In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations
Abstract
:1. Introduction
2. Results
2.1. Search for Candidate Mutation Sites
2.2. Identification of the Number and Position of Mutation Sites
2.3. Identification of Physicochemical Properties of Side Chains of PETase
2.4. Substrate Binding Visualizations from MD Trajectories of PETase and Variants
2.5. MM/PBSA Analysis on the Local Contribution of Amino Acids
2.6. Local Effects Induced by the S238C Mutation on the PET Substrate Binding
3. Discussion
4. Materials and Methods
4.1. Multiple Sequence Alignment
4.2. Preparation of Enzyme Structure for Molecular Docking
4.3. Molecular Docking
4.4. Candidate Mutation Selection
4.5. Alanine Scanning Mutagenesis
4.6. In Silico Site-Saturation Mutagenesis
4.7. Molecular Dynamics Simulations and Analysis
4.8. Binding Free Energy Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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PETase Variant | vdW Energy (kJ/mol) | Electrostatic Energy (kJ/mol) | Polar Solvation (kJ/mol) | Apolar Solvation (kJ/mol) | Total Binding Energy (kJ/mol) |
---|---|---|---|---|---|
WT-r0 | −215 ± 35 | −38 ± 27 | 121 ± 25 | −25 ± 4 | −156 ± 39 |
WT-r1 | −158 ± 53 | −55 ± 26 | 108 ± 44 | −19 ± 6 | −124 ± 62 |
Q119F-r0 | −160 ± 18 | −32 ± 19 | 94 ± 38 | −20 ± 2 | −118 ± 38 |
Q119F-r1 | −155 ± 27 | −31 ± 35 | 88 ± 19 | −19 ± 3 | −116 ± 51 |
D112M/S238F-r0 | −176 ± 45 | −30 ± 25 | 117 ± 24 | −21 ± 6 | −110 ± 70 |
D112M/S238F-r1 | −159 ± 33 | −32 ± 19 | 116 ± 42 | −18 ± 3 | −93 ± 46 |
S238C-r0 | −209 ± 36 | −53 ± 35 | 112 ± 31 | −24 ± 4 | −175 ± 40 |
S238C-r1 | −173 ± 23 | −39 ± 33 | 112 ± 42 | −20 ± 3 | −121 ± 37 |
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Charupanit, K.; Tipmanee, V.; Sutthibutpong, T.; Limsakul, P. In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations. Molecules 2022, 27, 3353. https://doi.org/10.3390/molecules27103353
Charupanit K, Tipmanee V, Sutthibutpong T, Limsakul P. In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations. Molecules. 2022; 27(10):3353. https://doi.org/10.3390/molecules27103353
Chicago/Turabian StyleCharupanit, Krit, Varomyalin Tipmanee, Thana Sutthibutpong, and Praopim Limsakul. 2022. "In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations" Molecules 27, no. 10: 3353. https://doi.org/10.3390/molecules27103353