By Eric J. Toone

This ebook covers important advances in enzymology, explaining the habit of enzymes and the way they are often applied to improve novel medicines, synthesize recognized and novel compounds, and comprehend evolutionary techniques.

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Phospholipid extrusion assay of reconstituted AcrB. 0, donor vesicles not containing any AcrB (bottom trace) do not show much change in fluorescence, nor do AcrB-containing vesicles in the absence of pH gradient (middle trace). However, when AcrB-containing vesicles are exposed to pH gradient, there is an expected gradual increase in NBD fluorescence in the presence of Mg2þ . Note that the rate of fluorescence increase is strongly accelerated if AcrA (15 mg/mL) is also added. ] STRUCTURE AND MECHANISM OF RND-TYPE MULTIDRUG EFFLUX PUMPS 27 medium for its function (93).

This protomer is called the binding protomer by the Murakami group or T (for “tight”) by others. Other protomers are called the access (or L for “loose”) and extrusion (or O for “open”) protomers. In the extrusion protomer, which shows the largest conformational alteration, the binding pocket becomes collapsed, and there appears to be an opening of the pathway from the binding pocket to the top (central funnel) of the periplasmic domain. Inspection of the structures of the transmembrane domains shows that the tight association of Asp407–Asp408–Lys940–Thr978 becomes disrupted in the extrusion protomer, probably as a consequence of the protonation of Asp407 and/or Asp408; indeed, the arrangement of these side chains here is nearly identical to that found in our mutant proteins (102) (Figure 10, green sticks).

When the crystal structures (without ligands) of these mutant proteins were examined (102), we found the following. 1. The tight interaction between Asp407, Asp408, Lys940, and Thr978 indeed became disrupted, and the Lys940 side chain, which interacted strongly with both of the carboxyl groups of Asp407 and Asp408 in the wild-type AcrB, went through a strong flipping motion and now faced away from these residues (Figure 10). Remarkably, the alterations were quite similar regardless of which residue was changed to Ala (102).

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