Metadynamics Study of Lipid-Mediated Antibacterial Toxin Binding to the EmrE Multiefflux Protein

EmrE
is a bacterial efflux protein in the small multidrug-resistant
(SMR) family present in Escherichia coli. Due to its small size, 110 residues in each dimer subunit, it is
an ideal model system to study ligand–protein–membrane
interactions. Here in our work, we have calculated the free energy
landscape of benzyltrimetylammonium (BTMA) and tetraphenyl phosphonium
(TPP) binding to EmrE using the enhanced sampling method-multiple
walker metadynamics. We estimate that the free energy of BTMA binding
to EmrE is −21.2 ± 3.3 kJ/mol and for TPP is −43.6
± 3.8 kJ/mol. BTMA passes through two metastable states to reach
the binding pocket, while TPP has a more complex binding landscape
with four metastable states and one main binding site. Our simulations
show that the ligands interact with the membrane lipids at a distance
1 nm away from the binding site which forms a broad local minimum,
consistent for both BTMA and TPP. This site can be an alternate entry
point for ligands to partition from the membrane into the protein,
especially for bulky and/or branched ligands. We also observed the
membrane lipid and C-terminal 110HisA form salt-bridge interactions
with the helix-1 residue 22LysB. Our free energy estimates and clusters
are in close agreement with experimental data and give us an atomistic
view of the ligand–protein–lipid interactions. Understanding
the binding pathway of these ligands can guide us in future design
of ligands that can alter or halt the function of EmrE.