An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(17), P. 11726 - 11739

Published: April 18, 2024

Lysine dioxygenase (KDO) is an important enzyme in human physiology involved bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs nature; however, little known about the factors govern regio- stereoselectivity of these enzymes. To understand how can selectively hydroxylate their substrate, we did a comprehensive computational study into mechanisms features 4-lysine dioxygenase. In particular, selected snapshot from MD simulation on KDO5 created large QM cluster models (A, B, C) containing 297, 312, 407 atoms, respectively. The largest model predicts regioselectivity matches experimental observation with rate-determining hydrogen atom abstraction C4–H position, followed by fast OH rebound to form 4-hydroxylysine products. calculations show C, dipole moment positioned along bond substrate and, therefore, electrostatic electric field perturbations protein assist creating hydroxylation selectivity. Furthermore, active site Tyr233 residue identified reacts through proton-coupled electron transfer akin axial Trp cytochrome c peroxidase. Thus, upon formation iron(IV)-oxo species catalytic cycle, phenol loses proton nearby Asp179 residue, while at same time, transferred iron create iron(III)-oxo species. This charged tyrosyl directs guides selectivity C4-hydroxylation substrate.

Language: Английский

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CO₂ Reduction by an Iron(I) Porphyrinate System: Effect of Hydrogen Bonding on the Second Coordination Sphere

Inorganic Chemistry, Journal Year: 2024, Volume and Issue: 63(10), P. 4474 - 4481

Published: Feb. 26, 2024

Transforming CO2 into valuable materials is an important reaction in catalysis, especially because concentrations the atmosphere have been growing steadily due to extensive fossil fuel usage. From environmental perspective, reduction of should be catalyzed by environmentally benign catalyst and avoid use heavy transition-metal ions. In this work, we present a computational study novel iron(I) porphyrin for reduction, namely, with tetraphenylporphyrin ligand analogues. particular, investigated one meso-phenyl groups substituted o-urea, p-urea, or o-2-amide groups. These substituents can provide hydrogen-bonding interactions second coordination sphere bound ligands assist proton relay. Furthermore, our studies bicarbonate phenol as stabilizers donors mechanism. Potential energy landscapes double protonation porphyrinate are reported. The work shows that bridges urea/amide iron center provides tight bonding pattern strong facilitates easy delivery CO2. Specifically, low-energy shuttle mechanism form CO water efficiently. o-urea group locks orientation helps ideal transfer, while there more mobility lesser stability o-amide position instead. Our calculations show leads proton-transfer barriers, line experimental observation. We then applied electric-field-effect estimate effects on two steps reaction. describe perturbations enhance driving forces used make predictions about how catalysts further engineered enhanced processes.

Language: Английский

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Revealing the Nature of the Second Branch Point in the Catalytic Mechanism of the Fe(II)/2OG-Dependent Ethylene Forming Enzyme

Chemical Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The study explores the second branchpoint of EFE catalytic mechanism, which determines product distribution ethylene and 3-hydroxypropionate formation using QM/MM simulations on WT A198L variants EFE.

Language: Английский

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Computational Study Into the Oxidative Ring‐Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin

Chemistry - A European Journal, Journal Year: 2024, Volume and Issue: 30(22)

Published: Feb. 7, 2024

The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into mechanism understand details pathways leading to products by-products we performed a comprehensive computational study. work shows that is bound tightly binding pocket with C

Language: Английский

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Quantum Mechanical Cluster Models for Calculations on Enzymatic Reaction Mechanisms: Set‐Up and Accuracy

Chemistry - A European Journal, Journal Year: 2024, Volume and Issue: 30(60)

Published: Aug. 7, 2024

Enzymes turnover substrates into products with amazing efficiency and selectivity as such have great potential for use in biotechnology pharmaceutical applications. However, details of their catalytic cycles the origins surrounding regio- chemoselectivity enzymatic reaction processes remain unknown, which makes engineering enzymes challenging. Computational modelling can assist experimental work field establish factors that influence rates product distributions. A popular approach is quantum mechanical cluster models take first- second coordination sphere enzyme active site consideration. These QM are widely applied but often results obtained dependent on model choice selection. Herein, we show give highly accurate reproduce distributions free energies activation within several kcal mol

Language: Английский

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Conformational Isomerization of the Fe(III)–OH Species Enables Selective Halogenation in Carrier-Protein-Independent Halogenase BesD and Hydroxylase-Evolved Halogenase

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(12), P. 9342 - 9353

Published: June 5, 2024

Despite extensive studies, how carrier-protein-independent BesD dictates the reaction toward thermodynamically unfavored halogenation is still elusive. Here, we investigated chlorination versus hydroxylation selectivity in both halogenase and hydroxylase-evolved Chi-14, employing MD simulations QM/MM calculations. In BesD, our calculations have shown that 2OG-assisted O2 activation affords axial Fe(IV)-oxo species responsible for substrate C–H activation. To facilitate following Cl-rebound reaction, nascent Fe(III)–OH has to undergo conformational isomerization equatorial one. This can remove steric effects between radical, thereby enhancing migration of radical Cl− ligand during Cl-rebound. Notably, hydrogen-bond interactions with second-sphere residue Asn are vital maintain unsaturated five-coordination shell Fe center. maintenance essential enabling transition from an orientation. Our results concordance existing experimental findings, underscoring pivotal influence iron coordination dynamics governing catalytic processes nonheme enzymes.

Language: Английский

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Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides

Angewandte Chemie International Edition, Journal Year: 2023, Volume and Issue: 62(42)

Published: Aug. 29, 2023

Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through 1,2-fluorine shift in electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, absence proton donor strong Fe-F bond be obtained as shown from calculations.

Language: Английский

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Substrate-Dependent Mechanism Switch in the Desaturation Reactions of the Mononuclear Nonheme Iron Enzyme PtlD

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(10), P. 7389 - 7401

Published: April 27, 2024

PtlD, a multifunctional mononuclear nonheme iron and α-ketoglutarate-dependent (NHFe/α-KG) dioxygenase involved in neopentalenoketolactone biosynthesis, catalyzes hydroxylation, desaturation, olefin epoxidation reactions. Investigating desaturation reactions of nonactivated carbons mediated by NHFe/α-KG enzymes is intriguing, especially for understanding the fate substrate radicals formed after hydrogen atom abstraction FeIV═O species. Here, we investigate reaction mechanism PtlD using two distinct substrates: neopentalenolactone D (1) features lone pair-containing oxygen adjacent to olefin-forming carbon atoms, whereas pentalenolactone (7) harbors carbonyl group at corresponding position. For 1, our isotope effect measurement protein mutagenesis experiments suggest formation carbocation intermediate, which subsequently deprotonated base generate products. Residue K288 serves as base, while Y113 likely stabilizes via π-cation interaction. 7, incorporation patterns indicated that intermediate also but unstable, leading hydroxylation due H2O quenching. Notably, 7's exhibits temperature-dependent large kinetic (KIE) an inverse solvent (SIE), suggesting tunneling contributes electron–proton transfer (EPT) process. These findings collectively reveal cases enzymes, where mechanisms switch with different substrates.

Language: Английский

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An Asynchronous, Concerted Mechanism for Cytochrome P450-Catalyzed Dehydrogenation: A Combined Deuterium Labeling and QM/MM Study

ACS Catalysis, Journal Year: 2025, Volume and Issue: 15(2), P. 1274 - 1286

Published: Jan. 7, 2025

Cytochromes P450 (P450s) commonly catalyze hydroxylation but can also be responsible for dehydrogenation reactions, important in drug metabolism and biosynthesis; the mechanism of latter transformation remains poorly understood. The well-characterized bacterial CYP199A4 catalyzes both p-alkylbenzoic acids thus provides an ideal model system which to investigate P450-catalyzed aliphatic dehydrogenation. Through use enantioselectively deuterated probes, metabolite analysis, protein crystallography, molecular dynamics simulations QM/MM (ONIOM) modeling, CYP199A4-catalyzed was found completely enantioselective postulated occur through asynchronous proton coupled electron transfer. No definitive evidence a cationic intermediate uncovered instead, positioning substrate key directing chemoselectivity reaction i.e., versus hydroxylation. This knowledge could exploited control other P450s helps explain common occurrence P450-desaturated metabolites alongside hydroxylated ones.

Language: Английский

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Defluorination of Fluorophenols by a Heme Dehaloperoxidase: Insights into the Defluorination Mechanism

ACS Catalysis, Journal Year: 2025, Volume and Issue: unknown, P. 3898 - 3912

Published: Feb. 19, 2025

Language: Английский

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