title: Computational study of correlated domain motions in the AcrB efflux transporter.
abstract: As active part of the major efflux system in E. coli bacteria, AcrB is responsible for the uptake and pumping of toxic substrates from the periplasm toward the extracellular space. In combination with the channel protein TolC and membrane fusion protein AcrA, this efflux pump is able to help the bacterium to survive different kinds of noxious compounds. With the present study we intend to enhance the understanding of the interactions between the domains and monomers, for example, the transduction of mechanical energy from the transmembrane domain into the porter domain, correlated motions of different subdomains within monomers, and cooperative effects between monomers. To this end, targeted molecular dynamics simulations have been employed either steering the whole protein complex or specific parts thereof. By forcing only parts of the complex towards specific conformational states, the risk for transient artificial conformations during the simulations is reduced. Distinct cooperative effects between the monomers in AcrB have been observed. Possible allosteric couplings have been identified providing microscopic insights that might be exploited to design more efficient inhibitors of efflux systems.
authors: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
authors: Robert
authors: 0000-0002-1711-1917
authors: R
authors: Schulz
authors: Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu km 0.7, 09042 Monserrato, Italy.
authors: Attilio V
authors: AV
authors: Vargiu
authors: Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu km 0.7, 09042 Monserrato, Italy.
authors: Paolo
authors: 0000-0003-0825-0824
authors: P
authors: Ruggerone
authors: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
authors: Ulrich
authors: 0000-0002-6114-7431
authors: U
authors: Kleinekathöfer
mesh_terms: D000494:Allosteric Regulation; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009038:Motion; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000737:chemistry* / Q000378:metabolism; D017434:Protein Structure, Tertiary
chemical_list: D029968:Escherichia coli Proteins; D027425:ATP-Binding Cassette, Sub-Family C Proteins; C083496:AcrB protein, E coli