短杆菌肽A-DMPC通道内离子输运的分子动力学模拟

用最近提出的构建膜体系初始构象的有效方法 ,构建了在DMPC脂膜环境下短杆菌肽A通道模型 (GA -DMPC)。通过对Na 、Ca2 、Cl-三种不同离子在GA -DMPC通道内不同位置的分子动力学模拟 ,研究离子在通道内输运过程中与通道及通道内水分子的相互作用 ,从分子动力学的角度阐明离子在通道内的输运机制。主要计算结果表明 :(1)离子在通道内的输运使GA的构象发生变化 ,GA的柔性是离子在通道内通透的重要因素 ;(2)Cl- 离子可扩大通道半径 ,Na 离子和Ca2 离子则减小通道半径。Cl-离子不能在GA通道内通透 ;(3)离子的出现使通道内水分子的偶极方向发生变化。上述结果均与实验相符。

MOLECULAR DYNAMICS SIMULATIONS OF THE ION TRASPORTATION IN THE GRAMICIDIN A-DMPC CHANNEL

The gramicidin A-DMPC (GA-DMPC) channel model was built with the new efficient approach for constructing the initial configuration. Molecular dynamics (MD) simulations were performed for different models with three different ions (Na , Ca2 and Cl-). The interactions of ion with the GA channel and water molecules in the channel pore were analyzed. The transportation mechanism of ion in the GA-DMPC channel was explained based on the MD simulations. The Main calculation results indicate the following points: (1) The conformational changes of GA are due to the ion permeation in the channel pore, and the flexibility of GA is the key factor for the ion permeation through the channel. (2) The Cl- ion can enlarge the local pore radius but the Na ion and Ca2 ion can reduce the local pore radius. Moreover, the Cl- ion can not permeate through the GA channel. (3) The dipole orientations of water molecules in the GA channel are changed when ions appear in the channel. All above three results are in agreement with experiment data.