THE EFFECT OF DIMER ADDITION ON HYDRATED HER2 PROTEIN MODEL USING COARSE-GRAINED AND FREE ENERGY PERTURBATION METHODS
Approximately 15 to 25% of breast cancer occurred by HER2 overexpression. HER2 is protein located in cell surface as signal pathway and active in dimer formation. Unlike HER1, HER3, and HER4 whose activity is ligand-dependent, HER2 is ligand-independent. This study performs molecular dynamics simula...
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| Format: | Final Project |
| Language: | Indonesia |
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| Online Access: | https://digilib.itb.ac.id/gdl/view/47567 |
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| Institution: | Institut Teknologi Bandung |
| Language: | Indonesia |
| Summary: | Approximately 15 to 25% of breast cancer occurred by HER2 overexpression. HER2 is protein located in cell surface as signal pathway and active in dimer formation. Unlike HER1, HER3, and HER4 whose activity is ligand-dependent, HER2 is ligand-independent. This study performs molecular dynamics simulation perceiving dimer addition effect on TMD and JMA of hydrated HER2 protein model using coarse-grained method. There are four models namely 1-dimer, 2-dimer, 3-dimer, and 4-dimer model. Simulations show that the difference amount of dimer affects interactions on TMD and JMA. Stability of each models in hydrated condition and vacuum are compared by free energy analysis using Free Energy Perturbation. The results show that hydration free energies in all model are less than free energy in vacuum. |
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