Systems analysis of molecular networks based on biochemical computational simulations

许多生物现象都是由其内在的生物网络所调控的。这些网络包含了线性和非线性的关系，这使得很难在系统层次上理解整个网络。在这项研究中，为了克服这些困难，我们试图利用两个相互依赖的方法，预测在硅片计算机模拟和验证体内实验。本论文主要研究了两个现象：1）肌球蛋白轻链（MLC）磷酸化的分子网络; 2）小脑长时程抑制（LTD）的定量分析。通过基于文献的模拟模型，我们成功地复制了只有初始阶段，但没有持续阶段。该模型精确地指出了我们缺失的通路可能是Rho激酶下游的基础。我们通过实验验证了MYPT 1磷酸化对Rho激酶的持续激活（肌球蛋白磷酸酶靶亚基1），Rho激酶的底物，2）我们建立了一个小脑突触后Ca^<2+>增加的计算模型，该模型揭示了Ca^<2+>增加是由Ca^<2+>诱导的Ca ^<2 +>释放（CICR）引起的再生周期引起的。PF刺激产生IP 3的潜伏期在小脑中产生尖峰时间依赖性LTD的时间窗。此外，我们开发了一个统一的模型的Ca^<2+>的增加和下游信号级联。这个统一的模型提出了一种可能性，即小脑突触后棘调节自身的突触强度，以获得足够的Ca^<2+>增加，从而实现稳定的LTD。

Many biological phenomena are regulated by their intrinsic biological networks. These networks contain both linear and non-linear relationship, which make difficult to understand the whole networks at the systems level. In this study, to overcome these difficulties we tried to utilize two interdependent approaches, prediction by in silico computational simulation and validation by in vivo experiments. We focused on two phenomena, 1) molecular network in myosin light chain (MLC) phosphorylation and 2) quantitative analysis of cerebellar long-term depression (LTD).1)Dynamics of throbin-induced MLC phosphorylation in endothelium is composed of initial and sustained phases. By the literature-based simulation model we succeeded in the reproduction of only the initial but not the sustained phase. The model pinpointed us the missing pathway may underlie downstream of Rho-kinase. We experimentally validated the sustained activation of Rho-kinase by the phosphorylation of MYPT1 (myosin phosphatase target subunit 1), a substrate of Rho-kinase, which exhibited hysteresis.2)We developed a computational model of postsynaptic Ca^<2+> increase in cerebellar LTD. The model revealed that Ca^<2+> increase is induced by a regenerative cycle by Ca^<2+>-induced Ca^<2+> release (CICR) via IP3 receptors, and that the latency of IP3 generation by PF stimulation produces timing window of spike-timing dependent LTD in the cerebellum. Moreover, we developed a unified model of the Ca^<2+> increase and downstream signaling cascades. The unified model raised the possibility that postsynaptic spines of the cerebellum tune their own synaptic strength for adequate Ca^<2+> increase for robust LTD.