dc.contributor.advisor | Wahyudi, Setyanto Tri | |
dc.contributor.advisor | Kurniati, Mersi | |
dc.contributor.author | Riadi, Aziz | |
dc.date.accessioned | 2024-02-23T00:01:41Z | |
dc.date.available | 2024-02-23T00:01:41Z | |
dc.date.issued | 2024 | |
dc.identifier.uri | http://repository.ipb.ac.id/handle/123456789/139668 | |
dc.description.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. | id |
dc.description.abstract | 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. | id |
dc.language.iso | id | id |
dc.publisher | IPB University | id |
dc.title | Variasi Model Molekul Air pada Simulasi Dinamika Molekuler: Studi Kasus Murine Double Minute 2 (MDM2) | id |
dc.title.alternative | Variations of Water Molecule Models in Molecular Dynamics Simulations: A Murine Double Minute 2 (MDM2) Case Study | id |
dc.type | Undergraduate Thesis | id |
dc.subject.keyword | Kestabilan protein | id |
dc.subject.keyword | MDM2 | id |
dc.subject.keyword | model molekul air | id |
dc.subject.keyword | simulasi dinamika molekuler | id |
dc.subject.keyword | Protein stability | id |
dc.subject.keyword | MDM2 | id |
dc.subject.keyword | water molecule model | id |
dc.subject.keyword | molecular dynamics simulation | id |