Drug Extrusion Process of Mate Multidrug Efflux Transporter Revealed by Molecular Dynamics Simulations

Abstract

MATE (the Multidrug And Toxic compound Extrusion) is one of the five multidrug efflux transporter super-families. It is featured as primary secondary active transporter and comprises of 12 trans-membrane helices. The first and last six transmembrane helices (TMs) form N-lobe and C-lobe domains, showing a two-fold rotational symmetry. It is considered that the drug release/capture related motions are characterized by switching of inward/outward-facing conformations (rocker-switch model).Recently, multiple structures of the MATE from P.furiosus (PfMATE), has been determined by X-ray crystallography in outward-facing conformation. Two distinct structures ‘Straight’ and ‘Bent’ are characterized by conformations of TM1. Furthermore, PfMATE is shown to be H+ driven antiporter, suggesting that D41 and D184 in N-lobe are involved as important proton pathway. It is also interesting that MATE has the hydrophobic surface of inner cavity, since other multidrug transporters exhibit hydrophilic. The sharply opened interface to the lipid molecules suggests the possibilities that the lipid molecules intensively interact with the inside of the cavity.To further elucidate the drug release mechanism in outward facing stage, we adopted several promising simulation methods, continuum electrostatic analysis to predict protonation states, a number of independent all-atom Molecular Dynamics (MD) simulations by changing conditions (initial conformations, protonations, lipid positions, etc.) for dynamics and interactions, and quantum mechanics calculation for drug forcefield development. Our results suggest that D41 is protonated in Straight, while D41 and D184 are both protonated in Bent. Furthermore, we successfully observed multiple drug release events in some conditions of MD simulations. In the poster presentation, we will report and discuss the dynamics and interactions of PfMATE revealed by different conditions of MDs. We will also discuss the insights of the drug release mechanism of PfMATE obtained by the simulations.