Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations

JACS Au, Journal Year: 2024, Volume and Issue: 4(4), P. 1591 - 1604

Published: April 9, 2024

P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (−)-naseseazine C (2) through intramolecular C–N bond formation and intermolecular C–C coupling. A thorough understanding its catalytic mechanism is crucial for engineering or design P450-catalyzed dimerization reactions. By employing MD simulations, QM/MM calculations, enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that most favorable pathway entails transfer a hydrogen atom N7–H Cpd I. Subsequently, there conformational change in substrate radical, shifting it Re-face Si-face N7 Substrate 1. The conformation 1 stabilized by protein environment π–π stacking interaction between indole ring heme porphyrin. subsequent C3–C6′ radical 2 occurs via attack mechanism. switch not only lowers barrier but also yields correct stereoselectivity observed experiments. In addition, evaluated reactivity ferric-superoxide species, showing reactive enough initiate abstraction NH group substrate. simulation provides comprehensive mechanistic insight into how enzyme precisely controls both cyclization current findings align with available experimental data, emphasizing pivotal role dynamics governing catalysis.

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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Unraveling the Catalytic Mechanism of Taxadiene-5α-hydroxylase from Crystallography and Computational Analyses

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(6), P. 3912 - 3925

Published: Feb. 26, 2024

Paclitaxel is a famous chemotherapeutic agent, but its microbial production poses long-standing challenge due to poor product selectivity. Taxadiene-5α-hydroxylase (CYP725A4) plays crucial role in the biosynthesis of paclitaxel, catalyzing oxidation taxadiene and iso-taxadiene. This process yields several products, including byproducts 5(12)-oxa-3(11)-cyclotaxane (OCT) 5(11)-oxa-3(11)-cyclotaxane (iso-OCT), as well target compound taxadien-5α-ol (T5OH). Despite extensive studies, molecular mechanism CYP725A4-catalyzed transformations still elusive, which could impede our understanding further engineering paclitaxel biosynthetic pathway. In this study, crystal structure CYP725A4 complex with elucidated. Through comprehensive computational analyses, catalytic mechanisms natural are deciphered. Our calculations indicate that affords zwitterion intermediate, can undergo two competing transformation routes. One involves formation epoxide, undergoes water-mediated rearrangement form T5OH product. alternative pathway, protonation oxygen intermediate facilitates subsequent hydride transfer carbon–oxygen coupling, resulting side products OCT/iso-OCT. Contrary taxadiene, hydroxylation at C5 iso-taxadiene directly T5OH. These crystallographic studies analyses have yielded valuable insights into laid foundation for CYP725A4.

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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Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments

Physical Chemistry Chemical Physics, Journal Year: 2024, Volume and Issue: 26(25), P. 17577 - 17587

Published: Jan. 1, 2024

Using molecular dynamics, machine learning, and density functional theory calculations we make predictions on engineered cytochrome P450 structures their product distributions.

Language: Английский

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Multiscale Study on the Intramolecular C–S Bond Formation Catalyzed by P450 Monooxygenase CxnD Involved in the Biosynthesis of Chuangxinmycin: The Critical Roles of Noncrystal Water Molecule and Conformational Change

Inorganic Chemistry, Journal Year: 2024, Volume and Issue: 63(9), P. 4086 - 4098

Published: Feb. 20, 2024

Cytochrome P450 monooxygenase CxnD catalyzes intramolecular C–S bond formation in the biosynthesis of chuangxinmycin, which is representative synthesis sulfur-containing natural heterocyclic compounds. The cyclization usually requires activation two reaction sites and a large conformational change; thus, illuminating its detailed mechanism remains challengeable. Here, pathway CxnD-catalyzed was clarified by series calculations, including Gaussian accelerated molecular dynamics simulations quantum mechanical-molecular mechanical calculations. Our results revealed that follows diradical coupling mechanism. first employs Cpd I to abstract hydrogen atom from imino group indole ring, then, resulted II further extracts another thiol side chain afford intermediate, noncrystal water molecule entering into active site after proved play an indispensable role. Moreover, intermediate cannot directly perform reaction. It should undergo changes leading proximity sites. flexibility enzyme substrate makes be successful.

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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Insights into Active Site Cysteine Residues in Mycobacterium tuberculosis Enzymes: Potential Targets for Anti-Tuberculosis Intervention

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3845 - 3845

Published: April 18, 2025

Cysteine, a semi-essential amino acid, is found in the active site of number vital enzymes bacterium Mycobacterium tuberculosis (Mtb) and particular those that relate to its survival, adaptability pathogenicity. Mtb causative agent tuberculosis, an infectious disease affects millions people globally. Common anti-tuberculosis targets are focused on immobilizing cysteine acid residue plays critical roles redox non-redox catalysis, modulation protein, enzyme activity, protein structure folding, metal coordination, posttranslational modifications newly synthesized proteins. This review examines five contain considered as key for drugs, namely alkyl hydroperoxide reductase (AhpC), dihydrolipoamide dehydrogenase (Lpd), aldehyde (ALDH), methionine aminopeptidase (MetAP) cytochromes P450. AhpC Lpd protect against oxidative nitrosative stress, whereas neutralizes peroxide/peroxynitrite substrates with two residues. ALDH detoxifies aldehydes, using nucleophilic form oxyanion thiohemiacetal intermediate, MtMetAP’s essential substrate recognition. The P450s metabolize various endogenous exogenous compounds. Targeting these residues could disrupt functions, presenting promising avenue developing anti-mycobacterial agents.

Language: Английский

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Mechanism of the Oxidative Ring-Closure Reaction during Gliotoxin Biosynthesis by Cytochrome P450 GliF

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(16), P. 8567 - 8567

Published: Aug. 6, 2024

During gliotoxin biosynthesis in fungi, the cytochrome P450 GliF enzyme catalyzes an unusual C-N ring-closure step while also aromatic ring is hydroxylated same reaction cycle, which may have relevance to drug synthesis reactions biotechnology. However, as details of mechanism are still controversial, no applications been developed yet. To resolve and gain insight into steps leading ring-closure, we ran a combination molecular dynamics density functional theory calculations on structure reactivity tested range possible mechanisms, pathways models. The show that, rather than hydrogen atom transfer from substrate Compound I, initial proton transition state followed by fast electron en route radical intermediate, hence non-synchronous abstraction takes place. intermediate then reacts OH rebound form biradical through between centers, gives products. Interestingly, energetics mechanisms appear little affected addition polar groups model predict that can be catalyzed other isozymes bind substrate. Alternative pathways, such pathway starting with electrophilic attack arene epoxide, high energy ruled out.

Language: Английский

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Molecular Basis for the P450-Catalyzed sp³ C–N Glycosidic Bond Formation in Staurosporine Biosynthesis

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(19), P. 14274 - 14284

Published: Sept. 12, 2024

Language: Английский

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