Selection of alkaliphilic Bacillus pectate lyases based on reactivity and pH-dependent stability in simulated...

Pectate lyases, known for their alkaliphilic nature, are ideal for industrial applications that require specific pH conditions, particularly in industries such as textiles and pulp extraction. These enzymes, primarily from the polysaccharide lyase family 1 (PL1) of different microbial sources, play a vital role in polysaccharide degradation. Given the potent pectinolytic activity of Bacillus pectate lyases, targeting these enzymes is crucial for identifying the most effective candidates. To address challenges in enzyme selection, we examined the initial catalytic interactions of Bacillus species N16-5 (sp_N16-5), Bacillus species TS-47 (sp_TS-47), and Bacillus species subtilis strain 168 (sub_168) with pectin using molecular docking, focusing on the binding of pectin to the active-site tunnel region. We employed steered molecular dynamics simulations to analyze the disassociation period of pectin, where sp_N16-5 demonstrated higher compactness and we applied a semi-empirical quantum mechanical approach for reaction modeling. Our analysis through NPT ensemble-based dynamics analysis emphasised the structural stability and compactness required to withstand high-production conditions. We identified Bacillus species N16-5 (sp_N16-5) as the most efficient pectinolytic lyase, as it showed strong affinity, reactivity and higher interaction, also sp_N16-5 shows its enthalpy of reaction at 9 kcal/mol with a lower activation energy barrier at 27 kcal/mol which is closest to the typical range among the chosen Bacillus pectate lyase, enabling rapid pectin conversion alongside low energy input. Outcomes from the pH-dependent molecular dynamics revealed the sp_N16-5 to possess a greater structural endurability, comparatively, this study streamlines the screening process for selecting optimal Bacillus pectate lyases through in-silico investigation for industrial applications.