In silico molecular modelling, structural dynamics simulation and characterization of antifungal nature of β-glucosidase enzyme from Sechium edule

Abstract

β-glucosidase is an enzyme that has ability to cleave β-glycosidic bonds present in oligosaccharides and glycoconjugates. They are known to be present across all domains of living organism and have important roles in many biological processes including plant defense mechanism. In the present study, a β-glucosidase enzyme identified from seeds of Sechium edule was characterized using various bioinformatics tools. A homology model (SeBG) was generated using a β-glucosidase crystal structure from Oryza sativa (PDB ID: 3PTK) as template. In silico structural binding studies on putative β-glucosidase protein revealed a stable and strong interaction indicative of higher GOLD fitness score with the substrates: p-nitrophenyl-β-d-glucopyranoside (pNPG), laminarin, chitotriose, N-acetylglucosamine and N-acetylmuramic acid suggesting its possible role in broad spectrum antifungal and antimicrobial activity. Assessment of the in vitro enzyme activity with pNPG showed a K_m and V_max values of 2.7 mM and 22 µMmin⁻¹mL⁻¹mg⁻¹, respectively. While, the in vitro enzyme activity with laminarin showed a K_m and V_max values of 0.31 mM and 0.043 µMmin⁻¹mL⁻¹mg⁻¹. The broad spectrum activity of the protein shown in our result indicates SeBG as a promising biocontrol agent against phytopathogens.

Communicated by Ramaswamy H. Sarma

Keywords:

• Antifungal
• β-glucosidase
• Sechium edule
• SeBG
• phytopathogen

Acknowledgements

The laboratory facilities provided by Joint Director, ICAR Research Complex for NEH Region, Manipur Centre and Director, ICAR Research Complex for NEH Region, Umiam are gratefully acknowledged.

Disclosure statement

The authors declare that they have no potential conflict of interest.

Additional information

Funding

The financial support from DBT Research Associateship Program in Biotechnology and Life sciences to Dr. Neeta Pathaw is gratefully acknowledged.