Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
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DOI：
10.1371/journal.pone.0000880
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发表时间：
2007-09-12
期刊：
影响因子：
3.7
通讯作者：
Im W
中科院分区：
文献类型：
--
作者：
Jo S;Kim T;Im W
膜蛋白的分子动力学模拟在原子水平上对其功能和与周围环境的相互作用提供了更深入的了解。然而，与球状蛋白的溶剂化相比，构建真实的蛋白质/膜复合物仍然具有挑战性，并且需要大量的模拟软件经验。CHARMM-GUI网站（http://www.charmm-gui.org）中的Membrane Builder可以帮助用户使用带有图形用户界面的web浏览器构建这样一个复杂的系统。通过一个广义的自动化构建过程，包括系统大小的确定以及脂质双分子层、孔隙水、散装水和离子的生成，根据系统大小的不同，一个具有几乎任何种类和形状的膜蛋白的现实膜系统可以在5分钟到2小时内生成。每个步骤都给出了经过详细阐述和广泛测试的默认值，为非专业用户和专业用户提供合理的选择和起点。在CHARMM-GUI网站上，可以免费获得12种跨膜蛋白和3种界面膜蛋白的完全平衡系统(三种不同类型的脂质分子（DMPC， DPPC和POPC）和两种类型的系统形状（矩形和六边形）。使用web环境的一个最重要的优点是，如果发现问题，用户可以在退出浏览器之前返回并重新生成整个系统。因此，Membrane Builder提供了直观和简单的方法来构建和模拟生物学上重要的膜系统。
Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org) helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC) and two types of system shapes (rectangular and hexagonal) are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.
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