Mechanism of the All-伪 to All-尾 Conformational Transition of RfaH-CTD: Molecular Dynamics Simulation and Markov State Model

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• 作者：Shanshan Li ; Bing Xiong ; Yuan Xu ; Tao Lu ; Xiaomin Luo ; Cheng Luo ; Jingkang Shen ; Kaixian Chen ; Mingyue Zheng ; Hualiang Jiang
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2014
• 出版时间：June 10, 2014
• 年：2014
• 卷：10
• 期：6
• 页码：2255-2264
• 全文大小：612K
• 年卷期：v.10,no.6(June 10, 2014)
• ISSN：1549-9626

文摘

The C-terminal domain of the bacterial transcription antiterminator RfaH undergoes a dramatic all-伪-helix to all-尾-barrel transition when released from its N-terminal domain. These two distinct folding patterns correspond to different functions: the all-伪 state acts as an essential regulator of transcription to ensure RNA polymerase binding, whereas the all-尾 state operates as an activator of translation by interacting with the ribosomal protein S10 and recruits ribosomal mRNA. Accordingly, this drastic conformational change enables RfaH to physically couple the transcription and translation processes in gene expression. To understand the mechanism behind this extraordinary functionally relevant structural transition, we constructed Markov state models using an adaptive seeding method. The constructed models highlight several parallel folding pathways with heterogeneous molecular mechanisms, which reveal the folding kinetics and atomic details of the conformational transition.