Yesylevskyy Semen O
Department of Physics of Biological Systems, Institute of Physics of National Academy of Science of Ukraine, Prospect Nauky 46, Kiev-28, 03680, Ukraine.
J Chem Inf Model. 2007 Sep-Oct;47(5):1986-94. doi: 10.1021/ci600553y. Epub 2007 Jul 25.
The major challenge in setting up membrane protein simulations is embedding the protein into the pre-equilibrated lipid bilayer. Several techniques were proposed to achieve optimal packing of the lipid molecules around the protein. However, all of them possess serious disadvantages, which limit their applicability and discourage the users of simulation packages from using them. In the present work, we analyzed existing approaches and proposed a new procedure of protein insertion into the lipid bilayer, which is implemented in the ProtSqueeze software. The advantages of ProtSqueeze are as follows: (1) the insertion algorithm is simple, understandable, and controllable; (2) the software can work with virtually any simulation package on virtually any platform; (3) no modification of the source code of the simulation package is needed; (4) the procedure of insertion is as automated as possible; (5) ProtSqueeze is distributed for free under a general public license. In this work, we present the architecture and the algorithm of ProtSqueeze and demonstrate its usage in case studies.
搭建膜蛋白模拟体系的主要挑战在于将蛋白质嵌入预先平衡好的脂质双分子层中。人们提出了多种技术来实现蛋白质周围脂质分子的最优堆积。然而，所有这些技术都存在严重缺陷，这限制了它们的适用性，也使得模拟软件的用户不愿使用它们。在本研究中，我们分析了现有方法，并提出了一种将蛋白质插入脂质双分子层的新程序，该程序已在ProtSqueeze软件中实现。ProtSqueeze的优点如下：（1）插入算法简单、易懂且可控；（2）该软件几乎可以在任何平台上与任何模拟软件配合使用；（3）无需修改模拟软件的源代码；（4）插入过程尽可能自动化；（5）ProtSqueeze根据通用公共许可免费分发。在本研究中，我们介绍了ProtSqueeze的架构和算法，并在案例研究中展示了其用法。
