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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Computational Insights into the Non-Heme Diiron Alkane Monooxygenase Enzyme AlkB: Electronic Structures, Dioxygen Activation, and Hydroxylation Mechanism of Liquid Alkanes

Inorganic Chemistry, Journal Year: 2024, Volume and Issue: 63(37), P. 17056 - 17066

Published: Sept. 6, 2024

Alkane monooxygenase (AlkB) is a membrane-spanning metalloenzyme that catalyzes the terminal hydroxylation of straight-chain alkanes involved in microbially mediated degradation liquid alkanes. According to cryoEM structures, AlkB features unique multihistidine ligand coordination environment with long Fe-Fe distance its active center. Up now, how employs diiron center activate dioxygen and which species responsible for triggering are still elusive. In this work, we constructed computational models performed quantum mechanics/molecular mechanics (QM/MM) calculations illuminate electronic characteristics carries out hydroxylation. Our revealed spin-spin interaction between two irons rather weak. The may ligate either Fe1 or Fe2 atom prefers act as linker increase irons, facilitating cleavage generate highly reactive Fe(IV)═O. Thus, Fe(IV)═O trigger hydrogen abstraction. addition, previously suggested mechanism uses both Fe-coordinated water perform was calculated be unlikely. Besides, our results indicate cannot use directly

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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The structural and functional investigation into an unusual nitrile synthase

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 16, 2023

Abstract The biosynthesis of neurotoxin aetokthonotoxin (AETX) that features a unique structure pentabrominated biindole nitrile involves first-of-its-kind synthase termed AetD, an enzyme shares very low sequence identity to known structures and catalyzes unprecedented mechanism. In this study, we resolve the crystal AetD in complex with substrate 5,7-di-Br-L-Trp. adopts heme oxygenase like fold forms hydrophobic cavity within helical bundle accommodate indole moiety. A diiron cluster comprising two irons serves as catalytic center binds carboxyl O amino N substrate. Notably, demonstrate AetD-catalyzed reaction is independent bromination also solved 5-Br-L-Trp L-Trp. Altogether, present study reveals substrate-binding pattern validates cluster-comprising active which should provide important basis support mechanistic investigations into class synthase.

Language: Английский

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Computational Exploration of Enzyme Promiscuity: Mechanisms of O₂ and NO Reduction Activities of the Desulfovibrio gigas Flavodiiron Protein

ACS Catalysis, Journal Year: 2023, Volume and Issue: 13(24), P. 16318 - 16336

Published: Dec. 6, 2023

Flavodiiron proteins possess reductive scavenging properties toward dioxygen and/or nitric oxide in various microorganisms. Among them, the Desulfovibrio gigas flavodiiron protein (Dg_ROO) was reported to be capable of catalyzing both O2 and NO reduction reactions, though it displays higher activity reducing than NO. In this study, quantum chemical methodology is employed investigate intricate mechanisms underlying these versatile reactions catalyzed by Dg_ROO. The calculations demonstrated that flavin mononucleotide (FMN) cofactor plays a pivotal role cleavage O–O bonds during four-electron providing two protons electrons reaction site. bond could take place from different metal oxidation states, namely, Fe(II)Fe(II)–HOOH or Fe(II)Fe(III)–OOH, depending on rate for electron/proton transfer FMN diiron Subsequently, water molecules are generated through consecutive outer-sphere proton-coupled electron steps. suggested commence with generation bridging hyponitrite (N–N) via direct coupling molecules. A directional rotation species then yields an N–O dianion, which triggers generates N2O. site transpires after forming N2O product. Further in-depth analyses comparisons highlight crucial played key second-shell tyrosine residues promiscuity selectivity These findings offer valuable insights into functional diversity other (FDPs) may contribute better understanding their catalytic properties.

Language: Английский

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N-Hydroxylation and Hydrolysis by the DnfA/B/C Multienzyme System Involved in the Aerobic N₂ Formation Process

ACS Catalysis, Journal Year: 2023, Volume and Issue: 13(18), P. 11963 - 11976

Published: Aug. 28, 2023

Nitrogen (N) loss is an important factor in N balance ecosystems. Traditionally, ammonia was considered as the sole initial oxidizing substrate for removal, and oxidation has long been a traditional cycle topic. Dirammox distinctive nitrogen removal mechanism it proceeds via direct aerobic conversion of to N2 single bacterium, yet its biocatalytic reactions enzymatic machinery remained elusive. By isotope tracing biochemical experiments, here we elucidate underlying N-oxidation [termed dinitrogen-forming (DNF) pathway], which have little precedent enzymology or organic amine utilization, expanding catalytic capabilities nonheme di-iron N-oxygenases (DnfA) glutamine amidotransferases (GATase I, DnfC) include formation. In DNF pathway, amide initially hydroxylated by DnfA with assistance DnfB l-glutamic acidγ-hydroxamate (l-GlnγHXM), then hydrolyzed DnfC hydroxylamine, turn oxidized DnfA/B N2. Further analyses revealed wide distribution N-hydroxylation–hydrolysis strategy dinitrogen generation various heterotrophic bacteria. These findings not only highlight unusual N-hydroxylation involved N–3-oxidation but also provide insights into universality pathway valuable biocatalysts removal.

Language: Английский

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Mechanistic Insights into the N‐Hydroxylations Catalyzed by the Binuclear Iron Domain of SznF Enzyme: Key Piece in the Synthesis of Streptozotocin

Chemistry - A European Journal, Journal Year: 2024, Volume and Issue: 30(16)

Published: Jan. 12, 2024

SznF, a member of the emerging family heme-oxygenase-like (HO-like) di-iron oxidases and oxygenases, employs two distinct domains to catalyze conversion N

Language: Английский

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Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non‐Heme Fe(II)/2‐Oxoglutarate‐Dependent Aspartyl Hydroxylase AspH

ChemPhysChem, Journal Year: 2024, Volume and Issue: 25(18)

Published: June 6, 2024

Abstract Aspartyl/asparaginyl hydroxylase (AspH) catalyzes the post‐translational hydroxylations of vital human proteins, playing an essential role in maintaining their biological functions. Single‐point mutations Second Coordination Sphere (SCS) and long‐range (LR) residues AspH have been linked to pathological conditions such as ophthalmologic condition Traboulsi syndrome chronic kidney disease (CKD). Although clinical impacts these are established, there is a critical knowledge gap regarding specific atomistic effects on catalytic mechanism AspH. In this study, we report integrated computational investigations potential mechanistic implications four mutant forms with importance: R735W, R735Q, R688Q, G434V. All exhibited altered binding interactions co‐substrate 2‐oxoglutarate (2OG) main substrate ferric‐superoxo ferryl complexes, which for catalysis, compared wild‐type (WT). Importantly, strongly influence energetics frontier molecular orbitals (FMOs) and, thereby, activation energies hydrogen atom transfer (HAT) step WT Insights from our study can contribute enzyme engineering development selective modulators mutants AspH, ultimately aiding treating cancers, CKD.

Language: Английский

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DFT mechanistic study of biomimetic diiron complex catalyzed dehydrogenation: Unexpected Fe(III)Fe(III)-1,1-μ-hydroperoxy active species for hydride abstraction

Journal of Inorganic Biochemistry, Journal Year: 2023, Volume and Issue: 251, P. 112426 - 112426

Published: Nov. 10, 2023

Language: Английский

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Recent Insights into the Reaction Mechanisms of Non‐Heme Diiron Enzymes Containing Oxoiron(IV) Complexes

ChemBioChem, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 7, 2024

Oxoiron(IV) complexes are key intermediates in the catalytic reactions of some non-heme diiron enzymes. These enzymes, across various subfamilies, activate dioxygen to generate high-valent diiron-oxo species, which, turn, drive activation substrates and mediate a variety challenging oxidative transformations. In this review, we summarize structures, formation mechanisms, functions eight representative enzymes (sMMO, RNR, ToMO, MIOX, PhnZ, SCD1, AlkB, SznF) spanning five subfamilies. We also categorize analyze structural mechanistic differences among these

Language: Английский

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