Molecular Dynamics Simulation Analyses of the Conformational Change of an Escherichia coli Multidrug Exporter, MdfA

Molecular dynamics (MD) simulations are a powerful tool to investigate the dynamics and the conformational distributions of proteins. My collaborators and I applied them to study the proton transport-coupled conformational change of an Escherichia coli multidrug exporter, MdfA. In this chapter, I first describe the theoretical basis for studying the dynamics and the conformational distributions of a protein using MD simulations. Second, I describe the methods to construct the simulation system, in which the protein is embedded in a solvated lipid bilayer, and those employed to conduct the MD simulations and to analyze the results. Finally, I describe the problems that remain unsolved and present a plan to further study the transport mechanism of MdfA using MD methods.