3.3.1 The acriflavine resistance protein B (AcrB) undergoes network rearrangement.
The acriflavine resistance protein B is a multidrug efflux pump found in the inner membrane component of the AcrAB-ToiC drug efflux system found in E coli . The overexpression of this protein machinery in the organism renders it resistant to a wide range of drugs as it functions to efflux the molecules out of the cell. The mechanism of function of the protein have been well studied. There are three distinct domains in each subunit of the AcrB protein, the transmembrane domain (TM-domain), pore domain and the ToiC docking domain. Drug molecules enter the protein from the central cavity in the TM-domain domain which are passed into the pore through channels that can open and close based on conformation coupling in the helices of the protein. The molecules efflux into the docking domain via the central funnel.
In the bound form, the AcrB trimer is bound to two molecules of designed ankyrin-repeat protein (DARPin) inhibitors (PDB ID 2J8S shown in Supplementary Figure 3A). This binding mimics the different functional states of the proteins, where the three chains of AcrB are locked in three different states which reveal the mechanism of drug efflux from the channels of each chain. Alteration of the network around the channel in the pore domain of AcrB (Chain A) is observed upon binding with the DARPin molecule (Figure 2A). The pore domain has an open channel that allows for the efflux of drug molecules which is closed in the inhibitor bound form of the protein. The closing of this channel is mediated by rearrangement of sidechain interactions facing outwards of the channel to face inwards thus closing the gate. This leads to a significant rearrangement of the network in the protein and hence the high network dissimilarity is observed.