Probing Mechanical and Thermodynamic Properties of Vibrio Cholerae ToxT Binding to DNA by Molecular Dynamics Simulations

The main objective of this research is to investigate DNA binding mechanisms to ToxT, a transcriptional activator of genes coding Cholera Toxin (CT) and Toxin Co-regulated Pilus (TCP). Determining the molecular mechanism of DNA-ToxT interaction is a milestone towards full understanding of the acute intestinal infection caused by the bacterium V. cholerae. ToxT binds to 13-bp sequences called toxboxes, which are located upstream of the genes whose transcription isactivated by ToxT. In the present study, all-atom Molecular Dynamics Simulations (MD) were performed to obtain trajectories of the solvated, neutralized, and equilibrated toxbox system in the NPT ensemble. These data were used to obtain thermodynamic properties of the toxbox system by calculating energies using the MD implementation of the generalized Born/surface area (GB/SA) implicit solvation method, and configurational entropies by normal mode analysis. The effects of sequence-dependent DNA conformation (DNA crookedness) on mechanical properties of the toxbox system was studied by performing MD on toxboxes subject to constant stretching forces.