Salmonella Typhi TolC protein: A molecular dynamics investigation

Introduction: The TolC family of proteins of Escherichia coli and other pathogenic Gram negative bacteria plays an important role as an outer membrane channel for the expulsion of drug and toxin from the cell. Typhoid fever, caused by Salmonella enterica serovar Typhi kills more than 200 000 lives annually. In S. Typhi, a TolC outer membrane protein was found to be antigenic for this pathogen. Understanding the dynamics of the S. Typhi TolC protein is essential towards development of diagnostics, therapeutics and vaccine towards typhoid fever. Therefore, molecular dynamics simulation has been performed on the protein. Objective: To refine homology structure of S. Typhi TolC protein by molecular dynamics simulation. Methods: A homology model of the S. Typhi TolC protein was embedded in phosphatidylethanolamine lipid bilayer. Water molecules were added and the system was subsequently neutralized. Minimization was performed by steepest descent method following which; temperature was equilibrated at 310.15K in the NVT ensemble. A 1 ns NPT run was performed with restraint on protein atoms to maintain pressure at 1 bar. Finally, production simulation was performed for 20 ns without restraints in the NPT ensemble. The average structure of the protein was generated by RMS fitting of all protein atoms from the production run and averaging over the coordinates. Results & Discussion: Results showed that the membrane simulation was energetically stable and reproduced experimental value. The protein conformation was also stable in simulation. Conformational analysis showed that the protein is highly mobile at the extracellular loops and periplasmic helices region. From Ramachandran plot and Errat analysis, the average structure showed improvements over the initial model. Conclusion: The average structure could be advantageous in aiding design efforts for inhibitors and binders against the S. Typhi TolC protein. � 2014 Asian Pacific Tropical Medicine Press.