Simulated Substrate Binding to the Inner Membrane Translocase AcrB

Abstract

Functioning as the engine of the AcrAB-TolC efflux pump, AcrB plays a key role in multidrug resistance in Escherichia coli. AcrB occurs as a trimer, where each monomer has a different conformation: loose (L), tight (T) or open (O) - representing different consecutive states in the reaction cycle. Here we report molecular dynamics simulations of the asymmetric 2GIF AcrB x-ray structure embedded in a phospholipid bilayer / 150 mM NaCl environment. To study the interaction with one of AcrB's simplest substrates, 25 hexane molecules were added to the system, with three hexanes placed directly in front of each monomer's porter domain. Using GroMACS 4.0.3 and the GROMOS96 53a6 force field we performed 5 independent MD runs, each 50ns long. Three runs were further extended by 150 ns. During one simulation, we observe a hexane entering the presumed drug transport channel of the (L) monomer. Binding occurs in a stepwise process during which the hexane moves towards the hydrophobic binding pocket inside the protein before reaching a final position after 25ns, 9.7 Å away from Phe-628. For the (T) monomer we observe hexane binding in a single step, reaching its final position 9.2 Å away from Phe-628. In none of the runs substrate binding takes place in the (O) monomer. However, an accumulation of hexane molecules in front of the closed porter domain could be observed here. In a second approach, we repeated the simulations now providing the antibiotic chloramphenicol as transport substrate instead. Correction et al.Biophysical JournalMay 04, 2011In Brief2963-Pos. Full-Text PDF Open Archive