| 极化蛋白专一性电荷在HIV-1蛋白酶-抑制剂结合自由能预测中的应用 |
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| 引用本文： | 李宇辰,冯国强,段莉莉.极化蛋白专一性电荷在HIV-1蛋白酶-抑制剂结合自由能预测中的应用[J].计算物理,2018,35(3):330-334. |
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| 作者姓名： | 李宇辰 冯国强 段莉莉 |
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| 作者单位： | 山东师范大学, 济南 250000 |
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| 基金项目： | 国家自然科学基金（11574184）及山东省优青项目（ZR2016JL003）资助 |
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| 摘 要： | 对人类免疫缺陷病毒（HIV-1）蛋白酶-抑制剂复合物分别在AMBER力场及极化专一性蛋白电荷（PPC）下进行10 ns的分子动力学模拟（MD），并用MM/PBSA方法计算结合自由能.PPC是基于线性标度的量子力学计算的静电势拟合的蛋白质电荷，能够更准确地描述蛋白质所处的静电环境.结果表明：PPC电荷计算的结合自由能比AMBER力场计算的结合自由能更接近实验值.
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| 关 键 词： | HIV-1蛋白酶 极化蛋白专一性电荷 结合自由能 |
| 收稿时间： | 2017-08-31 |
| 修稿时间： | 2017-09-06 |
Application of Protein-specific Polarized Charge on HIV-1 Protease-Inhibitor Binding Free Enengy |
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| LI Yuchen,FENG Guoqiang,DUAN Lili.Application of Protein-specific Polarized Charge on HIV-1 Protease-Inhibitor Binding Free Enengy[J].Chinese Journal of Computational Physics,2018,35(3):330-334. |
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| Authors: | LI Yuchen FENG Guoqiang DUAN Lili |
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| Institution: | Shandong Normal University, Jinan 250000, China |
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| Abstract: | Molecular dynamics simulations up to 10 ns are carried out to study binding of inhibitor to HIV-1 protease using standard AMBER force field and polarized protein-specific charge (PPC). Binding free energy was calculated by MM/PBSA method.PPC is derived from quantum mechanical calculation for protein in solution and therefore it includes electronic polarization effect. It shows that binding free energy calculated with PPC charge is closer to experimental result than that with AMBER force field. |
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| Keywords: | HIV-1 protease polarized protein-specific charge binding free energy |
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