Hiroi Noriko, Iba Keisuke, Tabira Akito, Okuhara Takahiro, Kubojima Takeshi, Hiraiwa Takumi, Kobayashi Tetsuya J, Oka Kotaro, Funahashi Akira
Annu Int Conf IEEE Eng Med Biol Soc. 2013;2013:2716-9. doi: 10.1109/EMBC.2013.6610101.
In vivo reaction space is constrained by complex structures which are made of entwined cytoskeletons and organelles; this create the difference between in vivo and in vitro in respect of molecular mobility, and it may affect reaction processes. Our motivation is to reveal the background mechanisms of the properties of molecular behaviors in vivo by numerical approach. For this object, we reassembled a pseudo-intracellular environment in 3D lattice space, and executed Monte Carlo simulation. By changing the relative amount of non-reactive obstacles in the simulation space, we tested the effect of the level of crowdedness to the molecular mobility and reaction processes. Our results showed that molecules demonstrated anomalous diffusion correlating to the restriction level of the reaction space. Reaction processes also showed distinct characteristics, that is increase of reaction rate at the beginning of reactions, with the decrease of the reaction rate at later time frame of reactions. Our results suggested that the anomalous behaviors at singe molecule level in vivo could bring an essential difference to the reaction processes and the results.
体内反应空间受到由缠绕的细胞骨架和细胞器构成的复杂结构的限制；这在分子流动性方面造成了体内和体外的差异，并且可能影响反应过程。我们的动机是通过数值方法揭示体内分子行为特性的背景机制。为了这个目标，我们在三维晶格空间中重新构建了一个伪细胞内环境，并进行了蒙特卡罗模拟。通过改变模拟空间中非反应性障碍物的相对数量，我们测试了拥挤程度对分子流动性和反应过程的影响。我们的结果表明，分子表现出与反应空间限制水平相关的反常扩散。反应过程也呈现出明显的特征，即在反应开始时反应速率增加，而在反应后期反应速率下降。我们的结果表明，体内单分子水平的反常行为可能给反应过程和结果带来本质差异。
