Binding of SoxR protein to two promoter-operator regions to regulate sox gene expression: A detailed molecular insight for structural changes and protein-DNA interactions

Abstract

Abstract SoxR protein is the repressor protein of the sulfur oxidizing sox operon. The most interesting feature of the sox operon is that the operon comes into play only when sulfur substrates are present in the environment. SoxR protein regulates the sox gene expression. Previously, different experimental procedures revealed that SoxR protein interacts with two promoter-operator regions referred to as sv (present between the soxS and soxV genes) and wx (present between the soxW and soxX genes). However, the mechanistic details of the SoxR-DNA interactions have not yet been fully understood. In order to find the mode of the binding interactions between the DNA and the SoxR protein, we employed molecular modeling techniques to build the models of SoxR-DNA complexes. The models of SoxR-DNA complexes were subjected to molecular mechanics and molecular dynamics simulations. The details of the binding interactions were then analyzed to predict the plausible mechanistic details. Additionally, the number of hydrogen bonds and ΔG values disclosed the statistically significant thermodynamic stability of the protein for better and firmer interaction with maximum participation of residues.