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.