title: Computer simulations suggest direct and stable tip to tip interaction between the outer membrane channel TolC and the isolated docking domain of the multidrug RND efflux transporter AcrB.
abstract: One way by which bacteria achieve antibiotics resistance is preventing drug access to its target molecule for example through an overproduction of multi-drug efflux pumps of the resistance nodulation division (RND) protein super family of which AcrAB-TolC in Escherichia coli is a prominent example. Although representing one of the best studied efflux systems, the question of how AcrB and TolC interact is still unclear as the available experimental data suggest that either both proteins interact in a tip to tip manner or do not interact at all but are instead connected by a hexamer of AcrA molecules. Addressing the question of TolC-AcrB interaction, we performed a series of 100 ns - 1 µs-molecular dynamics simulations of membrane-embedded TolC in presence of the isolated AcrB docking domain (AcrB(DD)). In 5/6 simulations we observe direct TolC-AcrB(DD) interaction that is only stable on the simulated time scale when both proteins engage in a tip to tip manner. At the same time we find TolC opening and closing freely on extracellular side while remaining closed at the inner periplasmic bottleneck region, suggesting that either the simulated time is too short or additional components are required to unlock TolC.
authors.affiliation: Department of Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany.
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Schmidt
authors.affiliation: MLL Münchner Leukämielabor GmbH, Max-Lebsche-Platz 31, 81377 München, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Raunest
authors.affiliation: Berlin-Chemie AG, Glienicker Weg 125, 12489 Berlin, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Fischer
authors.affiliation: Bonn-Rhein-Sieg University of Applied Sciences, Department of Electrical/Mechanical Engineering and Tech.Journalism, Grantham-Allee 20, 53757 Sankt Augustin, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Reith
authors.affiliation: Bonn-Rhein-Sieg University of Applied Sciences, Department of Electrical/Mechanical Engineering and Tech.Journalism, Grantham-Allee 20, 53757 Sankt Augustin, Germany. Electronic address: chkandt@mail.de.
authors.forename: Christian
authors.initials: C
authors.lastname: Kandt
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D001692:Biological Transport; D002462:Cell Membrane / Q000737:chemistry / Q000378:metabolism; D024901:Drug Resistance, Multiple, Bacterial; D004926:Escherichia coli / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D015870:Gene Expression; D008074:Lipoproteins / Q000737:chemistry* / Q000378:metabolism; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000378:metabolism; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D001425:Bacterial Outer Membrane Proteins; D029968:Escherichia coli Proteins; D008074:Lipoproteins; D026901:Membrane Transport Proteins; D027425:ATP-Binding Cassette, Sub-Family C Proteins; C083497:AcrA protein, E coli; C083496:AcrB protein, E coli; C073126:tolC protein, E coli
keywords: Access regulation; Antibiotics resistance; Membrane protein; Molecular dynamics; Multi-drug efflux; Outer membrane channel