Abstract
The current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global "one health" perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the smallest known ligand transporters that confers resistance to aromatic cations in a number of clinically relevant species. As an asymmetric homodimer undergoing an "alternating access" protomer-swap conformational change, it serves as a model for the mechanistic understanding of more complex drug transporters. Here, we present a free energy and solvent accessibility analysis that indicates the presence of two complementary ligand translocation pathways that remain operative in a broad range of conditions. Our simulations show a previously undescribed desolvated apo state and anticorrelated accessibility in the ligand-bound state, explaining on a structural level why EmrE does not disrupt the pH gradient through futile proton transfer. By comparing the behavior of a number of model charged and/or aromatic ligands, we also explain the origin of selectivity of EmrE towards a broad class of aromatic cations. Finally, we explore unbiased pathways of ligand entry and exit to identify correlated structural changes implicated in ligand binding and release, as well as characterize key intermediates of occupancy changes.
Highlights
Increasing bacterial resistance to many first-line drugs and antiseptics has long been seen as a global threat to public health
Many transporters target polyaromatic cations as they make up a significant fraction of both natural and man-made antibiotics, antiseptics or anti-pathogens [12,13,14,15]
After placing the structure in a model bacterial membrane, the system was first equilibrated for 1 μs
Summary
Increasing bacterial resistance to many first-line drugs and antiseptics has long been seen as a global threat to public health. One of the main culprits, and a possible therapeutic target, are the bacterial multidrug transporters (MDR) [1,2,3,4] These transporters play an important role in antibiotic resistance of several important human pathogens, such as Mycobacterium tuberculosis, Streptococcus pneumoniae, Pseudomonas aeruginosa or Vibrio cholerae [5,6,7]. Detailed knowledge about the molecular basis of drug recognition and transport by multi-drug transport systems is needed to develop inhibitors blocking the MDR transporters or new, non-extruded antibiotics. To work effectively, these proteins must recognize the universal characteristics of potentially toxic compounds and expel them from the cytoplasm in an energy-dependent manner [8,9,10,11]. Many transporters target polyaromatic cations as they make up a significant fraction of both natural and man-made antibiotics, antiseptics or anti-pathogens (e.g., benzalkonium chloride, ampicillin, erythromycin or tetracycline) [12,13,14,15]
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