<i>In silico</i> analysis of a putative dehalogenase from the genome of halophilic bacterium <i>Halomonas smyrnensis</i> AAD6T

Abstract

Microbial-assisted removal of natural or synthetic pollutants is the prevailing green, low-cost technology to treat polluted environments. However, the challenge with enzyme-assisted bioremediation is the laborious nature of dehalogenase-producing microorganisms' bioprospecting. This bottleneck could be circumvented by <i>in-silico analysis of certain microorganisms' whole-genome</i> sequences to predict their protein functions and enzyme versatility for improved biotechnological applications. Herein, this study performed structural analysis on a dehalogenase (<i>DehHsAAD6</i>) from the genome of <i>Halomonas smyrnensis</i> AAD6 by molecular docking and molecular dynamic (MD) simulations. Other bioinformatics tools were also employed to identify substrate preference (haloacids and haloacetates) of the <i>DehHsAAD6</i>. The <i>DehHsAAD6</i> preferentially degraded haloacids and haloacetates (-3.2-4.8 kcal/mol) and which formed three hydrogen bonds with Tyr12, Lys46, and Asp182. MD simulations data revealed the higher stability of <i>DehHsAAD6</i>-haloacid- (RMSD 0.22-0.3 nm) and <i>DehHsAAD6</i>-haloacetates (RMSF 0.05-0.14 nm) complexes, with the <i>DehHsAAD6</i>-L-2CP complex being the most stable. The detail of molecular docking calculations ranked complexes with the lowest binding free energies as: <i>DehHsAAD6</i>-L-2CP complex (-4.8 kcal/mol) = <i>DehHsAAD6</i>-MCA (-4.8 kcal/mol) < <i>DehHsAAD6-</i>TCA (-4.5 kcal/mol) < <i>DehHsAAD6-</i>2,3-DCP (-4.1 kcal/mol) < <i>DehHsAAD6-</i>D-2CP (-3.9 kcal/mol) < <i>DehHsAAD6-</i>2,2-DCP (-3.5 kcal/mol) < <i>DehHsAAD6-</i>3CP (-3.2 kcal/mol). In a nutshell, the study findings offer valuable perceptions into the elucidation of possible reaction mechanisms of dehalogenases for extended substrate specificity and higher catalytic activity.Communicated by Ramaswamy H. Sarma.