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Research Article

Exploring the potential of Halalkalibacterium halodurans laccase for endosulfan and chlorophacinone degradation: insights from molecular docking and molecular dynamics simulations

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Received 27 Mar 2023, Accepted 06 Nov 2023, Published online: 21 Nov 2023
 

Abstract

Pesticides are widely used in agriculture but at the same time, a majority of them are known to cause serious harm to health and the environment. In the recent past, laccases have been reported as key enzymes having the ability to degrade pollutants by converting them into less toxic forms. In this investigation, laccase from polyextremophilic bacterium Halalkalibacterium halodurans C-125 was analyzed for its structural, physicochemical, and functional characterization using in silico approaches. The 3D model of the said enzyme is unknown; therefore, the model was generated by template-independent modeling using ROBETTA, I-TASSER, and Alphafold server. The best-generated model from Alphafold with a confidence of 0.95 was validated from ERRAT and Verify 3D scores of 89.95 and 91.80%, respectively. The Ramachandran plot generated using the PROCHECK server further predicted the accuracy of the model with 93.7% and 5.9% of residues present in most favored and additional allowed regions of the plot respectively. The active sites, ion binding sites, and subcellular localization of laccase were also predicted. The generated model was docked with 121 pollutants (pesticides, insecticides, herbicides, fungicides, and rodenticides) for its degradation potential towards these pollutants. Two ligands chlorophacinone (based on the highest binding energy) and endosulfan (based on agricultural uses) were selected for molecular dynamic simulation studies. Endosulfan as a pesticide is banned but in some countries governments allow its use for special purposes which need serious consideration on developing bioremediation approaches for endosulfan degradation. MD simulation studies revealed that both chlorophacinone and endosulfan form hydrogen bonds and hydrophobic bonds with the active site of laccase and chlorophacinone-laccase complex were more stable in comparison to endosulfan. The present investigation provides insight into the structural features of laccase and its potential for the degradation of pesticides which can be further validated by experimental data.

Communicated by Ramaswamy H. Sarma

Consent to participate

All the authors agreed to participate in the scientific work.

Consent to publish

All the authors agreed to submit the manuscript.

Competing interests

The authors declare no competing interests.

Disclosure statement

No potential conflict of interest was reported by the authors.

Authors contributions

Shilpa Sharma and Ravi Kumar conceptualized the work. Rajat Pant and Ravi Kumar performed in silico characterization, docking studies and wrote the manuscript. Ramanathan Karuppasamy and Shanthi Veerappapillai performed MD studies. Shilpa Sharma and Ramanathan Karuppasamy provided critical feedback and reviewed the final manuscript. All the authors have read and finalized the manuscript.

Availability of data and materials

Available on request.

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