Enhancing the Thermostability of Bacillus licheniformis Alkaline Protease 2709 by Computation-Based Rational Design

The alkaline protease from <i>Bacillus licheniformis</i> strain 2709 (AprE 2709) is widely used in Chinese industries but faces stability challenges under high-temperature conditions. This study employed molecular modeling and mutagenesis to identify Asn residues at positions 61, 160, and 211 as key sites affecting the stability of AprE 2709. By leveraging the additive and cooperative effects of mutations, the mutant enzyme AprE 2709 (N61G/N160G/N211G) was engineered, exhibiting enhanced thermostability and catalytic activity. The mutant demonstrated a 2.89-fold increase in half-life at 60 °C and a 1.56-fold improvement in catalytic efficiency compared to the wild-type enzyme. Structural analysis revealed that the improved thermostability was due to altered electrostatic interactions and strengthened hydrophobic contacts. Targeting Asn residues prone to deamidation presents a promising strategy for improving protein heat tolerance. These findings not only enhance our understanding of enzyme stability but also lay a foundation for future research aimed at optimizing alkaline proteases for diverse industrial applications, particularly in high-temperature processes.