Electrostatic Perturbations from the Protein Affect C−H Bond Strengths of the Substrate and Enable Negative Catalysis in the TmpA Biosynthesis Enzyme

Lin, Yen-Ting; Ali, Hafiz Saqib; Visser, Sam P. de

doi:10.1002/chem.202100791

Cited by 25 publications

(29 citation statements)

References 128 publications

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“…50 However, for an isolated 2-(trimethylammonio)ethylphosphonate molecule in the gas phase a homolytic BDE C 1 −H = 96.1 kcal mol −1 was calculated, while the C 2 −H bond energy is significantly less, namely, BDE C 2 −H = 91.5 kcal mol −1 . 47 Therefore, based on the relative values of the BDEs for the C 1 −H and C 2 −H bonds, a regioselective C 2 -hydroxylation would be expected; however, the products distributions only find C 1 -hydroxylation instead. Previously, for a large test set of chemical compounds, we showed that the bond dissociation energy is linearly related to the change in polarizability along that chemical bond and consequently bond energies may be affected by electric field perturbations.…”

Section: Electric Field Affecting Substrate Bond Strengthsmentioning

confidence: 99%

“…44−46 Several examples of the substrates and reaction products obtained for these biosynthesis enzymes are given in Figure 2 with the respective BDE values of calculated C−H bond strengths. 26,39,43,47,48 Thus, prolyl-4-hydroxylase (P4H) chemoand enantioselectively hydroxylates the C 4 -position of a proline residue in a peptide chain to form R-4-hydroxyproline, an essential component of collagen strands that gives it its structure and function. 38 A series of computational studies on P4H, however, actually showed that the C 5 −H bonds in proline are significantly weaker than the C 4 −H bonds and hence C 5hydroxylation should be the dominant reaction pathway.…”

Section: Introductionmentioning

confidence: 99%

“…43 The final example shown in Figure 2 is for the 2-(trimethylammonio)ethylphosphonate dioxygenase (TmpA), which selectively hydroxylates the C 1 −H bond of the substrate to trigger the glycine betaine biosynthesis. 50 Interestingly, the calculated weakest C−H bond of 2-(trimethylammonio)ethylphosphonate in the gas phase is the C 2 −H bond and, 47 therefore, TmpA reacts through negative catalysis where the thermodynamically favored pathway is blocked in favor of an alternative reaction channel, namely, C 1 −H bond hydroxylation. 2 Below, we give details of our computational work on TmpA and how we believe this selectivity is obtained.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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...

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Section: Electric Field Affecting Substrate Bond Strengthsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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“…In addition, computational studies on the biosynthesis nonheme iron dioxygenase HygX identified a positively charged active site Lys residue that through charge-dipole interactions influences reactivity patterns and guides the selectivity of the reaction . However, in the analogous enzymes viomycin biosynthesis enzyme (VioL), the 2-(trimethylammonio)ethylphosphonate dioxygenase (TmpA) and the carbon starvation-induced protein D (CsiD), a combination of positively and negatively charged residues arranged local dipole moments in such a way that an otherwise unfavorable reaction pathway was stabilized. − These long-range interactions were shown to affect redox potentials and bond strengths and hence influence the catalytic cycle and enzymatic turnover. To understand the technical details of second- and first-coordination sphere effects of enzymes, many inorganic chemists have made links of enzymatic structures with synthetic (biomimetic) models.…”

Section: Second-coordination Sphere Effectsmentioning

confidence: 99%

Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants

et al. 2021

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Enzymes are highly efficient catalysts in Nature that often react with high stereo-, chemo-, and regioselectivity. Usually, enzymes achieve this selectivity through substrate binding and positioning in the active site. The second-coordination sphere effects (also called noncovalent interactions) position the substrate and oxidant in close vicinity, and their effects include electrostatic interactions, hydrogen-bonding interactions, salt-bridges, and also long-range charge-effects from bound cations and anions. Each of these environmental perturbations can affect the kinetics and selectivity of reactions differently. Over the past couple of years, a variety of biomimetic model complexes have been developed and designed that have a similar first-coordination sphere to mononuclear iron-containing enzymes. However, sometimes the reactivity patterns of the biomimetic models in solution are different from the analogous enzymatic systems, and often the selectivity of the reaction is lost. To understand the functional differences between enzymes and biomimetic models, large catalytic clusters have been developed that incorporate second-coordination sphere effects that influence spectroscopic features as well as reactivity patterns. In this Review, we summarize and highlight recent advances in biomimetic chemistry on the creation and design of iron catalysts and the insights that have been obtained when elaborate ligand features are added, which influence the substrate approach to the catalytic center. We start with a highlight of the axial and distal ligand effects of metal centers and how these can be perturbed by hydrogen bonding as well as steric restraints. The syntheses of the active oxidants through the addition of a proton-donating or -accepting groups to the structure have also been discussed in detail in this article. As shown in this work, second-coordination sphere effects can be useful not only to trap and characterize short-lived intermediates but also to enable high selectivity and specificity of a chemical reaction in analogy to enzymatic systems. These biomimetic models appear highly useful for biotechnological and engineering applications with reasonable turnover numbers and consequently have great potential for the future of stereo-and chemoselective synthetic catalytic reactions.

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“…Hence, we will focus on the mechanism starting from CpdI and a substrate only. Previous studies of ours showed that large QM cluster models of well over 150 atoms represent the oxidant and substrate binding pockets of enzymes highly accurately and give results at par with QM/MM methods [43][44][45][46]. Therefore, a large QM cluster model of the substrate-bound P450 OleT models was set up.…”

Section: Resultsmentioning

confidence: 99%

Product Distributions of Cytochrome P450 OleTJE with Phenyl-Substituted Fatty Acids: A Computational Study

Lin

Visser

2021

IJMS

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There are two types of cytochrome P450 enzymes in nature, namely, the monooxygenases and the peroxygenases. Both enzyme classes participate in substrate biodegradation or biosynthesis reactions in nature, but the P450 monooxygenases use dioxygen, while the peroxygenases take H2O2 in their catalytic cycle instead. By contrast to the P450 monooxygenases, the P450 peroxygenases do not require an external redox partner to deliver electrons during the catalytic cycle, and also no external proton source is needed. Therefore, they are fully self-sufficient, which affords them opportunities in biotechnological applications. One specific P450 peroxygenase, namely, P450 OleTJE, reacts with long-chain linear fatty acids through oxidative decarboxylation to form hydrocarbons and, as such, has been implicated as a suitable source for the biosynthesis of biofuels. Unfortunately, the reactions were shown to produce a considerable amount of side products originating from Ca and Cb hydroxylation and desaturation. These product distributions were found to be strongly dependent on whether the substrate had substituents on the Ca and/or Cb atoms. To understand the bifurcation pathways of substrate activation by P450 OleTJE leading to decarboxylation, Ca hydroxylation, Cb hydroxylation and Ca-Cb desaturation, we performed a computational study using 3-phenylpropionate and 2-phenylbutyrate as substrates. We set up large cluster models containing the heme, the substrate and the key features of the substrate binding pocket and calculated (using density functional theory) the pathways leading to the four possible products. This work predicts that the two substrates will react with different reaction rates due to accessibility differences of the substrates to the active oxidant, and, as a consequence, these two substrates will also generate different products. This work explains how the substrate binding pocket of P450 OleTJE guides a reaction to a chemoselectivity.

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Electrostatic Perturbations from the Protein Affect C−H Bond Strengths of the Substrate and Enable Negative Catalysis in the TmpA Biosynthesis Enzyme

Cited by 25 publications

References 128 publications

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

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

Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants

Product Distributions of Cytochrome P450 OleTJE with Phenyl-Substituted Fatty Acids: A Computational Study

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