Dimerization of the AtoC response regulator and modelling of its binding to DNA

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.

Figure optionsDownload high-quality image (156 K)Download as PowerPoint slideResearch highlights▶ The AtoC response regulator binds to a repeat of 20 nucleotides within the atoDAEB promoter. ▶ Molecular Modelling of the dimerization of AtoC and specifically its DNA-binding domain. ▶ Modelling of the inverted palindrome AtoC-target sequence. ▶ Docking of AtoC to its binding target. ▶ Biochemical study of the ability of AtoC to form oligomers in vitro.