Study on ubiquinol reaction site of cytochrome bo in Escherichia coli.

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Substrate binding sites of the Escherichia coli cytochromes bo and bd were probed with systematically synthesized ubiquinol analogues. The apparent K_m values of Q_2H_2 derivatives to the cytochrome bo were much lower than that of the corresponding 6-n-decyl derivatives. The isoprenoid structure is less hydrophobic than the saturated n-alkyl group with the same carbon number, therefore, the native isoprenoid side chain appears to play a specific role in quinol binding besides simply increasing hydrophobicity of the molecule. The V_<max> values of 2-methoxy-3-ethoxy analogues were greater than that of 2-ethoxy-3-methoxy analogues irrespective of the side chain structure. This result indicates not only that a methoxy group in the 2-position is recognized more strictly than the 3-position by the binding site, but also that the side chain structure does not affect binding of the quinol ring moiety. Systematic analysis of the electron-donating activities of the analogues with different substituents in the 5-position revealed that the 5-methyl group is important for the activity. In the parallel studies with the cytochrome bd, similar observations were obtained except that almost all quinol analogues, but not Q_1, elicited a remarkable substrate inhibition at higher concentrations. These results indicate that the structurally unrelated two terminal oxidases share common structural properties for the quinol oxidation site. In addition, to investigate the quinone binding site of cytochrome bo enzyme, convenient synthetic procedures which enable the preparation of photolable 2-azido-Q_2 and 3-azido-Q_2 have been established.