Computational Insights Into Serine and DHMA Binding to the Tsr Chemoreceptor of Escherichia Coli

Abstract

3,4-Dihydroxymandelic Acid (DHMA) has been reported to attract Escherichia coli by binding to the serine-binding sites of the bacteria’s Tsr chemoreceptor. Signaling via the Tsr chemoreceptor may promote the growth and virulence of E. coli and other bacteria with serine sensing receptors. In this study, we aimed to elucidate the binding conformation of DHMA in the Tsr chemoreceptor through implicit-solvent molecular dynamics (MD) simulations and free energy calculations. Our findings give insight to how DHMA binds to Tsr and suggests receptor residues that may be key to binding and signaling. We intend to continue this study by docking DHMA in one binding pocket at a time, rather than having both binding pockets of Tsr occupied, and using additional explicit-solvent MD simulations. These results provide impetus for new computational and experimental studies.