In silico assessment of dehalogenase from Bacillus thuringiensis H2 in relation to its salinity-stability and pollutants degradation

Abstract

Increased scientific interest has led to the rise in biotechnological uses of halophilic and halotolerant microbes for hypersaline wastewater bioremediation. Hence, this study performed molecular docking, molecular dynamic (MD) simulations, and validation by Molecular Mechanic Poisson-Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis H2. We aimed to identify the interactions of DehH2 with substrates haloacids, haloacetates, and chlorpyrifos under extreme salinity (35% NaCl). MD simulations revealed that DehH2 preferentially degraded haloacids and haloacetates (−6.3 to −4.7 kcal/mol) by forming three or four hydrogen bonds to the catalytic triad, Asp125, Arg201, and Lys202. Conversely, chlorpyrifos was the least preferred substrate in both MD simulations and MM-PBSA calculations. MD simulation results ranked the DehH2-L-2CP complex (RMSD □0.125−0.23 nm) as the most stable while the least was the DehH2-chlorpyrifos complex (RMSD 0.32 nm; RMSF 0.0 − 0.29). The order of stability was as follows: DehH2-L-2CP > DehH2-MCA > DehH2-D-2CP > DehH2-3CP > DehH2-2,2-DCP > DehH2-2,3-DCP > DehH2-TCA > DehH2-chlorpyrifos. The MM-PBSA calculations further affirmed the DehH2-L-2CP complex's highest stability with the lowest binding energy of −45.14 kcal/mol, followed closely by DehH2-MCA (−41.21 kcal/mol), DehH2-D-2CP (−31.59 kcal/mol), DehH2-3CP (−30.75 kcal/mol), DehH2-2,2- DCP (−29.72 kcal/mol), DehH2-2,3-DCP (−22.20 kcal/mol) and DehH2-TCA (−18.46 kcal/mol). The positive binding energy of the DehH2-chlorpyrifos complex (+180.57 kcal/mol) proved the enzyme's non-preference for the substrate. The results ultimately illustrated the unique specificity of the DehH2 to degrade the above-said pollutants under a hypersaline condition.

Communicated by Ramaswamy H. Sarma

Keywords:

• Dehalogenase
• salinity
• pollutant
• MD simulation
• MM-PBSA

Acknowledgements

The authors would like to express their gratitude to the Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia for their facilities. In addition, the HAO would like to thank the Ministry of Education through the Tertiary Education Trust Fund (TETFund) Nigeria for the studentship.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was funded by the Fundamental Research Grant Scheme (FRGS/1/2019/STG05/UTM/01/1) from the Ministry of Higher Education Malaysia (UTM code: R.J130000.7854.5F189) and the RUG-UTMHR: Q.J130000.2414.08G59 for financial assistance. Fundamental Research Grant Scheme (FRGS) from the Ministry of Higher Education Malaysia.