APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane
APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane
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DOI：
10.1371/journal.pone.0012722
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发表时间：
2010-09-29
期刊：
影响因子：
3.7
通讯作者：
Grabe, Michael
中科院分区：
文献类型：
--
作者：
Callenberg, Keith M.;Choudhary, Om P.;Grabe, Michael
静电力是分子间相互作用的主要决定因素之一。它们帮助引导蛋白质的折叠，增加一种蛋白质与另一种蛋白质的结合，并促进蛋白质-DNA和蛋白质-配体结合。计算生物系统静电性质的一种流行方法是数值求解泊松-玻尔兹曼（PB）方程，并且有几个易于使用的软件包可用于求解可溶性蛋白质的PB方程。在这里，我们提出了一个免费提供的程序，称为APBScore，进行这些计算中存在的膜。自适应Poisson-Boltzmann求解器（APBS）用作求解PB方程的后端，基于Java的图形用户界面（GUI）协调一组例程，这些例程引入膜的影响，确定其相对于蛋白质的位置，并设置膜电位。软件Jmol嵌入在GUI中，以在计算之前可视化插入膜中的蛋白质，并在完成计算之后可视化静电势。我们希望GUI允许人们轻松地进行这些计算，这将使该软件成为实验者和计算研究人员的有用资源。进行膜蛋白静电计算的三个例子来说明如何使用APBScore，并强调可以计算的感兴趣的不同数量。
Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated.