Universal Method for Embedding Proteins into Complex Lipid Bilayers for Molecular Dynamics Simulations
Universal Method for Embedding Proteins into Complex Lipid Bilayers for Molecular Dynamics Simulations
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DOI：
10.1021/ct500046e
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发表时间：
2014-06-01
影响因子：
5.5
通讯作者：
Javanainen, Matti
中科院分区：
文献类型：
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作者：
Javanainen, Matti
越来越多的兴趣对膜蛋白模拟要求一个通用的和有效的协议，同时嵌入到不对称的多组分脂质膜的多个蛋白质。为此，在这里，我们提出了一种新的和简单的技术的基础上推动蛋白质进入脂质膜从其一侧通过施加高侧压力的系统。这种方法与大多数（如果不是全部）仿真软件包兼容，并且独立于外部程序代码。最重要的是，我们的协议不改变宿主双层膜的脂质组成或跨膜脂质分布。它可以用于原子模型和粗粒度模型，并且它允许多个蛋白质同时嵌入膜中。结果表明，蛋白质结构是不受影响的压力施加到系统的过程中，蛋白质插入所需的模拟资源被证明是适度的，关于原子和粗粒度的模拟模型。
The growing interest toward membrane protein simulations calls for a universal and efficient protocol for embedding multiple proteins simultaneously into asymmetric many-component lipid membranes. To this end, here, we present a new and simple technique based on pushing proteins into a lipid membrane from its side by applying a high lateral pressure on the system. This approach is compatible with most (if not all) simulation software packages, and it is independent of external program codes. Most importantly, our protocol does not alter the lipid composition or the transmembrane lipid distribution of the host bilayer membrane. It can be employed with both atomistic and coarse-grained models, and it allows multiple proteins to be embedded into a membrane at the same time. It is shown that the protein structure is unaffected by the pressure applied to the system during the procedure, and the simulation resources required for protein insertion are shown to be modest, regarding both atomistic and coarse-grained simulation models.