Self-assembly of soybean peroxidase nanohybrid for activity enhancement and dye decolorization: experimental and computational studies

Abstract

The soybean peroxidase (SBP) mediated nanohybrid [SBP-Cu₃(PO₄)₂·3H₂O] synthesis was carried out in the present study. The scanning electron microscopy (SEM) analysis showed a characteristic flower-like hierarchical structure of the SBP-nanohybrid. The mechanism of SBP-nanohybrid formation was elucidated using computational approaches. The predicted Cu²⁺ binding sites followed by molecular docking studies showed the two lowest energy (−4.4 kcal/mol and −3.56 kcal/mol) Cu²⁺ binding sites. These two binding sites are located at the opposite position and might be involved in the formation of SBP-nanohybrid assemblies. Further, these sites are different than the catalytic active site pocket of SBP, and may facilitate more substrate catalysis. Obtained computational results were confirmed by in-vitro guaiacol oxidations studies using SBP-nanohybrid. The effect of various parameters on SBP-nanohybrid activity was studied. The pH 7.2 was found optimum for SBP-nanohybrid activity. The enzyme activity increased with an increase in temperature up to 50 °C temperature and then decreased with an increase in temperature. Around ∼138% enhanced activity was recorded using SBP-nanohybrid compared to crude SBP. Also, the SBP-nanohybrid showed around 95% decolorization of methylene blue (MB) in 1 h and the MB degradation was confirmed by high-pressure liquid chromatography analysis (HPLC).

Communicated by Ramaswamy H. Sarma

Keywords:

• Soybean peroxidase
• nanohybrid
• molecular docking
• binding sites
• dye decolorization

Acknowledgement

Mr. Sunil Bhapkar acknowledges Council of Scientific & Industrial Research for the research fellowship. Navanath Kumbhar sincerely acknowledges to Savitribai Phule Pune University (SPPU) (Formerly Pune University), Pune for providing the SPPU post-doctoral fellowship (ST/BL/2018-2018/0203).

Author contributions

Mr. Sunil Bhapkar: Experiments for Soybean peroxidase-nanohybrid synthesis, characterization, optimization of enzyme activity, dye decolorization study.

Dr. Navanath Kumbhar: In-silico studies, designing the protocols and studied the nanohybrid formation mechanism using computational approaches.

Mr. Prafful Sharma: Helped for nanohybrid synthesis and dye decolorization experiments.

Dr. Shweta Jagtap: Designed the experiments for nanohybrid synthesis and characterization.

Prof. Rajesh Gacche and Prof. Kailas D. Sonawane: Designed the experiments for molecular modelling.

Dr. Vitthal T. Barvkar: Designed the protocol for HPLC analysis of dye degradation.

Mr. Dnyaneshwar Sonune: Analyzed the dye degradation using HPLC.

Dr. Umesh Jadhav: Put forth the hypothesis that the molecular modeling/bioinformatics approaches can be used for identification of nanohybrid formation mechanism. He also designed the in-vitro studies. Collaborated with authors from various backgrounds and executed the whole study.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

Mr. Sunil Bhapkar acknowledges Council of Scientific & Industrial Research for the research fellowship. Navanath Kumbhar sincerely acknowledges to Savitribai Phule Pune University (SPPU) (Formerly Pune University), Pune for providing the SPPU post-doctoral fellowship (ST/BL/2018-2018/0203).