Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons

Li, Xingchun; Chu, Zhenhua; Du, Xianyuan; Qiu, Youli; Liu, Yu

doi:10.1039/c8ra10663k

Cited by 15 publications

(8 citation statements)

References 49 publications

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“…The molecular validation stage of docking (re-docking) was carried out to determine active-site binding through interactions between the native ligand and the receptor on the target protein. 45,46 The validation result showed that the native ligand had a good pose with the RMSD value of 0.93Å, which meets the criterion (Table 3). A smaller RMSD that is closer to $0Å represents increasingly accurate coordinates.…”

Section: Geometry Optimization Of Nordentatin Derivativesmentioning

confidence: 79%

In silicoapproach: biological prediction of nordentatin derivatives as anticancer agent inhibitors in the cAMP pathway

et al. 2020

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Section: Geometry Optimization Of Nordentatin Derivativesmentioning

confidence: 79%

In silicoapproach: biological prediction of nordentatin derivatives as anticancer agent inhibitors in the cAMP pathway

et al. 2020

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“…(bin5) by matching its 16S rRNA gene with a SIP identified OTU sequence. It is worth noting that a number of naphthalene/PAH dioxygenases, the key metabolic enzyme that carry out the first step in the aerobic degradation of NAP/PAHs (Li et al ., 2019c; Miyazawa et al ., 2020) were present, further confirming its involvement in the in situ degradation of NAP and confirming its important role in PAHs remediation. The results of naphthalene/PAH dioxygenase gene quantitation further supported the above conclusion.…”

Section: Discussionmentioning

confidence: 99%

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

Cai

Guan

et al. 2021

Environmental Microbiology

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Summary Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable‐isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the 13C‐DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non‐culturable microorganisms by combining both SIP and metagenome binning.

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“…The hydrophobic effect of amino acids is considered to be the most important factor in the structure and stability of proteins, and the relative hydrophilicity/hydrophobicity of amino acids has a significant effect on protein-receptor binding and other intermolecular bio-cognitive processes [23]. Studies have shown that replacing hydrophilic amino acid residues that reside in binding sites for hydrophobic molecules with hydrophobic amino acid residues can improve the affinity between target molecules and degrading enzymes [24]. Therefore, by replacing the hydrophobic amino acid residues at the binding site of each degrading enzyme with hydrophilic amino acid residues, the affinity between the degrading enzymes and the target fluoroquinolone molecules can be increased, and the degradation ability of fluoroquinolones by the degrading enzymes can be further improved.…”

Section: Determination Of Key Amino Acid Residues Of Fluoroquinolone mentioning

confidence: 99%

Molecular Modification of Fluoroquinolone-Biodegrading Enzymes Based on Molecular Docking and Homology Modelling

Sicheng

Sun

Cui

et al. 2019

IJERPH

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To improve the biodegradation efficiency of fluoroquinolone antibiotics during sewage treatment, fluoroquinolone aerobic, anaerobic and facultative degrading enzymes for fluoroquinolone degradation were modified by molecular docking and homology modelling. First, amino acid residues of the binding sites of degrading enzymes for the target fluoroquinolones ciprofloxacin (CIP), norfloxacin (NOR) and ofloxacin (OFL) were analysed by the molecular docking method. The hydrophobic amino acid residues within 5 Å of the target fluoroquinolone molecules were selected as the modification sites. The hydrophobic amino acid residues at the modified sites were replaced by the hydrophilic amino acid residues, and 150 amino acid sequence modification schemes of the degrading enzymes were designed. Subsequently, a reconstruction scheme of the degrading enzyme amino acid sequence reconstruction scheme was submitted to the SWISS-MODEL server and a selected homology modelling method was used to build a new structure of the degrading enzyme. At the same time, the binding affinities between the novel degrading enzymes and the target fluoroquinolones (represented by the docking scoring function) were evaluated by the molecular docking method. It was found that the novel enzymes can simultaneously improve the binding affinities for the three target fluoroquinolones, and the degradation ability of the six modification schemes was increased by more than 50% at the same time. Among the novel enzymes, the affinity effect of the novel anaerobic enzyme (6-1) with CIP, NOR and OFL was significantly increased, with increases of 129.24%, 165.06% and 169.59%, respectively, followed by the facultative enzyme and aerobic enzyme. In addition, the designed degrading enzymes had certain selectivity for the degradation of the target quinolone. Among the novel enzymes, the binding affinities of the novel anaerobic enzyme (6-3) and CIP, the novel aerobic enzyme (3-6) and NOR, and the novel facultative enzyme (13-6) and OFL were increased by 149.71%, 178.57% and 297.12% respectively. Calculations using the Gaussian09 software revealed that the degradation reaction barrier of the novel degrading enzyme (7-1) and CIP NOR and OFL decreased by 37.65 kcal·mol−1, 6.28 kcal·mol−1 and 6.28 kcal·mol−1, respectively, which would result in efficient degradation of the target fluoroquinolone molecules. By analysing the binding affinity of the degrading enzymes before and after the modification with methanol, it was further speculated that the degradation effect of the modified aerobic degrading enzymes on organic matter was lower than that before the modification, and the increase or decrease in the degradation effect was less than 10%. The mechanism analysis found that the interaction between the modified amino acid residues of the degrading enzymes and the fluoroquinolone molecules increased. The average distance between the amino acid residues and the fluoroquinolone molecules represented a comprehensive affinity effect, and its value was positively correlated with the degradation effect of the novel degrading enzymes.

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Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons

Abstract: To promote the biodegradation of aromatic hydrocarbons in petroleum-contaminated soils, naphthalene dioxygenase (NDO), which is the key metabolic enzyme that degrades aromatic hydrocarbons, was modified using molecular docking and homology modelling.

Cited by 15 publications

References 49 publications

In silicoapproach: biological prediction of nordentatin derivatives as anticancer agent inhibitors in the cAMP pathway

In silicoapproach: biological prediction of nordentatin derivatives as anticancer agent inhibitors in the cAMP pathway

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

Molecular Modification of Fluoroquinolone-Biodegrading Enzymes Based on Molecular Docking and Homology Modelling

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