Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic

Abstract

According to the literature review, microbial degradation of polyethylene terephthalate by PETases has been detected effective and eco-friendly. However, the number of microorganisms capable of such feats is limited with some undesirable bioprospecting results. BTA-hydrolase has been already reported capable of degrading polyethylene terephthalate. Therefore, mutation by in silico sitedirected mutagenesis means to introduce current isomer of PETase for polyethylene terephthalate degradative capability as a better approach to resolve this issue. This study aimed to use in silico site-directed mutagenesis to convert a carboxylesterase from Archaeoglobus fulgidus to BTA-hydrolase from Thermobifida fusca by replacing six amino acids in specific locations. This work was followed by molecular docking analysis with polyethylene terephthalate and polypropylene to compare their interactions. The best-docked enzyme-substrate complex was further subjected to molecular dynamics simulation to gauge the binding quality of the BTA-hydrolase, wild-type and mutant-carboxylesterase with only polyethylene terephthalate as a substrate. Results of molecular docking revealed lowest binding energy for the wild-type carboxylesterase-polypropylene complex (-7.5 kcal/mol). The root-mean-square deviation value was observed stable for BTA-hydrolase. Meanwhile, root-mean-square fluctuation was assessed with higher fluctuation for the mutated residue Lys178. Consequently, the Rg value for BTA-hydrolase-ligand complex (∼1.68 nm) was the lowest compared to the mutant and wild-type carboxylesterase. The collective data conveyed that mutations imparted a minimal change in the ability of the mutant carboxylesterase to bind to polyethylene terephthalate.

Biotechnological methods to remove microplastics: a review

“…On the other hand, site-directed mutagenesis is also used to alter the activity of genes associated with microplastic degradation. In a recent study, Lameh et al ( 2022 ) reported mutation of carboxylesterase by in silico site‐directed mutagenesis to produce BTA‐hydrolase in Archaeoglobus fulgidus to enhance its ability to degrade polyethylene terephthalate.…”

In silico protein engineering shows that novel mutations affecting NAD+ binding sites may improve phosphite dehydrogenase stability and activity

“…The polar hydrogen atoms and Gasteiger charges were added to the protein chain 19 . The ligands were subjected to the same procedure to ensure that the torsions for rotation were accurately adopted during docking 20 . The macromolecules were under rigid conditions when interacting with the ligand under flexible conditions, using the Lamarckian Genetic Algorithm (LGA) method 21 .…”

Elucidating the Role of Pelargonidin-3-O-Glucoside on C1QL3, CYBB, and CYTIP Involved in Glucose Metabolism: An In Silico Approach

“…Energy minimization techniques were applied to optimize the ligand conformation and lower its energy state, ensuring it was in a suitable form for subsequent molecular docking experiments. [ 10 ]…”