STUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH
Polyethylene terephthalate (PET) is one of the most widely produced synthetic polymers and is commonly used as the base material for food containers and disposable bottles. The accumulation of PET waste has become a serious environmental issue that needs to be addressed. The recent discovery of Ideo...
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id-itb.:755312023-08-02T13:49:59ZSTUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH Hadi Saputro, Dwi Kimia Indonesia Final Project PETase, thermostability, molecular dynamics simulation INSTITUT TEKNOLOGI BANDUNG https://digilib.itb.ac.id/gdl/view/75531 Polyethylene terephthalate (PET) is one of the most widely produced synthetic polymers and is commonly used as the base material for food containers and disposable bottles. The accumulation of PET waste has become a serious environmental issue that needs to be addressed. The recent discovery of Ideonella sakaiensis bacteria has brought new hope in PET waste management. Ideonella sakaiensis is known to produce the PETase enzyme, which can degrade PET. However, the application of this enzyme in industrial waste treatment faces challenges as PETase starts to lose its activity above 45° C. Therefore, engineering methods are needed to enhance the thermostability of PETase. Previous molecular docking studies have predicted that a combination of mutations L117F/Q119Y/S121E/G165A/D186H/R280A/ S214H/S238F can improve the stability and affinity of PETase towards bis(2-hydroxyethyl) terephthalate (BHET) and (mono(2-hydroxyethyl)terephthalate)2 (2MHET) ligands. However, the prediction methods used in the study were relatively simple, and further comprehensive validation is required to understand the interactions and molecular dynamics of the PETase- ligand complex. This research aims to determine the stability and binding affinity of the combined mutant PETase through molecular dynamics simulation (MD) approach. Simulations were performed on wildtype PETase and its mutant variants using the GROMACS program with a simulation time of 100 ns. The stability of PETase was evaluated based on the Root Mean Square Deviation (RMSD) obtained from MD simulations, while the binding affinity towards BHET and 2MHET ligands was evaluated based on the changes in Gibbs free energy (?G) using the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method. The simulation results showed that the combined mutations in PETase can enhance its thermostability, with R280A being the dominant mutation point. The combined mutations can reduce the structural coil flexibility at residues 234 – 247, making the structure more stable at higher temperatures. Furthermore, the combined mutations are also predicted to increase the binding affinity of PETase towards BHET and 2MHET ligands, with a decrease in ?G values of -5.30 kJ/mol and -5.33 kJ/mol respectively. Based on these findings, it can be concluded that the combined mutations performed on PETase can enhance its potential as a bioremediation agent for PET waste. This research has successfully validated the molecular docking simulation predictions at a more detailed atomic level. text |
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Kimia Hadi Saputro, Dwi STUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH |
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Polyethylene terephthalate (PET) is one of the most widely produced synthetic polymers and is commonly used as the base material for food containers and disposable bottles. The accumulation of PET waste has become a serious environmental issue that needs to be addressed. The recent discovery of Ideonella sakaiensis bacteria has brought new hope in PET waste management. Ideonella sakaiensis is known to produce the PETase enzyme, which can degrade PET. However, the application of this enzyme in industrial waste treatment faces challenges as PETase starts to lose its activity above 45° C. Therefore, engineering methods are needed to enhance the thermostability of PETase. Previous molecular docking studies have predicted that a combination of mutations L117F/Q119Y/S121E/G165A/D186H/R280A/ S214H/S238F can improve the stability and affinity of PETase towards bis(2-hydroxyethyl) terephthalate (BHET) and (mono(2-hydroxyethyl)terephthalate)2 (2MHET) ligands. However, the prediction methods used in the study were relatively simple, and further comprehensive validation is required to understand the interactions and molecular dynamics of the PETase- ligand complex. This research aims to determine the stability and binding affinity of the combined mutant PETase through molecular dynamics simulation (MD) approach. Simulations were performed on wildtype PETase and its mutant variants using the GROMACS program with a simulation time of 100 ns. The stability of PETase was evaluated based on the Root Mean Square Deviation (RMSD) obtained from MD simulations, while the binding affinity towards BHET and 2MHET ligands was evaluated based on the changes in Gibbs free energy (?G) using the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method. The simulation results showed that the combined mutations in PETase can enhance its thermostability, with R280A being the dominant mutation point. The combined mutations can reduce the structural coil flexibility at residues 234 – 247, making the structure more stable at higher temperatures. Furthermore, the combined mutations are also predicted to increase the binding affinity of PETase towards BHET and 2MHET ligands, with a decrease in ?G values of -5.30 kJ/mol and -5.33 kJ/mol respectively. Based on these findings, it can be concluded that the combined mutations performed on PETase can enhance its potential as a bioremediation agent for PET waste. This research has successfully validated the molecular docking simulation predictions at a more detailed atomic level.
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Final Project |
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Hadi Saputro, Dwi |
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Hadi Saputro, Dwi |
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Hadi Saputro, Dwi |
title |
STUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH |
title_short |
STUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH |
title_full |
STUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH |
title_fullStr |
STUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH |
title_full_unstemmed |
STUDY OF IMPROVING PETASE THERMOSTABILITY AND ACTIVITY WITH MOLECULAR DYNAMICS SIMULATION APPROACH |
title_sort |
study of improving petase thermostability and activity with molecular dynamics simulation approach |
url |
https://digilib.itb.ac.id/gdl/view/75531 |
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1822994403981000704 |