are different due to local electric dipole moments and electric field strengths. These examples show that enzymes have an intricately designed structure that enables a chemical reaction under ambient conditions through the positioning of positively and negatively charged residues that influence and enhance reaction mechanisms. These computational insights create huge possibilities in bioengineering to apply local electric field and dip...

Can Second Coordination Sphere and Long-Range Interactions Modulate Hydrogen Atom Transfer in a Non-Heme Fe(II)-Dependent Histone Demethylase?

“… 26 , 41 Recent studies demonstrated that electrostatic perturbations could be a promising tool to modulate the rate and specificity of chemical reactions. 42 − 44 Computational methods thus have an important role in studying factors away from the active site that regulates the kinetics of individual steps in oxygenase catalysis. 28 , 29 , 45 …”

Which is the real oxidant in competitive ligand self-hydroxylation and substrate oxidation—a biomimetic iron(ii)-hydroperoxo species or an oxo-iron(iv)-hydroxy one?

“…Experimental investigations demonstrated that ligand self-hydroxylation can be inhibited by adding external substrates, which can intercept the oxidant generated from dioxygen activation mediated by iron( ii )-α-hydroxy acid complex. 3,36,37 Although high-valent iron-oxo species have often been implicated as reactive intermediates in many oxygen activating enzymes, 1,4–15 there is also evidence for the oxidation capability of the iron-hydroperoxo species. 39–41,76 Thus, the two intermediates ( i.e.…”

“…Comparison of the oxidation capability of Fe II (OOH) and Fe IV (O)(OH) toward different external substrates Experimental investigations demonstrated that ligand selfhydroxylation can be inhibited by adding external substrates, which can intercept the oxidant generated from dioxygen activation mediated by iron(II)-α-hydroxy acid complex. 3,36,37 Although high-valent iron-oxo species have often been implicated as reactive intermediates in many oxygen activating enzymes, 1,[4][5][6][7][8][9][10][11][12][13][14][15] there is also evidence for the oxidation capability of the iron-hydroperoxo species. [39][40][41]76 Thus, the two intermediates (i.e., Fe II (OOH) (1) and Fe IV (O)(OH) ( 2)) involved in this dioxygen activation process described above may serve as the oxidants to complete the following oxidations.…”

“…[1][2][3] High-valent iron-oxo species, derived from the activation of dioxygen at the iron(II) centers, have often been implicated (and in some cases, characterized) as reactive intermediates to exert these oxidative transformations in metalloenzymes, like peroxidases, catalases, cytochrome P450s, halogenases, and 2-oxoglutarate dependent dioxygenases (2-ODDs). 1,[4][5][6][7][8][9][10][11][12][13][14][15] Therein, in cytochrome P450 enzymes, an iron(IV)-oxo-porphyrin cation radical complex (called Cpd I) has been generally accepted as the active species and the direct experimental evidence of such reactive species has been provided by Schlichting et al in 2000 16 and by Green et al in 2010. 17 However, in 2-ODDs (e.g., isopenicillin N synthase), an oxo-iron(IV)-hydroxo intermediate is postulated to be responsible for the cyclisation reaction.…”

Oriented External Electric Fields Regurating the Reaction Mechanism of CH4 Oxidation Catalyzed by Fe(IV)-Oxo-Corrolazine: Insight from Density Functional Calculations

“…Recently, Sason Shaik et al ( Hirao et al, 2008 ; Gorin et al, 2012 ; Fried and Boxer, 2015 ; Li et al, 2015 ; Akamatsu et al, 2017 ; Che et al, 2018 ; Ciampi et al, 2018 ; He et al, 2018 ; Yu and Coote, 2019 ; Shaik et al, 2020 ; Shaik et al, 2004b ; Kraskov et al, 2021 ; Yu et al, 2021 ; Zhang et al, 2021 ; de Visser et al, 2022 ) found that oriented external electric fields (OEEFs) can be used as a new type of catalyst to catalyze reactions by stabilizing transition states through the interactions between OEEFs and the molecular dipole moments, and even can increase the selectivity of reactions through adjusting the direction of OEEFs. Through theoretical calculations, our group also found that the OEEFs can modulate the reaction process through the interactions with the dipole moment of the reaction molecules ( Wang et al, 2019 ).…”