Molecular dynamics simulations of temperature-dependent PET binding in PETase, ThermoPETase, and FAST-PETase

Polyethylene terephthalate (PET) biodegradation has gained significant attention following the 2016 discovery of the PET-hydrolyzing enzyme <i>Is</i>PETase from <i>Ideonella sakaiensis</i> 201-F6. Although <i>Is</i>PETase operates under mild temperature conditions, its limited catalytic activity and poor thermal stability restrict large-scale industrial applications. To overcome these limitations, several engineered variants have been developed. In this study, the wild-type <i>Is</i>PETase was systematically compared with two engineered variants, ThermoPETase and FAST-PETase, under four temperature conditions (300, 313, 323, and 333 K) using fully detailed atomistic molecular dynamics (MD) simulations. A PET dimer was docked into the active site of each enzyme, followed by 150 ns of restrained and unrestrained MD simulations to evaluate structural stability and substrate interactions. Both engineered variants exhibited improved thermal stability relative to <i>Is</i>PETase, with FAST-PETase demonstrating the highest stability across all temperatures. Increased flexibility of the catalytic triad was observed in both engineered variants, suggesting enhanced catalytic adaptability compared to <i>Is</i>PETase. Key residues, Tyr87 and Met161, were identified as essential for stabilizing the PET dimer within the active-site cavity. At elevated temperature (333 K), <i>Is</i>PETase showed increased flexibility, leading to disrupted PET dimer binding. In contrast, ThermoPETase and FAST-PETase preserved stable PET dimer positioning at elevated temperatures, with FAST-PETase displaying the most favourable structural characteristics across all temperature conditions. Furthermore, binding energy calculations revealed a correlation between structural stability and reduced enthalpic binding energies at each enzyme's optimal temperature. Based on these analyses, the optimal temperatures for PET degradation were found to be 323 K for <i>Is</i>PETase, 333 K for ThermoPETase, and 300-313 K for FAST-PETase. These findings provide molecular-level insights into the structure-stability-activity relationships of PETase variants and highlight key determinants for the rational design of improved PET-degrading enzymes.