Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability

Abstract

Understanding the mechanisms influencing poly(ethylene terephthalate) (PET) biodegradation is crucial for developing innovative strategies to accelerate the breakdown of this persistent plastic. In this study, we employed all-atom molecular dynamics simulation to investigate the adsorption process of the LCC-ICCG cutinase enzyme onto the PET surface. Our results revealed that hydrophobic, π−π, and H bond interactions, specifically involving aliphatic, aromatic, and polar uncharged amino acids, were the primary driving forces for the adsorption of the cutinase enzyme onto PET. Additionally, we observed a negligible change in the enzyme's tertiary structure during the interaction with PET (RMSD = 1.35 Å), while its secondary structures remained remarkably stable. Quantitative analysis further demonstrated that there is about a 24% decrease in the number of enzyme−water hydrogen bonds upon adsorption onto the PET surface. The significance of this study lies in unraveling the molecular intricacies of the adsorption process, providing valuable insights into the initial steps of enzymatic PET degradation.

Metagenome-derived SusD-homologs affiliated with Bacteroidota bind to synthetic polymers

“…Recently, Sahihi and collaborators ( 71 ) provided relevant data on the molecular dynamics between a PETase and PET. It was reported that hydrophobic interactions were important for enzymatic adsorption toward PET ( 71 ).…”

“…Recently, Sahihi and collaborators ( 71 ) provided relevant data on the molecular dynamics between a PETase and PET. It was reported that hydrophobic interactions were important for enzymatic adsorption toward PET ( 71 ). In our work, we observed a similar trend with SusD, revealed by the predicted presence of hydrophobic pockets within the proteins’ surface.…”