Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation

Abstract

EmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE+POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the transporter, but to understand molecular aspects of its mode of action, a monomer was also included in our work. We analyzed hydrogen bonds which include inter- and intra-molecular interactions. Analyzing the long-lasting H-bond interactions, we found that water access to the internal transmembrane segments is regulated by residues with aromatic or basic side chains and fluctuating transmembrane helices. Our finding supports that GLU14 in EmrE apo-form is ready to interact or bind with substrate molecule. The analysis of distance center of masses and water entrance area indicate the feasibility of the dimer to undergo induced fit in order to accommodate a ligand. The results indicate that a binding pattern can be formed in the EmrE in such a way that GLU14 binds to the positively charged fragment of a substrate molecule, and other aromatic residues (i.e., TRP63 and TYR40) located in vicinity may accommodate other non-polar parts of substrate molecule. The results of our simulation also allow us to support experimentally testable hypotheses concerning functional inward-outward conformational changes of the protein.

Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE

“…Over the course of an aggregate simulation time of 12.5 s, the secondary structure of the faRM remained intact, with a more expansive helical architecture compared with prior models for EmrE ( 10 , 28 , 29 ), similar to other membrane proteins. EmrE is highly dynamic within the simulations, and aromatic residues around the binding site play a pivotal role in controlling the observed conformational heterogeneity.…”

In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis

“…Unfortunately, they may be regarded only as static snapshots of highly dynamic proteins, like this key factor of NMD. Computational studies of peptides for predicting and rationalizing already available data are used more often to analyze their mechanistic details [ 77 , 78 ]. To further examine the results obtained from the structural modeling and the possible functional relevance of certain domains, we conducted MDS for the crystal structure of the UPF2-interacting domain of UPF1 in both H .…”

Influence of quaternary cation compound on the size of the Escherichia coli small multidrug resistance protein, EmrE

“…High-resolution 3D analysis using cryo-electron microscopy and X-ray crystallography have reported on the conformational state of the topologically asymmetric dimer of EmrE [12] , [17] , [18] . NMR spectroscopy has also confirmed the presence of EmrE homodimers, wherein the putative active site involves Glu14 and residues from each monomer in structurally inequivalent environments [19] , [20] , [21] , [22] , [23] . In addition to Glu14, aromatic residues have been shown to play a role in defining the active site: for example, Trp63 was demonstrated to be located close to the QCC binding pocket, and a variant of this residue abolished ligand binding [8] , [24] .…”