Studi Biofisika dan Kimia Molekuler terhadap Termostabilitas Enzim PETase melalui Simulasi Dinamika Molekuler Multitemperatur
Keywords:
PETase; Termostabilitas; Simulasi Dinamika Molekuler; RMSD, Biodegradasi Plastik.Abstract
Pencemaran plastik akibat akumulasi poli(etilena tereftalat) (PET) menjadi tantangan lingkungan global yang mendesak. Enzim PETase memiliki potensi dalam upaya bioremediasi plastik melalui proses degradasi enzimatis, namun aplikasinya masih terkendala oleh rendahnya stabilitas termal. Penelitian ini bertujuan untuk mengevaluasi stabilitas struktural dan termodinamika enzim PETase pada berbagai variasi temperatur menggunakan metode simulasi dinamika molekuler (molecular dynamics/MD) berbasis perangkat lunak GROMACS. Perlakuan temperatur yang digunakan meliputi 300 K, 310 K, 373 K, 440 K, dan 500 K untuk merepresentasikan kondisi temperatur ruang, fisiologis, hingga ekstrem. Analisis dilakukan terhadap parameter RMSD, RMSF, radius girasi (Rg), jumlah ikatan hidrogen, luas permukaan yang dapat diakses pelarut (solvent accessible surface area, SASA), energi total sistem, serta evaluasi konformasi visual melalui snapshot struktur 3D. Hasil simulasi menunjukkan bahwa PETase tetap stabil pada 300 K dan 310 K, namun mulai mengalami destabilisasi struktural pada 373 K. Perubahan struktural yang signifikan, termasuk unfolding protein dan peningkatan paparan permukaan hidrofobik, diamati pada 440 K dan 500 K. Studi ini memberikan informasi biofisika molekuler penting terkait batas toleransi termal PETase, yang dapat menjadi referensi dalam pengembangan varian enzim dengan termostabilitas yang lebih tinggi untuk aplikasi bioteknologi lingkungan.
References
Abraham, M., Alekseenko, A., Bergh, C., Blau, C., Briand, E., Doijade, M., Fleischmann, S., Gapsys, V., Garg, G., Gorelov, S., Gouaillardet, G., Gray, A., Irrgang, M. E., Jalalypour, F., Jordan, J., Junghans, C., Kanduri, P., Keller, S., Kutzner, C., … Lindahl, E. (2023). GROMACS 2023.3 Manual. Zenodo. https://doi.org/10.5281/zenodo.10017699
Aier, I., Varadwaj, P. K., & Raj, U. (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports, 6(1), 34984. https://doi.org/10.1038/srep34984
Apicella, A., Marascio, M., Colangelo, V., Soncini, M., Gautieri, A., & Plummer, C. J. G. (2017). Molecular dynamics simulations of the intrinsically disordered protein amelogenin. Journal of Biomolecular Structure and Dynamics, 35(8), 1813–1823. https://doi.org/10.1080/07391102.2016.1196151
Bagewadi, Z. K., Yunus Khan, T. M., Gangadharappa, B., Kamalapurkar, A., Mohamed Shamsudeen, S., & Yaraguppi, D. A. (2023). Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target of Micrococcus luteus with secondary metabolites from Bacillus licheniformis recognized by genome mining approach. Saudi Journal of Biological Sciences, 30(9), 103753. https://doi.org/https://doi.org/10.1016/j.sjbs.2023.103753
Burgin, T., Pollard, B. C., Knott, B. C., Mayes, H. B., Crowley, M. F., McGeehan, J. E., Beckham, G. T., & Woodcock, H. L. (2024). The reaction mechanism of the Ideonella sakaiensis PETase enzyme. Communications Chemistry, 7(1). https://doi.org/10.1038/s42004-024-01154-x
Deng, B., Yue, Y., Yang, J., Yang, M., Xing, Q., Peng, H., Wang, F., Li, M., Ma, L., & Zhai, C. (2023). Improving the activity and thermostability of PETase from Ideonella sakaiensis through modulating its post-translational glycan modification. Communications Biology, 6(1), 1–10. https://doi.org/10.1038/s42003-023-04413-0
Gao, Y., Mei, Y., & Zhang, J. Z. H. (2015). Treatment of Hydrogen Bonds in Protein Simulations. Advanced Materials for Renewable Hydrogen Production, Storage and Utilization. https://doi.org/10.5772/61049
Ghahremanian, S., Rashidi, M. M., Raeisi, K., & Toghraie, D. (2022). Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review. Journal of Molecular Liquids, 354, 118901. https://doi.org/10.1016/j.molliq.2022.118901
Gordon, J. C., Myers, J. B., Folta, T., Shoja, V., Heath, L. S., & Onufriev, A. (2005). H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research, 33(Web Server issue), W368-71. https://doi.org/10.1093/nar/gki464
Han, X., Liu, W., Huang, J. W., Ma, J., Zheng, Y., Ko, T. P., Xu, L., Cheng, Y. S., Chen, C. C., & Guo, R. T. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-02255-z
Hollingsworth, S. A., & Dror, R. O. (2018). Molecular Dynamics Simulation for All. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
Ke, Q., Gong, X., Liao, S., Duan, C., & Li, L. (2022). Effects of thermostats/barostats on physical properties of liquids by molecular dynamics simulations. Journal of Molecular Liquids, 365, 120116. https://doi.org/https://doi.org/10.1016/j.molliq.2022.120116
Kim, H., Fábián, B., & Hummer, G. (2023). Neighbor List Artifacts in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 19(23), 8919–8929. https://doi.org/10.1021/acs.jctc.3c00777
Kumar, G., Mishra, R. R., & Verma, A. (2022). Introduction to Molecular Dynamics Simulations. In A. Verma, S. Mavinkere Rangappa, S. Ogata, & S. Siengchin (Eds.), Forcefields for Atomistic-Scale Simulations: Materials and Applications (pp. 1–19). Springer Nature Singapore. https://doi.org/10.1007/978-981-19-3092-8_1
Lemkul, J. A. (2024). Introductory Tutorials for Simulating Protein Dynamics with GROMACS. The Journal of Physical Chemistry B, 128(39), 9418–9435. https://doi.org/10.1021/acs.jpcb.4c04901
Mackay, D. H. J., Cross, A. J., & Hagler, A. T. (1989). The Role of Energy Minimization in Simulation Strategies of Biomolecular Systems. Prediction of Protein Structure and the Principles of Protein Conformation, 317–358. https://doi.org/10.1007/978-1-4613-1571-1_7
Masson, P., & Lushchekina, S. (2022). Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules (Basel, Switzerland), 27(20). https://doi.org/10.3390/molecules27206861
Oktafiansyah, R., Herry Santjojo, D. J. D., Sakti, S. P., Zafirah, T. N., Ghufron, M., Khusnah, N. F., & Masruroh. (2020). Swelling Effect Observation of The Copper Phthalocyanine Layer on QCM and Its Effect on Surface Roughness and Morphology Changes. IOP Conference Series: Materials Science and Engineering, 833(1), 12082. https://doi.org/10.1088/1757-899X/833/1/012082
Rasjava, A. R., Kurniawati, D., Rizki, W. O. S., Kurniati, N. F., & Hertadi, R. (2025). Development of inulin nanocarrier for effective oral delivery of insulin: synthesize, optimization, characterization, and biophysical study. Journal of Biomaterials Science, Polymer Edition, 36(8), 963–986. https://doi.org/10.1080/09205063.2024.2436297
Sabari V L, D., Rajmohan, G., S B, R., S, S., Nagasubramanian, K., G, S. K., & Venkatachalam, P. (2025). Improving the binding affinity of plastic degrading cutinase with polyethylene terephthalate (PET) and polyurethane (PU); an in-silico study. Heliyon, 11(2), e41640. https://doi.org/https://doi.org/10.1016/j.heliyon.2025.e41640
Skarmoutsos, I., & Guardia, E. (2025). Molecular Dynamics of High-Pressure Liquid Water: Going from Ambient to Near-Critical Temperatures. Chemistry – A European Journal, 31(28), e202500423. https://doi.org/https://doi.org/10.1002/chem.202500423
Soong, Y. H. V., Sobkowicz, M. J., & Xie, D. (2022). Recent Advances in Biological Recycling of Polyethylene Terephthalate (PET) Plastic Wastes. Bioengineering, 9(3), 1–27. https://doi.org/10.3390/bioengineering9030098
Tanasupawat, S., Takehana, T., Yoshida, S., Hiraga, K., & Oda, K. (2016). Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate). International Journal of Systematic and Evolutionary Microbiology, 66(8), 2813–2818. https://doi.org/10.1099/ijsem.0.001058
Urbanek, A. K., Kosiorowska, K. E., & Mirończuk, A. M. (2021). Current Knowledge on Polyethylene Terephthalate Degradation by Genetically Modified Microorganisms. Frontiers in Bioengineering and Biotechnology, 9(November), 1–15. https://doi.org/10.3389/fbioe.2021.771133
