By Eric J. Toone
This e-book covers important advances in enzymology, explaining the habit of enzymes and the way they are often applied to boost novel medicinal drugs, synthesize recognized and novel compounds, and comprehend evolutionary procedures.
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Additional info for Advances in Enzymology and Related Areas of Molecular Biology (Volume 77)
Because binding of fluorescent substrates to a large AcrB trimer is expected to slow the tumbling of these molecules, this method offers advantages. 5 mM for rhodamine 6G to 74 mM for ciprofloxacin. However, the method does not give reliable information on binding stoichiometry, and because the authors did not use, as controls, mutant AcrB proteins that are altered in substrate binding, it is unclear whether the binding occurred to the true binding sites or to some extraneous pockets that bind lipophilic molecules in a nonspecific manner.
The efflux of fluorescent dyes from cells after their energization was followed in several studies. Typically, cells are preloaded with dyes that become fluorescent only within the membrane or the cytosol. The preloading requires deenergization of the RND pump by a proton conductor such as CCCP (carbonyl cyanide m-chlorophenylhydrazone), and reener- 16 HIROSHI NIKAIDO gization of the cells is done by adding compounds such as glucose or formate. If everything goes perfectly, the time-dependent decrease in fluorescence intensity should follow the integrated form of the Michaelis–Menten equation, which should give us the kinetic constants Km and Vmax.
Finally, its physiological significance is supported further by a comparison of its surface in AcrB and in the homology-modeled AcrD (36); although the surface is entirely hydrophobic in AcrB, in the aminoglycoside pump AcrD it contains many oxygen atoms that may function in the binding of the hydrophilic basic substrates. B. PATHWAYS FOR DRUGS: A CURRENT HYPOTHESIS How do the substrates reach the binding pocket? All three groups that studied the asymmetric trimer structure agree that there is an open pathway in the binding protomer between the binding pocket and the external large cleft of the periplasmic domain of the binding protomer (102–104) (see Figure 12).
Advances in Enzymology and Related Areas of Molecular Biology (Volume 77) by Eric J. Toone