DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.
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DOI：
10.1002/jcc.24715
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发表时间：
2017-04-05
影响因子：
3
通讯作者：
Alexov E
中科院分区：
文献类型：
--
作者：
Li L;Chakravorty A;Alexov E
远距离静电力在分子生物学中起着重要作用，特别是在大分子相互作用中。然而，计算浸入水中的不规则形状分子的静电力是一项困难的任务。在这里，我们报告了一个新的工具，DelPhiForce，这是DelPhi包中的一个工具，用于计算和可视化生物分子系统中的静电力。同时，用于在用户自定义位置建模静电势的DelPhi算法也得到了增强，包括三二次和三次插值方法。三次插值方法已经对解析解进行了测试，结果表明，在分辨率为4格/Å时，相应的误差可以忽略不计。DelPhiForce进一步应用于研究三种蛋白质-蛋白质复合物之间的作用力。已经证明，静电力通过引导结合伙伴（使伙伴识别其原生界面）和施加静电扭矩（如果伙伴的相互方向不是原生的）来发挥双重作用。DelPhiForce的输出是VMD可以读取和可视化的格式，并为蛋白质-蛋白质结合的分析提供了额外的选择。DelPhiForce可从DelPhi网页http://compbio.clemson.edu/downloadDir/delphiforce.tar.gz下载。一个新的工具，DelPhiForce，开发并提供DelPhi分布计算和可视化静电力和扭矩之间的受体和配体。如图所示，静电力不仅将结合伙伴相互吸引，而且通过施加扭矩将天然结合界面定位在正确的结合模式上，使配体定向在天然结合模式上。
Long-range electrostatic forces play an important role in molecular biology, particularly in macromolecular interactions. However, calculating the electrostatic forces for irregularly shaped molecules immersed in water is a difficult task. Here we report a new tool, DelPhiForce, which is a tool in the DelPhi package that calculates and visualizes the electrostatic forces in biomolecular systems. In parallel, the DelPhi algorithm for modeling electrostatic potential at user-defined positions has been enhanced to include triquadratic and tricubic interpolation methods. The tricubic interpolation method has been tested against analytical solutions and it has been demonstrated that the corresponding errors are negligibly small at resolution 4 grids/Å. The DelPhiForce is further applied in the study of forces acting between partners of three protein-protein complexes. It has been demonstrated that electrostatic forces play a dual role by steering binding partners (so that the partners recognize their native interfaces) and exerting an electrostatic torque (if the mutual orientations of the partners are not native-like). The output of DelPhiForce is in a format that VMD can read and visualize, and provides additional options for analysis of protein-protein binding. DelPhiForce is available for download from the DelPhi webpage at http://compbio.clemson.edu/downloadDir/delphiforce.tar.gz. A new tool, DelPhiForce, is developed and made available within DelPhi distribution to calculate and visualize electrostatic forces and torques acting between receptor and ligand. As illustrated in the figure, the electrostatic forces not only attract the binding partners to each other, but orient the ligand in the native binding mode via applying a torque that positions the native binding interfaces in the correct binding mode.