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Title: | Variasi Model Molekul Air pada Simulasi Dinamika Molekuler: Studi Kasus Murine Double Minute 2 (MDM2) |
Other Titles: | Variations of Water Molecule Models in Molecular Dynamics Simulations: A Murine Double Minute 2 (MDM2) Case Study |
Authors: | Wahyudi, Setyanto Tri Kurniati, Mersi Riadi, Aziz |
Issue Date: | 2024 |
Publisher: | IPB University |
Abstract: | Dalam simulasi dinamika molekuler diperlukan molekul air sebagai pelarut
agar sistem sesuai dengan kondisi yang sebenarnya. Adanya keterbatasan daya
komputasi dan tidak ada satu pun model yang mereproduksi semua nilai eksperimen
dengan akurat sehingga perlu dilakukan perbandingan efisiensi komputasi dan
akurasi model molekul air yang umum digunakan. Penelitian ini bertujuan
mengetahui pengaruh variasi dari model molekul air pada kestabilan protein
MDM2, serta menentukan model dengan ketepatan dan kecepatan simulasi yang
optimal. Metode yang digunakan berupa simulasi dinamika molekuler selama 100
ns pada suhu 300 K dan 340 K dengan parameter yang dianalisis terdiri dari waktu
simulasi, RMSD, radius girasi, jarak protein-ligan, RMSF, ikatan hidrogen, serta
energi. Hasil simulasi menunjukkan bahwa meningkatnya suhu sistem dapat
menurunkan kestabilan protein dan sebaliknya, serta variasi model molekul air
menghasilkan fluktuasi grafik yang berbeda meskipun tidak signifikan.
Berdasarkan hasil analisis, diperoleh bahwa simulasi yang menggunakan model
SPC/E dan TIP3P lebih cepat daripada yang menggunakan model TIP4P-Ew dan
OPC. Selain itu, analisis RMSD model SPC/E lebih sesuai dibandingkan TIP3P. In molecular dynamics simulations, water molecules are required as a solvent so that the system conforms to the real conditions. Due to limited computing power and no single model reproduced all experimental values exactly, it was necessary to compare the computational efficiency and accuracy of the widely used water molecule models. This research aimed to identify the effect of the variations for water molecule models on the stability of the MDM2 protein and determine a model with optimal accuracy and simulation quickness. The method utilised was molecular dynamics simulations for 100 ns at temperatures of 300 K and 340 K, with the parameters analysed consisting of time simulation, RMSD, radius of gyration, protein-ligand distance, RMSF, hydrogen bonds, and energy. Simulation results showed that increasing system temperature could decrease protein stability and vice versa, as well as that variations of water molecule models produced different, albeit insignificant, graph fluctuations. Based on the analysis results, it was obtained that the simulations using SPC/E and TIP3P models were quicker than those using TIP4P-Ew and OPC models. In addition, the RMSD analysis of the SPC/E model was more appropriate than TIP3P. |
URI: | http://repository.ipb.ac.id/handle/123456789/139668 |
Appears in Collections: | UT - Physics |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
G74180055_Aziz Riadi_Cover.pdf Restricted Access | Cover | 560.67 kB | Adobe PDF | View/Open |
G74180055_Aziz Riadi_Fulltext.pdf Restricted Access | Fulltext | 4.31 MB | Adobe PDF | View/Open |
G74180055_Aziz Riadi_Lampiran.pdf Restricted Access | Lampiran | 3.33 MB | Adobe PDF | View/Open |
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