A Model for Allosteric Communication in Drug Transport by the AcrAB-TolC Tripartite Efflux Pump.

Anya Webber,Malitha Ratnaweera,Ben F Luisi,Véronique Yvette Ntsogo Enguéné,Andrzej Harris

doi:10.3390/antibiotics11010052

Abstract

RND family efflux pumps are complex macromolecular machines involved in multidrug resistance by extruding antibiotics from the cell. While structural studies and molecular dynamics simulations have provided insights into the architecture and conformational states of the pumps, the path followed by conformational changes from the inner membrane protein (IMP) to the periplasmic membrane fusion protein (MFP) and to the outer membrane protein (OMP) in tripartite efflux assemblies is not fully understood. Here, we investigated AcrAB-TolC efflux pump’s allostery by comparing resting and transport states using difference distance matrices supplemented with evolutionary couplings data and buried surface area measurements. Our analysis indicated that substrate binding by the IMP triggers quaternary level conformational changes in the MFP, which induce OMP to switch from the closed state to the open state, accompanied by a considerable increase in the interface area between the MFP subunits and between the OMPs and MFPs. This suggests that the pump’s transport-ready state is at a more favourable energy level than the resting state, but raises the puzzle of how the pump does not become stably trapped in a transport-intermediate state. We propose a model for pump allostery that includes a downhill energetic transition process from a proposed ‘activated’ transport state back to the resting pump.

Highlights

Antimicrobial resistance rates are rising: it is predicted that by 2050 there could be ten million deaths per year due to drug-resistant infections [1]
The remaining strongly coupled pairs were mapped onto molecular structure models, and residue pairs on the same helix were removed from the analysis, as these are unlikely to reflect allosteric interactions
The open state of AcrA and to Colicins protein (TolC) appeared to be at a lower energy than the closed state. This raises the paradox that the pump would be trapped in an energy minimum and not be able to efflux substrate. To reconcile this finding with the logical requirement for energetic transitions during Acriflavine resistance protein B (AcrB) pump cycling, we propose a model for conformational changes in AcrAB-TolC (Figure 8)

Summary

Introduction

Antimicrobial resistance rates are rising: it is predicted that by 2050 there could be ten million deaths per year due to drug-resistant infections [1]. An important multidrug resistance mechanism is the overexpression of drug efflux pumps [5]. These pumps can export diverse antibiotics, preventing them from reaching their cellular targets [6]. Despite the wide range of existing pumps among bacteria showing diverse structure and activities, those systems share broad similarities including a potential requirement for allosteric switching. Their functional importance make them attractive targets for inhibitors design that either occlude or lock substrate binding sites or impede allosteric transitions [8]

Methods

Results

Discussion

Conclusion