Functional Rotation of the Transporter AcrB Insights into Drug Extrusion from Simulations 英文参考文献.docVIP

FunctionalRotationoftheTransporterAcrB:Insightsinto DrugExtrusionfromSimulations RobertSchulz1.,AttilioV.Vargiu2*.,FrancescaCollu2,UlrichKleinekatho¨fer1,PaoloRuggerone2 1School of Engineering and Science, Jacobs University Bremen, Bremen, Germany, 2Istituto Officina dei Materiali del CNR, UOS SLACS and Dipartimento di Fisica, Universita’degliStudidiCagliari,Monserrato,Italy Abstract The tripartite complex AcrAB-TolC is the major efflux system in Escherichia coli. It extrudes a wide spectrum of noxious compounds out of the bacterium, including many antibiotics. Its active part, the homotrimeric transporter AcrB, is responsible for the selective binding of substrates and energy transduction. Based on available crystal structures and biochemicaldata,thetransportofsubstratesbyAcrBhasbeenproposedtotakeplaceviaafunctionalrotation,inwhich eachmonomerassumesaparticularconformation.However,thereisnomolecular-leveldescriptionoftheconformational changes associated with the rotation and their connection to drug extrusion. To obtain insights thereon, we have performed extensive targeted molecular dynamics simulations mimicking the functional rotation of AcrB containing doxorubicin, one of the two substrates that were co-crystallized so far. The simulations, including almost half a million atoms, have been used to test several hypotheses concerning the structure-dynamics-function relationship of this transporter.Ourresultsindicatethat,uponinductionofconformationalchanges,thesubstratedetachesfromthebinding pocketandapproachesthegatetothecentralfunnel.Furthermore,weprovidestrongevidencefortheproposedperistaltic transportinvolvingazipper-likeclosureofthebindingpocket,responsibleforthedisplacementofthedrug.Aconcerted opening of the channel between the binding pocket and the gate further favors the displacement of the drug. This microscopicallywell-fundedinformationallowsonetoidentifytheroleofspecificaminoacidsduringthetransitionsandto shedlightonthefunctioningofAcrB. Citation: Sch