Department of Biochemistry & Biotechnology, University of Thessaly Ploutonos 26 & Aeolou, Larisa GR-41221, Greece.
J Mol Graph Model. 2010 Dec;29(4):565-72. doi: 10.1016/j.jmgm.2010.10.004. Epub 2010 Oct 23.
Bacterial signal transduction systems can be viewed as an entity of multi-sensory and output domains, whereas the functions of response regulators play a pivotal role in the complex network interactions. One crucial property among response regulators functions is their oligomerization and subsequent binding to DNA. The AtoS-AtoC two component system, functionally modulated by various agents, influences fundamental cellular processes such as short-chain fatty acid catabolism and poly-(R)-3-hydroxybutyrate biosynthesis in Escherichia coli. Among the already reported characteristic properties, AtoC binds to a specific site, a palindromic repeat of 20 nucleotides within the atoDAEB promoter. Since experimental structures of AtoC or its complex with DNA are not yet available, an almost complete homology model of AtoC and of its putative entity as a dimer is constructed for this study, as well as a model of its binding to its target DNA sequence. The latter is associated with large conformational changes, as shown by molecular dynamics simulations. Subsequent biochemical study, including cross-linking via chemical agents, revealed the ability of AtoC to form oligomers in vitro.
细菌信号转导系统可以看作是多感觉和输出域的实体，而响应调节剂的功能在复杂的网络相互作用中起着关键作用。在响应调节剂功能中，一个关键特性是它们的寡聚化和随后与 DNA 的结合。阿托斯-阿托 C 双组分系统受各种因素的功能调节，影响大肠杆菌中基本的细胞过程，如短链脂肪酸代谢和聚（R）-3-羟基丁酸的生物合成。在已经报道的特征性质中，阿托 C 与一个特定的位点结合，即在 atoDAEB 启动子内的 20 个核苷酸的回文重复。由于阿托 C 或其与 DNA 的复合物的实验结构尚不可用，因此为这项研究构建了阿托 C 及其假定二聚体的几乎完整的同源模型，以及其与靶 DNA 序列结合的模型。后者如分子动力学模拟所示，伴随着大的构象变化。随后的生化研究，包括通过化学试剂进行交联，揭示了阿托 C 在体外形成寡聚体的能力。
