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首页> 外文期刊>Journal of theoretical & computational chemistry >Study on complexes of trypsin and its inhibitors by means of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM)
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Study on complexes of trypsin and its inhibitors by means of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM)

机译：通过融合到分子力学中的原子键电负性均衡方法研究胰蛋白酶及其抑制剂的配合物（ABEEM / MM）

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Trypsin is one of the most important enzymes and plays important roles in the regulation of biological processes. The newly developed trypsin-inhibitor interaction potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) was employed to study complexes of trypsin and its inhibitors. Some structural properties, including root-mean-square deviations (RMSD) of bond length, bond angle and key dihedral, and coordinated RMS Shifts of atoms and hydrogen bond, were studied using ABEEM/MM method and compared with OPLS-AA force-field. At the same time, comparative study on the charges of the hydrogen atoms at the tail of the ligand was also discussed in order to investigate the effect of hydrogen bond between trypsin and its ligand. This work demonstrates that ABEEM/MM model can well reproduce good structures for these trypsin-inhibitor complexes with rather small RMSD of bond length, bond angles, key dihedrals, and RMS Shifts of atomic coordinates with respect to the experimental crystal structures, compared with the results from the OPLS-AA method. The charges obtained by ABEEM/MM model are in good accordance with those from an ab initio calculation. Moreover, both the polarization and the salt-bridge effects have been taken into account. It is shown that ABEEM charges can properly describe the electrostatic interactions between the protein trypsin and its inhibitors.
机译：胰蛋白酶是最重要的酶之一，并且在调节生物过程中起重要作用。基于融合了分子力学的原子键电负性均等化方法（ABEEM / MM），新开发的胰蛋白酶-抑制剂相互作用势模型被用于研究胰蛋白酶及其抑制剂的配合物。使用ABEEM / MM方法研究了一些结构特性，包括键长，键角和键二面体的均方根偏差（RMSD）以及原子和氢键的协调RMS位移，并与OPLS-AA力场进行了比较。同时，还讨论了配体尾部氢原子电荷的比较研究，以研究胰蛋白酶与其配体之间氢键的作用。这项工作表明，对于这些胰蛋白酶-抑制剂复合物，ABEEM / MM模型可以很好地重现良好的结构，与键合长度，键角，键二面体以及相对于实验晶体结构的原子坐标的RMS位移相比，RMSD较小。 OPLS-AA方法得出的结果。通过ABEEM / MM模型获得的电荷与从头算得到的电荷非常一致。此外，已经考虑了极化和盐桥效应。结果表明，ABEEM电荷可以恰当地描述蛋白胰蛋白酶及其抑制剂之间的静电相互作用。

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