Monte Carlo analysis of obstructed diffusion in three dimensions:: Application to molecular diffusion in organelles
Monte Carlo analysis of obstructed diffusion in three dimensions:: Application to molecular diffusion in organelles
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DOI：
10.1016/s0006-3495(98)77978-0
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发表时间：
1998-05-01
影响因子：
3.4
通讯作者：
Verkman, AS
中科院分区：
文献类型：
--
作者：
ﾃ僕veczky, BP;Verkman, AS
分子在细胞器房水腔中的传输涉及到复杂几何结构的受限隔室中的扩散。用蒙特卡罗方法模拟了颗粒在三维空间中的扩散，以评价细胞器结构对扩散输运的影响，并将实验光漂白数据与本征扩散系数联系起来。模拟了两种细胞器结构：一种是含有数量和大小可变的固定管腔阻塞物的线粒体状长封闭圆柱体，另一种是由直径和密度可变的相互连接的圆柱体组成的内质网状网络。在每次模拟中计算>；10(5)粒子的轨迹，通常是计算>；10(5)时间步长。对于简单几何结构，计算的随时间变化的浓度分布与扩散方程的解析解定量地吻合。对于线粒体样的圆柱体，要显著减缓扩散，需要较大或较宽的单一障碍，或多个障碍。在模拟的斑点光漂白实验中，对于单个遮挡93%的管腔面积的薄横向障碍、宽度为53%的单一遮挡障碍物(16个格点(圆柱体长度的8%)、10个等间距的53%障碍物交替遮挡圆柱体内腔的对侧半部分、或粒子结合到壁上(平均停留时间=10个时间步长)，表观扩散传输速率(由到75%荧光恢复的时间定义)的下降类似于25%。有障碍物的恢复曲线形状呈长尾，显示异常扩散。模拟还证明了在远离漂白区的点上测量荧光耗竭的实用性。对于网状网络，粒子的扩散输运比在无障碍的三维空间中的扩散输运略有减少。在模拟光漂白实验中，当90-97%的空间被遮挡时，网状结构的表观扩散传输减少了39%-60%。这些计算提供了一种根据微观扩散特性分析光漂白数据的方法，并支持细胞器势垒必须相当严重才能严重阻碍溶质扩散的范式。
Molecular transport in the aqueous lumen of organelles involves diffusion in a confined compartment with complex geometry. Monte Carlo simulations of particle diffusion in three dimensions were carried out to evaluate the influence of organelle structure on diffusive transport and to relate experimental photobleaching data to intrinsic diffusion coefficients. Two organelle structures were modeled: a mitochondria-like long closed cylinder containing fixed luminal obstructions of variable number and size, and an endoplasmic reticulum-like network of interconnected cylinders of variable diameter and density. Trajectories were computed in each simulation for >10(5) particles, generally for >10(5) time steps. Computed time-dependent concentration profiles agreed quantitatively with analytical solutions of the diffusion equation for simple geometries. For mitochondria-like cylinders, significant slowing of diffusion required large or wide single obstacles, or multiple obstacles. In simulated spot photobleaching experiments, a similar to 25% decrease in apparent diffusive transport rate (defined by the time to 75% fluorescence recovery) was found for a single thin transverse obstacle occluding 93% of lumen area, a single 53%-occluding obstacle of width 16 lattice points (8% of cylinder length), 10 equally spaced 53% obstacles alternately occluding opposite halves of the cylinder lumen, or particle binding to walls (with mean residence time = 10 time steps). Recovery curve shape with obstacles showed long tails indicating anomalous diffusion. Simulations also demonstrated the utility of measurement of fluorescence depletion at a spot distant from the bleach zone. For a reticulum-like network, particle diffusive transport was mildly reduced from that in unobstructed three-dimensional space. In simulated photobleaching experiments, apparent diffusive transport was decreased by 39-60% in reticular structures in which 90-97% of space was occluded. These computations provide an approach to analyzing photobleaching data in terms of microscopic diffusive properties and support the paradigm that organellar barriers must be quite severe to seriously impede solute diffusion.