Date of Award
12-1-2024
Degree Name
Master of Science
Department
Physics
First Advisor
Jayasekera, Thushari
Abstract
The petroleum-based polyethylene terephthalate (PET) is a versatile and synthetic polymer that plays a pivotal role in the economy, including packaging, textiles, 3D printers, and even medical-related applications. There is a need for plastic waste management. Biological up-cycling of PET is a promising method for a clean and sustainable future. In 2012, a group of researchers, Tournier et. al., performed experiments and molecular dynamics simulations on the Leaf-branch Compost Cutinase, LCC (PDB Code: 4EB0), which outperformed the PET hydrolysis activity compared to three other PET hydrolyzing enzymes. The LCC and PET depolymerization rate of wildtype LCC was reported to be 93.2 mg/hour at 65 °C. However, depolymerization is found to be limited by thermostability of the enzyme. With the detailed investigation of number of variants, they reported 4 variants of LCC, WCCG, WCCM, ICCG, and ICCM, which shows increased performance. In this study, the thermostability seems to be enhanced by adding a disulfide bonding at a place where the homolog enzyme reported to have a Calcium ion (Ca2+). No studies are available to see the effect of the metal ions at the same location of LCC. The primary goal of this thesis is to perform the MD simulations to understand the effect of metal ions on the dynamics of LCC and a PET trimer of monohydroxyethyl terephthalate, 2HE (MHET)3. We used a Quantum Mechanical (QM) simulation to optimize the metal geometry, thus the metal specific force fields are developed using the Metal Center Parameter Builder (MCPB). Our results suggest adding a metal ion with a S238E mutation for further investigations.
In 2016, a group of researchers discovered a bacterium cutinase that contains two enzymes, polyethylene terephthalate hydrolase and mono(2-hydroxyethyl) terephthalate hydrolase (PETase and MHETase) that degrades PET and mono(2 hydroxyethyl) terephthalate (MHET). Further research has shown LCC, PETase, and MHETase, have the potential to depolymerize PET and MHET with a disulfide bond or a metal added to the structure of LCC. We will dive deep into the methodology of adding a Ca2+ and Mg2+ to LCC’s metal site, and run the molecular dynamics of that metal site. Using molecular dynamic simulations, we observe the root mean deviation (RMSD) of a metal mutation inside wild-type LCC bacterium. Wild-type LCC has no metal in the protein structure. We will highlight potential metal site mutations to wild-type LCC.
Access
This thesis is Open Access and may be downloaded by anyone.