Amide binding site positions

In the first step of the peptidyl transferase reaction, a peptidyl tRNA molecule is bound in the P-site with its nascent peptide extending down the peptide exit tunnel (Fig. 4.1). An elongation factor binds to a factor binding site (FBS) and positions an aminoacyl-tRNA in the A-site. The a amino group of the aminoacyl-tRNA nucleophilically attacks the ester bond which connects the peptide to the tRNA bound in the P-site (Fig. 4.2). The ester bond is broken as an amide bond forms, and the peptide becomes one amino acid longer, and is now attached to the tRNA that in the A-site. Translocation of the products follows peptide bond formation, as the newly formed deacylated- tRNA of the P-site moves into the E-site, and as the newly elongated peptidyl-tRNA moves from the A-site into the P-site. 

If our hypothesis is correct, this hypothetical binding site should also accommodate fluridone, norflurazon and difunone and some possible binding orientations of these molecules are compared with furanone 13 in Figures 7-9. Note that we have attempted to depict the molecules in such a way that key structural features, e.g., the CF3 phenyl and vinylogous amide subunits, occupy the same positions as nearly as possible. Finally, it should be emphasized that considerable further work is required to demonstrate that the furanones actually inhibit phytoene desaturase and to further probe the possibility of a common binding site for the proven inhibitors including those such as fluorochloridone (10) and the m-phenoxybenzamides (4), which do not incorporate the vinylogous amide substructure. 

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