Tieleman D P, Berendsen H J
BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands.
Biophys J. 1998 Jun;74(6):2786-801. doi: 10.1016/S0006-3495(98)77986-X.
In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square deviation from the crystal structure of 0.23 nm and a stable secondary structure. No evidence is found for large-scale motions of the L3 loop. We investigate the pore dimensions, conductance, and the properties of water inside the pore. This water forms a complicated pattern, even when averaged over 1 ns of simulation time. Around the pore constriction zone the water dipoles are highly structured in the plane of the membrane, oriented by the strong transversal electric field. In addition, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The diffusion coefficients of water inside the pore are greatly reduced compared to bulk. We compare our results to results from model pores (Breed et al., 1996. Biophys. J. 70:1 643-1 661; Sansom et al. 1997. Biophys. J. 73:2404-241 5) and discuss implications for further theoretical work.
在本文中，我们基于对大肠杆菌外膜孔蛋白F（OmpF）三聚体、318个棕榈酰油酰磷脂酰乙醇胺脂质、27个钠离子和12992个水分子的分子动力学模拟，研究了由OmpF形成的孔的性质。经过平衡和纳秒级的生产运行后，OmpF三聚体与晶体结构的C-α均方根偏差为0.23纳米，且具有稳定的二级结构。未发现L3环有大规模运动的证据。我们研究了孔的尺寸、电导率以及孔内水的性质。即使在1纳秒的模拟时间内进行平均，这种水也形成了复杂的模式。在孔的收缩区周围，水偶极子在膜平面内高度有序排列，由强横向电场定向。此外，沿孔轴存在从双层膜的细胞外侧指向细胞内侧的净取向。与本体相比，孔内水的扩散系数大大降低。我们将我们的结果与模型孔的结果（Breed等人，1996年。《生物物理杂志》70:1 643 - 1 661；Sansom等人，1997年。《生物物理杂志》73:2404 - 241 5）进行了比较，并讨论了对进一步理论工作的影响。
