Chen C-M, Zuckermann M
Department of Physics, National Taiwan Normal University, Taipei, Taiwan.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Nov;86(5 Pt 1):051905. doi: 10.1103/PhysRevE.86.051905. Epub 2012 Nov 5.
We use a minimal model to study the processive motion of coupled synthetic molecular motors along a DNA track and we present data from Monte Carlo (MC) computer simulations based on this model. The model was originally proposed by Bromley et al. [HFSP J. 3, 204 (2009)] for studying the properties of a synthetic protein motor, the "Tumbleweed" (TW), and involves rigid Y-shaped motors diffusively rotating along the track while controlled by a series of periodically injected ligand pulses into the solution. The advantage of the model is that it mimics the mechanical properties of the TW motor in detail. Both the average first passage time which measures the diffusive motion of the motors, and the average dwell time on the track which measures their processivity are investigated by varying the parameters of the model. The latter includes ligand concentration and the range and strength of the binding interaction between motors and the track. In particular, it is of experimental interest to study the dependence of these dynamic time scales of the motors on the ligand concentration. Single rigid TW motors were first studied since no previous MC simulations of these motors have been performed. We first studied single motors for which we found a logarithmic decrease of the average first passage time and a logarithmic increase of the average dwell time with increasing ligand concentration. For two coupled motors, the dependence on ligand concentration is still logarithmic for the average first passage time but becomes linear for the average dwell time. This suggests a much greater stability in the processive motion of coupled motors as compared to single motors in the limit of large ligand concentration. By increasing the number of coupled motors, m, it was found that the average first passage time of the coupled motors only increases slowly with m while the average dwell time increases exponentially with m. Thus the stability of coupled motors on the track can be considerably enhanced by their cooperative motion.
我们使用一个最小模型来研究耦合的合成分子马达沿DNA轨道的持续运动，并展示基于该模型的蒙特卡罗（MC）计算机模拟数据。该模型最初由Bromley等人[《HFSP杂志》3, 204 (2009)]提出，用于研究合成蛋白马达“风滚草”（TW）的特性，涉及刚性Y形马达在轨道上进行扩散旋转，同时由一系列周期性注入溶液中的配体脉冲进行控制。该模型的优点是它详细地模拟了TW马达的机械特性。通过改变模型参数，研究了测量马达扩散运动的平均首次通过时间以及测量其持续性的在轨道上的平均停留时间。后者包括配体浓度以及马达与轨道之间结合相互作用的范围和强度。特别地，研究马达的这些动态时间尺度对配体浓度的依赖性具有实验意义。由于此前尚未对这些马达进行过MC模拟，所以首先研究了单个刚性TW马达。我们首先研究了单个马达，发现随着配体浓度增加，平均首次通过时间呈对数下降，平均停留时间呈对数增加。对于两个耦合马达，平均首次通过时间对配体浓度的依赖性仍然是对数关系，但平均停留时间变为线性关系。这表明在大配体浓度极限下，与单个马达相比，耦合马达的持续运动具有更高的稳定性。通过增加耦合马达的数量m，发现耦合马达的平均首次通过时间仅随m缓慢增加，而平均停留时间随m呈指数增加。因此，耦合马达在轨道上的稳定性可通过它们的协同运动得到显著增强。
