Molecular Dynamics to Elucidate the DNA-Binding Activity of AlpZ, a Member of the Gamma-Butyrolactone Receptor Family in Streptomyces ambofaciens.

摘要: Signaling molecule receptors play a central role in quorum sensing and the coordination onset of specialized metabolite biosynthesis Streptomyces due to their dual function signal detection gene expression control through DNA-binding promoter region target genes. In ambofaciens alp biosynthetic cluster includes signaling receptor AlpZ that negatively regulates complex regulatory cascade key genes involved kinamycin antibiotic production until its cognate ligand, yet unidentified molecule, prompts release from promoters. Here we use an original molecular dynamics method evaluate properties DNA sequence impact has on interaction. It is first time this approach used characterize regulator γ-butyrolactone family. The observed KD nanomolar range indicates AlpZ-DNA constitute particularly stable complex. ably disturbs binding while no effect activity AlpZ. Regulator size was determined found be considerably large regarding protein sequence, indicating by as homodimer, structural modeling comparison with closely related supports conclusion.