Yesudhas Dhanusha, Anwar Muhammad Ayaz, Choi Sangdun
Department of Molecular Science and Technology, Ajou University Suwon 16499 Korea
RSC Adv. 2019 Mar 13;9(14):8121-8130. doi: 10.1039/c8ra10085c. eCollection 2019 Mar 6.
The efficiency of stem cell transcriptional regulation always depends on the cooperative association and expression of transcription factors (TFs). Among these, Oct4, Sox2, and Nanog play major roles. Their cooperativity is facilitated direct protein-protein interactions or DNA-mediated interactions, yet the mechanism is not clear. Most biochemical studies have examined Oct4/Sox2 cooperativity, whereas few studies have evaluated how Nanog competes in the connection between these TFs. In this study, using computational models and molecular dynamics simulations, we built a framework representing the DNA-mediated cooperative interaction between Nanog and Sox2 and analyzed the plausible interaction factors experienced by Nanog because of Sox2, its cooperative binding partner. Comparison of a wild-type and mutant Nanog/Sox2 model with the Nanog crystal structure revealed the regulatory structural mechanism between Nanog/Sox2-DNA-mediated cooperative bindings. Along with the transactivation domains interaction, the DNA-mediated allosteric interactions are also necessary for Nanog cooperative binding. DNA-mediated Nanog-Sox2 cooperativity influences the protein conformational changes and a stronger interaction profile was observed for Nanog-Mut (L103E) in comparison with the Nanog-WT complex.
干细胞转录调控的效率总是依赖于转录因子（TFs）的协同结合与表达。其中，Oct4、Sox2和Nanog发挥着主要作用。它们的协同作用通过直接的蛋白质-蛋白质相互作用或DNA介导的相互作用来促进，但具体机制尚不清楚。大多数生化研究都考察了Oct4/Sox2的协同作用，而很少有研究评估Nanog在这些转录因子之间的联系中是如何竞争的。在本研究中，我们使用计算模型和分子动力学模拟，构建了一个代表Nanog和Sox2之间DNA介导的协同相互作用的框架，并分析了Nanog因其协同结合伙伴Sox2而可能经历的相互作用因素。将野生型和突变型Nanog/Sox2模型与Nanog晶体结构进行比较，揭示了Nanog/Sox2-DNA介导的协同结合之间的调控结构机制。除了反式激活结构域相互作用外，DNA介导的变构相互作用对于Nanog的协同结合也是必要的。DNA介导的Nanog-Sox2协同作用影响蛋白质构象变化，并且与Nanog-WT复合物相比，观察到Nanog-Mut（L103E）具有更强的相互作用谱。
