Particle simulation approach for subcellular dynamics and interactions of biological molecules.
Particle simulation approach for subcellular dynamics and interactions of biological molecules.
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DOI：
10.1186/1471-2105-7-s4-s20
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发表时间：
2006-12-12
影响因子：
3
通讯作者：
Konagaya, Akihiko
中科院分区：
文献类型：
--
作者：
Azuma, Ryuzo;Kitagawa, Tetsuji;Kobayashi, Hiroshi;Konagaya, Akihiko
由于分子成像技术的进步，细胞内的时空动态现在可以以适当的分辨率可视化。甚至单粒子跟踪（SPT）和单荧光团视频成像（SFVI）现在也被应用于分子水平动力学的观察。然而，关于分子水平的动力学如何影响细胞水平的性质知之甚少。我们提出了一种算法，设计用于三维模拟的反应扩散动力学的分子，基于粒子模型。化学反应通过空间中粒子的相互作用进行，活化能决定了每次相互作用时这些化学反应的速率。这种基于能量的模型可以包括细胞膜、其他细胞器的膜和细胞骨架。通过对一个可逆酶反应模型的仿真实验，验证了该算法的有效性。从细胞表面上模拟的分子相互作用拍摄的快照图像显示与筏相关的聚集域（尺寸约0.2 μm）。筏构造的样本轨迹表现出“跳跃扩散”。这些结构域控制着膜蛋白的扩散运动。这些发现表明，我们的方法是有前途的生物现象的本地化特性建模。
Spatio-temporal dynamics within cells can now be visualized at appropriate resolution, due to the advances in molecular imaging technologies. Even single-particle tracking (SPT) and single fluorophore video imaging (SFVI) are now being applied to observation of molecular-level dynamics. However, little is known concerning how molecular-level dynamics affect properties at the cellular level. We propose an algorithm designed for three-dimensional simulation of the reaction-diffusion dynamics of molecules, based on a particle model. Chemical reactions proceed through the interactions of particles in space, with activation energies determining the rates of these chemical reactions at each interaction. This energy-based model can include the cellular membrane, membranes of other organelles, and cytoskeleton. The simulation algorithm was tested for a reversible enzyme reaction model and its validity was confirmed. Snapshot images taken from simulated molecular interactions on the cell-surface revealed clustering domains (size ~0.2 μm) associated with rafts. Sample trajectories of raft constructs exhibited "hop diffusion". These domains corralled the diffusive motion of membrane proteins. These findings demonstrate that our approach is promising for modelling the localization properties of biological phenomena.