Molecular Simulation Elaborating the Structural Mechanism of Spiri forming nitrilase from Bacillus safensis

Nitrilases are indispensable in the biocatalytic hydrolysis of nitrile compounds, which presents promising applications in industrial biocatalysis and environmental remediation. In this study, we conduct an extensive investigation into the structural and functional properties of Bacillus safensis nitrilase (BsNIT), highlighting its assembly, substrate binding mechanisms, stability, evolutionary relationships, and active site conservation. Using a combination of molecular modeling and extensive molecular dynamics simulations, we unveil the intricate architecture of BsNIT, which exhibits a left-handed spiri-forming structure stabilized by interchain interactions and salt-bridge formations. The substrate-binding pocket, surrounded by aromatic residues, displays multifaceted accessibility through distinct channels. Our simulations reveal substrate-specific catalytic orientations, with glutaronitrile and 4-cyanobutanoic acid displaying stable binding, while benzonitrile exhibits a propensity for rapid product diffusion. Analysis of active site conservation emphasizes the functional significance of preserved catalytic residues, providing insights into BsNIT's catalytic efficiency. This comprehensive study offers a thorough understanding of BsNIT's structure-function relationships, paving the way for future advancements in enzyme engineering and bioremediation strategies targeting nitrile pollutants.