Homology modeling and thermostability enhancement of Vibrio palustris PETase via hydrophobic interactions

The quest for sustainable solutions to plastic pollution has driven research into plastic-degrading enzymes, offering promising avenues for polymer recycling applications. However, enzymes derived from natural sources often exhibit suboptimal thermostability, hindering their industrial viability. Protein engineering techniques have emerged as a powerful approach to enhance the desired properties of these biocatalysts. This study aims to conduct a comprehensive analysis of the thermostability of Vibrio palustris PETase (VpPETase) through an integrated computational approach encompassing homology modeling, site-specific molecular docking, molecular dynamics (MD) simulations, and comparative evaluation of a single-point mutation (V195F) against the wild-type enzyme. Homology modeling was used to predict VpPETase model using multiple templates. Model quality was rigorously assessed using Ramachandran plot analysis, ProSA, Verify 3D, and ERRAT. Molecular docking elucidated the catalytic region comprising residues His149, Asp117, and Ser71, while highlighting the pivotal roles of His149, Tyr1, and Ser71 in substrate binding affinity. MD simulations at various temperatures revealed higher stability at 313.15 K over a 100 ns trajectory, as evidenced by analyses of root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), hydrogen bonding, and root-mean-square fluctuation (RMSF). The V195F mutant exhibited a slight increase in stability compared to wild-type. While this study provides valuable insights into the thermostability of VpPETase, further investigations, including experimental validation of thermostability enhancements and in vitro characterization, are warranted to fully exploit the potential of this enzyme for industrial applications in plastic recycling.