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• W2415634955 abstract "AcrB is the inner membrane transporter of the tripartite multidrug efflux pump AcrAB-TolC in E. coli, which poses a major obstacle to the treatment of bacterial infections. X-ray structures have identified two types of substrate-binding pockets in the porter domains of AcrB trimer: the proximal binding pocket (PBP) and the distal binding pocket (DBP), and suggest a functional rotating mechanism in which each protomer cycles consecutively through three distinct conformational states (access, binding and extrusion). However, the details of substrate binding and translocation between the binding pockets remain elusive. In this work, we performed atomic simulations to obtain the free energy profile of the translocation of an antibiotic drug doxorubicin (DOX) inside AcrB. Our simulation indicates that DOX binds at the PBP and DBP with comparable affinities in the binding state protomer, and overcomes a 3 kcal/mol energy barrier to transit between them. Obvious conformational changes including closing of the PC1/PC2 cleft and shrinking of the DBP were observed upon DOX binding in the PBP, resulting in an intermediate state between the access and binding states. Taken together, the simulation results reveal a detailed stepwise substrate binding and translocation process in the framework of functional rotating mechanism." @default.
• W2415634955 created "2016-06-24" @default.
• W2415634955 creator A5002073070 @default.
• W2415634955 creator A5012022141 @default.
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• W2415634955 date "2015-09-14" @default.
• W2415634955 modified "2023-09-27" @default.
• W2415634955 title "Stepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB" @default.
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• W2415634955 doi "https://doi.org/10.1038/srep13905" @default.
• W2415634955 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4595977" @default.
• W2415634955 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26365278" @default.
• W2415634955 hasPublicationYear "2015" @default.
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