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空间不均匀膜中带电脂质和外周蛋白的侧向动力学:连续和蒙特卡罗方法的比较。

Lateral dynamics of charged lipids and peripheral proteins in spatially heterogeneous membranes: comparison of continuous and Monte Carlo approaches.

机构信息

Centre for Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom.

出版信息

J Chem Phys. 2011 Oct 21;135(15):155103. doi: 10.1063/1.3652958.

Abstract

Biological membranes are complex environments whose physico-chemical properties are of utmost importance for the understanding of many crucial biological processes. Much attention has been given in the literature to the description of membranes along the z-axis perpendicular to the membrane. Here, we instead consider the lateral dynamics of lipids and peripheral proteins due to their electrostatic interaction. Previously, we constructed a Monte Carlo automaton capable of simulating mutual diffusive dynamics of charged lipids and associated positively charged peptides. Here, we derive and numerically analyze a system of Poisson-Boltzmann-Nernst-Planck (PBNP) equations that provide a mean-field approximation compatible with our Monte Carlo model. The thorough comparison between the mean-field PBNP equations and Monte Carlo simulations demonstrates that both the approaches are in a good qualitative agreement in all tested scenarios. We find that the two methods quantitatively deviate when the local charge density is high, presumably because the Poisson-Boltzmann formalism is applicable in the so-called weak coupling limit, whose validity is restricted to low charge densities. Nevertheless, we conclude that the mean-field PBNP approach provides a good approximation for the considerably more detailed Monte Carlo model at only a fraction of the associated computational cost and allows simulation of the membrane lateral dynamics on the space and time scales relevant for the realistic biological problems.

摘要

生物膜是复杂的环境,其物理化学性质对于理解许多关键的生物过程至关重要。文献中已经有很多关于沿垂直于膜的 z 轴描述膜的内容。在这里,我们则考虑由于静电相互作用而导致的脂质和外周蛋白的侧向动力学。此前,我们构建了一个蒙特卡罗自动机,能够模拟带电脂质和相关带正电荷肽的相互扩散动力学。在这里,我们推导出并数值分析了一个泊松-玻尔兹曼-能斯特-普朗克(PBNP)方程组系统,该系统提供了与我们的蒙特卡罗模型兼容的平均场近似。平均场 PBNP 方程与蒙特卡罗模拟的彻底比较表明,在所有测试场景中,这两种方法在定性上都非常吻合。我们发现,当局部电荷密度较高时,两种方法在定量上存在差异,这可能是因为泊松-玻尔兹曼公式适用于所谓的弱耦合极限,其有效性仅限于低电荷密度。然而,我们得出的结论是,平均场 PBNP 方法在计算成本仅为相关蒙特卡罗模型的一小部分的情况下,为更详细的蒙特卡罗模型提供了良好的近似,并允许在与实际生物问题相关的空间和时间尺度上模拟膜的侧向动力学。

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