Homology Modeling of Laccase Enzyme of Filamentous Fungus Trichoderma sp. CNSC-2 and Its Role in Pyrene Degradation

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants that impart several hazardous effects on the environment. Extracellular enzymes released by filamentous fungi are well-known participants in the degradation of such organic pollutants. The present study aims to determine the interaction of pyrene with Lac1 protein, coding for the extracellular laccase enzyme from Trichoderma sp. CNSC-2. Lac1 sequence analysis revealed the stable and acidic nature of the laccase enzyme. The dominance of random coils (54.8%) and extended strands (28.3%) in secondary structure defined protein flexibility. 3D homology modeling followed by validation revealed a high-quality model with 94.8% residues in the favored zone of Ramachandran plot. Molecular docking study with pyrene displayed a significant binding affinity of −7.82 kcal mol⁻¹ with the amino acid residues at the active binding site of Lac1, indicating a strong role in pyrene binding. Trichoderma sp. CNSC-2 achieved 69.42 ± 0.4% of pyrene removal efficiency at 100 mg l⁻¹ pyrene concentration on day 12 of incubation. Laccase activity during pyrene degradation simultaneously increased, and the highest activity was observed on day 6 of incubation. Enzyme production was found to be optimum at pH 6 (p < 0.001) and 30°C temperature (p < 0.0001). FTIR analysis showed deviation in the amide bands of laccase in the presence of pyrene, and additional peaks coinciding with pyrene metabolites were observed. The decrease in intensity of laccase due to quenching by pyrene interaction was determined by fluorescence spectroscopy. Thus, this study suggested a strong binding affinity of pyrene to the laccase active site implying the potential role of laccase enzyme from Trichoderma sp. CNSC-2 in pyrene degradation.

Keywords:

• Binding affinity
• docking
• homology modeling
• laccase
• pyrene
• Trichoderma

Acknowledgements

The authors would like to acknowledge the authorities of NIT Rourkela, Odisha for providing the necessary facilities.

Authors’ contributions

ADB and NC conducted the experiments. ADB acquired and analyzed the data. ADB and SK drafted the original manuscript. SD designed the research, secured the fund, interpreted the data and revised this manuscript. All the authors read and agreed to this final manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

All the data generated or analyzed during this study have been included in the manuscript and supplementary material. The sequencing raw data of laccase was deposited in the NCBI Sequence Read Archive database under the accession number OP858805 (Lac1).

Additional information

Funding

Authors would like to thank the Department of Biotechnology, Government of India, for the financial assistance [BT/PR9465/NDB/39/360/2013]. ADB is grateful to the Council of Scientific and Industrial Research, Government of India [09/983(0048)/2020-EMR-I] for the fellowship for doctoral study.