利用AMOEBA进行胰蛋白酶-配体结合自由能计算。
Trypsin-ligand binding free energy calculation with AMOEBA.
作者信息
Shi Yue, Jiao Dian, Schnieders Michael J, Ren Pengyu
机构信息
Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA.
出版信息
Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:2328-31. doi: 10.1109/IEMBS.2009.5335108.
Abstract
The binding free energies of several benzamidine -like inhibitors to trypsin were examined using a polarizable molecular mechanics potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was indicated to be the driving force for the binding. MD simulations show that the ligands form hydrogen bonds with trypsin and water molecules nearby in a competitive fashion. While the binding free energy is independent of the ligand dipole moment, it shows a strong correlation with the ligand molecular polarizability.
摘要
使用可极化分子力学势研究了几种苯甲脒类抑制剂与胰蛋白酶的结合自由能。所有计算得到的结合自由能与实验数据吻合良好。通过自由能分解表明，静电相互作用是结合的驱动力。分子动力学模拟表明，配体以竞争方式与胰蛋白酶及附近的水分子形成氢键。虽然结合自由能与配体偶极矩无关，但它与配体分子极化率有很强的相关性。
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