Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

Journal of the American Chemical Society, Год журнала: 2024, Номер 146(24), С. 16670 - 16680

Опубликована: Июнь 7, 2024

To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory of protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field entire active site is tracked through dynamics, clustered using affinity propagation algorithm, subjected principal component analysis. This analysis reveals notable changes with DE, where distinct topologies influence transition state energetics mechanism. A chemically meaningful emerges takes lead facilitates crossing barrier transfer. Our findings underscore intrinsic dynamic's on enzyme function, ability switch mechanisms within same protein, crucial role design.

Язык: Английский

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

Chemistry - A European Journal, Год журнала: 2024, Номер 30(60)

Опубликована: Авг. 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

Язык: Английский

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

Physical Chemistry Chemical Physics, Год журнала: 2024, Номер 26(25), С. 17577 - 17587

Опубликована: Янв. 1, 2024

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

Язык: Английский

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

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(16), С. 8567 - 8567

Опубликована: Авг. 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.

Язык: Английский

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CO2 Adsorption in Natural Deep Eutectic Solvents: Insights from Quantum Mechanics and Molecular Dynamics

Physical Chemistry Chemical Physics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

CO2 capture is an important process for mitigating emissions in the atmosphere. Recently, ionic liquids have been identified as possible systems processes. Major drawbacks of such are mostly high cost synthesis and poor biodegradability. Natural deep eutectic solvents, a class solvents using materials natural origin, developed, which compared to low-cost more environmentally benign. However, very little known on details at molecular level that govern adsorption these what limits features. Elucidating aspects would represent step forward design implementation promising emissions. Herein, we report computational study mechanisms characteristics containing arginine/glycerol mixtures. We establish hydrogen bonding effects drive carbon dioxide composed L-arginine glycerol dynamics quantum mechanics simulations. Our findings indicate that, although both arginine contain multiple atoms capable acting bond donors acceptors, primarily functions acceptor while serves donor most interactions. Furthermore, compounds contribute participate binding. This provides valuable insights into behaviour enhances our understanding from perspective

Язык: Английский

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easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms

Journal of Chemical Theory and Computation, Год журнала: 2025, Номер unknown

Опубликована: Фев. 6, 2025

The dynamics of metal centers are challenging to describe due the vast variety ligands, metals, and coordination spheres, hampering existence general databases transferable force field parameters for classical molecular simulations. Here, we present easyPARM, a Python-based tool that can calculate wide range complexes from routine frequency calculations with electronic structure methods. approach is based on unique labeling strategy, in which each ligand atom coordinates receives type. This design prevents parameter shortage, duplication, necessity post-process output files, even very complicated whose parametrization process remain automatic. program requires Cartesian Hessian matrix, geometry xyz file, atomic charges provide reliable force-field extensively benchmarked against density functional theory both gas condensed phases. procedure allows description at low computational cost an accuracy as good quality matrix obtained by quantum chemistry easyPARM v2.00 reads vibrational frequencies Gaussian (version 09 or 16) ORCA 5 6) format provides refined Amber format. These be directly used NAMD engines converted other formats. available free charge GitHub platform (https://github.com/Abdelazim-Abdelgawwad/easyPARM.git).

Язык: Английский

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

ACS Catalysis, Год журнала: 2025, Номер unknown, С. 3898 - 3912

Опубликована: Фев. 19, 2025

Язык: Английский

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Cluster model study of the mechanism and origins of enantio- and chemoselectivity in non-heme iron enzyme-catalyzed C–H azidation

RSC Advances, Год журнала: 2025, Номер 15(12), С. 8931 - 8937

Опубликована: Янв. 1, 2025

Computational insights reveal the origin of enantio- and chemoselectivity in non-heme iron enzyme-catalyzed C–H azidation.

Язык: Английский

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Debate of Nucleophilic versus Electrophilic Oxidative Aldehyde Deformylation by Mononuclear Nonheme Iron(III)-Peroxo and Iron(IV)-Oxo Complexes

Journal of the American Chemical Society, Год журнала: 2025, Номер unknown

Опубликована: Апрель 28, 2025

High-valent iron(IV)-oxo species are fleeting intermediates that perform vital reactions in enzymatic catalysis. In contrast, heme and nonheme iron(III)-peroxo usually act as nucleophiles converted to high-valent iron-oxo for electrophilic oxidation reactions. Herein, we report a study on aldehyde deformylation of 2-phenylpropionaldehyde (2-PPA) its derivatives by complexes bearing tetramethylated cyclam (TMC) analogues, including [FeIII(O2)(12-TMC)]+ (1), [FeIII(O2)(13-TMC)]+ (2), [FeIII(O2)(14-TMC)]+ (3). Reactivity studies employing deuterated substrates, such α-[D1]-2-phenylpropionaldehyde aldehyde-[D]-2-phenylpropionaldehyde, demonstrate 2-PPA the occurs via abstraction stronger C-H atom, rather than expected nucleophilic attack or weaker α-C-H atom Interestingly, preference is retained during complexes, i.e., [FeIV(O)(13-TMC)]2+ (4) [FeIV(O)(N4Py)]2+ (5). DFT calculations reproduce experimental trends reactivity reveal peroxide O-O bond cleaved form an iron(III)-dioxyl conducts abstraction; this chemoselectivity achieved through stabilizing noncovalent interactions between oxidants aromatic ring substrate positions close proximity FeIII-O2/FeIV═O cores. These new theoretical findings together with previous demonstrations ability 1-3 hydrogen transfer, oxygen cis-dihydroxylation highlight cores not inherently can have more important functions chemical biological reactions, acting transient en route metal-oxo intermediates.

Язык: Английский

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Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code

ACS Catalysis, Год журнала: 2024, Номер 14(15), С. 11584 - 11590

Опубликована: Июль 20, 2024

The ability to introduce noncanonical amino acids as axial ligands in heme enzymes has provided a powerful experimental tool for studying the structure and reactivity of their FeIV═O ("ferryl") intermediates. Here, we show that similar approach can be used perturb conserved Fe coordination environment 2-oxoglutarate (2OG) dependent oxygenases, versatile class employ highly-reactive ferryl intermediates mediate challenging C–H functionalizations. Replacement one cis-disposed histidine oxygenase VioC with less electron donating Nδ-methyl-histidine (MeHis) preserves both catalytic function reaction selectivity. Significantly, key intermediate responsible activation accumulated wildtype modified protein. In contrast enzymes, where metal-oxo is extremely sensitive nature proximal ligand, rates observed large kinetic isotope effects are only minimally affected by ligand replacement VioC. This study showcases modulating sphere nonheme iron will enhance our understanding factors governing divergent activities.

Язык: Английский

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