Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study
Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study
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不同环境下聚酰胺B通道内溶剂分子的结构和动力学：分子动力学研究
DOI：
10.1039/c7cp06299k
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发表时间：
2018
影响因子：
3.3
通讯作者：
Saito Shinji
中科院分区：
文献类型：
--
作者：
Kalathingal Mahroof;Sumikama Takashi;Mori Toshifumi;Oiki Shigetoshi;Saito Shinji
用全原子分子动力学模拟方法研究了海洋细胞毒性肽聚茶酰胺B（pTB）在水、POPC双层膜和1：1氯仿/甲醇混合物中的β6.3螺旋通道。 研究了pTB β6.3-螺旋在三种环境中的结构和涨落。在混合溶剂中计算的pTB的平均结构与混合溶剂中的NMR解析结构良好一致，表明用于pTB中的非标准基团的参数的有效性。详细研究了孔内溶剂分子的构型和动力学。研究发现，由于相邻甲醇分子之间没有强氢键，甲醇分子在孔内的运动不相关。另一方面，由于相邻水分子之间的强氢键，孔隙内的水分子的运动在方向和方向上都高度相关。这表明，在膜中的孔内的水分子的集体行为是至关重要的离子通过pTB通道的渗透。
The β6.3-helical channel of the marine cytotoxic peptide, polytheonamide B (pTB), is examined in water, the POPC bilayer, and a 1 : 1 chloroform/methanol mixture using all-atom molecular dynamics simulations. The structures and fluctuations of the β6.3-helix of pTB are investigated in the three environments. The average structure of pTB calculated in the mixed solvent is in good agreement with the NMR-resolved structure in the mixed solvent, indicating the validity of the parameters used for the non-standard groups in pTB. The configuration and dynamics of solvent molecules inside the pore are examined in detail. It is found that the motions of methanol molecules inside the pore are not correlated because of the absence of strong hydrogen bonds (HBs) between adjacent methanol molecules. On the other hand, the motions of water molecules inside the pore are highly correlated, both translationally and orientationally, due to the strong HBs between neighboring water molecules. It is suggested that the collective behavior of water molecules inside the pore in the membrane is crucial for the permeation of ions through the pTB channel.