All-Atom Molecular Dynamics Simulation of Multidrug Efflux Transporter AcrB

Abstract

In E. coli, it is known that the tripartite multidrug efflux system (AcrB/ AcrA/ TolC) exists, and AcrB resides in the inner membrane region and take part in substrate recognition and energy transduction for drug export through proton transfer. Recently, x-ray structures provided that AcrB forms trimeric protein where each subunit is different conformation, “binding state”, “extrusion state” and “access state”. Especially, only extrusion state subunit has different side chain conformation of residues (Asp407, Asp408 and Lys940), which are essential for proton translocation (protonation site). These results suggest that drugs are exported by a three-step structural change involved in proton motive force which is inferred to be caused by change of protonation states of the protonation site residues. However, the structural change process which involved in proton motive force is still unclear. In the present study, we performed 100 ns all-atom molecular dynamics (MD) simulations of three types of AcrB-membrane-water systems which are different from protonation state of Asp407 and/or Asp408 in extrusion state protomer. During all of the 100 ns MD simulations, the global structures of each subunit were conserved. However, in extrusion state protomer, the conformation of the protonation site residues were changed to those of other state protomers only when Asp 407 and 408 residues were deprotonated. In this presentation, we will discuss the structural change and proton transfer mechanism.