A computational study of the dechlorination of β-hexachlorocyclohexane (β-HCH) catalyzed by the haloalkane dehalogenase LinB

Manna, Rabindra Nath; Dybała-Defratyka, Agnieszka

doi:10.1016/j.abb.2014.07.028

Cited by 16 publications

(10 citation statements)

References 34 publications

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“…The other tool is based on the theoretical KIEs prediction. The theoretical insight from some of us, based on full enzymatic model [15] allowed to characterize mechanistic pathways viable for the transformation of γ-HCH by LinA and eventually led to the carbon, chlorine, and hydrogen KIEs prediction [16,17]. Some discrepancies, such as much larger predicted hydrogen KIE, have been found in the data coming from these two approaches, thus opening room for debate.…”

Section: Introductionmentioning

confidence: 99%

Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?

Kannath

Adamczyk

et al. 2019

IJMS

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Hexachlorocyclohexane (HCH) isomers constitute a group of persistent organic pollutants. Their mass production and treatment have led to a global environmental problem that continues to this day. The characterization of modes of degradation of HCH by isotope fractionation is a current challenge. Multi isotope fractionation analysis provides a concept to characterize the nature of enzymatic and chemical transformation reactions. The understanding of the kinetic isotope effects (KIE) on bond cleavage reaction contributes to analyses of the mechanism of chemical and enzymatic reactions. Herein, carbon, chlorine, and hydrogen kinetic isotope effects are measured and predicted for the dehydrochlorination reaction of γ-HCH promoted by the hydroxyl ion in aqueous solution. Quantum mechanical (QM) microsolvation with an implicit solvation model and path integral formalism in combination with free-energy perturbation and umbrella sampling (PI-FEP/UM) and quantum mechanical/molecular mechanical QM/MM potentials for including solvent effects as well as calculating isotope effects are used and analyzed with respect to their performance in reproducing measured values. Reaction characterization is discussed based on the magnitudes of obtained isotope effects. The comparative analysis between the chemical dehydrochlorination of γ-HCH in aqueous media and catalyzed reaction by dehydrochlorinase, LinA is presented and discussed. Based on the values of isotope effects, these two processes seem to occur via the same net mechanism.

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Section: Introductionmentioning

confidence: 99%

Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?

Kannath

Adamczyk

et al. 2019

IJMS

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“…Minimization was performed as previously described. 39 Then, the systems were heated from 100 to 300 K during 300 ps using the NVT ensemble with a time step of 1 fs and equilibrated using the NPT ensemble. Three replicas of classical MM MD simulations were performed for each complex.…”

Section: Methodsmentioning

confidence: 99%

“…The resulting systems consisted of approximately 51 000 atoms. Minimization was performed as previously described . Then, the systems were heated from 100 to 300 K during 300 ps using the NVT ensemble with a time step of 1 fs and equilibrated using the NPT ensemble.…”

Section: Methodsmentioning

confidence: 99%

Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA

et al. 2020

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Herein we present the results of an in-depth simulation study of LinA and its two variants. In our analysis, we combined the exploration of protein conformational dynamics with and without bound substrates (hexachlorocyclohexane (HCH) isomers) performed using molecular dynamics simulation followed by the extraction of the most frequently visited conformations and their characteristics with a detailed description of the interactions taking place in the active site between the respective HCH molecule and the first shell residues by using symmetry-adapted perturbation theory (SAPT) calculations. A detailed investigation of the conformational space of LinA substates has been accompanied by description of enzymatic catalytic steps carried out using a hybrid quantum mechanics/molecular mechanics (QM/MM) potential along with the computation of the potential of mean force (PMF) to estimate the free energy barriers for the studied transformations: dehydrochlorination of γ-, (−)-α-, and (+)-α-HCH by LinA-type I and -type II variants. The applied combination of computational techniques allowed us not only to characterize two LinA types but also to point to the most important differences between them and link their features to catalytic efficiency each of them possesses toward the respective ligand. More importantly it has been demonstrated that type I protein is more mobile, its active site has a larger volume, and the dehydrochlorination products are stabilized more strongly than in the case of type II enzyme, due to differences in the residues present in the active sites. Additionally, interaction energy calculations revealed very interesting patterns not predicted before but having the potential to be utilized in any attempts of improving LinA catalytic efficiency. On the basis of all these observations, LinA-type I protein seems to be more preorganized for the dehydrochlorination reaction it catalyzes than the type II variant.

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“…Initial structure energy minimization was performed as previously described. 21 Next, the systems were heated from 100 to 300 K during 300 ps using the NVT ensemble with a time step of 1 fs and equilibrated using the NPT ensemble. The production runs were performed using the NPT ensemble with a time step of 1 fs and the length of the simulations was equal to 100 ns or 60 ns in the case of LinB and DhaA complexes, respectively, which provided stable complexes according to RMSD and system density (data not shown).…”

Section: 𝑙𝑛 (mentioning

confidence: 99%

The Fate of Various Halogenated Organics in the Active Sites of LinB and DhaA Dehalogenases – A Combined Experimental and Computational Study

Sowińska

Krzemińska

Englman

et al. 2022

Preprint

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LinB and DhaA are well-known haloalkane dehalogenases (HLDs) capable of converting a plethora of halogenated alkanes, also those considered persistent pollutants. One way of studying the nature and efficiency of these important enzymes is to measure the kinetic isotope effect (KIE) on the metabolized reaction, in particular leaving group (either chloride or bromide) KIE. Although the general mechanism via which these two dehalogenating enzymes operate has been already studied and described, the isotope effects data providing information on the mechanistic details, especially Br KIE are scarce. In this work we aimed at gaining insights into the enzymatic dehalogenation of dibromo- and bromo-chloro- ethanes by LinB and DhaA, by combining experimental and computational methods. A model developed this way has been subsequently extended to dihalopropanes. Using the predicted free energy surface of the reaction catalyzed by HLD and kinetic isotope effects based on QM/MM calculations it has been demonstrated that with respect to the magnitudes of Br KIE conversion of 1,2-dibromoethane, 1-bromo-2-chloroethane or 1,2-dibromopropane, and therefore also other propanes should not differ. In the case of C KIE the scenario might be different as depending on the carbon position adjacent to the eliminated bromine substituent one can observe either larger or smaller isotope effect (~1.06 or 1.04 for the primary and secondary position, respectively). By predicting halogen binding isotope effects (BIEs) as well as computing interaction energy for each HLD-ligand complex the binding event preceding a chemical change in the active site has been characterized. The magnitude and direction of BIEs are discussed thoroughly by invoking the dynamics and the architecture of each active site, the strength of interactions with the first shell residues, and pointing to the dominating forces determining the binding of each of the studied ligands.

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A computational study of the dechlorination of β-hexachlorocyclohexane (β-HCH) catalyzed by the haloalkane dehalogenase LinB

Cited by 16 publications

References 34 publications

Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?

Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?

Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA

The Fate of Various Halogenated Organics in the Active Sites of LinB and DhaA Dehalogenases – A Combined Experimental and Computational Study

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