THE EFFECTS OF HYDRATION ON PROTEIN OF AZURIN USING COARSE-GRAINED METHOD AND THE FREE-ENERGY ANALYSIS
Proteins play important roles in body metabolism. However, to reveal hydration effects, it is cost computing especially for all-atom calculation. Coarse-grained method is one of potential solution to reduce the calculation and computable in longer timescale. Furthermore, the protein of Azurin is in...
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| Format: | Theses |
| Language: | Indonesia |
| Online Access: | https://digilib.itb.ac.id/gdl/view/21722 |
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| Institution: | Institut Teknologi Bandung |
| Language: | Indonesia |
| Summary: | Proteins play important roles in body metabolism. However, to reveal hydration effects, it is cost computing especially for all-atom calculation. Coarse-grained method is one of potential solution to reduce the calculation and computable in longer timescale. Furthermore, the protein of Azurin is interesting protein and potentially applicable to cancer medicine for the stability property reason. We <br />
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investigate the effects of hydration on Azurin, the conformation and the stabilities. Furthermore, we analyze the free-energy of the conformation system to find the <br />
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favorable structure using free energy perturbation (FEP) calculation. Our calculation results show that free energy value of azurin is -136.9 kJ/mol. It shows a good agreement with experimental results with relative error index remained at 0.07%. |
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