Plant-microorganism combined remediation of polychlorinated naphthalenes contaminated soils based on molecular directed transformation and Taguchi experimental design-assisted dynamics simulation

Gu, Wenwen; Zhao, Yuanyuan; Li, Qing; Liu, Yu

doi:10.1016/j.jhazmat.2020.122753

Cited by 34 publications

(16 citation statements)

References 38 publications

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“…Previous studies [ 53 ] have shown that the smaller the absolute value of the binding energy, the weaker the affinity of the molecule to bind to the receptor protein; namely, the molecule exhibits lower anti-oestrogenic activity. As explained in Table 7 , under the same external conditions of the 7 types of PCB-44 derivatives, only the absolute value of the binding energy of PCB-44-6 and PCB-44-7 to the oestrogen receptor showed a decreasing trend; the reduction rates were 13.77% to 33.66% and 19.99% to 31.68%, respectively, indicating that the anti-oestrogenic activity of these two molecules was expressed to a much lesser extent than the standard molecule PCB-44.…”

Section: Resultsmentioning

confidence: 99%

Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

Zhang

Chu

et al. 2021

IJERPH

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The aim of this paper is to explore the mechanism of the change in oestrogenic activity of PCBs molecules before and after modification by designing new PCBs derivatives in combination with molecular docking techniques through the constructed model of oestrogenic activity of PCBs molecules. We found that the weakened hydrophobic interaction between the hydrophobic amino acid residues and hydrophobic substituents at the binding site of PCB derivatives and human oestrogen receptor alpha (hERα) was the main reason for the weakened binding force and reduced anti-oestrogenic activity. It was consistent with the information that the hydrophobic field displayed by the 3D contour maps in the constructed oestrogen activity CoMSIA model was one of the main influencing force fields. The hydrophobic interaction between PCB derivatives and oestrogen-active receptors was negatively correlated with the average distance between hydrophobic substituents and hydrophobic amino acid residues at the hERα-binding site, and positively correlated with the number of hydrophobic amino acid residues. In other words, the smaller the average distance between the hydrophobic amino acid residues at the binding sites between the two and the more the number of them, and the stronger the oestrogen activity expression degree of PCBS derivative molecules. Therefore, hydrophobic interactions between PCB derivatives and the oestrogen receptor can be reduced by altering the microenvironmental conditions in humans. This reduces the ability of PCB derivatives to bind to the oestrogen receptor and can effectively modulate the risk of residual PCB derivatives to produce oestrogenic activity in humans.

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Section: Resultsmentioning

confidence: 99%

Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

Zhang

Chu

et al. 2021

IJERPH

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“…A catalyst enhances the activity of the degradation enzymes. The concentration of resveratrol, a catalyst, at 150 mg/L promotes the degradation of pollutants by the degradation enzymes, while at 200 mg/L, the degradation slows down [19]. Therefore, in the present study, the lower (150 mg/L) and higher (200 mg/L) values of resveratrol concentration were selected as the two levels of the factor catalyst.…”

Section: Determination Of the External Environment Conditions To Promote The Plant-microbe Combined Remediation Using Taguchi Experimentamentioning

confidence: 99%

“…The magnitude of the binding energy of the PCBs for the plant absorption enzyme (6QIM), plant degradation enzyme (3GZX), and microbial mineralization enzyme (1B85) represents the strength of binding of the PCB pollutants to these three enzymes [19]. In the present study, ten multifunctional plant degradation enzyme) were subjected to molecular dynamics simulations performed in the Gromacs software using the Dell PowerEdge R7525 server.…”

Section: Suitable External Conditions For Promoting Plant-microbe Combined Remediation Of Pcb-contaminated Soilmentioning

confidence: 99%

“…Biphenyl dioxygenase was modified to enhance its ability to degrade contaminants in the plant along with enabling its secretion from the root system into the soil environment to promote contaminant degradation in the soil as well [18]. The main processes involved in the plant-microbe combined remediation of organic soil contamination are plant absorption, plant degradation, and microbial mineralization [19]. The water channel enzyme in the plant roots mediates the transport of PCBs within the plant and consequently influences the ability of the plant to absorb PCBs [20].…”

Section: Introductionmentioning

confidence: 99%

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Enhanced plant-microbe remediation of PCBs in soil using enzyme modification technique combined with molecular docking and molecular dynamics

Li¹,

He²,

Liu

2021

Biochemical Journal

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The study on the enhanced mechanisms of the enzymes involved in plant absorption, plant degradation, and microbial mineralization in the remediation of soils contaminated with polychlorinated biphenyls (PCBs) is of great significance for the application of plant-microbe combined remediation technique in PCB-contaminated soils. The present study first used a combination of molecular docking and molecular dynamics methods to calculate the effects of the plant absorption enzyme, plant degradation enzyme, and microbial mineralization enzyme on the PCBs in the soil environment. A multifunctional plant degradation enzyme was constructed with three functional roles of absorption, degradation, and mineralization using amino acid sequence recombination and site-directed mutagenesis to modify the template of plant degradation enzyme. Finally, using the Taguchi experimental design-assisted molecular dynamics simulation method, the suitable external environmental conditions of plant-microbe combined remediation of the PCB-contaminated soil were determined. In total, six multifunctional plant degradation enzymes were designed, which exhibited a significantly improved efficiency of PCB degradation. In comparison to the complex of plant absorption enzyme, plant degradation enzyme, and microorganism mineralization enzyme (6QIM-3GZX-1B85), the six multifunctional plant degradation enzymes exhibited significantly higher efficiency (2.10–2.38 times) in degrading the PCBs, with a maximum of 2.69 times under suitable external environmental conditions.

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“…The source modification based on molecular modification and the process control based on molecular dynamics are the focus and hotspot of the collaborative degradation of pollutants by plants and microorganisms. Gu et al [ 18 ] explored the types of polychlorinated naphthalene (PCN) contaminated soil and determined the practicable scheme of combined remediation using an integrated method of genetic engineering and environmental remediation technology. Gu et al [ 19 ] designed thirteen new proteins/enzymes, which significantly promoted the absorption, degradation and mineralization of the plant-microorganism combined remediation on PCN-contaminated soil.…”

Section: Introductionmentioning

confidence: 99%

Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method

Xiao

et al. 2021

Molecules

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In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants.

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Plant-microorganism combined remediation of polychlorinated naphthalenes contaminated soils based on molecular directed transformation and Taguchi experimental design-assisted dynamics simulation

Cited by 34 publications

References 38 publications

Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

Enhanced plant-microbe remediation of PCBs in soil using enzyme modification technique combined with molecular docking and molecular dynamics

Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method

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