Dimer interface engineering significantly boosts the performance of organophosphate hydrolase for degrading methyl...

Multimeric enzymes are prevalent in nature and widely applied in industrial applications, so the stabilization of multimeric enzymes is of significance and practical value in enzyme engineering. Here, we proposed an energy-guided molecular dynamics (MD)-aided interface engineering (MDAIE) strategy aiming at enhancing the catalytic performance of a dimeric enzyme, organophosphate hydrolase (OPH), for degrading methyl parathion, one of the widely used organophosphorus pesticides. By identifying the key amino acid residues influencing the dimeric subunit interactions and filtering out unreasonable residues, 13 single-site mutations with potentially stabilizing performance were generated, and eight of them showed significantly improved activity compared to the wild-type enzyme (WT). By further combination of beneficial single-site mutations, four combinatorial mutants (Q155R/E181L, T147V/E181L, T147V/Q155R, and T147V/E159L) with significantly improved performance compared to the WT were achieved from six double-site mutations. Thus, a total of 12 mutants that efficiently degraded organophosphorus pesticide over the WT were obtained, and the best mutant, Q155R/E181L, exhibited 3.0-fold increase in catalytic efficiency, >1.8-fold extension in half-life (t_1/2) at 60 °C, and 2.1 °C rise in melting temperature (T_m). Comprehensive structural analysis and MD simulations unraveled the mechanism underlying simultaneous gains in both activation and stabilization by the dimer engineering. The results validated the MDAIE strategy as a reliable and effective approach to boosting the performance of multimeric enzymes. In this specific case, the dimer engineering of OPH offered a promising and robust biocatalyst for bioremediation and environmental protection.