Molecular docking and molecular dynamics simulation of mutant carboxylesterase in enhancing microplastics binding affinity

Abstract

Literature survey has shown that microbial and biodegradation of polyethylene terephthalate (PET) by PETases are eco-friendly. However, microbes capable of such feat are few in conjunction with being time-consuming and the laborious bioprospecting efforts are undesirable. Therefore, mutation by in silico means of current isomer of PETase to introduce PET degradative capability could be a better approach to resolve this issue. Previously, BTA-hydrolase was reported capable of degrading PET. This study aimed to convert a carboxylesterase from Archaeoglobus fulgidus (AFEST) to BTA-hydrolase of Thermobifida fusca by in silico site-directed mutagenesis of six amino acids. This was followed by molecular docking analysis with PET and polypropylene (PP) to compare their interactions. The best-docked enzyme-substrate complex was further subjected to molecular dynamics (MD) simulation using GROMACS to gauge the binding quality of the above-said proteins PET. Results of molecular docking revealed the mutated residues, Glu34Asn, Gly177Lys, Asp179 Ala, Leu120Phe, Ala168 Met, and Leu82Thr on the AFEST yielded the lowest binding energy for the wild-type AFEST-PP complex (-7.5 kcal/mol), followed by mutant AFEST-PP complex (-7.1 kcal/mol) and lastly, the BTA-hydrolase-PP complex with (-5.9 kcal/mol). The mutant-AFEST also showed lower binding energy (- 6.7 kcal/mol) than BTA-hydrolase (-5.6 kcal/mol) when complexed with PET. The energy-minimized wild-type-, mutant-AFEST and BTA-hydrolase docked ligand complexes showed that the RMSD value for the BTA-hydrolase-PET complex was stable (0.12 – 0.18 nm) after 5 ns compared to the mutant AFEST-PET complex (~0.22 nm) after 18 ns. The RMSF for the mutant AFEST-PET complex fluctuated at 0.43 nm for the mutated residue Lys177, while the RMSF value of the BTA-hydrolase-PET complex was 0.32 nm for Leu248. Finally, the Rg value for BTA-hydrolase-PET complex (~1.68 nm) was the lowest compared to the mutant-AFEST-PET and wild-type AFEST-PET complexes which both showed the same range (~1.80 – 1.84 nm). The collective in silico data conveyed the six residue mutations on the wild-type AFEST imparted a minimal change in the ability of the mutant-AFEST to bind to PET. This suggests that amino acid mutations that are closer and more centrally-located in the tunnel leading up to the catalytic site might yield a mutant-AFEST with better PET-degrading ability.