Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations.

Nathaniel J Traaseth,Ampon Sae Her,Maureen Leninger

doi:10.7554/elife.48909

Abstract

Transporters from bacteria to humans contain inverted repeat domains thought to arise evolutionarily from the fusion of smaller membrane protein genes. Association between these domains forms the functional unit that enables transporters to adopt distinct conformations necessary for function. The small multidrug resistance (SMR) family provides an ideal system to explore the role of mutations in altering conformational preference since transporters from this family consist of antiparallel dimers that resemble the inverted repeats present in larger transporters. Here, we show using NMR spectroscopy how a single conservative mutation introduced into an SMR dimer is sufficient to change the resting conformation and function in bacteria. These results underscore the dynamic energy landscape for transporters and demonstrate how conservative mutations can influence structure and function.

Highlights

Membrane transport proteins catalyze the movement of ions and molecules across the membrane by binding substrates on one side of the bilayer and undergoing conformational changes (Jardetzky, 1966; Zhang et al, 2016)
One class of these proteins is the small multidrug resistance (SMR) family (Schuldiner, 2014; Schuldiner, 2009; Paulsen et al, 1996) found in bacteria and archaea that contain four TM domains and assemble into antiparallel homodimers or heterodimers which resemble the inverted repeat structure in larger transporters. Homodimer transporters such as the multidrug efflux pump EmrE are able to insert into two opposing directions in the membrane whereas heterodimers are comprised of two genes that each insert into the membrane in a single orientation
It is important to note that the mixture of wild-type EmrE and the L51I or I62L mutant produces a statistical fraction of heterodimers and homodimers in the samples

Summary

Introduction

Membrane transport proteins catalyze the movement of ions and molecules across the membrane by binding substrates on one side of the bilayer and undergoing conformational changes (Jardetzky, 1966; Zhang et al, 2016). Proteins with structural repeats are thought to arise evolutionarily from the fusion of smaller membrane protein genes, such as three or four transmembrane (TM) domain transporters that associate into oligomers to achieve the functional state (Xu et al, 2014; Bay and Turner, 2009) One class of these proteins is the small multidrug resistance (SMR) family (Schuldiner, 2014; Schuldiner, 2009; Paulsen et al, 1996) found in bacteria and archaea that contain four TM domains and assemble into antiparallel homodimers or heterodimers which resemble the inverted repeat structure in larger transporters. The widespread prevalence of inverted repeats and divergent evolution from

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