Imaging α-hemolysin with molecular dynamics:: Ionic conductance, osmotic permeability, and the electrostatic potential map
Imaging α-hemolysin with molecular dynamics:: Ionic conductance, osmotic permeability, and the electrostatic potential map
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DOI：
10.1529/biophysj.104.058727
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发表时间：
2005-06-01
影响因子：
3.4
通讯作者：
Schulten, K
中科院分区：
文献类型：
--
作者：
Aksimentiev, A;Schulten, K
金黄色葡萄球菌α-溶血素是一种自组装毒素，在脂膜上齐聚形成充满水的跨膜通道。除了是研究最充分的细菌源毒素之一，α-溶血素还是几种生物技术应用的主要成分，包括控制小溶质通过脂膜输送的系统，小溶质的随机传感器，以及传统DNA测序技术的替代技术。通过大规模分子动力学模拟，研究了α-溶血素/脂双层复合体对水和离子的渗透性。所研究的体系由300,000个原子组成，包括一个蛋白质拷贝，一个DPPC脂质双层贴片和一个1M的KCl水溶液。监测孔结构的变化显示，α-溶血素茎的平均横截面不对称。施加外加静电场产生跨膜离子电流；在几个电压偏置下重复模拟，得到α-溶血素的电流/电压曲线和一组静电电位图。发现α-溶血素对氯离子的选择性依赖于外加偏压的方向和大小。我们的模拟结果与现有的实验数据有很好的定量一致性。分析了所有水分子的运动轨迹，计算了α-溶血素对水的渗透渗透率和电渗透效应，并表征了其七个侧通道的渗透性。侧通道被发现连接蛋白质茎周围的7个His-144残基和主体溶液；观察到这些残基的质子化影响离子电导，表明7个His-144组成了门控a-溶血素通道电导的pH传感器。
alpha-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being one of the best-studied toxins of bacterial origin, alpha-hemolysin is the principal component in several biotechnological applications, including systems for controlled delivery of small solutes across lipid membranes, stochastic sensors for small solutes, and an alternative to conventional technology for DNA sequencing. Through large-scale molecular dynamics simulations, we studied the permeability of the alpha-hemolysin/lipid bilayer complex for water and ions. The studied system, composed of; 300,000 atoms, included one copy of the protein, a patch of a DPPC lipid bilayer, and a 1 M water solution of KCl. Monitoring the fluctuations of the pore structure revealed an asymmetric, on average, cross section of the alpha-hemolysin stem. Applying external electrostatic fields produced a transmembrane ionic current; repeating simulations at several voltage biases yielded a current/voltage curve of alpha-hemolysin and a set of electrostatic potential maps. The selectivity of alpha-hemolysin to Cl- was found to depend on the direction and the magnitude of the applied voltage bias. The results of our simulations are in excellent quantitative agreement with available experimental data. Analyzing trajectories of all water molecule, we computed the alpha-hemolysin's osmotic permeability for water as well as its electroosmotic effect, and characterized the permeability of its seven side channels. The side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk solution; the protonation of these residues was observed to affect the ion conductance, suggesting the seven His-144 to comprise the pH sensor that gates conductance of the a-hemolysin channel.