PRISKILA KELLY ANGELIKA, - (2020) SIMULASI DINAMIKA MOLEKUL TERHADAP KESTABILAN ANTIBODI SCFV 6D4B10 ANTI-NS1 DENV DENGAN KONSTRUK VL-LINKER-VH-BAD. Skripsi thesis, Sekolah Tinggi Farmasi Indonesia.
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Abstract
Demam Berdarah Dengue (DBD) merupakan penyakit infeksi virus dengue (DENV) yang dibawa oleh vektor nyamuk Aedes aegepyti atau Aedes albopictus. Sebagai negara tropis, Indonesia mengalami kasus kematian dan jumlah pasien yang tinggi akibat penyakit ini. Namun sayangnya, pengobatan imunoterapi antiDENV yang spesifik masih belum tersedia. Tahapan diagnosis yang cepat dan interpretasi yang tepat menjadi dasar yang penting dalam pengobatan demam berdarah. Dengan perkembangan teknologi antibodi, ditemukan molekul singlechain variable Fragment (scFv) 6D4B10 memiliki potensi anti-DENV spesifik, sehingga dapat berperan sebagai komponen diagnostik untuk deteksi DENV berbasis antibodi. Adapun penelitian ini mengarah pada kajian kestabilan scFv 6D4B10 yang dirancang dengan penambahan linker dan Biotin Acceptor Domain (BAD) guna meningkatkan kualitas struktur VL-VH dari scFv pada media deteksi. Studi in-sillico scFv dimulai dengan pemodelan dan optimasi struktur protein menggunakan aplikasi Modeller 9.23, evaluasi model, hingga simulasi dinamika molekul dengan aplikasi Amber 16 dan Amber tools 17. Sedangkan visualisasi dan analisis hasil simulasi dinamika molekul menggunakan Visual Molecular Dynamics. Pemodelan scFv natif dan scFv-BAD berbasis homologi menggunakan templat protein 4F9L memberikan hasil evaluasi stereokimia yang baik pada plot Ramachandran dan Z-score pada ProSA. Grafik RMSD menyatakan bahwa struktur BAD pada scFv mulai stabil pada waktu 45 ns dan nilai RMSF BAD hingga 20,4409 Å. Sedangkan visualisasi hasil simulasi dinamika molekul menyatakan bahwa struktur linker maupun BAD tidak mengganggu sisi pengikatan scFv. --- Dengue Haemorrhagic Fever (DHF) is a dengue virus infection disease (DENV) carried by the mosquito vector Aedes aegepyti or Aedes albopictus. As a tropical country, Indonesia faces high cases of death and number of patients due to this disease. Unfortunately, specific anti-DENV immunotheraphy treatment is still not available. Rapid diagnosis and proper interpretation are important bases in the treatment of dengue fever. With the development of antibody technology, it was found that the 6D4B10 single-chain variable Fragment (scFv) molecule has specific anti-DENV potential, so that it can act as a diagnostic component for antibody-based DENV detection. This research leads to a study of the stability of scFv 6D4B10 which is designed with the addition of linker and Biotin Acceptor Domain (BAD) to improve the quality of the VL-VH structure of scFv in the detection medium. The in-sillico study begins with modelling and optimization of protein structure using Modeller 9.23 aplication, model evaluation, and molecular dynamics simulations using Amber 18 and Amber tools 17 application. Meanwhile, visualization and analysis of molecular dynamics simulation results using Visual Molecular Dynamics. Homology modeling using 4F9L protein template gave good stereochemical evaluation results on the Ramachandran plot and Z-score on ProSA. RMSD graph shows that the BAD structure on scFv begins to stabilize at 45 ns and RMSF value of BAD was up to 20,4409 Å. Meanwhile, the visualization results states that neither the linker nor BAD interfere with the binding site of scFv.
| Item Type: | Thesis (Skripsi) |
|---|---|
| Uncontrolled Keywords: | Demam Berdarah Dengue, Homology modelling, ScFv 6D4B10, .........................Linker, BAD, Simulasi Dinamika Molekul. --- Dengue Haemorrhagic Fever, Homology modelling, ScFv 6D4B10, ..................... Linker, BAD, Molecular Dynamic Simulations. |
| Subjects: | Q Science > Q Science (General) R Medicine > R Medicine (General) |
| Divisions: | Program Studi S1 Farmasi |
| Depositing User: | pustakawan - - |
| Date Deposited: | 04 Oct 2024 01:08 |
| Last Modified: | 04 Oct 2024 01:08 |
| URI: | http://repository.stfi.ac.id/id/eprint/1343 |
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