Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations
Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations
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DOI：
10.1021/la0106485
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发表时间：
2002-01-08
期刊：
影响因子：
3.9
通讯作者：
Woolf, TB
中科院分区：
文献类型：
--
作者：
Grossfield, A;Woolf, TB
几个实验结构的膜蛋白的整合已经证明，色氨酸侧链被发现优先在膜界面内，但没有明确的物理解释，这种偏好已被证明。目前的工作包含一系列的分子动力学模拟，旨在提供深入了解这种现象。具体而言，我们进行了传统的无偏模拟，以及偏吲哚和N-甲基吲哚内棕榈油酰磷脂酰胆碱（POPC）双层的分子动力学。无偏计算考察了吲哚在膜中心、头基区和膜外水三种环境中的行为。使用一种新的动态窗口程序，有效地移动的吲哚通过双层偏置计算。这些计算使我们能够探索方向，氢键，和能量的吲哚，作为其位置的函数沿着膜正常。此外，自由能配置文件构建从有偏见的模拟，便于比较实验和吲哚的分配行为的可能解释。
Several experimental structures of integral membrane proteins have demonstrated that tryptophan side chains are found preferentially within the membrane interface, but no clear physical explanation for this preference has been demonstrated. The present work contains a series of molecular dynamics simulations designed to provide insight into this phenomenon. Specifically, we performed conventional unbiased simulations, as well as biased molecular dynamics of indole and N-methylindole within palmitoyloleoyl phosphatidylcholine (POPC) bilayers. The unbiased calculations examined the behavior of the indoles in three environments-the membrane center, the headgroup region, and the water outside the membrane. The biased calculations were performed using a new dynamic windowing procedure, which efficiently moved the indoles through the bilayer. These calculations allowed us to explore the orientation, hydrogen bonding, and energetics of the indole, as a function of its location along the membrane normal. Furthermore, free energy profiles were constructed from the biased simulations, facilitating comparison to experiment and a possible explanation of indole's partitioning behavior.