Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface

Cesar A López,Klaas M Pos,S Gnanakaran,Helen I Zgurskaya,Timothy Travers

doi:10.1038/s41598-017-16497-w

Abstract

Antibiotic efflux is one of the most critical mechanisms leading to bacterial multidrug resistance. Antibiotics are effluxed out of the bacterial cell by a tripartite efflux pump, a complex machinery comprised of outer membrane, periplasmic adaptor, and inner membrane protein components. Understanding the mechanism of efflux pump assembly and its dynamics could facilitate discovery of novel approaches to counteract antibiotic resistance in bacteria. We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM pump in a Gram-negative membrane model that contained both inner and outer membranes separated by a periplasmic space. All-atom molecular dynamics (MD) simulations confirm that the fully assembled pump is stable in the microsecond timescale. Using a combination of all-atom and coarse-grained MD simulations and sequence covariation analysis, we characterized the interface between MexA and OprM in the context of the entire efflux pump. These analyses suggest a plausible mechanism by which OprM is activated via opening of its periplasmic aperture through a concerted interaction with MexA.

Highlights

Previous structural and functional analyses showed that the clinically important efflux pumps of P. aeruginosa and other Gram-negative bacteria consist of an inner membrane protein component belonging to the Resistance Nodulation cell Division (RND) superfamily of secondary transporters, a channel-forming outer membrane factor (OMF), and a periplasmic membrane fusion protein (MFP)[30,31,32,33,34]
The conformation adopted by the MexA hexamer α-hairpin helices was similar to that observed for the AcrA hexamer in a recent high-resolution cryo-EM structure of drug-bound AcrAB-TolC56 (Figure S3), even though there were no bound drugs to MexAB-OprM during the MD flexible fitting (MDFF) fitting
The interactions between MFPs and the outer membrane channels are essential for functionalities of efflux pumps and their versatility in complex assemblies

Summary

Introduction

Previous structural and functional analyses showed that the clinically important efflux pumps of P. aeruginosa and other Gram-negative bacteria consist of an inner membrane protein component belonging to the Resistance Nodulation cell Division (RND) superfamily of secondary transporters, a channel-forming outer membrane factor (OMF), and a periplasmic membrane fusion protein (MFP)[30,31,32,33,34]. These three components are believed to form a protein complex that extends across both the inner and the outer membranes, allowing the extrusion of drugs from the periplasm directly into the extracellular milieu[34,35,36,37]. The α-helices in combination with the β-barrel domain form a hollow structure, accessible from the extracellular compartment

Methods

Results

Conclusion