The Effects of Hydration on Protein of Azurin using Coarse-Grained Method and The Free-Energy Analysis

International Conference on Energy Sciences 2016

能源学;物理学

Fitrasari, Dian^1 ; Purqon, Acep^1

Physics of Earth and Complex Systems, Institute of Technology Bandung, Indonesia^1

关键词: Atom calculations;    Calculation results;    Coarse-grained;    Free energy analysis;    Free energy perturbation;    Hydration effects;    Relative errors;    Stability properties;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/877/1/012034/pdf
DOI  :  10.1088/1742-6596/877/1/012034

来源: IOP

【 摘 要 】

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 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 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%.