Jiang Hanlun, Sheong Fu Kit, Zhu Lizhe, Gao Xin, Bernauer Julie, Huang Xuhui
Bioengineering Graduate Program, Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; The HKUST Shenzhen Research Institute, Shenzhen, China.
Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
PLoS Comput Biol. 2015 Jul 16;11(7):e1004404. doi: 10.1371/journal.pcbi.1004404. eCollection 2015 Jul.
Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems.
Argonaute（Ago）蛋白和微小RNA（miRNA）是RNA干扰的核心组成部分，RNA干扰是一种关键的细胞机制，用于序列特异性基因沉默。尽管进行了深入研究，但Ago如何识别miRNA的分子机制仍不清楚。在本研究中，我们提出了这种分子识别的两步机制：选择性结合，随后是结构重排。我们的模型基于马尔可夫状态模型（MSM）、大规模蛋白质-RNA对接和分子动力学（MD）模拟相结合的结果。使用MSM，我们确定了无配体人Ago-2的一种开放状态，它与部分开放和封闭状态处于快速平衡。如我们的蛋白质-RNA对接研究所表明的，这种开放状态下的构象的特点是其结合凹槽大部分暴露，能够在几何上容纳miRNA。然后，miRNA可能选择性地结合到这些开放构象上。在初始结合后，复合物可能如我们的MD模拟所示进行进一步的结构重排，并最终达到稳定的二元复合物结构。我们的结果为Ago-miRNA识别机制提供了新的见解，并且我们的方法在研究其他重要的分子识别系统方面具有广泛应用的巨大潜力。
