Computational approach to ensure the stability of the favorable ATP binding site in E. coli Hfq
Computational approach to ensure the stability of the favorable ATP binding site in E. coli Hfq
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DOI：
10.1016/j.jmgm.2010.11.003
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发表时间：
2010-12-01
影响因子：
2.9
通讯作者：
Lee, Keun Woo
中科院分区：
文献类型：
--
作者：
Lazar, Prettina;Kim, Songmi;Lee, Keun Woo
细菌Hfq是一种高度保守的热稳定蛋白，分子量约为10 kDa。Hfq蛋白是在1968年作为一种E.大肠杆菌宿主因子，这是必不可少的复制噬菌体Q β。现在很明显，HFq具有许多重要的生理作用。在大肠杆菌Hfq突变体表现出多种应激反应相关的表型。目前已知Hfq调节肠杆菌中两种主要应激转录因子RpoS和RpoE的翻译，并通过多种机制介导其多营养效应。它与调控sRNA相互作用，并促进它们与其靶标的反义相互作用。它还独立地调节mRNA降解，此外还作为mRNA翻译的阻遏物。最近Arluison等人的论文[9]提供了第一个证据表明Hfq是一种ATP结合蛋白。他们确定了Hfq中一个合理的ATP结合位点，并测试了Hfq的ATP结合亲和力和化学计量。实验数据表明，通过Hfq-RNA复合物的ATP结合导致蛋白质的显著不稳定，并且结果还证明了Tyr 25的重要作用，Tyr 25位于裂缝的侧翼并稳定ATP的腺嘌呤部分，可能通过芳香堆积。在我们的研究中，使用GOLD对接软件将ATP分子对接到预测的结合裂缝中。利用分子动力学模拟研究了ATP的结合性质及其对Hfq-RNA复合物的影响。Tyr 25残基的重要性进行了监测，并显示使用突变研究的建模系统。我们的数据和相应的结果指出，由于ATP结合和Tyr 25 Ala突变的Hfq功能结构的后果之一。(C)2010年由Elsevier Inc.出版
Bacterial Hfq is a highly conserved thermostable protein of about 10 kDa. The Hfq protein was discovered in 1968 as an E. coli host factor that was essential for replication of the bacteriophage Q beta. It is now clear that Hfq has many important physiological roles. In E. coli. Hfq mutants show a multiple stress response related phenotypes. Hfq is now known to regulate the translation of two major stress transcription factors RpoS and RpoE in Enterobacteria and mediates its plieotrophic effects through several mechanisms. It interacts with regulatory sRNA and facilitates their antisense interaction with their targets. It also acts independently to modulate mRNA decay and in addition acts as a repressor of mRNA translation. Recent paper from Arluison et al. [9] provided the first evidence indicating that Hfq is an ATP-binding protein. They determined a plausible ATP-binding site in Hfq and tested Hfq's ATP-binding affinity and stoichiometry. Experimental data suggest that the ATP-binding by the Hfq-RNA complex results in its significant destabilization of the protein and the result also proves important role of Tyr25 that flanks the cleft and stabilizes the adenine portion of ATP, possibly via aromatic stacking. In our study, the ATP molecule was docked into the predicted binding cleft using GOLD docking software. The binding nature of ATP and its effect on Hfq-RNA complex was studied using molecular dynamics simulations. Importance of Tyr25 residue was monitored and revealed using mutational study on the modeled systems. Our data and the corresponding results point to one of Hfq functional structural consequences due to ATP binding and Tyr25Ala mutation. (C) 2010 Published by Elsevier Inc.